Major update: obiarrays with columns containing indices referring to

character strings.

doc/.gitignore

@@ -1,3 +1,5 @@
 /build/
 /doxygen/
 /build_dir.txt
+/.DS_Store
+/.gitignore

doc/Makefile

@@ -57,7 +57,7 @@ html:
 	@echo "Generating Doxygen documentation..."
 	doxygen Doxyfile
 	@echo "Doxygen documentation generated. \n"
-	$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
+	$(SPHINXBUILD) -b html -c ./ $(ALLSPHINXOPTS) $(BUILDDIR)/html
 	@echo
 	@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
 

doc/conf.py

@@ -36,7 +36,7 @@ extensions = [
     'sphinx.ext.pngmath',
     'sphinx.ext.ifconfig',
     'sphinx.ext.viewcode',
-    'breathe',
+#    'breathe',
 ]
 
 # Add any paths that contain templates here, relative to this directory.
@@ -51,7 +51,7 @@ source_suffix = '.rst'
 #source_encoding = 'utf-8-sig'
 
 # The master toctree document.
-master_doc = 'index'
+master_doc = 'source/index'
 
 # General information about the project.
 project = u'OBITools3'
@@ -292,7 +292,7 @@ texinfo_documents = [
 #texinfo_no_detailmenu = False
 
 #Breathe configuration
-sys.path.append( "../breathe/" )
-breathe_projects = { "OBITools3": "../doxygen/xml/" }
+sys.path.append( "breathe/" )
+breathe_projects = { "OBITools3": "doxygen/xml/" }
 breathe_default_project = "OBITools3"
 

doc/doxygen/xml/.gitignore

@@ -1,4 +0,0 @@
-# Ignore everything in this directory
-*
-# Except this file
-!.gitignore

doc/source/DMS.rst

@@ -13,7 +13,7 @@ Up to now, each of these categories of data were stored in separate
 files, and nothing made it mandatory to keep them together.
 
 
-The `Data Management System` (DMS) of OBITools3 can be regarded as a basic 
+The `Data Management System` (DMS) of OBITools3 can be viewed like a basic 
 database system.
 
 
@@ -27,9 +27,7 @@ OBIDMS UML
 
 An OBIDMS directory contains :
   * one `OBIDMS history file <#obidms-history-files>`_
-  * Two different kinds of directories :
-     * OBIDMS column directories
-     * OBIDMS column group directories containing OBIDMS column directories
+  * OBIDMS column directories
 
 
 OBIDMS column directories
@@ -39,16 +37,9 @@ OBIDMS column directories contain :
     * all the different versions of one OBIDMS column, under the form of different files (`OBIDMS column files <#obidms-column-files>`_)
     * one `OBIDMS version file <#obidms-version-files>`_
 
-The directory name is the column attribute, or sub-attribute if the column directory is in a column group directory.
+The directory name is the column attribute with the extension ``.obicol``.
 
-
-OBIDMS column group directories
-===============================
-
-OBIDMS column group directories contain OBIDMS column directories. They are used to store dictionary-like data, where 
-each key corresponds to an OBIDMS column.
-
-The directory name is the dictionary attribute. Each key is considered a sub-attribute and is associated to its column.
+Example: ``count.obicol``
 
 
 OBIDMS column files
@@ -57,7 +48,7 @@ OBIDMS column files
 Each OBIDMS column file contains :
 	* a header of a size equal to a multiple of PAGESIZE (PAGESIZE being equal to 4096 bytes
 	  on most systems) containing metadata
-	* one column of data with the same `OBIType <types.html#obitypes>`_
+	* Lines of data with the same `OBIType <types.html#obitypes>`_
 
 
 Header
@@ -79,7 +70,14 @@ The header of an OBIDMS column contains :
 Data
 ----
 
-A column of data with the same `OBIType <types.html#obitypes>`_.
+A line of data corresponds to a vector of elements. Each element is associated with an element name. 
+Elements names are stored in the header. The correspondance between an element and its name is done 
+using their order in the lists of elements and elements names.  This structure allows the storage of 
+dictionary-like data.
+
+Example: In the header, the attribute ``elements_names`` will be associated with the value ``"sample_1;
+sample_2;sample_3"``, and a line of data with the type ``OBInt_t`` will be stored as an ``OBInt_t`` vector 
+of size three e.g. ``5|8|4``.
 
 
 Mandatory columns
@@ -158,3 +156,5 @@ operations ever done in the OBIDMS directory and the views in between them :
 .. image:: ./images/history.png
     :width: 150 px
     :align: center
+
+

doc/source/data.rst

@@ -2,8 +2,8 @@
 Data in OBITools3
 #################
 
-The OBITools3 inaugure a new way to manage DNA metabarcoding data. 
-They rely on a `Data management System` (DMS) that can be considered as
+The OBITools3 introduce a new way to manage DNA metabarcoding data. 
+They rely on a `Data management System` (DMS) that can be viewed like 
 a simplified database system.
 
 

doc/source/guidelines.rst

@@ -70,7 +70,7 @@ Tickets should always be labeled with the branches for which they are relevant.
 Documentation
 *************
 
-C functions are documented in the header files.
+C functions are documented in the header files for public functions, and in the source file for private functions.
 
 
 **************
@@ -92,7 +92,7 @@ C99 :
 	* Object layer
 	* OBITools3 library
 
-`Python 3 <https://www.python.org/>`_ :
+`Python 3.5 <https://www.python.org/>`_ :
 	* Top layer code (scripts)	
 	
 For the documentation, `Sphinx <http://sphinx-doc.org/>`_ should be used for both the original 
@@ -111,6 +111,8 @@ Enum members, macros, constants:                ``ALL_CAPS``
 
 Functions, local variables:                     ``lower_case``
 
+Public functions:                               ``obi_lower_case``
+
 Functions that shouldn't be called directly:    ``_lower_case`` (``_`` prefix)
 
 Global variables:                                ``g_lower_case`` (``g_`` prefix)
@@ -120,9 +122,6 @@ Pointers:                                        ``pointer_ptr`` (``_ptr`` suffi
 .. note::
     Underscores are used to delimit 'words'.
 
-.. todo::
-    ``obi_function`` for public functions names?
-
 
 *****************
 Programming rules

doc/source/index.rst

@@ -11,7 +11,6 @@ OBITools3 documentation
 
    Programming guidelines <guidelines>
    Data structures <data>
-   Pistes de reflexion <pistes>
 
 
 Indices and tables

doc/source/specialvalues.rst

@@ -7,13 +7,16 @@ NA values
 =========
 
 All OBITypes have an associated NA (Not Available) value. 
-NA values are implemented by specifying an explicit NA value for each type, corresponding to the R standards:
+NA values are implemented by specifying an explicit NA value for each type, 
+corresponding to the R standards as much as possible:
 
-* For the types ``OBIInt_t``, ``OBIBool_t``, ``OBIIdx_t`` and ``OBITaxid_t``, the NA value is ``INT_MIN``.
+* For the type ``OBIInt_t``, the NA value is ``INT_MIN``.
 
-* For the type ``OBIChar_t``: the NA value is ``\0`` (?).
+* For the type ``OBIBool_t``, the NA value is ``2``.
 
-* For the type ``OBIStr_t`` : the NA value is ``\0`` (?).
+* For the type ``OBIIdx_t`` and ``OBITaxid_t``, the NA value is ``SIZE_MAX``.
+
+* For the type ``OBIChar_t``: the NA value is ``\0``.
 
 * For the type ``OBIFloat_t``::
 
@@ -29,7 +32,7 @@ NA values are implemented by specifying an explicit NA value for each type, corr
         x.word[hw] = 0x7ff00000;
         x.word[lw] = 1954;
         return x.value;
-    }   
+    }
 
 
 Minimum and maximum values for ``OBIInt_t``

doc/source/types.rst

@@ -7,11 +7,14 @@ OBITypes
 :download:`html version of the OBITypes UML file <UML/OBITypes_UML.class.violet.html>`
 
 
+.. image:: ./UML/Obicolumn_classes_UML.png
+
+:download:`html version of the OBIDMS classes UML file <UML/Obicolumn_classes_UML.class.violet.html>`
+
+
 .. toctree::
    :maxdepth: 2
 
    The elementary types <elementary>
    The containers <containers>
    Special values <specialvalues>
-
-

doc/sphinx/build_dir.txt

@@ -0,0 +1 @@
+build/lib.macosx-10.6-intel-3.5

doc/sphinx/source/pistes.rst

@@ -1,23 +0,0 @@
-###################
-Pistes de reflexion
-###################
-
-
-******************************
-Ce que l'on veut pouvoir faire
-******************************
-
-    * Gerer les valeurs manquantes
-    * Modifier une colonne en cours d'ecriture (mmap)
-    * Ajouter des valeurs a la fin du fichier d'une colonne en cours d'ecriture (mmap)
-    
-
-******
-Divers
-******
-
-* Si l'ordre d'une colonne est change, elle est reecrite (pas d'index).
-* Utilisation de semaphores pour la lecture
-* Utilisation de tas pour l'indexation des chaines de caracteres. Chaque colonne dont 
-  le type est OBIStr_t est stockee dans 3 fichiers : un fichier contenant les chaines, un 
-  fichier contenant les index, et un fichier contenant le tas.

python/obitools3/obicount.py

@@ -1,31 +0,0 @@
-import sys
-import argparse
-
-
-from obitools3.obidms.obidmscolumn.capidmscolumn import OBIDMS_column
-
-
-if __name__ == '__main__': 
-    
-    parser = argparse.ArgumentParser(description='Computes the sum of a column.')
-    
-    parser.add_argument('-d', '--dms', dest='dms_name', type=str,
-                       help='Name of the OBIDMS containing the column')
-    parser.add_argument('-c', '--column', dest='column_name', type=str, default='count',
-                       help="Name of the OBIDMS column (default: 'count')")
-    parser.add_argument('-v', '--version', dest='version_number', type=int, default=-1,
-                       help='Version number of the column (default: latest version)')
-    
-    args = parser.parse_args()
-   
-    c = OBIDMS_column.open(args.dms_name, args.column_name, version_number=args.version_number)
-    
-    # check that 1 element / line and summable type?
-
-    total = 0    
-    
-    for count in c :
-        total+=count
-    
-    print("Total count = ", total)    
-

python/obitools3/obidms/_obidms.cfiles

@@ -12,3 +12,5 @@
 ../../../src/obitypes.c
 ../../../src/private_at_functions.h
 ../../../src/private_at_functions.c
+../../../src/obiarray.h
+../../../src/obiarray.c

python/obitools3/obidms/_obidms.pxd

@@ -2,9 +2,11 @@
 
 from .capi.obidms       cimport OBIDMS_p
 from .capi.obidmscolumn cimport OBIDMS_column_p
-from .capi.obitypes     cimport obiversion_t, OBIType_t
+from .capi.obitypes     cimport obiversion_t, OBIType_t, index_t
+
 
 cdef class OBIDMS_column
+
             
 cdef class OBIDMS:
 
@@ -12,27 +14,34 @@ cdef class OBIDMS:
     cdef str dms_name
     
     cpdef dict list(self)
-    
+    cpdef close(self)
     cpdef OBIDMS_column open_column(self,
                                     str column_name,
                                     bint create=*, 
                                     bint clone=*, bint clone_data=*,
                                     obiversion_t version_number=*, 
                                     OBIType_t data_type=*,
-                                    size_t nb_lines=*, 
-                                    size_t nb_elements_per_line=*, 
-                                    str elements_names=*)
+                                    index_t nb_lines=*, 
+                                    index_t nb_elements_per_line=*, 
+                                    list elements_names=*,
+                                    str array_name=*)
 
 
 cdef class OBIDMS_column:
 
-    cdef OBIDMS_column_p pointer
-    cdef OBIDMS dms
-    cdef str data_type   # TODO keep as OBIType_t? both?
-    cdef str dms_name
-    cdef str column_name
+    cdef OBIDMS_column_p    pointer
+    cdef OBIDMS             dms
+    cdef str                data_type   # TODO keep as OBIType_t? both?
+    cdef str                dms_name
+    cdef str                column_name
+    cdef index_t             nb_elements_per_line
+    cdef list               elements_names
+
+#    cpdef object get_item(self, index_t line_nb, str element_name)                  TODO can't declare because not the same in all subclasses
+#    cpdef        set_item(self, index_t line_nb, str element_name, object value)    TODO can't declare because object value
+    cpdef list    get_elements_names(self)
+    cpdef str     get_data_type(self)
+    cpdef index_t get_nb_lines_used(self)
+    cpdef str     get_creation_date(self)
+    cpdef         close(self)
 
-    cpdef object get_item(self, size_t line_nb, str element_name)
-    cpdef list   get_elements_names(self)
-    cpdef str    get_data_type(self)
-    cpdef size_t get_nb_lines_used(self)

python/obitools3/obidms/_obidms.pyx

@@ -4,36 +4,48 @@ from pathlib import Path
 
 from obitools3.utils cimport bytes2str, str2bytes
 
-from .capi.obidms cimport obi_dms
-from .capi.obidmscolumn cimport obi_column_get_data_type_from_name, \
+from .capi.obidms cimport obi_dms, \
+                          obi_close_dms
+from .capi.obidmscolumn cimport obi_column_get_header_from_name, \
+                                obi_unmap_header, \
                                 obi_column_get_latest_version_from_name, \
-                                obi_column_get_line_count_from_name, \
-                                obi_column_get_nb_lines_used, \
-                                obi_column_get_elements_names, \
                                 obi_create_column, \
                                 obi_clone_column, \
                                 obi_open_column, \
-                                obi_close_column
-from .capi.obitypes cimport const_char_p, name_data_type
-
+                                obi_close_column, \
+                                obi_column_format_date, \
+                                OBIDMS_column_header_p
+from .capi.obitypes cimport const_char_p, \
+                            name_data_type
+                            
 
 from ._obidms cimport OBIDMS
 from ._obidms cimport OBIDMS_column
 
 from ._obidmscolumn_int cimport OBIDMS_column_int, \
-                                OBIDMS_column_int_writable
-
+                                OBIDMS_column_int_writable, \
+                                OBIDMS_column_int_multi_elts, \
+                                OBIDMS_column_int_multi_elts_writable
+                                
 from ._obidmscolumn_float cimport OBIDMS_column_float, \
-                                  OBIDMS_column_float_writable
+                                  OBIDMS_column_float_writable, \
+                                  OBIDMS_column_float_multi_elts, \
+                                  OBIDMS_column_float_multi_elts_writable
 
 from ._obidmscolumn_bool cimport OBIDMS_column_bool, \
-                                 OBIDMS_column_bool_writable
+                                 OBIDMS_column_bool_writable, \
+                                 OBIDMS_column_bool_multi_elts, \
+                                 OBIDMS_column_bool_multi_elts_writable
 
 from ._obidmscolumn_char cimport OBIDMS_column_char, \
-                                 OBIDMS_column_char_writable
+                                 OBIDMS_column_char_writable, \
+                                 OBIDMS_column_char_multi_elts, \
+                                 OBIDMS_column_char_multi_elts_writable
 
-from ._obidmscolumn_idx cimport OBIDMS_column_idx, \
-                                OBIDMS_column_idx_writable
+from ._obidmscolumn_str cimport OBIDMS_column_str, \
+                                OBIDMS_column_str_writable, \
+                                OBIDMS_column_str_multi_elts, \
+                                OBIDMS_column_str_multi_elts_writable
 
 
 cdef class OBIDMS :
@@ -49,10 +61,13 @@ cdef class OBIDMS :
         # Fill structure and create or open the DMS
         self.dms_name = dms_name
         self.pointer = obi_dms(<const_char_p> dms_name_b)
+        # TODO: test pointer and raise Exception("Failed opening or creating an OBIDMS")
 
 
-#    def __del__(self) :                        # TODO problem with closing dir breaking everything
-#        obi_close_dms(self.pointer)
+    cpdef close(self) :
+        #TODO close all columns
+        if (obi_close_dms(self.pointer)) < 0 :
+            raise Exception("Problem closing an OBIDMS")
 
 
     cpdef dict list(self):
@@ -63,125 +78,151 @@ cdef class OBIDMS :
         cdef str column_name
         cdef bytes column_name_b
         cdef str data_type
+        cdef str creation_date
         cdef obiversion_t latest_version
-        cdef size_t line_count
+        cdef index_t line_count
+        cdef OBIDMS_column_header_p header
         
         p = Path(self.dms_name+'.obidms')
 
-        print("{:<25} {:<25} {:<25} {:<25}".format('-Column name-','-Data type-','-Latest version number-', '-Line count of latest version-'))
+        print("{:<30} {:<12} {:<25} {:<30} {:<40}".format('-Column name-', 
+                                                   '-Data type-', 
+                                                   '-Latest version number-', 
+                                                   '-Line count of latest version-',
+                                                   '-Creation date of latest version-'))
         for entry in p.iterdir():
             if entry.suffix == ".obicol":
                 column_name = entry.stem
                 column_name_b = str2bytes(column_name)
                 dms[column_name] = {}
-                data_type = bytes2str(name_data_type(obi_column_get_data_type_from_name(self.pointer, column_name_b)))
+                header = obi_column_get_header_from_name(self.pointer, column_name_b)
+                data_type = bytes2str(name_data_type(header.data_type))
+                line_count = header.line_count
+                creation_date = bytes2str(obi_column_format_date(header.creation_date))
+                obi_unmap_header(header)    # TODO check if error? but C will already warn and there's nothing to do
                 latest_version = obi_column_get_latest_version_from_name(self.pointer, column_name_b)
-                line_count = obi_column_get_line_count_from_name(self.pointer, column_name_b)
                 dms[column_name]['data_type'] = data_type
                 dms[column_name]['latest_version'] = latest_version
                 dms[column_name]['line_count'] = line_count
-                print("{:<25} {:<25} {:<25} {:<25}".format(column_name, data_type, latest_version, line_count))
+                dms[column_name]['creation_date'] = creation_date
+                # TODO : actually get all the informations in the header
+                print("{:<30} {:<12} {:<25} {:<30} {:<40}".format(column_name, data_type, latest_version, line_count, creation_date))
 
         return dms
      
+     
     cpdef OBIDMS_column open_column(self,
                                     str column_name,
                                     bint create=False, 
                                     bint clone=False, bint clone_data=True,
                                     obiversion_t version_number=-1, 
                                     OBIType_t data_type= <OBIType_t> 0,
-                                    size_t nb_lines=0, 
-                                    size_t nb_elements_per_line=1, 
-                                    str elements_names=None):
+                                    index_t nb_lines=0, 
+                                    index_t nb_elements_per_line=0, 
+                                    list elements_names=None,
+                                    str array_name="default_obiarray"):
         
         # Declarations
         cdef OBIDMS_column column
+        cdef object subclass        # TODO object?
         cdef bytes column_name_b
+        cdef OBIDMS_column_header_p header
+        
+        header = NULL
         
         # Format the character string to send to C function
         column_name_b = str2bytes(column_name)
         
+        # Get the header of the latest version of the column if 
+        # some needed informations are not provided
+        if ((not data_type or not nb_elements_per_line) and not create) :
+            header = obi_column_get_header_from_name(self.pointer, column_name_b)
+            
         # Get the data type if not provided
         if not data_type :
             if create :
                 raise Exception("A data type must be specified")
             else :
-                data_type = obi_column_get_data_type_from_name(self.pointer, column_name_b)
+                data_type = header.data_type
 
-        # Open the column with the right subclass depending on the data type and the mode (read-only or writable)
+        # Get the number of elements per line if not provided and needed
+        if not nb_elements_per_line :
+            if create : # Set to one if not provided (default value)
+                nb_elements_per_line = 1
+            else :
+                nb_elements_per_line = header.nb_elements_per_line
+                if nb_elements_per_line > 1 :
+                    elements_names = bytes2str(header.elements_names).split(';')
+
+        if header != NULL :
+            obi_unmap_header(header)        # TODO check if error? but C will already warn and there's nothing to do
+        
+        # Open the column with the right subclass depending on the data type, the mode 
+        # (read-only or writable) and whether there are multiple elements per line or not  
         if data_type == 1 :
             if (create or clone) :
-                column = OBIDMS_column_int_writable(self, column_name, 
-                                                    create, clone, clone_data, 
-                                                    version_number, data_type, 
-                                                    nb_lines, nb_elements_per_line, 
-                                                    elements_names)
+                if nb_elements_per_line == 1 :
+                    subclass = OBIDMS_column_int_writable
+                else :
+                    subclass = OBIDMS_column_int_multi_elts_writable
             else :
-                 column = OBIDMS_column_int(self, column_name, 
-                                                 create, clone, clone_data, 
-                                                 version_number, data_type, 
-                                                 nb_lines, nb_elements_per_line, 
-                                                 elements_names)
-               
+                if nb_elements_per_line == 1 :
+                    subclass = OBIDMS_column_int
+                else :
+                    subclass = OBIDMS_column_int_multi_elts
         elif data_type == 2 :
             if (create or clone) :
-                column = OBIDMS_column_float_writable(self, column_name, 
-                                                      create, clone, clone_data, 
-                                                      version_number, data_type, 
-                                                      nb_lines, nb_elements_per_line, 
-                                                      elements_names)
+                if nb_elements_per_line == 1 :
+                    subclass = OBIDMS_column_float_writable
+                else :
+                    subclass = OBIDMS_column_float_multi_elts_writable
             else :
-                 column = OBIDMS_column_float(self, column_name, 
-                                                   create, clone, clone_data, 
-                                                   version_number, data_type, 
-                                                   nb_lines, nb_elements_per_line, 
-                                                   elements_names)
-
+                if nb_elements_per_line == 1 :
+                    subclass = OBIDMS_column_float
+                else :
+                    subclass = OBIDMS_column_float_multi_elts
         elif data_type == 3 :
             if (create or clone) :
-                column = OBIDMS_column_bool_writable(self, column_name, 
-                                                     create, clone, clone_data, 
-                                                     version_number, data_type, 
-                                                     nb_lines, nb_elements_per_line, 
-                                                     elements_names)
+                if nb_elements_per_line == 1 :
+                    subclass = OBIDMS_column_bool_writable
+                else :
+                    subclass = OBIDMS_column_bool_multi_elts_writable
             else :
-                 column = OBIDMS_column_bool(self, column_name, 
-                                                  create, clone, clone_data, 
-                                                  version_number, data_type, 
-                                                  nb_lines, nb_elements_per_line, 
-                                                  elements_names)
-
+                if nb_elements_per_line == 1 :
+                    subclass = OBIDMS_column_bool
+                else :
+                    subclass = OBIDMS_column_bool_multi_elts
         elif data_type == 4 :
             if (create or clone) :
-                column = OBIDMS_column_char_writable(self, column_name, 
-                                                     create, clone, clone_data, 
-                                                     version_number, data_type, 
-                                                     nb_lines, nb_elements_per_line, 
-                                                     elements_names)
+                if nb_elements_per_line == 1 :
+                    subclass = OBIDMS_column_char_writable
+                else :
+                    subclass = OBIDMS_column_char_multi_elts_writable
             else :
-                 column = OBIDMS_column_char(self, column_name, 
-                                                  create, clone, clone_data, 
-                                                  version_number, data_type, 
-                                                  nb_lines, nb_elements_per_line, 
-                                                  elements_names)
-    
-#         elif data_type == 5 :
-#             if (create or clone) :
-#                 column = OBIDMS_column_idx_writable(self, column_name, 
-#                                                     create, clone, clone_data, 
-#                                                     version_number, data_type, 
-#                                                     nb_lines, nb_elements_per_line, 
-#                                                     elements_names)
-#             else :
-#                  column = OBIDMS_column_idx(self, column_name, 
-#                                             create, clone, clone_data, 
-#                                             version_number, data_type, 
-#                                             nb_lines, nb_elements_per_line, 
-#                                             elements_names)
-   
+                if nb_elements_per_line == 1 :
+                    subclass = OBIDMS_column_char
+                else :
+                    subclass = OBIDMS_column_char_multi_elts
+        elif data_type == 5 :
+            if (create or clone) :
+                if nb_elements_per_line == 1 :
+                    subclass = OBIDMS_column_str_writable
+                else :
+                    subclass = OBIDMS_column_str_multi_elts_writable
+            else :
+                if nb_elements_per_line == 1 :
+                    subclass = OBIDMS_column_str
+                else :
+                    subclass = OBIDMS_column_str_multi_elts
         else :
             raise Exception("Problem with the data type")
             
+        column = subclass(self, column_name, 
+                          create, clone, clone_data, 
+                          version_number, data_type, 
+                          nb_lines, nb_elements_per_line, 
+                          elements_names, array_name)
+
         return column
 
 
@@ -196,88 +237,90 @@ cdef class OBIDMS_column :
                  bint clone, bint clone_data,
                  obiversion_t version_number, 
                  OBIType_t type,
-                 size_t nb_lines, 
-                 size_t nb_elements_per_line, 
-                 str elements_names):
+                 index_t nb_lines, 
+                 index_t nb_elements_per_line, 
+                 list elements_names,
+                 str array_name):
         
         # Declarations
         cdef bytes column_name_b
         cdef bytes dms_name_b
+        cdef bytes array_name_b
         cdef bytes elements_names_b
         
         # Fill structure
         self.dms = dms
         self.data_type = bytes2str(name_data_type(type))
         self.column_name = column_name
+        self.nb_elements_per_line = nb_elements_per_line
+        self.elements_names = elements_names
         
         # Format the character strings to send them to C functions
         column_name_b = str2bytes(column_name)
         dms_name_b = str2bytes(self.dms.dms_name)
+        array_name_b = str2bytes(array_name)
         
         # Create, clone or open column
         if create :
             if elements_names == None :  
                 elements_names_b = column_name_b
             else :
-                elements_names_b = str2bytes(elements_names)
-            self.pointer = obi_create_column(self.dms.pointer, column_name_b, type, nb_lines, nb_elements_per_line, elements_names_b)
+                elements_names_b = str2bytes(";".join(elements_names))
+            self.pointer = obi_create_column(self.dms.pointer, column_name_b, type, 
+                                             nb_lines, nb_elements_per_line, 
+                                             elements_names_b, array_name_b)
         else :
             if clone :
                 self.pointer = obi_clone_column(self.dms.pointer, column_name_b, version_number, clone_data)
             else :
                 self.pointer = obi_open_column(self.dms.pointer, column_name_b, version_number)
-    
+        
     
     def __iter__(self):
     
         # Declarations
-        cdef list elements_names
-        cdef str element_name
-        cdef bint multiple_elements
-        cdef object line               # TODO
-        cdef size_t lines_used
-        cdef size_t line_nb
-        
-        # Check if there are multiple elements per line anf if yes, get their names
-        elements_names = self.get_elements_names()
-        if len(elements_names) > 1 :
-            multiple_elements = True
-        else :
-            element_name = elements_names[0]
+        cdef index_t lines_used
+        cdef index_t line_nb
         
         # Yield each line
-        lines_used = obi_column_get_nb_lines_used(self.pointer)
-        for line_nb in xrange(lines_used):
-            if multiple_elements :
-                line = []
-                for element_name in elements_names :
-                    line.append(self.get_item(line_nb, element_name))
-            else :
-                line = self.get_item(line_nb, element_name)
-            yield line
+        lines_used = self.pointer.header.lines_used
+        for line_nb in range(lines_used):
+            yield self.get_line(line_nb)
 
 
-    def __setitem__(self, size_t line_nb, object value):
-        self.set_item(line_nb, "", value)
+    def __setitem__(self, index_t line_nb, object value):
+        self.set_line(line_nb, value)
 
-        
-    def __getitem__(self, size_t line_nb):
-        return self.get_item(line_nb, "")
 
-    cpdef object get_item(self, size_t line_nb, str element_name):
-        raise NotImplementedError
+    def __getitem__(self, index_t line_nb):
+        return self.get_line(line_nb)
+
+
+#    cpdef object get_item(self, index_t line_nb, str element_name):           TODO
+#        raise NotImplementedError
+
+
+#    cpdef set_item(self, index_t line_nb, str element_name, object value):    TODO
+#        raise NotImplementedError
+
     
     cpdef list get_elements_names(self):
-        cdef bytes elements_names
-        elements_names = obi_column_get_elements_names(self.pointer)
-        return (bytes2str(elements_names)).split(';')
+        return self.elements_names
 
              
     cpdef str get_data_type(self):
         return self.data_type
-
     
-    cpdef size_t get_nb_lines_used(self):
-        return obi_column_get_nb_lines_used(self.pointer)
-        
+    
+    cpdef index_t get_nb_lines_used(self):
+        return self.pointer.header.lines_used
+    
+    
+    cpdef str get_creation_date(self):
+        return bytes2str(obi_column_format_date(self.pointer.header.creation_date))
+    
+    
+    cpdef close(self):
+        raise NotImplementedError
+   
    

python/obitools3/obidms/_obidmscolumn_bool.cfiles

@@ -14,3 +14,5 @@
 ../../../src/obitypes.c
 ../../../src/private_at_functions.h
 ../../../src/private_at_functions.c
+../../../src/obiarray.h
+../../../src/obiarray.c

python/obitools3/obidms/_obidmscolumn_bool.pxd

@@ -1,17 +1,25 @@
 #cython: language_level=3
 
-from .capi.obitypes cimport obibool_t
-from .capi.obidmscolumn cimport OBIDMS_column_p
-                                                
-from ._obidms cimport OBIDMS_column
+from .capi.obitypes cimport obibool_t, index_t
+from ._obidms       cimport OBIDMS_column
 
 
 cdef class OBIDMS_column_bool(OBIDMS_column):
-    cpdef object get_item(self, size_t line_nb, str element_name)
-    cpdef set_item(self, size_t line_nb, str element_name, obibool_t value)
+    cpdef object get_line(self, index_t line_nb)
+    cpdef set_line(self, index_t line_nb, object value)
     cpdef close(self)
 
-cdef class OBIDMS_column_bool_writable(OBIDMS_column_bool):
-    cpdef set_item(self, size_t line_nb, str element_name, obibool_t value)
+cdef class OBIDMS_column_bool_writable(OBIDMS_column_bool):     
+    cpdef set_line(self, index_t line_nb, object value)
     cpdef close(self)
 
+cdef class OBIDMS_column_bool_multi_elts(OBIDMS_column_bool):
+    cpdef object get_item(self, index_t line_nb, str element_name)
+    cpdef object get_line(self, index_t line_nb)
+    cpdef set_item(self, index_t line_nb, str element_name, obibool_t value)
+    cpdef set_line(self, index_t line_nb, object values)
+
+cdef class OBIDMS_column_bool_multi_elts_writable(OBIDMS_column_bool_multi_elts):
+    cpdef set_item(self, index_t line_nb, str element_name, obibool_t value)
+    cpdef set_line(self, index_t line_nb, object values)
+    cpdef close(self)

python/obitools3/obidms/_obidmscolumn_bool.pyx

@@ -3,7 +3,9 @@
 from .capi.obidmscolumn cimport obi_close_column,\
                                 obi_truncate_and_close_column, \
                                 obi_column_get_obibool_with_elt_name, \
-                                obi_column_set_obibool_with_elt_name
+                                obi_column_get_obibool_with_elt_idx, \
+                                obi_column_set_obibool_with_elt_name, \
+                                obi_column_set_obibool_with_elt_idx
 from .capi.obierrno     cimport obi_errno
 from .capi.obitypes     cimport OBIBool_NA
 
@@ -13,8 +15,41 @@ from cpython.bool cimport PyBool_FromLong
 
 
 cdef class OBIDMS_column_bool(OBIDMS_column):
- 
-    cpdef object get_item(self, size_t line_nb, str element_name):
+
+    cpdef object get_line(self, index_t line_nb):
+        cdef obibool_t value
+        cdef object result
+        value = obi_column_get_obibool_with_elt_idx(self.pointer, line_nb, 0)
+        if obi_errno > 0 :
+            raise IndexError(line_nb)
+        if value == OBIBool_NA :
+            result = None
+        else :
+            result = PyBool_FromLong(value)
+        return result
+
+    cpdef set_line(self, index_t line_nb, object value):
+        raise Exception("Column is read-only")
+    
+    cpdef close(self):
+        if obi_close_column(self.pointer) < 0 :
+            raise Exception("Problem closing a column")
+
+
+cdef class OBIDMS_column_bool_writable(OBIDMS_column_bool):     
+
+    cpdef set_line(self, index_t line_nb, object value):
+        if obi_column_set_obibool_with_elt_idx(self.pointer, line_nb, 0, <obibool_t> value) < 0:
+            raise Exception("Problem setting a value in a column")
+
+    cpdef close(self):
+        if obi_truncate_and_close_column(self.pointer) < 0 :
+            raise Exception("Problem closing a column")
+
+
+cdef class OBIDMS_column_bool_multi_elts(OBIDMS_column_bool):
+
+    cpdef object get_item(self, index_t line_nb, str element_name):
         cdef obibool_t value
         cdef object result
         value = obi_column_get_obibool_with_elt_name(self.pointer, line_nb, str2bytes(element_name))
@@ -25,22 +60,45 @@ cdef class OBIDMS_column_bool(OBIDMS_column):
         else :
             result = PyBool_FromLong(value)
         return result
-     
-    cpdef set_item(self, size_t line_nb, str element_name, obibool_t value):
+    
+    cpdef object get_line(self, index_t line_nb) :
+        cdef obibool_t value
+        cdef object result
+        cdef index_t i
+        cdef bint all_NA
+        result = {}
+        all_NA = True
+        for i in range(self.nb_elements_per_line) :
+            value = obi_column_get_obibool_with_elt_idx(self.pointer, line_nb, i)
+            if obi_errno > 0 :
+                raise IndexError(line_nb)           
+            result[self.elements_names[i]] = PyBool_FromLong(value)
+            if all_NA and (value != OBIBool_NA) :
+                all_NA = False
+        if all_NA :
+            result = None
+        return result
+
+    cpdef set_item(self, index_t line_nb, str element_name, obibool_t value):
+        raise Exception("Column is read-only")
+
+    cpdef set_line(self, index_t line_nb, object values):
         raise Exception("Column is read-only")
-     
-    cpdef close(self):
-        if obi_close_column(self.pointer) < 0 :
-            raise Exception("Problem closing a column")
 
 
-cdef class OBIDMS_column_bool_writable(OBIDMS_column_bool):     
-   
-    cpdef set_item(self, size_t line_nb, str element_name, obibool_t value):
-        if obi_column_set_obibool_with_elt_name(self.pointer, line_nb, str2bytes(element_name), value) < 0 :
+cdef class OBIDMS_column_bool_multi_elts_writable(OBIDMS_column_bool_multi_elts):     
+
+    cpdef set_item(self, index_t line_nb, str element_name, obibool_t value):
+        if obi_column_set_obibool_with_elt_name(self.pointer, line_nb, str2bytes(element_name), value) < 0:
             raise Exception("Problem setting a value in a column")
- 
+    
+    cpdef set_line(self, index_t line_nb, object values):
+        cdef obibool_t value
+        for element_name in values :
+            value = <obibool_t> values[element_name]
+            self.set_item(line_nb, element_name, value)
+
     cpdef close(self):
         if obi_truncate_and_close_column(self.pointer) < 0 :
             raise Exception("Problem closing a column")
-     
+

python/obitools3/obidms/_obidmscolumn_char.cfiles

@@ -14,3 +14,5 @@
 ../../../src/obitypes.c
 ../../../src/private_at_functions.h
 ../../../src/private_at_functions.c
+../../../src/obiarray.h
+../../../src/obiarray.c

python/obitools3/obidms/_obidmscolumn_char.pxd

@@ -1,17 +1,25 @@
 #cython: language_level=3
 
-from .capi.obitypes cimport obichar_t
-from .capi.obidmscolumn cimport OBIDMS_column_p
-                                                
-from ._obidms cimport OBIDMS_column
+from .capi.obitypes cimport obichar_t, index_t
+from ._obidms       cimport OBIDMS_column
 
 
 cdef class OBIDMS_column_char(OBIDMS_column):
-    cpdef object get_item(self, size_t line_nb, str element_name)
-    cpdef set_item(self, size_t line_nb, str element_name, bytes value)
+    cpdef object get_line(self, index_t line_nb)
+    cpdef set_line(self, index_t line_nb, object value)
     cpdef close(self)
 
-cdef class OBIDMS_column_char_writable(OBIDMS_column_char):
-    cpdef set_item(self, size_t line_nb, str element_name, bytes value)
+cdef class OBIDMS_column_char_writable(OBIDMS_column_char):     
+    cpdef set_line(self, index_t line_nb, object value)
     cpdef close(self)
 
+cdef class OBIDMS_column_char_multi_elts(OBIDMS_column_char):
+    cpdef object get_item(self, index_t line_nb, str element_name)
+    cpdef object get_line(self, index_t line_nb)
+    cpdef set_item(self, index_t line_nb, str element_name, bytes value)
+    cpdef set_line(self, index_t line_nb, object values)
+
+cdef class OBIDMS_column_char_multi_elts_writable(OBIDMS_column_char_multi_elts):
+    cpdef set_item(self, index_t line_nb, str element_name, bytes value)
+    cpdef set_line(self, index_t line_nb, object values)
+    cpdef close(self)

python/obitools3/obidms/_obidmscolumn_char.pyx

@@ -3,17 +3,52 @@
 from .capi.obidmscolumn cimport obi_close_column,\
                                 obi_truncate_and_close_column, \
                                 obi_column_get_obichar_with_elt_name, \
-                                obi_column_set_obichar_with_elt_name
+                                obi_column_get_obichar_with_elt_idx, \
+                                obi_column_set_obichar_with_elt_name, \
+                                obi_column_set_obichar_with_elt_idx
 from .capi.obierrno     cimport obi_errno
 from .capi.obitypes     cimport OBIChar_NA
 
 from obitools3.utils cimport str2bytes
 
 
-cdef class OBIDMS_column_char(OBIDMS_column) :
- 
-    cpdef object get_item(self, size_t line_nb, str element_name):
-        cdef char value
+cdef class OBIDMS_column_char(OBIDMS_column):
+
+    cpdef object get_line(self, index_t line_nb):
+        cdef obichar_t value
+        cdef object result
+        value = obi_column_get_obichar_with_elt_idx(self.pointer, line_nb, 0)
+        if obi_errno > 0 :
+            raise IndexError(line_nb)
+        if value == OBIChar_NA :
+            result = None
+        else :
+            result = <bytes> value
+        return result
+
+    cpdef set_line(self, index_t line_nb, object value):
+        raise Exception("Column is read-only")
+    
+    cpdef close(self):
+        if obi_close_column(self.pointer) < 0 :
+            raise Exception("Problem closing a column")
+
+
+cdef class OBIDMS_column_char_writable(OBIDMS_column_char):     
+
+    cpdef set_line(self, index_t line_nb, object value):
+        if obi_column_set_obichar_with_elt_idx(self.pointer, line_nb, 0, <bytes> value[0]) < 0:
+            raise Exception("Problem setting a value in a column")
+
+    cpdef close(self):
+        if obi_truncate_and_close_column(self.pointer) < 0 :
+            raise Exception("Problem closing a column")
+
+
+cdef class OBIDMS_column_char_multi_elts(OBIDMS_column_char):
+
+    cpdef object get_item(self, index_t line_nb, str element_name):
+        cdef obichar_t value
         cdef object result
         value = obi_column_get_obichar_with_elt_name(self.pointer, line_nb, str2bytes(element_name))
         if obi_errno > 0 :
@@ -23,22 +58,81 @@ cdef class OBIDMS_column_char(OBIDMS_column) :
         else :
             result = <bytes> value
         return result
+    
+    cpdef object get_line(self, index_t line_nb) :
+        cdef obichar_t value
+        cdef object result
+        cdef index_t i
+        cdef bint all_NA
+        result = {}
+        all_NA = True
+        for i in range(self.nb_elements_per_line) :
+            value = obi_column_get_obichar_with_elt_idx(self.pointer, line_nb, i)
+            if obi_errno > 0 :
+                raise IndexError(line_nb)           
+            result[self.elements_names[i]] = <bytes> value
+            if all_NA and (value != OBIChar_NA) :
+                all_NA = False
+        if all_NA :
+            result = None
+        return result
 
-    cpdef set_item(self, size_t line_nb, str element_name, bytes value):
+    cpdef set_item(self, index_t line_nb, str element_name, bytes value):
         raise Exception("Column is read-only")
- 
-    cpdef close(self):
-        if obi_close_column(self.pointer) < 0 :
-            raise Exception("Problem closing a column")
- 
-         
-cdef class OBIDMS_column_char_writable(OBIDMS_column_char) :     
- 
-    cpdef set_item(self, size_t line_nb, str element_name, bytes value):
+
+    cpdef set_line(self, index_t line_nb, object values):
+        raise Exception("Column is read-only")
+
+
+cdef class OBIDMS_column_char_multi_elts_writable(OBIDMS_column_char_multi_elts):     
+
+    cpdef set_item(self, index_t line_nb, str element_name, bytes value):
         if obi_column_set_obichar_with_elt_name(self.pointer, line_nb, str2bytes(element_name), value[0]) < 0:
             raise Exception("Problem setting a value in a column")
- 
+    
+    cpdef set_line(self, index_t line_nb, object values):
+        cdef bytes value
+        for element_name in values :
+            value = <bytes> values[element_name]
+            self.set_item(line_nb, element_name, value)
+
     cpdef close(self):
         if obi_truncate_and_close_column(self.pointer) < 0 :
             raise Exception("Problem closing a column")
-      
+
+
+
+
+
+# cdef class OBIDMS_column_char(OBIDMS_column) :
+#  
+#     cpdef object get_item(self, index_t line_nb, str element_name):
+#         cdef char value
+#         cdef object result
+#         value = obi_column_get_obichar_with_elt_name(self.pointer, line_nb, str2bytes(element_name))
+#         if obi_errno > 0 :
+#             raise IndexError(line_nb, element_name)
+#         if value == OBIChar_NA :
+#             result = None
+#         else :
+#             result = <bytes> value
+#         return result
+# 
+#     cpdef set_item(self, index_t line_nb, str element_name, bytes value):
+#         raise Exception("Column is read-only")
+#  
+#     cpdef close(self):
+#         if obi_close_column(self.pointer) < 0 :
+#             raise Exception("Problem closing a column")
+#  
+#          
+# cdef class OBIDMS_column_char_writable(OBIDMS_column_char) :     
+#  
+#     cpdef set_item(self, index_t line_nb, str element_name, bytes value):
+#         if obi_column_set_obichar_with_elt_name(self.pointer, line_nb, str2bytes(element_name), value[0]) < 0:
+#             raise Exception("Problem setting a value in a column")
+#  
+#     cpdef close(self):
+#         if obi_truncate_and_close_column(self.pointer) < 0 :
+#             raise Exception("Problem closing a column")
+#       

python/obitools3/obidms/_obidmscolumn_float.cfiles

@@ -14,3 +14,5 @@
 ../../../src/obitypes.c
 ../../../src/private_at_functions.h
 ../../../src/private_at_functions.c
+../../../src/obiarray.h
+../../../src/obiarray.c

python/obitools3/obidms/_obidmscolumn_float.pxd

@@ -1,16 +1,25 @@
 #cython: language_level=3
 
-from .capi.obitypes cimport obifloat_t
-from .capi.obidmscolumn cimport OBIDMS_column_p
-                                                
-from ._obidms cimport OBIDMS_column
+from .capi.obitypes cimport obifloat_t, index_t
+from ._obidms       cimport OBIDMS_column
 
 
 cdef class OBIDMS_column_float(OBIDMS_column):
-    cpdef object get_item(self, size_t line_nb, str element_name)
-    cpdef set_item(self, size_t line_nb, str element_name, obifloat_t value)
+    cpdef object get_line(self, index_t line_nb)
+    cpdef set_line(self, index_t line_nb, object value)
     cpdef close(self)
-    
-cdef class OBIDMS_column_float_writable(OBIDMS_column_float):
-    cpdef set_item(self, size_t line_nb, str element_name, obifloat_t value)
+
+cdef class OBIDMS_column_float_writable(OBIDMS_column_float):     
+    cpdef set_line(self, index_t line_nb, object value)
+    cpdef close(self)
+
+cdef class OBIDMS_column_float_multi_elts(OBIDMS_column_float):
+    cpdef object get_item(self, index_t line_nb, str element_name)
+    cpdef object get_line(self, index_t line_nb)
+    cpdef set_item(self, index_t line_nb, str element_name, obifloat_t value)
+    cpdef set_line(self, index_t line_nb, object values)
+
+cdef class OBIDMS_column_float_multi_elts_writable(OBIDMS_column_float_multi_elts):
+    cpdef set_item(self, index_t line_nb, str element_name, obifloat_t value)
+    cpdef set_line(self, index_t line_nb, object values)
     cpdef close(self)

python/obitools3/obidms/_obidmscolumn_float.pyx

@@ -3,7 +3,9 @@
 from .capi.obidmscolumn cimport obi_close_column,\
                                 obi_truncate_and_close_column, \
                                 obi_column_get_obifloat_with_elt_name, \
-                                obi_column_set_obifloat_with_elt_name
+                                obi_column_get_obifloat_with_elt_idx, \
+                                obi_column_set_obifloat_with_elt_name, \
+                                obi_column_set_obifloat_with_elt_idx
 from .capi.obierrno     cimport obi_errno
 from .capi.obitypes     cimport OBIFloat_NA
 
@@ -12,7 +14,40 @@ from obitools3.utils cimport str2bytes
 
 cdef class OBIDMS_column_float(OBIDMS_column):
 
-    cpdef object get_item(self, size_t line_nb, str element_name):
+    cpdef object get_line(self, index_t line_nb):
+        cdef obifloat_t value
+        cdef object result
+        value = obi_column_get_obifloat_with_elt_idx(self.pointer, line_nb, 0)
+        if obi_errno > 0 :
+            raise IndexError(line_nb)
+        if value == OBIFloat_NA :
+            result = None
+        else :
+            result = <double> value
+        return result
+
+    cpdef set_line(self, index_t line_nb, object value):
+        raise Exception("Column is read-only")
+    
+    cpdef close(self):
+        if obi_close_column(self.pointer) < 0 :
+            raise Exception("Problem closing a column")
+
+
+cdef class OBIDMS_column_float_writable(OBIDMS_column_float):     
+
+    cpdef set_line(self, index_t line_nb, object value):
+        if obi_column_set_obifloat_with_elt_idx(self.pointer, line_nb, 0, <obifloat_t> value) < 0:
+            raise Exception("Problem setting a value in a column")
+
+    cpdef close(self):
+        if obi_truncate_and_close_column(self.pointer) < 0 :
+            raise Exception("Problem closing a column")
+
+
+cdef class OBIDMS_column_float_multi_elts(OBIDMS_column_float):
+
+    cpdef object get_item(self, index_t line_nb, str element_name):
         cdef obifloat_t value
         cdef object result
         value = obi_column_get_obifloat_with_elt_name(self.pointer, line_nb, str2bytes(element_name))
@@ -21,24 +56,48 @@ cdef class OBIDMS_column_float(OBIDMS_column):
         if value == OBIFloat_NA :
             result = None
         else :
-            result = <float> value
+            result = <double> value
         return result
     
-    cpdef set_item(self, size_t line_nb, str element_name, obifloat_t value):
+    cpdef object get_line(self, index_t line_nb) :
+        cdef obifloat_t value
+        cdef object result
+        cdef index_t i
+        cdef bint all_NA
+        result = {}
+        all_NA = True
+        for i in range(self.nb_elements_per_line) :
+            value = obi_column_get_obifloat_with_elt_idx(self.pointer, line_nb, i)
+            if obi_errno > 0 :
+                raise IndexError(line_nb)           
+            result[self.elements_names[i]] = <double> value
+            if all_NA and (value != OBIFloat_NA) :
+                all_NA = False
+        if all_NA :
+            result = None
+        return result
+
+    cpdef set_item(self, index_t line_nb, str element_name, obifloat_t value):
         raise Exception("Column is read-only")
 
-    cpdef close(self):
-        if obi_close_column(self.pointer) < 0 :
-            raise Exception("Problem closing a column")
-                  
+    cpdef set_line(self, index_t line_nb, object values):
+        raise Exception("Column is read-only")
 
-cdef class OBIDMS_column_float_writable(OBIDMS_column_float):     
 
-    cpdef set_item(self, size_t line_nb, str element_name, obifloat_t value):
+cdef class OBIDMS_column_float_multi_elts_writable(OBIDMS_column_float_multi_elts):     
+
+    cpdef set_item(self, index_t line_nb, str element_name, obifloat_t value):
         if obi_column_set_obifloat_with_elt_name(self.pointer, line_nb, str2bytes(element_name), value) < 0:
             raise Exception("Problem setting a value in a column")
+    
+    cpdef set_line(self, index_t line_nb, object values):
+        cdef obifloat_t value
+        for element_name in values :
+            value = <obifloat_t> values[element_name]
+            self.set_item(line_nb, element_name, value)
 
     cpdef close(self):
         if obi_truncate_and_close_column(self.pointer) < 0 :
             raise Exception("Problem closing a column")
+
  

python/obitools3/obidms/_obidmscolumn_idx.pxd

@@ -1,16 +0,0 @@
-#cython: language_level=3
-
-from .capi.obitypes cimport obiidx_t
-from .capi.obidmscolumn cimport OBIDMS_column_p
-                                                
-from ._obidms cimport OBIDMS_column
-
-
-cdef class OBIDMS_column_idx(OBIDMS_column):
-    cpdef object get_item(self, size_t line_nb, str element_name)
-    cpdef set_item(self, size_t line_nb, str element_name, obiidx_t value)
-    cpdef close(self)
-    
-cdef class OBIDMS_column_idx_writable(OBIDMS_column_idx):
-    cpdef set_item(self, size_t line_nb, str element_name, obiidx_t value)
-    cpdef close(self)

python/obitools3/obidms/_obidmscolumn_idx.pyx

@@ -1,46 +0,0 @@
-#cython: language_level=3
-
-from .capi.obidmscolumn cimport obi_close_column,\
-                                obi_truncate_and_close_column, \
-                                obi_column_get_obiidx_with_elt_name, \
-                                obi_column_set_obiidx_with_elt_name
-from .capi.obierrno     cimport obi_errno
-from .capi.obitypes     cimport OBIIdx_NA
-
-from obitools3.utils cimport str2bytes
-
-from cpython.int cimport PyInt_FromSsize_t
-
-
-cdef class OBIDMS_column_idx(OBIDMS_column):
-
-    cpdef object get_item(self, size_t line_nb, str element_name):
-        cdef obiidx_t value
-        cdef object result
-        value = obi_column_get_obiidx_with_elt_name(self.pointer, line_nb, str2bytes(element_name))
-        if obi_errno > 0 :
-            raise IndexError(line_nb, element_name)
-        if value == OBIIdx_NA :
-            result = None
-        else :
-            result = PyInt_FromSsize_t(value)
-        return result
-    
-    cpdef set_item(self, size_t line_nb, str element_name, obiidx_t value):
-        raise Exception("Column is read-only")
-
-    cpdef close(self):
-        if obi_close_column(self.pointer) < 0 :
-            raise Exception("Problem closing a column")
-                  
-
-cdef class OBIDMS_column_idx_writable(OBIDMS_column_idx):     
-
-    cpdef set_item(self, size_t line_nb, str element_name, obiidx_t value):
-        if obi_column_set_obiidx_with_elt_name(self.pointer, line_nb, str2bytes(element_name), value) < 0:
-            raise Exception("Problem setting a value in a column")
-
-    cpdef close(self):
-        if obi_truncate_and_close_column(self.pointer) < 0 :
-            raise Exception("Problem closing a column")
- 

python/obitools3/obidms/_obidmscolumn_int.cfiles

@@ -14,3 +14,5 @@
 ../../../src/obitypes.c
 ../../../src/private_at_functions.h
 ../../../src/private_at_functions.c
+../../../src/obiarray.h
+../../../src/obiarray.c

python/obitools3/obidms/_obidmscolumn_int.pxd

@@ -1,16 +1,25 @@
 #cython: language_level=3
 
-from .capi.obitypes cimport obiint_t
-from .capi.obidmscolumn cimport OBIDMS_column_p
-                                                
-from ._obidms cimport OBIDMS_column
+from .capi.obitypes cimport obiint_t, index_t
+from ._obidms       cimport OBIDMS_column
 
 
 cdef class OBIDMS_column_int(OBIDMS_column):
-    cpdef object get_item(self, size_t line_nb, str element_name)
-    cpdef set_item(self, size_t line_nb, str element_name, obiint_t value)
+    cpdef object get_line(self, index_t line_nb)
+    cpdef set_line(self, index_t line_nb, object value)
     cpdef close(self)
-    
-cdef class OBIDMS_column_int_writable(OBIDMS_column_int):
-    cpdef set_item(self, size_t line_nb, str element_name, obiint_t value)
+
+cdef class OBIDMS_column_int_writable(OBIDMS_column_int):     
+    cpdef set_line(self, index_t line_nb, object value)
+    cpdef close(self)
+
+cdef class OBIDMS_column_int_multi_elts(OBIDMS_column_int):
+    cpdef object get_item(self, index_t line_nb, str element_name)
+    cpdef object get_line(self, index_t line_nb)
+    cpdef set_item(self, index_t line_nb, str element_name, obiint_t value)
+    cpdef set_line(self, index_t line_nb, object values)
+
+cdef class OBIDMS_column_int_multi_elts_writable(OBIDMS_column_int_multi_elts):
+    cpdef set_item(self, index_t line_nb, str element_name, obiint_t value)
+    cpdef set_line(self, index_t line_nb, object values)
     cpdef close(self)

python/obitools3/obidms/_obidmscolumn_int.pyx

@@ -3,7 +3,9 @@
 from .capi.obidmscolumn cimport obi_close_column,\
                                 obi_truncate_and_close_column, \
                                 obi_column_get_obiint_with_elt_name, \
-                                obi_column_set_obiint_with_elt_name
+                                obi_column_get_obiint_with_elt_idx, \
+                                obi_column_set_obiint_with_elt_name, \
+                                obi_column_set_obiint_with_elt_idx
 from .capi.obierrno     cimport obi_errno
 from .capi.obitypes     cimport OBIInt_NA
 
@@ -11,12 +13,43 @@ from obitools3.utils cimport str2bytes
 
 from cpython.int cimport PyInt_FromLong
 
-from ._obidms cimport OBIDMS_column
-
 
 cdef class OBIDMS_column_int(OBIDMS_column):
 
-    cpdef object get_item(self, size_t line_nb, str element_name):
+    cpdef object get_line(self, index_t line_nb):
+        cdef obiint_t value
+        cdef object result
+        value = obi_column_get_obiint_with_elt_idx(self.pointer, line_nb, 0)
+        if obi_errno > 0 :
+            raise IndexError(line_nb)
+        if value == OBIInt_NA :
+            result = None
+        else :
+            result = PyInt_FromLong(value)
+        return result
+
+    cpdef set_line(self, index_t line_nb, object value):
+        raise Exception("Column is read-only")
+    
+    cpdef close(self):
+        if obi_close_column(self.pointer) < 0 :
+            raise Exception("Problem closing a column")
+
+
+cdef class OBIDMS_column_int_writable(OBIDMS_column_int):     
+
+    cpdef set_line(self, index_t line_nb, object value):
+        if obi_column_set_obiint_with_elt_idx(self.pointer, line_nb, 0, <obiint_t> value) < 0:
+            raise Exception("Problem setting a value in a column")
+
+    cpdef close(self):
+        if obi_truncate_and_close_column(self.pointer) < 0 :
+            raise Exception("Problem closing a column")
+
+
+cdef class OBIDMS_column_int_multi_elts(OBIDMS_column_int):
+
+    cpdef object get_item(self, index_t line_nb, str element_name):
         cdef obiint_t value
         cdef object result
         value = obi_column_get_obiint_with_elt_name(self.pointer, line_nb, str2bytes(element_name))
@@ -28,21 +61,44 @@ cdef class OBIDMS_column_int(OBIDMS_column):
             result = PyInt_FromLong(value)
         return result
     
-    cpdef set_item(self, size_t line_nb, str element_name, obiint_t value):
+    cpdef object get_line(self, index_t line_nb) :
+        cdef obiint_t value
+        cdef object result
+        cdef index_t i
+        cdef bint all_NA
+        result = {}
+        all_NA = True
+        for i in range(self.nb_elements_per_line) :
+            value = obi_column_get_obiint_with_elt_idx(self.pointer, line_nb, i)
+            if obi_errno > 0 :
+                raise IndexError(line_nb)           
+            result[self.elements_names[i]] = PyInt_FromLong(value)
+            if all_NA and (value != OBIInt_NA) :
+                all_NA = False
+        if all_NA :
+            result = None
+        return result
+
+    cpdef set_item(self, index_t line_nb, str element_name, obiint_t value):
         raise Exception("Column is read-only")
 
-    cpdef close(self):
-        if obi_close_column(self.pointer) < 0 :
-            raise Exception("Problem closing a column")
-                  
+    cpdef set_line(self, index_t line_nb, object values):
+        raise Exception("Column is read-only")
 
-cdef class OBIDMS_column_int_writable(OBIDMS_column_int):     
 
-    cpdef set_item(self, size_t line_nb, str element_name, obiint_t value):
+cdef class OBIDMS_column_int_multi_elts_writable(OBIDMS_column_int_multi_elts):     
+
+    cpdef set_item(self, index_t line_nb, str element_name, obiint_t value):
         if obi_column_set_obiint_with_elt_name(self.pointer, line_nb, str2bytes(element_name), value) < 0:
             raise Exception("Problem setting a value in a column")
+    
+    cpdef set_line(self, index_t line_nb, object values):
+        cdef obiint_t value
+        for element_name in values :
+            value = <obiint_t> values[element_name]
+            self.set_item(line_nb, element_name, value)
 
     cpdef close(self):
         if obi_truncate_and_close_column(self.pointer) < 0 :
             raise Exception("Problem closing a column")
- 
+

python/obitools3/obidms/_obidmscolumn_str.cfiles

@@ -1,5 +1,5 @@
-../../../src/obidmscolumn_idx.c
-../../../src/obidmscolumn_idx.h
+../../../src/obidmscolumn_str.c
+../../../src/obidmscolumn_str.h
 ../../../src/obidmscolumn.h
 ../../../src/obidmscolumn.c
 ../../../src/obidmscolumndir.h
@@ -14,3 +14,5 @@
 ../../../src/obitypes.c
 ../../../src/private_at_functions.h
 ../../../src/private_at_functions.c
+../../../src/obiarray.h
+../../../src/obiarray.c

python/obitools3/obidms/_obidmscolumn_str.pxd

@@ -0,0 +1,25 @@
+#cython: language_level=3
+
+from .capi.obitypes cimport index_t
+from ._obidms       cimport OBIDMS_column
+
+
+cdef class OBIDMS_column_str(OBIDMS_column):
+    cpdef object get_line(self, index_t line_nb)
+    cpdef set_line(self, index_t line_nb, object value)
+    cpdef close(self)
+
+cdef class OBIDMS_column_str_writable(OBIDMS_column_str):     
+    cpdef set_line(self, index_t line_nb, object value)
+    cpdef close(self)
+
+cdef class OBIDMS_column_str_multi_elts(OBIDMS_column_str):
+    cpdef object get_item(self, index_t line_nb, str element_name)
+    cpdef object get_line(self, index_t line_nb)
+    cpdef set_item(self, index_t line_nb, str element_name, str value)
+    cpdef set_line(self, index_t line_nb, object values)
+
+cdef class OBIDMS_column_str_multi_elts_writable(OBIDMS_column_str_multi_elts):
+    cpdef set_item(self, index_t line_nb, str element_name, str value)
+    cpdef set_line(self, index_t line_nb, object values)
+    cpdef close(self)

python/obitools3/obidms/_obidmscolumn_str.pyx

@@ -0,0 +1,103 @@
+#cython: language_level=3
+ 
+from .capi.obidmscolumn cimport obi_close_column,\
+                                obi_truncate_and_close_column, \
+                                obi_column_get_obistr_with_elt_name, \
+                                obi_column_get_obistr_with_elt_idx, \
+                                obi_column_set_obistr_with_elt_name, \
+                                obi_column_set_obistr_with_elt_idx
+from .capi.obierrno     cimport obi_errno
+from .capi.obitypes     cimport OBIIdx_NA, const_char_p
+
+from obitools3.utils cimport str2bytes, bytes2str
+
+
+cdef class OBIDMS_column_str(OBIDMS_column):
+
+    cpdef object get_line(self, index_t line_nb):
+        cdef bytes value
+        cdef object result
+        value = <bytes> obi_column_get_obistr_with_elt_idx(self.pointer, line_nb, 0)
+        if obi_errno > 0 :
+            raise IndexError(line_nb)
+        if value == OBIIdx_NA :
+            result = None
+        else :
+            result = bytes2str(value)
+        return result
+
+    cpdef set_line(self, index_t line_nb, object value):
+        raise Exception("Column is read-only")
+    
+    cpdef close(self):
+        if obi_close_column(self.pointer) < 0 :
+            raise Exception("Problem closing a column")
+
+
+cdef class OBIDMS_column_str_writable(OBIDMS_column_str):     
+
+    cpdef set_line(self, index_t line_nb, object value):
+        if obi_column_set_obistr_with_elt_idx(self.pointer, line_nb, 0, str2bytes(value)) < 0:
+            raise Exception("Problem setting a value in a column")
+
+    cpdef close(self):
+        if obi_truncate_and_close_column(self.pointer) < 0 :
+            raise Exception("Problem closing a column")
+
+
+cdef class OBIDMS_column_str_multi_elts(OBIDMS_column_str):
+
+    cpdef object get_item(self, index_t line_nb, str element_name):
+        cdef bytes value
+        cdef object result
+        value = <bytes> obi_column_get_obistr_with_elt_name(self.pointer, line_nb, str2bytes(element_name))
+        if obi_errno > 0 :
+            raise IndexError(line_nb, element_name)
+        if value == OBIIdx_NA :
+            result = None
+        else :
+            result = bytes2str(value)
+        return result
+    
+    cpdef object get_line(self, index_t line_nb) :
+        cdef bytes value
+        cdef object result
+        cdef index_t i
+        cdef bint all_NA
+        result = {}
+        all_NA = True
+        for i in range(self.nb_elements_per_line) :
+            value = <bytes> obi_column_get_obistr_with_elt_idx(self.pointer, line_nb, i)
+            if obi_errno > 0 :
+                raise IndexError(line_nb)           
+            result[self.elements_names[i]] = bytes2str(value)
+            if all_NA and (value != OBIIdx_NA) :
+                all_NA = False
+        if all_NA :
+            result = None
+        return result
+
+    cpdef set_item(self, index_t line_nb, str element_name, str value):
+        raise Exception("Column is read-only")
+
+    cpdef set_line(self, index_t line_nb, object values):
+        raise Exception("Column is read-only")
+
+
+cdef class OBIDMS_column_str_multi_elts_writable(OBIDMS_column_str_multi_elts):     
+
+    cpdef set_item(self, index_t line_nb, str element_name, str value):
+        if obi_column_set_obistr_with_elt_name(self.pointer, line_nb, str2bytes(element_name), str2bytes(value)) < 0:
+            raise Exception("Problem setting a value in a column")
+    
+    cpdef set_line(self, index_t line_nb, object values):
+        cdef str value
+        for element_name in values :
+            value = values[element_name]
+            self.set_item(line_nb, element_name, value)
+
+    cpdef close(self):
+        if obi_truncate_and_close_column(self.pointer) < 0 :
+            raise Exception("Problem closing a column")
+
+ 

python/obitools3/obidms/capi/obidmscolumn.pxd

@@ -8,38 +8,48 @@ from ..capi.obitypes cimport const_char_p, \
                              obibool_t, \
                              obichar_t, \
                              obifloat_t, \
-                             obiidx_t
+                             index_t, \
+                             time_t
+
 
 cdef extern from "obidmscolumn.h" nogil:
+    
+    struct OBIDMS_column_header_t:
+        bint            little_endian
+        int             header_size
+        index_t         line_count
+        index_t         lines_used
+        index_t         nb_elements_per_line
+        const_char_p    elements_names
+        OBIType_t       data_type
+        time_t          creation_date
+        obiversion_t    version
+        obiversion_t    cloned_from
+        const_char_p    name
+        const_char_p    array_name
+        const_char_p    comments
+    
+    ctypedef OBIDMS_column_header_t* OBIDMS_column_header_p
+
     struct OBIDMS_column_t:
-        pass
+        OBIDMS_column_header_p header
 
     ctypedef OBIDMS_column_t* OBIDMS_column_p
 
     OBIDMS_column_p obi_create_column(OBIDMS_p dms, 
                                       const_char_p column_name, 
                                       OBIType_t type, 
-                                      size_t nb_lines, 
-                                      size_t nb_elements_per_line, 
-                                      const_char_p elements_names)
-    
-    size_t obi_column_get_nb_lines_used(OBIDMS_column_p column)
-    
-    const_char_p obi_column_get_elements_names(OBIDMS_column_p column)
-    
-    void obi_column_make_unwritable(OBIDMS_column_p column)
-    
+                                      index_t nb_lines, 
+                                      index_t nb_elements_per_line, 
+                                      const_char_p elements_names,
+                                      const_char_p array_name)
+                
     OBIDMS_column_p obi_open_column(OBIDMS_p dms, 
                                     const_char_p column_name, 
                                     obiversion_t version_number)
-    
-    OBIType_t obi_column_get_type(OBIDMS_column_p column)
-    
+        
     int obi_close_column(OBIDMS_column_p column)
-    
-    OBIType_t obi_column_get_data_type_from_name(OBIDMS_p dms, 
-                                                 const_char_p column_name)
-    
+        
     OBIDMS_column_p obi_clone_column(OBIDMS_p dms, 
                                      const_char_p column_name, 
                                      obiversion_t version_number, 
@@ -49,65 +59,112 @@ cdef extern from "obidmscolumn.h" nogil:
     
     obiversion_t obi_column_get_latest_version_from_name(OBIDMS_p dms, 
                                                          const_char_p column_name)
+        
+    OBIDMS_column_header_p obi_column_get_header_from_name(OBIDMS_p dms, 
+                                                           const_char_p column_name)
     
-    OBIType_t obi_column_get_data_type_from_name(OBIDMS_p dms, 
-                                                 const_char_p column_name)
-    
-    size_t obi_column_get_line_count_from_name(OBIDMS_p dms, 
-                                               const_char_p column_name)
-    
+    int obi_unmap_header(OBIDMS_column_header_p header)
+        
+    char* obi_column_format_date(time_t date)
+
     
 cdef extern from "obidmscolumn_int.h" nogil:
     int obi_column_set_obiint_with_elt_name(OBIDMS_column_p column, 
-                                            size_t line_nb, 
+                                            index_t line_nb, 
                                             const_char_p element_name, 
                                             obiint_t value)
+
+    int obi_column_set_obiint_with_elt_idx(OBIDMS_column_p column, 
+                                           index_t line_nb, 
+                                           index_t element_idx, 
+                                        obiint_t value)
     
     obiint_t obi_column_get_obiint_with_elt_name(OBIDMS_column_p column, 
-                                                 size_t line_nb, 
+                                                 index_t line_nb, 
                                                  const_char_p element_name)
+    
+    obiint_t obi_column_get_obiint_with_elt_idx(OBIDMS_column_p column, 
+                                                index_t line_nb, 
+                                                index_t element_idx)
+
 
 cdef extern from "obidmscolumn_bool.h" nogil:
 
     int obi_column_set_obibool_with_elt_name(OBIDMS_column_p column, 
-                                             size_t line_nb, 
+                                             index_t line_nb, 
                                              const_char_p element_name, 
                                              obibool_t value)
     
+    int obi_column_set_obibool_with_elt_idx(OBIDMS_column_p column, 
+                                            index_t line_nb, 
+                                            index_t element_idx, 
+                                            obibool_t value)
+    
     obibool_t obi_column_get_obibool_with_elt_name(OBIDMS_column_p column, 
-                                                   size_t line_nb, 
+                                                   index_t line_nb, 
                                                    const_char_p element_name)
+    
+    obibool_t obi_column_get_obibool_with_elt_idx(OBIDMS_column_p column, 
+                                                  index_t line_nb, 
+                                                  index_t element_idx)
 
 cdef extern from "obidmscolumn_char.h" nogil:
 
     int obi_column_set_obichar_with_elt_name(OBIDMS_column_p column, 
-                                             size_t line_nb, 
+                                             index_t line_nb, 
                                              const_char_p element_name, 
                                              obichar_t value)
     
+    int obi_column_set_obichar_with_elt_idx(OBIDMS_column_p column, 
+                                            index_t line_nb, 
+                                            index_t element_idx, 
+                                            obichar_t value)
+    
     obichar_t obi_column_get_obichar_with_elt_name(OBIDMS_column_p column, 
-                                                   size_t line_nb, 
+                                                   index_t line_nb, 
                                                    const_char_p element_name)
+    
+    obichar_t obi_column_get_obichar_with_elt_idx(OBIDMS_column_p column, 
+                                                  index_t line_nb, 
+                                                  index_t element_idx)
 
 cdef extern from "obidmscolumn_float.h" nogil:
 
     int obi_column_set_obifloat_with_elt_name(OBIDMS_column_p column, 
-                                              size_t line_nb, 
+                                              index_t line_nb, 
                                               const_char_p element_name, 
                                               obifloat_t value)
     
-    obifloat_t obi_column_get_obifloat_with_elt_name(OBIDMS_column_p column, 
-                                                     size_t line_nb, 
-                                                     const_char_p element_name)
-
-cdef extern from "obidmscolumn_idx.h" nogil:
-
-    int obi_column_set_obiidx_with_elt_name(OBIDMS_column_p column, 
-                                            size_t line_nb, 
-                                            const_char_p element_name, 
-                                            obiidx_t value)
+    int obi_column_set_obifloat_with_elt_idx(OBIDMS_column_p column, 
+                                             index_t line_nb, 
+                                             index_t element_idx, 
+                                             obifloat_t value)
     
-    obiidx_t obi_column_get_obiidx_with_elt_name(OBIDMS_column_p column, 
-                                                 size_t line_nb, 
-                                                 const_char_p element_name)
+    obifloat_t obi_column_get_obifloat_with_elt_name(OBIDMS_column_p column, 
+                                                     index_t line_nb, 
+                                                     const_char_p element_name)
+    
+    obifloat_t obi_column_get_obifloat_with_elt_idx(OBIDMS_column_p column, 
+                                                    index_t line_nb, 
+                                                    index_t element_idx)
+
+cdef extern from "obidmscolumn_str.h" nogil:
+
+    int obi_column_set_obistr_with_elt_name(OBIDMS_column_p column, 
+                                            index_t line_nb, 
+                                            const_char_p element_name, 
+                                            char* value)
+    
+    int obi_column_set_obistr_with_elt_idx(OBIDMS_column_p column, 
+                                           index_t line_nb, 
+                                           index_t element_idx, 
+                                           char* value)
+    
+    const_char_p obi_column_get_obistr_with_elt_name(OBIDMS_column_p column, 
+                                              index_t line_nb, 
+                                              const_char_p element_name)
+    
+    const_char_p obi_column_get_obistr_with_elt_idx(OBIDMS_column_p column, 
+                                             index_t line_nb, 
+                                             index_t element_idx)
 

python/obitools3/obidms/capi/obitypes.pxd

@@ -1,7 +1,8 @@
 #cython: language_level=3
 
 
-from libc.stdint cimport int32_t
+from libc.stdint cimport int32_t, int64_t
+from posix.types cimport time_t
 
 
 cdef extern from *:
@@ -32,10 +33,10 @@ cdef extern from "obitypes.h" nogil:
     ctypedef int32_t obiint_t
     ctypedef double obifloat_t
     ctypedef char obichar_t  
-    ctypedef size_t obiidx_t
+    ctypedef int64_t index_t
 
     extern obiint_t   OBIInt_NA
-    extern obiidx_t   OBIIdx_NA
+    extern index_t    OBIIdx_NA
     extern obifloat_t OBIFloat_NA
     extern obichar_t  OBIChar_NA
     extern obibool_t  OBIBool_NA

python/obitools3/unit_tests.py

@@ -0,0 +1,271 @@
+import os
+import sys
+import shutil
+import unittest
+from random import randint, uniform, choice
+import string
+
+from obitools3.obidms._obidms import OBIDMS
+
+
+LINE_COUNT_FOR_TEST_COLUMN = 10000         # TODO randomize?
+SMALLER_LINE_COUNT_FOR_TEST_COLUMN = 1000  # TODO randomize?
+NB_ELEMENTS_PER_LINE = 20                  # TODO randomize?
+DMS_NAME = "unit_test_dms"
+DATA_TYPES = ['OBI_INT', 'OBI_FLOAT', 'OBI_BOOL', 'OBI_CHAR', 'OBI_IDX']
+
+
+def create_test_obidms():
+    dms_name = DMS_NAME
+    dms_dir_name = dms_name+'.obidms'
+    dms = OBIDMS(dms_name)
+    return (dms, dms_name, dms_dir_name)
+
+
+def create_test_column(dms, data_type_code, multiple_elements_per_line=False):
+    data_types = DATA_TYPES
+    data_type_code = data_type_code
+    data_type_str = data_types[data_type_code-1]
+    col_name = "unit_test_"+data_type_str
+        
+    if multiple_elements_per_line :
+        elts_names = elements_names()
+        col = dms.open_column(col_name, 
+                              create=True, 
+                              data_type=data_type_code, 
+                              nb_elements_per_line=NB_ELEMENTS_PER_LINE,
+                              elements_names=elts_names)
+        return (col, col_name, elts_names, data_type_str)
+
+    else :
+        col = dms.open_column(col_name, 
+                              create=True, 
+                              data_type=data_type_code)
+        return (col, col_name, data_type_str)
+
+
+def elements_names():
+    names = [str(i) for i in range(NB_ELEMENTS_PER_LINE)]
+    return names
+
+
+def random_obivalue(data_type):
+    r = 1000000
+    if data_type == "OBI_INT" :
+        return randint(-r,r)
+    elif data_type == "OBI_FLOAT" :
+        return uniform(-r,r)
+    elif data_type == "OBI_BOOL" :
+        return randint(0,1)
+    elif data_type == "OBI_CHAR" :
+        nucs = 'atgc'
+        return bytes(nucs[randint(0,3)], 'utf-8')
+    elif data_type == "OBI_IDX" :
+        length = randint(1,500)
+        randoms = ''.join(choice(string.ascii_lowercase) for i in range(length))
+        return randoms
+
+class OBIDMS_Column_TestCase(unittest.TestCase):
+    def tearDown(self):
+        self.col.close()
+        self.dms.close()
+        shutil.rmtree(self.dms_dir_name, ignore_errors=True)
+    def test_OBIDMS_column_type(self):
+        assert self.col.get_data_type() == self.data_type_str, 'Wrong data type associated with column'
+    def test_OBIDMS_column_cloning(self):
+        for i in range(LINE_COUNT_FOR_TEST_COLUMN):
+            self.col[i]= random_obivalue(self.data_type_str)
+        self.col.close()
+        clone = self.dms.open_column(self.col_name, clone=True)
+        self.col = self.dms.open_column(self.col_name)
+        assert clone.get_nb_lines_used() == self.col.get_nb_lines_used(), "Cloned column doesn't have the same number of lines used"
+        i=0
+        for i in range(clone.get_nb_lines_used()) :
+            assert clone[i] == self.col[i], "Different value in original column and cloned column"
+            assert clone[i] is not None, "None value"
+        clone.close()
+    def test_OBIDMS_column_set_and_get(self):
+        for i in range(LINE_COUNT_FOR_TEST_COLUMN):
+            v = random_obivalue(self.data_type_str)
+            self.col[i] = v
+            assert self.col[i] == v, "Different value than the set value"
+            assert self.col[i] is not None, "None value"
+
+
+class OBIDMS_Column_multiple_elements_TestCase(OBIDMS_Column_TestCase):
+    def test_OBIDMS_column_cloning(self):
+        pass
+        for i in range(SMALLER_LINE_COUNT_FOR_TEST_COLUMN):
+            v = {}
+            for e in self.elts_names :
+                v[e] = random_obivalue(self.data_type_str)
+            self.col[i] = v
+        self.col.close()
+        clone = self.dms.open_column(self.col_name, clone=True)
+        self.col = self.dms.open_column(self.col_name)
+        assert clone.get_nb_lines_used() == self.col.get_nb_lines_used(), "Cloned column doesn't have the same number of lines used"
+        i=0
+        for i in range(SMALLER_LINE_COUNT_FOR_TEST_COLUMN):
+            assert self.col[i] == clone[i], "Different value in original column and cloned column"
+            assert self.col[i] is not None, "None value"
+        clone.close()
+    def test_OBIDMS_column_set_and_get_with_elements_names(self):
+        for i in range(SMALLER_LINE_COUNT_FOR_TEST_COLUMN):
+            for e in range(NB_ELEMENTS_PER_LINE) :
+                v = random_obivalue(self.data_type_str)
+                self.col.set_item(i, self.elts_names[e], v)
+                assert self.col.get_item(i, self.elts_names[e]) == v, "Different value than the set value"
+                assert self.col.get_item(i, self.elts_names[e]) is not None, "None value"
+    def test_OBIDMS_column_set_and_get(self):
+        for i in range(SMALLER_LINE_COUNT_FOR_TEST_COLUMN):
+            v = {}
+            for e in self.elts_names :
+                v[e] = random_obivalue(self.data_type_str)
+            self.col[i] = v
+            assert self.col[i] == v, "Different value than the set value"
+            assert self.col[i] is not None, "None value"
+
+
+class OBIDMS_Column_OBI_INT_TestCase(OBIDMS_Column_TestCase):
+    def setUp(self):
+        self.data_type_code = 1
+        self.dms, \
+        self.dms_name, \
+        self.dms_dir_name = create_test_obidms()
+        self.col, \
+        self.col_name, \
+        self.data_type_str = create_test_column(self.dms, 
+                                                self.data_type_code)
+       
+
+class OBIDMS_Column_OBI_INT_multiple_elements_TestCase(OBIDMS_Column_multiple_elements_TestCase):
+    def setUp(self):
+        self.data_type_code = 1
+        self.dms, \
+        self.dms_name, \
+        self.dms_dir_name = create_test_obidms()
+        self.col, \
+        self.col_name, \
+        self.elts_names, \
+        self.data_type_str = create_test_column(self.dms, 
+                                                self.data_type_code,
+                                                multiple_elements_per_line=True)
+
+
+class OBIDMS_Column_OBI_FLOAT_TestCase(OBIDMS_Column_TestCase):
+    def setUp(self):
+        self.data_type_code = 2
+        self.dms, \
+        self.dms_name, \
+        self.dms_dir_name = create_test_obidms()
+        self.col, \
+        self.col_name, \
+        self.data_type_str = create_test_column(self.dms, 
+                                                self.data_type_code)
+       
+
+class OBIDMS_Column_OBI_FLOAT_multiple_elements_TestCase(OBIDMS_Column_multiple_elements_TestCase):
+    def setUp(self):
+        self.data_type_code = 2
+        self.dms, \
+        self.dms_name, \
+        self.dms_dir_name = create_test_obidms()
+        self.col, \
+        self.col_name, \
+        self.elts_names, \
+        self.data_type_str = create_test_column(self.dms, 
+                                                self.data_type_code,
+                                                multiple_elements_per_line=True)
+
+
+class OBIDMS_Column_OBI_BOOL_TestCase(OBIDMS_Column_TestCase):
+    def setUp(self):
+        self.data_type_code = 3
+        self.dms, \
+        self.dms_name, \
+        self.dms_dir_name = create_test_obidms()
+        self.col, \
+        self.col_name, \
+        self.data_type_str = create_test_column(self.dms, 
+                                                self.data_type_code)
+       
+
+class OBIDMS_Column_OBI_BOOL_multiple_elements_TestCase(OBIDMS_Column_multiple_elements_TestCase):
+    def setUp(self):
+        self.data_type_code = 3
+        self.dms, \
+        self.dms_name, \
+        self.dms_dir_name = create_test_obidms()
+        self.col, \
+        self.col_name, \
+        self.elts_names, \
+        self.data_type_str = create_test_column(self.dms, 
+                                                self.data_type_code,
+                                                multiple_elements_per_line=True)
+
+
+class OBIDMS_Column_OBI_CHAR_TestCase(OBIDMS_Column_TestCase):
+    def setUp(self):
+        self.data_type_code = 4
+        self.dms, \
+        self.dms_name, \
+        self.dms_dir_name = create_test_obidms()
+        self.col, \
+        self.col_name, \
+        self.data_type_str = create_test_column(self.dms, 
+                                                self.data_type_code)
+       
+
+class OBIDMS_Column_OBI_CHAR_multiple_elements_TestCase(OBIDMS_Column_multiple_elements_TestCase):
+    def setUp(self):
+        self.data_type_code = 4
+        self.dms, \
+        self.dms_name, \
+        self.dms_dir_name = create_test_obidms()
+        self.col, \
+        self.col_name, \
+        self.elts_names, \
+        self.data_type_str = create_test_column(self.dms, 
+                                                self.data_type_code,
+                                                multiple_elements_per_line=True)
+
+
+class OBIDMS_Column_OBI_STR_TestCase(OBIDMS_Column_TestCase):
+    def setUp(self):
+        self.data_type_code = 5
+        self.dms, \
+        self.dms_name, \
+        self.dms_dir_name = create_test_obidms()
+        self.col, \
+        self.col_name, \
+        self.data_type_str = create_test_column(self.dms, 
+                                                self.data_type_code)
+       
+
+class OBIDMS_Column_OBI_STR_multiple_elements_TestCase(OBIDMS_Column_multiple_elements_TestCase):
+    def setUp(self):
+        self.data_type_code = 5
+        self.dms, \
+        self.dms_name, \
+        self.dms_dir_name = create_test_obidms()
+        self.col, \
+        self.col_name, \
+        self.elts_names, \
+        self.data_type_str = create_test_column(self.dms, 
+                                                self.data_type_code,
+                                                multiple_elements_per_line=True)
+
+
+if __name__ == '__main__': 
+     unittest.main(verbosity=2, defaultTest=["OBIDMS_Column_OBI_INT_TestCase",
+                                             "OBIDMS_Column_OBI_INT_multiple_elements_TestCase",
+                                             "OBIDMS_Column_OBI_FLOAT_TestCase",
+                                             "OBIDMS_Column_OBI_FLOAT_multiple_elements_TestCase",
+                                             "OBIDMS_Column_OBI_BOOL_TestCase",
+                                             "OBIDMS_Column_OBI_BOOL_multiple_elements_TestCase",
+                                             "OBIDMS_Column_OBI_CHAR_TestCase",
+                                             "OBIDMS_Column_OBI_CHAR_multiple_elements_TestCase",
+                                             "OBIDMS_Column_OBI_STR_TestCase",
+                                             "OBIDMS_Column_OBI_STR_multiple_elements_TestCase"])
+
+

python/obitools3/version.py

@@ -2,4 +2,4 @@ major = 1
 minor = 1
 serial= '16'
 
-version ="%2d.%02d.%s" % (major,minor,serial)
+version ="%d.%02d.%s" % (major,minor,serial)

src/obiarray.h

@@ -0,0 +1,285 @@
+/****************************************************************************
+ * OBIDMS array header file	                                                *
+ ****************************************************************************/
+
+/**
+ * @file obiarray.h
+ * @author Celine Mercier
+ * @date October 19th 2015
+ * @brief Header file for handling arrays for storing and retrieving byte arrays (i.e. coding for character strings).
+ */
+
+
+#ifndef OBIARRAY_H_
+#define OBIARRAY_H_
+
+
+#include <stdlib.h>
+#include <stdio.h>
+#include <stdint.h>
+#include <time.h>
+#include <sys/types.h>
+#include <dirent.h>
+
+#include "obidms.h"
+#include "obitypes.h"
+
+
+#define ARRAY_MAX_NAME (2048) 		/**< The maximum length of an array name.
+                              	  	 */
+#define ARRAY_GROWTH_FACTOR (2)		/**< The growth factor when an array is enlarged.
+                                	 */
+#define BYTE_ARRAY_HEADER_SIZE (5)  /**< The size of the header of a byte array.
+                              	  	 */
+
+
+typedef char byte_t;		/**< Defining byte type since data is stored in bits
+							 *	 and char (stored on one byte) is the smallest addressable unit.
+ 	 	 	 	 	 	 	 */
+
+
+/**
+ * @brief OBIDMS array data header structure.
+ */
+typedef struct OBIDMS_array_data_header {
+	int			header_size;						/**< Size of the header in bytes.
+	 	 	 	 	 	 	 	 	 	 	 	 	 */
+	index_t		data_size_used;						/**< Size of the data used in bytes.
+	 	 	 	 	 	 	 	 	 	 	 	 	 */
+	index_t		data_size_max;						/**< Max size of the data in bytes.
+	 	 	 	 	 	 	 	 	 	 	 	 	 */
+	index_t		nb_items;							/**< Number of items.
+	 	 	 	 	 	 	 	 	 	 	 	 	 */
+	char    	array_name[ARRAY_MAX_NAME+1];		/**< The array name as a NULL terminated string.
+													 */
+	time_t		creation_date;			    	    /**< Date of creation of the file.
+												     */
+} OBIDMS_array_data_header_t, *OBIDMS_array_data_header_p;
+
+
+/**
+ * @brief OBIDMS array data structure.
+ */
+typedef struct OBIDMS_array_data {
+	OBIDMS_array_data_header_p	header; 		 	/**< A pointer to the header of the array data.
+	 	 	 	 	 	 	 	 	 	 	 	 	 */
+	byte_t*                   	data;   		 	/**< A pointer to the beginning of the data.
+													 */
+} OBIDMS_array_data_t, *OBIDMS_array_data_p;
+
+
+/**
+ * @brief OBIDMS array header structure.
+ */
+typedef struct OBIDMS_array_header {
+	int			header_size;						/**< Size of the header in bytes.
+	 	 	 	 	 	 	 	 	 	 	 	 	 */
+	size_t		array_size;							/**< Size of the array in bytes.
+	 	 	 	 	 	 	 	 	 	 	 	 	 */
+	index_t		nb_items;							/**< Number of items in the array.
+	 	 	 	 	 	 	 	 	 	 	 	 	 */
+	index_t		nb_items_max;						/**< Maximum number of items in the array before it has to be enlarged.
+	 	 	 	 	 	 	 	 	 	 	 	 	 */
+	char    	array_name[ARRAY_MAX_NAME+1];		/**< The array name as a NULL terminated string.
+													 */
+	time_t		creation_date;			    	    /**< Date of creation of the file.
+												     */
+} OBIDMS_array_header_t, *OBIDMS_array_header_p;
+
+
+/**
+ * @brief OBIDMS array structure.
+ */
+typedef struct OBIDMS_array {
+	OBIDMS_array_header_p		header; 		 	/**< A pointer to the header of the array.
+	 	 	 	 	 	 	 	 	 	 	 	 	 */
+	index_t*                 	first;   		 	/**< A pointer to the beginning of the array itself.
+													 */
+	OBIDMS_array_data_p			data;				/**< A pointer to the structure containing the data
+													 *   that the array references.
+	 	 	 	 	 	 	 	 	 	 	 	 	 */
+	DIR*						directory;			/**< A directory entry usable to
+										 	 	 	 *    refer and scan the array directory.
+										 	 	 	 */
+} OBIDMS_array_t, *OBIDMS_array_p;
+
+
+/**
+ * @brief Checks if an obiarray already exists or not.
+ *
+ * @param dms The OBIDMS to which the obiarray belongs.
+ * @param array_name The name of the obiarray.
+ *
+ * @returns A value indicating whether the obiarray exists or not.
+ * @retval 1 if the obiarray exists.
+ * @retval 0 if the obiarray does not exist.
+ * @retval -1 if an error occurred.
+ *
+ * @since October 2015
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+int obi_array_exists(OBIDMS_p dms, const char* array_name);
+
+
+/**
+ * @brief Opens an obiarray and creates it if it does not already exist.
+ *
+ * Note: An obiarray is made of two files (referred to by two structures).
+ * 		 One file contains the indices referring to the data, and the other
+ * 		 file contains the data itself. The obiarray as a whole is referred
+ * 		 to via the OBIDMS_array structure.
+ *
+ * @param dms The OBIDMS to which the obiarray belongs.
+ * @param array_name The name of the obiarray.
+ *
+ * @returns A pointer to the obiarray structure.
+ * @retval NULL if an error occurred.
+ *
+ * @since October 2015
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+OBIDMS_array_p obi_array(OBIDMS_p dms, const char* array_name);
+
+
+/**
+ * @brief Creates an obiarray. Fails if it already exists.
+ *
+ * Note: An obiarray is made of two files (referred to by two structures).
+ * 		 One file contains the indices referring to the data, and the other
+ * 		 file contains the data itself. The obiarray as a whole is referred
+ * 		 to via the OBIDMS_array structure.
+ *
+ * @param dms The OBIDMS to which the obiarray belongs.
+ * @param array_name The name of the obiarray.
+ *
+ * @returns A pointer to the newly created obiarray structure.
+ * @retval NULL if an error occurred.
+ *
+ * @since October 2015
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+OBIDMS_array_p obi_create_array(OBIDMS_p dms, const char* array_name);
+
+
+/**
+ * @brief Opens an obiarray. Fails if it does not already exist.
+ *
+ * Note: An obiarray is made of two files (referred to by two structures).
+ * 		 One file contains the indices referring to the data, and the other
+ * 		 file contains the data itself. The obiarray as a whole is referred
+ * 		 to via the OBIDMS_array structure.
+ *
+ * @param dms The OBIDMS to which the obiarray belongs.
+ * @param array_name The name of the obiarray.
+ *
+ * @returns A pointer to the obiarray structure.
+ * @retval NULL if an error occurred.
+ *
+ * @since October 2015
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+OBIDMS_array_p obi_open_array(OBIDMS_p dms, const char* array_name);
+
+
+/**
+ * @brief Closes an obiarray.
+ *
+ * Note: An obiarray is made of two files (referred to by two structures).
+ * 		 One file contains the indices referring to the data, and the other
+ * 		 file contains the data itself. The obiarray as a whole is referred
+ * 		 to via the OBIDMS_array structure.
+ *
+ * @param array A pointer to the obiarray structure to close and free.
+ *
+ * @retval 0 if the operation was successfully completed.
+ * @retval -1 if an error occurred.
+ *
+ * @since October 2015
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+int obi_close_array(OBIDMS_array_p array);
+
+
+/**
+ * @brief Adds a value (byte array) in an obiarray, checking first if it is already in it.
+ *
+ * @warning The byte array to add must already be encoded and contain its header.
+ *
+ * @param array A pointer to the obiarray.
+ * @param value The byte array to add in the obiarray.
+ *
+ * @returns The index of the value, whether it was added or already in the obiarray.
+ * @retval -1 if an error occurred.
+ *
+ * @since October 2015
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+index_t obi_array_add(OBIDMS_array_p array, byte_t* value);
+
+
+/**
+ * @brief Recovers a value (byte array) in an obiarray.
+ *
+ * @warning The byte array recovered is encoded and contains its header.
+ *
+ * @param array A pointer to the obiarray.
+ * @param index The index of the value in the data array.
+ *
+ * @returns A pointer to the byte array recovered.
+ *
+ * @since October 2015
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+byte_t* obi_array_get(OBIDMS_array_p array, index_t index);
+
+
+/**
+ * @brief Searches a value (byte array) in an obiarray performing a binary search.
+ *
+ * @warning The byte array to search must already be encoded and contain its header.
+ *
+ * @param array A pointer to the obiarray.
+ * @param value The byte array to add in the obiarray.
+ *
+ * @returns If the value is found, its data index is returned.
+ * 			If the value is not found, the array index indicating where the value's data index
+ * 			should be in the array is returned in the form (- (index + 1)), as data indices in an
+ * 			obiarray are sorted according to the ascending order of the values (byte arrays) themselves.
+ *
+ * @since October 2015
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+index_t obi_array_search(OBIDMS_array_p array, byte_t* value);
+
+
+/**
+ * @brief Converts a character string to a byte array with a header.
+ *
+ * @warning The byte array must be freed by the caller.
+ *
+ * @param value The character string to convert.
+ *
+ * @returns A pointer to the byte array created.
+ * @retval NULL if an error occurred.
+ *
+ * @since October 2015
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+byte_t* obi_str_to_obibytes(char* value);
+
+
+/**
+ * @brief Converts a byte array to a character string.
+ *
+ * @param value_b The byte array to convert.
+ *
+ * @returns A pointer to the character string contained in the byte array.
+ *
+ * @since October 2015
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+const char* obi_obibytes_to_str(byte_t* value_b);
+
+
+#endif /* OBIARRAY_H_ */
+

src/obidebug.h

@@ -1,8 +1,12 @@
-/*
- * obidebug.h
- *
- *  Created on: June 25th 2015
- *      Author: Celine Mercier (celine.mercier@metabarcoding.org)
+/****************************************************************************
+ * Header file for the debugging code                                       *
+ ****************************************************************************/
+
+/**
+ * @file obidebug.h
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ * @date 25 June 2015
+ * @brief Header file for the debugging code.
  */
 
 
@@ -12,7 +16,7 @@
 #include <limits.h>
 
 
-//#ifndef DEBUG_LEVEL
+//#ifndef DEBUG_LEVEL			// TODO
 //#define DEBUG_LEVEL MAXINT
 //#endif
 

src/obidms.c

@@ -1,14 +1,20 @@
-/*
- * obidms.c
- *
- *  @date 23 May 2015
- *  @Author: coissac
+/********************************************************************
+ * OBIDMS functions                                                 *
+ ********************************************************************/
+
+/**
+ * @file obidms.c
+ * @author Eric Coissac (eric.coissac@metabarcoding.org)
+ * @date 23 May 2015
+ * @brief OBIDMS functions.
  */
 
+
 #include <stdlib.h>
 #include <stdio.h>
 #include <string.h>
 #include <sys/stat.h>
+#include <fcntl.h>
 #include <sys/types.h>
 #include <dirent.h>
 
@@ -16,9 +22,10 @@
 #include "obierrno.h"
 #include "obidebug.h"
 #include "obidmscolumn.h"
+#include "private_at_functions.h"
 
 
-#define DEBUG_LEVEL 0
+#define DEBUG_LEVEL 0	// TODO has to be defined somewhere else (cython compil flag?)
 
 
 /**************************************************************************
@@ -29,27 +36,22 @@
 
 
 /**
- * Internal function building the directory name from an OBIDMS name.
+ * Internal function building the OBIDMS directory name from an OBIDMS name.
  *
  * The function builds the directory name corresponding to an OBIDMS.
- * It checks also that the name is not too long.
+ * It also checks that the name is not too long.
  *
  * @warning The returned pointer has to be freed by the caller.
  *
- * @param dms_name the name of the OBIDMS
+ * @param dms_name The name of the OBIDMS.
  *
- * @return a pointer to the directory name
- * @retvalue <directory_name> if everything is ok
- * @retvalue NULL if an error occurs
- *
- * ###Error values
- * 		- OBIDMS_MEMORY_ERROR    : something wrong occurred during memory allocation.
- * 		- OBIDMS_LONG_NAME_ERROR : the database name exceeds the limit.
+ * @returns A pointer to the directory name.
+ * @retval NULL if an error occurred.
  *
  * @since May 2015
  * @author Eric Coissac (eric.coissac@metabarcoding.org)
  */
-static char *build_directory_name(const char *dms_name);
+static char* build_directory_name(const char* dms_name);
 
 
 /************************************************************************
@@ -58,9 +60,9 @@ static char *build_directory_name(const char *dms_name);
  *
  ************************************************************************/
 
-static char *build_directory_name(const char *dms_name)
+static char* build_directory_name(const char* dms_name)
 {
-	char *directory_name;
+	char* directory_name;
 
 	// Build the database directory name
 	if (asprintf(&directory_name, "%s.obidms", dms_name) < 0)
@@ -113,7 +115,9 @@ int obi_dms_exists(const char* dms_name)
 
 OBIDMS_p obi_create_dms(const char* dms_name)
 {
-	char *directory_name;
+	char* directory_name;
+	DIR* dms_dir;
+	int dms_file_descriptor;
 
 	// Build and check the directory name
 	directory_name = build_directory_name(dms_name);
@@ -132,6 +136,33 @@ OBIDMS_p obi_create_dms(const char* dms_name)
 		return NULL;
 	}
 
+	// Get file descriptor of DMS directory to create the arrays directory
+	dms_dir = opendir(directory_name);
+	if (dms_dir == NULL)
+	{
+		obi_set_errno(OBIDMS_UNKNOWN_ERROR);
+		obidebug(1, "\nProblem opening a newly created OBIDMS directory");
+		free(directory_name);
+		return NULL;
+	}
+	dms_file_descriptor = dirfd(dms_dir);
+	if (dms_file_descriptor < 0)
+	{
+		obi_set_errno(OBIDMS_UNKNOWN_ERROR);
+		obidebug(1, "\nProblem getting the file descriptor of a newly created OBIDMS directory");
+		free(directory_name);
+		return NULL;
+	}
+
+	// Create the arrays directory
+	if (mkdirat(dms_file_descriptor, ARRAY_DIR_NAME, 00777) < 0)
+	{
+		obi_set_errno(OBI_ARRAY_ERROR);
+		obidebug(1, "\nProblem creating an arrays directory");
+		free(directory_name);
+		return NULL;
+	}
+
 	free(directory_name);
 
 	return obi_open_dms(dms_name);
@@ -143,6 +174,7 @@ OBIDMS_p obi_open_dms(const char* dms_name)
 	OBIDMS_p	dms;
 	char*	 	directory_name;
 	DIR*		directory;
+	int			dms_file_descriptor;
 
 	dms = NULL;
 
@@ -191,6 +223,26 @@ OBIDMS_p obi_open_dms(const char* dms_name)
 	strcpy(dms->directory_name, directory_name);
 	dms->directory = directory;
 
+	// Get file descriptor of DMS directory to open the arrays directory
+	dms_file_descriptor = dirfd(directory);
+	if (dms_file_descriptor < 0)
+	{
+		obi_set_errno(OBIDMS_UNKNOWN_ERROR);
+		obidebug(1, "\nError getting the file descriptor for a newly created OBIDMS directory");
+		free(directory_name);
+		return NULL;
+	}
+
+	// Open the arrays directory
+	dms->array_directory = private_opendirat(dms_file_descriptor, ARRAY_DIR_NAME);
+	if (dms->array_directory == NULL)
+	{
+		obi_set_errno(OBIDMS_UNKNOWN_ERROR);
+		obidebug(1, "\nError opening the arrays directory");
+		free(directory_name);
+		return NULL;
+	}
+
 	free(directory_name);
 
 	return dms;
@@ -223,7 +275,14 @@ int obi_close_dms(OBIDMS_p dms)
 		if (closedir(dms->directory) < 0)
 		{
 			obi_set_errno(OBIDMS_MEMORY_ERROR);
-			obidebug(1, "\nError closing an OBIDSM directory");
+			obidebug(1, "\nError closing an OBIDMS directory");
+			free(dms);
+			return -1;
+		}
+		if (closedir(dms->array_directory) < 0)
+		{
+			obi_set_errno(OBI_ARRAY_ERROR);
+			obidebug(1, "\nError closing an array directory");
 			free(dms);
 			return -1;
 		}

src/obidms.h

@@ -1,13 +1,19 @@
-/*
- * obidms.h
- *
- *  Created on: 23 mai 2015
- *      Author: coissac
+/********************************************************************
+ * OBIDMS header file                                               *
+ ********************************************************************/
+
+/**
+ * @file obidmscolumn.h
+ * @author Eric Coissac (eric.coissac@metabarcoding.org)
+ * @date 23 May 2015
+ * @brief Header file for the OBIDMS functions and structures.
  */
 
+
 #ifndef OBIDMS_H_
 #define OBIDMS_H_
 
+
 #include <stdlib.h>
 #include <sys/stat.h>
 #include <errno.h>
@@ -17,38 +23,42 @@
 
 #include "obierrno.h"
 
-#define OBIDMS_MAX_NAME (2048) /**< The maximum length of an OBIDMS name
-                                */
 
-/** @brief A structure describing an OBIDMS instance
+#define OBIDMS_MAX_NAME (2048) 	   /**< The maximum length of an OBIDMS name.
+                                	*/
+#define ARRAY_DIR_NAME "arrays"	   /**< The name of the arrays directory.
+                                	*/
+
+
+/**
+ * @brief A structure describing an OBIDMS instance
  *
  * A pointer to this structure is returned on creation
  * and opening of an OBITools Data Management System (DMS)
  */
-
 typedef struct OBIDMS {
 	char	directory_name[OBIDMS_MAX_NAME+1];	/**< The name of the directory
-	                                     	 	 *   containing the DMS
+	                                     	 	 *   containing the DMS.
 	                                     	 	 */
 	DIR*	directory;							/**< A directory entry usable to
-										 	 	 *   refer and scan the database directory
+										 	 	 *   refer and scan the database directory.
+										 	 	 */
+	DIR*	array_directory;					/**< A directory entry usable to
+										 	 	 *   refer and scan the array directory.
 										 	 	 */
 } OBIDMS_t, *OBIDMS_p;
 
 
-/*@
- * @brief Checks if an OBIDMS exists
+/**
+ * @brief Checks if an OBIDMS exists.
  *
- * @param dms_name a pointer to a C string containing the name of the database.
- *             The actual directory name used to store the DMS will be
- *             `<dms_name>.obidms`.
+ * @param dms_name A pointer to a C string containing the name of the database.
  *
- * @return an integer value indicating the status of the database
- * @retvalue 1 the database exist
- * @retvalue 0 the database does not exist
- * @retvalue -1 an error occurred
+ * @returns An integer value indicating the status of the database
+ * @retval 1 if the database exists.
+ * @retval 0 if the database does not exist.
+ * @retval -1 if an error occurred.
  *
- * @see obi_close_dms()
  * @since May 2015
  * @author Eric Coissac (eric.coissac@metabarcoding.org)
  */
@@ -62,79 +72,64 @@ int obi_dms_exists(const char* dms_name);
  * if a directory with this name does not already exist
  * before creating the new database.
  *
- * @param dms_name a pointer to a C string containing the name of the database.
- *             The actual directory name used to store the DMS will be
- *             `<name>.obidms`
+ * A directory to store obiarrays is also created.
  *
- * @return a pointer to an OBIDMS structure describing the newly created DMS
- * @retval NULL on error and the `obi_errno` variable is set.
+ * @param dms_name A pointer to a C string containing the name of the database.
+ *                 The actual directory name used to store the DMS will be
+ *                 `<dms_name>.obidms`.
  *
- * ###Error values
- * 		- OBIDMS_EXIST_ERROR     : a database with the same name already exists.
- * 		- OBIDMS_LONG_NAME_ERROR : the database name exceeds the limit.
- * 		- OBIDMS_MEMORY_ERROR    : something wrong occurred during memory allocation.
+ * @returns A pointer to an OBIDMS structure describing the newly created DMS.
+ * @retval NULL if an error occurred.
  *
  * @see obi_close_dms()
  * @since May 2015
  * @author Eric Coissac (eric.coissac@metabarcoding.org)
  */
-OBIDMS_p obi_create_dms(const char *dms_name);
+OBIDMS_p obi_create_dms(const char* dms_name);
 
 
 /**
  * @brief Opens an existing OBITools Data Management instance (OBIDMS).
  *
- * @param dms_name a pointer to a C string containing the name of the database.
- *             The actual directory name used to store the DMS will be
- *             `<name>.obidms`
+ * @param dms_name A pointer to a C string containing the name of the database.
  *
- * @return a pointer to an OBIDMS structure describing the newly created DMS
- * @retval NULL on error and the `obi_errno`variable is set.
- *
- * ###Error values
- * 		- OBIDMS_LONG_NAME_ERROR : the database name exceeds the limit.
- * 		- OBIDMS_MEMORY_ERROR    : something wrong occurred during memory allocation.
+ * @returns A pointer to an OBIDMS structure describing the opened DMS.
+ * @retval NULL if an error occurred.
  *
  * @see obi_close_dms()
  * @since May 2015
  * @author Eric Coissac (eric.coissac@metabarcoding.org)
  */
-OBIDMS_p obi_open_dms(const char *dms_name);
+OBIDMS_p obi_open_dms(const char* dms_name);
 
 
 /**
- * @brief Creates a new OBIDMS instance.
+ * @brief Creates or opens a new OBIDMS instance.
  *
  * If the database already exists, this function opens it, otherwise it
  * creates a new database.
  *
- * @param dms_name a pointer to a C string containing the name of the database.
- *             The actual directory name used to store the DMS is
- *             `<name>.obidms`
+ * @param dms_name A pointer to a C string containing the name of the database.
  *
- * @return a pointer to an OBIDMS structure describing the newly created DMS
- * @retval NULL on error and the `obi_errno`variable is set.
- *
- * ###Error values
- * 		- OBIDMS_LONG_NAME_ERROR : the database name exceeds the limit.
- * 		- OBIDMS_MEMORY_ERROR    : something wrong occurred during memory allocation.
+ * @returns A pointer to an OBIDMS structure describing the OBIDMS.
+ * @retval NULL if an error occurred.
  *
  * @see obi_close_dms()
  * @since May 2015
  * @author Eric Coissac (eric.coissac@metabarcoding.org)
  */
-OBIDMS_p obi_dms(const char *dms_name);
+OBIDMS_p obi_dms(const char* dms_name);
 
 
 /**
  * @brief Closes an opened OBITools Data Management instance (OBIDMS).
  *
- * @param dms a pointer as returned by obi_create_dms() or obi_open_dms()
+ * @param dms A pointer as returned by obi_create_dms() or obi_open_dms().
  *
- * @return an integer value indicating the success of the operation. Even on
- * 		   error, the `OBIDMS` structure is freed
- * @retvalue 0 on success
- * @retvalue -1 on failure and the `obi_errno` variable is set.
+ * @returns An integer value indicating the success of the operation. Even on
+ * 		    error, the `OBIDMS` structure is freed.
+ * @retval 0 on success.
+ * @retval -1 if an error occurred?-.
  *
  * @see obi_create_dms()
  * @see obi_open_dms()

src/obidmscolumn.c

@@ -1,12 +1,12 @@
 /****************************************************************************
- * OBIDMS_column functions                                                  *
+ * OBIDMS columns functions                                                 *
  ****************************************************************************/
 
 /**
  * @file obidmscolumn.c
- * @author Celine Mercier
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
  * @date 22 May 2015
- * @brief Functions for the shared elements of all the OBIColumn structures.
+ * @brief Functions shared by all the OBIDMS columns.
  */
 
 
@@ -16,10 +16,11 @@
 #include <sys/types.h>
 #include <dirent.h>
 #include <unistd.h>
+#include <time.h>
 #include <fcntl.h>
 #include <stdbool.h>
 #include <math.h>
-#include <sys/mman.h>	/* mmap() is defined in this header */
+#include <sys/mman.h>
 
 #include "obidmscolumn.h"
 #include "obidmscolumndir.h"
@@ -28,9 +29,10 @@
 #include "obierrno.h"
 #include "obidebug.h"
 #include "obilittlebigman.h"
+#include "obiarray.h"
 
 
-#define DEBUG_LEVEL 0
+#define DEBUG_LEVEL 0	// TODO has to be defined somewhere else (cython compil flag?)
 
 
 /**************************************************************************
@@ -47,18 +49,16 @@
  *
  * @warning The returned pointer has to be freed by the caller.
  *
- * @param column_name the name of the OBIDMS column.
+ * @param column_name The name of the OBIDMS column file.
+ * @param version_number The version number of the OBIDMS column file.
  *
- * @return a pointer to the column file name
- * @retvalue NULL if an error occurs
- *
- * ###Error values
- * 		- OBIDMS_MEMORY_ERROR    : something wrong occurred during memory allocation.
+ * @returns A pointer to the column file name.
+ * @retval NULL if an error occurred.
  *
  * @since May 2015
  * @author Eric Coissac (eric.coissac@metabarcoding.org)
  */
-static char *build_column_file_name(const char *column_name, obiversion_t version_number);
+static char* build_column_file_name(const char* column_name, obiversion_t version_number);
 
 
 /**
@@ -69,32 +69,28 @@ static char *build_column_file_name(const char *column_name, obiversion_t versio
  *
  * @warning The returned pointer has to be freed by the caller.
  *
- * @param column_name the name of the OBIDMS column.
+ * @param column_name The name of the OBIDMS column.
  *
- * @return a pointer to the version file name
- * @retvalue NULL if an error occurs
- *
- * ###Error values
- * 		- OBIDMS_MEMORY_ERROR    : something wrong occurs during memory allocation.
+ * @returns A pointer to the version file name.
+ * @retval NULL if an error occurred.
  *
  * @since May 2015
  * @author Eric Coissac (eric.coissac@metabarcoding.org)
  */
-static char *build_version_file_name(const char *column_name);
+static char* build_version_file_name(const char* column_name);
 
 
 /**
  * @brief Internal function returning a new column version number
- *        in the `dms` database
+ *        in the OBIDMS database.
  *
- * @param dms a pointer as returned by obi_create_dms() or obi_open_dms()
- * @param column_name the name of the column
- * @param block is the call is blocking or not
- *                 - `true` the call is blocking
- *                 - `false` the call is not blocking
+ * @param column_directory A pointer as returned by obi_create_column_directory() or obi_open_column_directory().
+ * @param block Whether the call is blocking or not:
+ *              	- `true` the call is blocking
+ *                  - `false` the call is not blocking.
  *
- * @return the bigger version number used for this column
- * @retvalue -1 if the column does not exist
+ * @returns The next version number for this column.
+ * @retval -1 if an error occurred.
  *
  * @since May 2015
  * @author Eric Coissac (eric.coissac@metabarcoding.org)
@@ -104,50 +100,50 @@ static obiversion_t obi_get_new_version_number(OBIDMS_column_directory_p column_
 
 /**
  * @brief Internal function creating a new column version file
- *        in the `dms` database
+ *        in the OBIDMS database.
  *
  * The new file is initialized with the minimum version number `0`.
  *
- * @param dms a pointer as returned by obi_create_dms() or obi_open_dms()
- * @param column_name the name of the column
+ * @param column_directory A pointer as returned by obi_create_column_directory() or obi_open_column_directory().
  *
- * @return the next usable version number for this column : `0`
- * @retvalue -1 if the column does not exist
+ * @returns The next usable version number for this column : `0`.
+ * @retval -1 if an error occurred.
  *
  * @since May 2015
  * @author Eric Coissac (eric.coissac@metabarcoding.org)
  */
-static int create_version_file(OBIDMS_column_directory_p column_directory);
+static obiversion_t create_version_file(OBIDMS_column_directory_p column_directory);
 
 
 /**
  * @brief Internal function setting the elements names of the lines of a
- * column in the header of the OBIDMS column structure.
+ *        column in the header of the OBIDMS column structure.
  *
- * @param column a pointer as returned by obi_create_column()
- * @param elements_names the names of the elements with ';' as separator
+ * @param column A pointer as returned by obi_create_column().
+ * @param elements_names The names of the elements with ';' as separator.
  *
- * @return 0 if the operation was successfully completed
- * @retvalue -1 if an error occurred
+ * @retval 0 if the operation was successfully completed.
+ * @retval -1 if an error occurred.
  *
  * @since July 2015
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-int obi_column_set_elements_names(OBIDMS_column_p column, const char* elements_names);
+static int obi_column_set_elements_names(OBIDMS_column_p column, const char* elements_names);
 
 
 /**
- * @brief Internal function computing how many lines of an OBIDMS column fill in a memory page.
+ * @brief Internal function computing how many lines of an OBIDMS column
+ *        fit in a memory page.
  *
- * @param data_type the data OBIType
- * @param nb_elements_per_line the number of elements per line
+ * @param data_type The data OBIType.
+ * @param nb_elements_per_line The number of elements per line.
  *
- * @return the line count for one memory page
+ * @returns The line count for one memory page.
  *
  * @since September 2015
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-size_t get_line_count_per_page(OBIType_t data_type, size_t nb_elements_per_line);
+static index_t get_line_count_per_page(OBIType_t data_type, index_t nb_elements_per_line);
 
 
 /************************************************************************
@@ -157,35 +153,35 @@ size_t get_line_count_per_page(OBIType_t data_type, size_t nb_elements_per_line)
  ************************************************************************/
 
 
-static char *build_column_file_name(const char *column_name, obiversion_t version_number)
+static char* build_column_file_name(const char* column_name, obiversion_t version_number)
 {
-	char *filename;
+	char* file_name;
 
-	// Build the database directory name
-	if (asprintf(&filename,"%s@%d.odc", column_name, version_number) < 0)
+	// Build the file name
+	if (asprintf(&file_name,"%s@%d.odc", column_name, version_number) < 0)
 	{
 		obi_set_errno(OBICOL_MEMORY_ERROR);
 		obidebug(1, "\nError building a column file name");
 		return NULL;
 	}
 
-	return filename;
+	return file_name;
 }
 
 
-static char *build_version_file_name(const char *column_name)
+static char* build_version_file_name(const char* column_name)
 {
-	char *filename;
+	char* file_name;
 
-	// Build the database directory name
-	if (asprintf(&filename,"%s.odv", column_name) < 0)
+	// Build the file name
+	if (asprintf(&file_name,"%s.odv", column_name) < 0)
 	{
 		obi_set_errno(OBICOL_MEMORY_ERROR);
 		obidebug(1, "\nError building a version file name");
 		return NULL;
 	}
 
-	return filename;
+	return file_name;
 }
 
 
@@ -232,10 +228,10 @@ static obiversion_t obi_get_new_version_number(OBIDMS_column_directory_p column_
 		else
 		{
 			obi_set_errno(OBICOL_UNKNOWN_ERROR);
+			obidebug(1, "\nError opening a version file");
+			free(version_file_name);
 			return -1;
 		}
-		obidebug(1, "\nError opening a version file");
-		free(version_file_name);
 	}
 
 	// Test if the version file size is ok
@@ -346,7 +342,7 @@ static obiversion_t obi_get_new_version_number(OBIDMS_column_directory_p column_
 }
 
 
-static int create_version_file(OBIDMS_column_directory_p column_directory)
+static obiversion_t create_version_file(OBIDMS_column_directory_p column_directory)
 {
 	off_t 			loc_size;
 	obiversion_t 	version_number;
@@ -467,7 +463,7 @@ int obi_column_set_elements_names(OBIDMS_column_p column, const char* elements_n
 	return 0;
 }
 
-size_t get_line_count_per_page(OBIType_t data_type, size_t nb_elements_per_line)
+index_t get_line_count_per_page(OBIType_t data_type, index_t nb_elements_per_line)
 {
 	return getpagesize() / (obi_sizeof(data_type) * nb_elements_per_line);
 }
@@ -599,28 +595,30 @@ obiversion_t obi_column_get_latest_version_from_name(OBIDMS_p dms, const char* c
 
 size_t obi_get_platform_header_size()
 {
-	return getpagesize() * 1;
+	return getpagesize() * 2;
 }
 
 
 OBIDMS_column_p obi_create_column(OBIDMS_p dms,
 		                          const char* column_name,
 								  OBIType_t data_type,
-								  size_t nb_lines,
-								  size_t nb_elements_per_line,
-								  const char* elements_names)
+								  index_t nb_lines,
+								  index_t nb_elements_per_line,
+								  const char* elements_names,
+								  const char* array_name)
 {
-	OBIDMS_column_p 		new_column;
+	OBIDMS_column_p 			new_column;
 	OBIDMS_column_directory_p	column_directory;
-	OBIDMS_column_header_p 	header;
-	size_t 					file_size;
-	obiversion_t 			version_number;
-	char* 					column_file_name;
-	int 					column_file_descriptor;
-	int						column_dir_file_descriptor;
-	size_t 					header_size;
-	size_t 					data_size;
-	size_t					minimum_line_count;
+	OBIDMS_column_header_p 		header;
+	OBIDMS_array_p				array;
+	size_t 						file_size;
+	obiversion_t 				version_number;
+	char* 						column_file_name;
+	int 						column_file_descriptor;
+	int							column_dir_file_descriptor;
+	size_t 						header_size;
+	size_t 						data_size;
+	index_t						minimum_line_count;
 
 	new_column = NULL;
 
@@ -635,24 +633,29 @@ OBIDMS_column_p obi_create_column(OBIDMS_p dms,
 		obidebug(1, "\nCan't create column because of empty column name");
 		return NULL;
 	}
-	if ((data_type < 1) || (data_type > 4))
+	if ((data_type < 1) || (data_type > 5))
 	{
 		obidebug(1, "\nCan't create column because of invalid data type");
 		return NULL;
 	}
+	if ((data_type == 5) && (array_name == NULL))
+	{
+		obidebug(1, "\nCan't create column because of empty array name");
+		return NULL;
+	}
+
 
 	// The initial line count should be between the minimum (corresponding to the page size) and the maximum allowed
 	minimum_line_count = get_line_count_per_page(data_type, nb_elements_per_line);
 	if (nb_lines > MAXIMUM_LINE_COUNT)
 	{
-		obidebug(1, "\nCan't create column because of line count greater than the maximum allowed (%lld)", MAXIMUM_LINE_COUNT);
+		obidebug(1, "\nCan't create column because of line count greater than the maximum allowed (%d)", MAXIMUM_LINE_COUNT);
 		return NULL;
 	}
 	else if (nb_lines < minimum_line_count)
 		nb_lines = minimum_line_count;
 
 	// The number of elements names should be equal to the number of elements per line
-
 	if ((elements_names == NULL) && (nb_elements_per_line > 1))
 	{
 		obidebug(1, "\nCan't create column because no elements names were given for a number of elements per line greater than 1");
@@ -661,7 +664,7 @@ OBIDMS_column_p obi_create_column(OBIDMS_p dms,
 	else if ((elements_names != NULL) && (nb_elements_per_line > 1))
 	{
 		char* token;
-		size_t n = 0;
+		index_t n = 0;
 		token = strdup(elements_names);
 		token = strtok(token, ";");
 		while (token != NULL)
@@ -723,6 +726,7 @@ OBIDMS_column_p obi_create_column(OBIDMS_p dms,
 	if (column_file_descriptor < 0)
 	{
 		obi_set_errno(OBICOL_UNKNOWN_ERROR);
+		obidebug(1, "\nError opening a column file");
 		free(column_file_name);
 		return NULL;
 	}
@@ -800,11 +804,28 @@ OBIDMS_column_p obi_create_column(OBIDMS_p dms,
 	header->creation_date 		 = time(NULL);
 	header->version       		 = version_number;
 	header->cloned_from    		 = -1;
-	header->comments[0]   		 = 0x0;
+	header->comments[0]   		 = 0x0;		// TODO
 
 	obi_column_set_elements_names(new_column, elements_names);
 
-	strncpy(header->name, column_name, OBIDMS_MAX_COLNAME);
+	strncpy(header->name, column_name, OBIDMS_COLUMN_MAX_NAME);
+
+	// If the data type is OBI_IDX, the associated obi_array is opened or created
+	if (data_type == 5)
+	{
+		array = obi_array(dms, array_name);
+		if (array == NULL)
+		{
+			obidebug(1, "\nError opening or creating the array associated with a column");
+			munmap(new_column->header, header_size);
+			close(column_file_descriptor);
+			free(column_file_name);
+			free(new_column);
+			return NULL;
+		}
+		new_column->array = array;
+		strncpy(header->array_name, array_name, ARRAY_MAX_NAME);
+	}
 
 	// Fill the data with NA values
 	obi_ini_to_NA_values(new_column, 0, nb_lines);
@@ -816,10 +837,13 @@ OBIDMS_column_p obi_create_column(OBIDMS_p dms,
 }
 
 
-OBIDMS_column_p obi_open_column(OBIDMS_p dms, const char* column_name, obiversion_t version_number)
+OBIDMS_column_p obi_open_column(OBIDMS_p dms,
+								const char* column_name,
+								obiversion_t version_number)
 {
 	OBIDMS_column_p 		    column;
 	OBIDMS_column_directory_p	column_directory;
+	OBIDMS_array_p				array;
 	char* 						column_file_name;
 	int 						column_file_descriptor;
 	int							column_dir_file_descriptor;
@@ -911,8 +935,9 @@ OBIDMS_column_p obi_open_column(OBIDMS_p dms, const char* column_name, obiversio
 	// TODO Check endianness?
 
 	// Compute data size from the informations in the header
-	data_size = ((column->header)->line_count) * sizeof((column->header)->data_type);
+	data_size = obi_array_sizeof((column->header)->data_type, (column->header)->line_count, (column->header)->nb_elements_per_line);
 
+	// Map the data
 	column->data   			 = mmap(NULL,
 			                 	 	data_size,
 			                 	 	PROT_READ,
@@ -934,6 +959,22 @@ OBIDMS_column_p obi_open_column(OBIDMS_p dms, const char* column_name, obiversio
 
 	column->writable  = false;
 
+	// If the data type is OBI_IDX, the associated obi_array is opened or created
+	if ((column->header)->data_type == 5)
+	{
+		array = obi_array(dms, (column->header)->array_name);
+		if (array == NULL)
+		{
+			obidebug(1, "\nError opening the array associated with a column");
+			munmap(column->header, header_size);
+			close(column_file_descriptor);
+			free(column_file_name);
+			free(column);
+			return NULL;
+		}
+		column->array = array;
+	}
+
 	free(column_file_name);
 	close(column_file_descriptor);
 
@@ -941,12 +982,15 @@ OBIDMS_column_p obi_open_column(OBIDMS_p dms, const char* column_name, obiversio
 }
 
 
-OBIDMS_column_p obi_clone_column(OBIDMS_p dms, const char* column_name, obiversion_t version_number, bool clone_data)
+OBIDMS_column_p obi_clone_column(OBIDMS_p dms,
+								 const char* column_name,
+								 obiversion_t version_number,
+								 bool clone_data)
 {
 	OBIDMS_column_p   column_to_clone;
 	OBIDMS_column_p   new_column;
-	size_t 			  nb_lines;
-	size_t			  nb_elements_per_line;
+	index_t 			  nb_lines;
+	index_t			  nb_elements_per_line;
 	size_t			  data_size;
 	OBIType_t		  data_type;
 
@@ -972,7 +1016,8 @@ OBIDMS_column_p obi_clone_column(OBIDMS_p dms, const char* column_name, obiversi
 								   data_type,
 								   nb_lines,
 								   nb_elements_per_line,
-								   (column_to_clone->header)->elements_names);
+								   (column_to_clone->header)->elements_names,
+								   (column_to_clone->header)->array_name);
 
 	if (new_column == NULL)
 	{
@@ -1010,7 +1055,7 @@ int obi_close_column(OBIDMS_column_p column)
 	size_t data_size;
 
 	// Munmap data
-	data_size = (column->header)->line_count * (column->header)->nb_elements_per_line * sizeof((column->header)->data_type);
+	data_size = obi_array_sizeof((column->header)->data_type, (column->header)->line_count, (column->header)->nb_elements_per_line);
 	if (munmap(column->data, data_size) < 0)
 	{
 		obi_set_errno(OBICOL_UNKNOWN_ERROR);
@@ -1026,25 +1071,27 @@ int obi_close_column(OBIDMS_column_p column)
 		return -1;
 	}
 
+	obi_close_column_directory(column->column_directory);
+
 	free(column);
 
 	return 0;
 }
 
 
-int obi_truncate_column_to_lines_used(OBIDMS_column_p column)
+int obi_truncate_column_to_lines_used(OBIDMS_column_p column)	// TODO is it necessary to unmap/remap?
 {
 	size_t file_size;
 	size_t data_size;
-	size_t new_line_count;
+	index_t new_line_count;
 	double multiple;
 	int column_dir_file_descriptor;
 	int column_file_descriptor;
 	char* column_file_name;
 
-	// Compute the new line count = the number of lines used rounded to the nearest multiple of page size
-	multiple = ceil((double) ((column->header)->lines_used * (column->header)->nb_elements_per_line * obi_sizeof((column->header)->data_type)) / (double) getpagesize());
-	new_line_count = (int) multiple * getpagesize();
+	// Compute the new line count = the number of lines used rounded to the nearest greater multiple of page size greater than 0
+	multiple = ceil((double) (ONE_IF_ZERO((column->header)->lines_used) * (column->header)->nb_elements_per_line * obi_sizeof((column->header)->data_type)) / (double) getpagesize());
+	new_line_count = floor((((int) multiple) * getpagesize()) / ((column->header)->nb_elements_per_line * obi_sizeof((column->header)->data_type))); // TODO is it safe to cast like this?
 
 	// Check that it is actually greater than the current number of lines allocated in the file, otherwise no need to truncate
 	if ((column->header)->line_count == new_line_count)
@@ -1133,8 +1180,8 @@ int obi_enlarge_column(OBIDMS_column_p column)
 	size_t old_data_size;
 	size_t new_data_size;
 	size_t header_size;
-	size_t old_line_count;
-	size_t new_line_count;
+	index_t old_line_count;
+	index_t new_line_count;
 	int column_dir_file_descriptor;
 	int column_file_descriptor;
 	char* column_file_name;
@@ -1168,7 +1215,7 @@ int obi_enlarge_column(OBIDMS_column_p column)
 
 	// Calculate the new file size
 	old_line_count = (column->header)->line_count;
-	new_line_count = old_line_count * GROWTH_FACTOR;
+	new_line_count = old_line_count * COLUMN_GROWTH_FACTOR;
 
 	if (new_line_count > MAXIMUM_LINE_COUNT)
 	{
@@ -1179,7 +1226,7 @@ int obi_enlarge_column(OBIDMS_column_p column)
 		return -1;
 	}
 	old_data_size = obi_array_sizeof((column->header)->data_type, old_line_count, (column->header)->nb_elements_per_line);
-	new_data_size = old_data_size * GROWTH_FACTOR;
+	new_data_size = old_data_size * COLUMN_GROWTH_FACTOR;
 	header_size = (column->header)->header_size;
 	file_size = header_size + new_data_size;
 
@@ -1193,7 +1240,8 @@ int obi_enlarge_column(OBIDMS_column_p column)
 		return -1;
 	}
 
-	// Remap the data: try enlarging mapped region (this actually never works on my mac without the MAP_FIXED flag which overwrites everything)
+	// Remap the data: try enlarging mapped region (TODO this actually never works on my mac without the MAP_FIXED flag which overwrites everything)
+	// TODO : makes separate function even if it's only used here?
 	//obidebug(2, "\ntry enlarging mapped region: old size = %ld, new size = %ld, size = %ld", old_data_size, new_data_size, new_data_size - old_data_size);
 	new_data	   			 = mmap(column->data,
 			                 	 	new_data_size - old_data_size,
@@ -1267,11 +1315,14 @@ int obi_truncate_and_close_column(OBIDMS_column_p column)
 }
 
 
-void obi_ini_to_NA_values(OBIDMS_column_p column, size_t start, size_t nb_lines)
+void obi_ini_to_NA_values(OBIDMS_column_p column,
+						  index_t first_line_nb,
+						  index_t nb_lines)
 {
-	size_t i, end, nb_elements;
+	index_t i, start, end, nb_elements;
 
 	nb_elements = nb_lines*((column->header)->nb_elements_per_line);
+	start = first_line_nb*((column->header)->nb_elements_per_line);
 	end = start + nb_elements;
 
 	switch ((column->header)->data_type) {
@@ -1304,38 +1355,14 @@ void obi_ini_to_NA_values(OBIDMS_column_p column, size_t start, size_t nb_lines)
 
 	case OBI_IDX:   for (i=start;i<end;i++)
 					{
-						*(((obiidx_t*) (column->data)) + i) = OBIIdx_NA;
+						*(((index_t*) (column->data)) + i) = OBIIdx_NA;
 					}
 					break;
 	}
 }
 
 
-void obi_column_make_unwritable(OBIDMS_column_p column)
-{
-	column->writable = false;
-}
-
-
-size_t obi_column_get_line_count(OBIDMS_column_p column)
-{
-	return (column->header)->line_count;
-}
-
-
-size_t obi_column_get_nb_lines_used(OBIDMS_column_p column)
-{
-	return (column->header)->lines_used;
-}
-
-
-OBIType_t obi_column_get_data_type(OBIDMS_column_p column)
-{
-	return (column->header)->data_type;
-}
-
-
-OBIType_t obi_column_get_data_type_from_name(OBIDMS_p dms, const char* column_name)
+OBIDMS_column_header_p obi_column_get_header_from_name(OBIDMS_p dms, const char* column_name)	// TODO ADD VERSION ARGUMENT
 {
 	OBIDMS_column_header_p 		header;
 	OBIDMS_column_directory_p	column_directory;
@@ -1343,7 +1370,6 @@ OBIType_t obi_column_get_data_type_from_name(OBIDMS_p dms, const char* column_na
 	int 						column_file_descriptor;
 	int							column_dir_file_descriptor;
 	size_t 						header_size;
-	OBIType_t					data_type;
 	obiversion_t	   			version_number;
 
 	// Get the column directory structure associated to the column
@@ -1351,7 +1377,7 @@ OBIType_t obi_column_get_data_type_from_name(OBIDMS_p dms, const char* column_na
 	if (column_directory == NULL)
 	{
 		obidebug(1, "\nError opening a column directory structure");
-		return -1;
+		return NULL;
 	}
 
 	// Get the file descriptor associated to the column directory
@@ -1361,25 +1387,25 @@ OBIType_t obi_column_get_data_type_from_name(OBIDMS_p dms, const char* column_na
 		obi_set_errno(OBICOLDIR_UNKNOWN_ERROR);
 		obidebug(1, "\nError getting the file descriptor of a column directory");
 		obi_close_column_directory(column_directory);
-		return -1;
+		return NULL;
 	}
 
 	// Calculate the header size
-	header_size = obi_get_platform_header_size();
+	header_size = obi_get_platform_header_size();	// TODO read in header itself
 
 	// Get the latest version number
 	version_number = obi_get_latest_version_number(column_directory);
 	if (version_number < 0)
 	{
 		obidebug(1, "\nError getting the latest version number in a column directory");
-		return -1;
+		return NULL;
 	}
 
 	// Get the column file name
 	column_file_name = build_column_file_name(column_name, version_number);
 	if (column_file_name == NULL)
 	{
-		return -1;
+		return NULL;
 	}
 
 	// Open the column file (READ-ONLY)
@@ -1389,7 +1415,7 @@ OBIType_t obi_column_get_data_type_from_name(OBIDMS_p dms, const char* column_na
 		obidebug(1, "\nError opening a column file");
 		obi_set_errno(OBICOL_UNKNOWN_ERROR);
 		free(column_file_name);
-		return -1;
+		return NULL;
 	}
 
 	// Fill the header structure
@@ -1407,124 +1433,42 @@ OBIType_t obi_column_get_data_type_from_name(OBIDMS_p dms, const char* column_na
 		obidebug(1, "\nError mmapping the header of a column");
 		close(column_file_descriptor);
 		free(column_file_name);
-		return -1;
+		return NULL;
 	}
 
-	// Check endianness?
-
-	data_type = header->data_type;
+	// TODO Check endianness?
 
 	free(column_file_name);
 	close(column_file_descriptor);
-	munmap(header, header_size);
-	return data_type;
+
+	return header;
 }
 
 
-size_t obi_column_get_line_count_from_name(OBIDMS_p dms, const char* column_name)
+int obi_unmap_header(OBIDMS_column_header_p header)
 {
-	OBIDMS_column_header_p 		header;
-	OBIDMS_column_directory_p	column_directory;
-	char* 						column_file_name;
-	int 						column_file_descriptor;
-	int							column_dir_file_descriptor;
-	size_t 						header_size;
-	size_t						line_count;
-	obiversion_t	   			version_number;
-
-	// Get the column directory structure associated to the column
-	column_directory = obi_open_column_directory(dms, column_name);
-	if (column_directory == NULL)
-	{
-		obidebug(1, "\nError opening a column directory structure");
-		return -1;
-	}
-
-	// Get the file descriptor associated to the column directory
-	column_dir_file_descriptor = dirfd(column_directory->directory);
-	if (column_dir_file_descriptor < 0)
-	{
-		obi_set_errno(OBICOLDIR_UNKNOWN_ERROR);
-		obidebug(1, "\nError getting the file descriptor of a column directory");
-		obi_close_column_directory(column_directory);
-		return -1;
-	}
-
-	// Calculate the header size
-	header_size = obi_get_platform_header_size();
-
-	// Get the latest version number
-	version_number = obi_get_latest_version_number(column_directory);
-	if (version_number < 0)
-	{
-		obidebug(1, "\nError getting the latest version number in a column directory");
-		return -1;
-	}
-
-	// Get the column file name
-	column_file_name = build_column_file_name(column_name, version_number);
-	if (column_file_name == NULL)
-	{
-		return -1;
-	}
-
-	// Open the column file (READ-ONLY)
-	column_file_descriptor = openat(column_dir_file_descriptor, column_file_name, O_RDONLY);
-	if (column_file_descriptor < 0)
-	{
-		obidebug(1, "\nError opening a column file");
-		obi_set_errno(OBICOL_UNKNOWN_ERROR);
-		free(column_file_name);
-		return -1;
-	}
-
-	// Fill the header structure
-	header = mmap(NULL,
-			 header_size,
-			 PROT_READ,
-			 MAP_SHARED,
-			 column_file_descriptor,
-			 0
-			 );
-
-	if (header == MAP_FAILED)
+	if (munmap(header, header->header_size) < 0)
 	{
 		obi_set_errno(OBICOL_UNKNOWN_ERROR);
-		obidebug(1, "\nError mmapping the header of a column");
-		close(column_file_descriptor);
-		free(column_file_name);
+		obidebug(1, "\nError munmapping a column header");
 		return -1;
 	}
-
-	// Check endianness?
-
-	line_count = header->line_count;
-
-	free(column_file_name);
-	close(column_file_descriptor);
-	munmap(header, header_size);
-	return line_count;
-}
-
-
-const char* obi_column_get_elements_names(OBIDMS_column_p column)
-{
-	return (column->header)->elements_names;
+	return 0;
 }
 
 
 // TODO to be rewritten in an optimized and safe way
-size_t obi_column_get_element_index_from_name(OBIDMS_column_p column, const char* element_name)
+index_t obi_column_get_element_index_from_name(OBIDMS_column_p column, const char* element_name)
 {
 	char* elements_names;
 	char* name;
-	size_t element_index;
+	index_t element_index;
 
 	elements_names = strdup((column->header)->elements_names);
 	if (elements_names == NULL)
 	{
 		obidebug(1, "\nError strdup-ing the elements names");
-		return -1;
+		return OBIIdx_NA;
 	}
 
 	element_index = 0;
@@ -1550,14 +1494,32 @@ size_t obi_column_get_element_index_from_name(OBIDMS_column_p column, const char
 
 	obidebug(1, "\nCan't find an element name");
 	free(elements_names);
-	return -1;
+	return OBIIdx_NA;
 }
 
 
-size_t obi_column_get_nb_elements_per_line(OBIDMS_column_p column)
+char* obi_column_format_date(time_t date)
 {
-	return (column->header)->nb_elements_per_line;
+	char* formatted_time;
+	struct tm* tmp;
+
+	formatted_time = (char*) malloc(FORMATTED_TIME_LENGTH*sizeof(char));
+
+	tmp = localtime(&date);
+	if (tmp == NULL)
+	{
+		obi_set_errno(OBICOL_UNKNOWN_ERROR);
+		obidebug(1, "\nError formatting a date");
+		return NULL;
+	}
+
+	if (strftime(formatted_time, FORMATTED_TIME_LENGTH, "%c", tmp) == 0)
+	{
+		obi_set_errno(OBICOL_UNKNOWN_ERROR);
+		obidebug(1, "\nError formatting a date");
+		return NULL;
+	}
+
+	return formatted_time;
 }
 
-
-

src/obidmscolumn.h

@@ -1,14 +1,15 @@
 /****************************************************************************
- * OBIDMS_column header file                                                    *
+ * OBIDMS columns header file                                               *
  ****************************************************************************/
 
 /**
  * @file obidmscolumn.h
- * @author Celine Mercier
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
  * @date 12 May 2015
- * @brief Header file for the shared elements of all the OBIDMS column structures.
+ * @brief Header file for the functions and structures shared by all the OBIDMS columns.
  */
 
+
 #ifndef OBIDMSCOLUMN_H_
 #define OBIDMSCOLUMN_H_
 
@@ -24,65 +25,86 @@
 #include "obierrno.h"
 #include "obilittlebigman.h"
 #include "obidmscolumndir.h"
+#include "obiarray.h"
 
-#define ELEMENTS_NAMES_MAX (2048)
-#define GROWTH_FACTOR (2)
-#define MAXIMUM_LINE_COUNT (1000000)
+
+#define ONE_IF_ZERO(x) (((x)==0)?1:(x))	/**< If x is equal to 0, x takes the value 1.
+                                	   	 */
+#define ELEMENTS_NAMES_MAX (2048)     	/**< The maximum length of the list of elements names.
+                                	     */
+#define COLUMN_GROWTH_FACTOR (2)	 	/**< The growth factor when a column is enlarged.
+                                	   	 */
+#define MAXIMUM_LINE_COUNT (1000000)    /**< The maximum line count for the data of a column. //TODO
+                                	     */
+#define FORMATTED_TIME_LENGTH (1024)    /**< The length allocated for the character string containing a formatted date
+ 	 	 	 	 	 	 	 	 	     */
 
 
 typedef int32_t obiversion_t; 	/**< Used to store the column version number
                                  */
 
-/**
- * @brief OBIColumnHeader structure.
- */
 
+/**
+ * @brief OBIDMS column header structure.
+ */
 typedef struct OBIDMS_column_header {
-	bool			little_endian;		        /**< endianness of the column:
-											     *   	- `true`  on little endian platforms
-												 *		- `false` on big endian platforms
-												 *
-												 *   @see obi_is_little_endian()
-	 	 	 	 	 	 	 	 	 	 	     */
-	int				header_size;		        /**< size of the header in bytes */
-	size_t			line_count;				    /**< number of lines of data */
-	size_t			lines_used;				    /**< number of lines of data used */
-	size_t			nb_elements_per_line;       /**< number of elements per line (default : 1) */
-	char			elements_names[ELEMENTS_NAMES_MAX+1];				/**< names of the line elements (default : "["column_name"]") */
-	OBIType_t		data_type;				    /**< type of the data */
-	time_t			creation_date;			    /**< date of creation of the file */
-	obiversion_t	version;				    /**< version of the OBIColumn */
-	obiversion_t	cloned_from;			    /**< version of the OBIColumn from which the column was cloned from (-1 if it does not come from cloning).*/
-	char            name[OBIDMS_MAX_COLNAME+1]; /**< The column name as a NULL
-	                                             *   terminated string.
-	                                             */
-	char 			comments[1];				/**< comments stored as a classical
-												 zero end C string.
-												 The size of the comment is only limited
-												 by the header size
-	 	 	 	 	 	 	 	 	 	 	 */
+	bool			little_endian;		        			/**< Endianness of the column:
+											     	 	 	 *   	- `true`  on little endian platforms
+											     	 	 	 *		- `false` on big endian platforms
+											     	 	 	 *   @see obi_is_little_endian()
+											     	 	 	 */
+	size_t			header_size;		   				    /**< Size of the header in bytes.
+	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 */
+	index_t			line_count;							    /**< Number of lines of data allocated.
+	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 */
+	index_t			lines_used;							    /**< Number of lines of data used.
+	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 */
+	index_t			nb_elements_per_line;       			/**< Number of elements per line (default: 1).
+	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 */
+	char			elements_names[ELEMENTS_NAMES_MAX+1];	/**< Names of the line elements with ';' as separator
+															 *	 (should be the column name if one element per line).
+															 */
+	OBIType_t		data_type;				    			/**< Type of the data.
+	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 */
+	time_t			creation_date;			    			/**< Date of creation of the file.
+	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 */
+	obiversion_t	version;				   				/**< Version of the column.
+	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 */
+	obiversion_t	cloned_from;			    			/**< Version of the column from which this column
+															 *   was cloned from (-1 if it was not created by cloning
+															 *   another column).
+															 */
+	char            name[OBIDMS_COLUMN_MAX_NAME+1]; 	    /**< The column name as a NULL terminated string.
+	                                             	 	 	 */
+	char            array_name[ARRAY_MAX_NAME+1]; 	    	/**< If there is one, the obi_array name as a NULL terminated string.
+	                                             	 	 	 */
+	char 			comments[1];							/**< Comments stored as a classical zero end C string.
+												 	 	 	 *	 The size of the comment is only limited by the header size.
+												 	 	 	 */
 } OBIDMS_column_header_t, *OBIDMS_column_header_p;
 
 
 /**
- * @brief Structure describing a Column of the OBITools DMS
+ * @brief OBIDMS column structure.
  *
  * A data structure of this type is returned by the functions
- * creating, opening or cloning an OBIDMS_column.
+ * creating, opening or cloning an OBIDMS column.
  */
 typedef struct OBIDMS_column {
-	OBIDMS_p                	dms;			 	/**< A pointer to a DMS instance */
-	OBIDMS_column_directory_p   column_directory;	/**< A pointer to an OBIDMS column directory instance */
-	OBIDMS_column_header_p		header; 		 	/**< A pointer to the header of the column */
-	void*                   	data;   		 	/**< A `void` pointer to the beginning of the
-	                                 	 	  	  	 *   data.
+	OBIDMS_p                	dms;			 	/**< A pointer to the OBIDMS structure to which the column belongs.
+	 	 	 	 	 	 	 	 	 	 	 	 	 */
+	OBIDMS_column_directory_p   column_directory;	/**< A pointer to the OBIDMS column directory structure to which the column belongs.
+	 	 	 	 	 	 	 	 	 	 	 	 	 */
+	OBIDMS_column_header_p		header; 		 	/**< A pointer to the header of the column.
+	 	 	 	 	 	 	 	 	 	 	 	 	 */
+	OBIDMS_array_p 				array;				/**< A pointer to the array associated with the column if there is one.
+	 	 	 	 	 	 	 	 	 	 	 	 	 */
+	void*                   	data;   		 	/**< A `void` pointer to the beginning of the data.
 	                                 	 	         *
-													 *   @warning never use this member directly
-													 *            outside of the code of the
-													 *            low level functions
-													 *            of the OBITools DMS
+													 *   @warning Never use this member directly outside of the code of the
+													 *            low level functions of the OBIDMS.
 													 */
-	bool						writable;	     	/**< Indicates if the column is writable or not.
+	bool						writable;	     	/**< Indicates if the column is writable or not.	TODO delete?
 													 *       - `true` the column is writable
 													 *       - `false` the column is read-only
 													 *
@@ -93,23 +115,30 @@ typedef struct OBIDMS_column {
 
 
 /**
- * @brief Returns the latest version of a column in a column directory
+ * @brief Returns the latest version number of a column in a column directory using the column directory structure.
  *
- * @param column_directory
+ * @param column_directory A pointer as returned by obi_create_column_directory() or obi_open_column_directory().
  *
- * @return the latest version number kept in the version file
- * @return -1 if an error occurred
+ * @returns The latest version number kept in the version file.
+ * @retval -1 if an error occurred.
+ *
+ * @since May 2015
+ * @author Eric Coissac (eric.coissac@metabarcoding.org)
  */
 obiversion_t obi_get_latest_version_number(OBIDMS_column_directory_p column_directory);
 
 
 /**
- * @brief Returns the latest version of a column in a column directory
+ * @brief Returns the latest version of a column in a column directory using the column name.
  *
- * @param column_name
+ * @param dms A pointer on an OBIDMS.
+ * @param column_name The column name.
  *
- * @return the latest version number kept in the version file
- * @return -1 if an error occurred
+ * @returns The latest version number kept in the version file.
+ * @retval -1 if an error occurred.
+ *
+ * @since May 2015
+ * @author Eric Coissac (eric.coissac@metabarcoding.org)
  */
 obiversion_t obi_column_get_latest_version_from_name(OBIDMS_p dms, const char* column_name);
 
@@ -118,9 +147,9 @@ obiversion_t obi_column_get_latest_version_from_name(OBIDMS_p dms, const char* c
  * @brief Returns the header size in bytes of a column on this platform.
  *
  * The header size is defined as a multiple of the memory page size.
- * Up to now the header size is defined as one time the page size.
+ * As of now the header size is defined as one time the page size.
  *
- * @return a `size_t` value corresponding to the header size in bytes
+ * @returns The header size in bytes.
  *
  * @since May 2015
  * @author Eric Coissac (eric.coissac@metabarcoding.org)
@@ -131,30 +160,43 @@ size_t obi_get_platform_header_size();
 /**
  * @brief Creates a column.
  *
- * @param dms a pointer on an OBIDMS
- * @param column_name the name of the new column
- * @param type the OBIType code used to create the column
- * @param nb_lines the number of lines to be stored
+ * The minimum data size allocated is one memory page, and the data is initialized to the NA value of the OBIType.
+ * If there is an array associated with the column, it is opened or created if it does not already exist.
+ *
+ * @warning If there is one element per line, elements_names should be equal to column_name.	// TODO change this condition?
+ *
+ * @param dms A pointer on an OBIDMS.
+ * @param column_name The name of the new column.
+ * @param data_type The OBIType code of the data.
+ * @param nb_lines The number of lines to be stored.
+ * @param nb_elements_per_line The number of elements per line.
+ * @param elements_names The names of the elements with ';' as separator.
+ * @param array_name The name of the array if there is one associated with the column.
+ *
+ * @returns A pointer on the newly created column structure.
+ * @retval NULL if an error occurred.
  *
  * @since May 2015
  * @author Eric Coissac (eric.coissac@metabarcoding.org)
  */
 OBIDMS_column_p obi_create_column(OBIDMS_p dms,
-								  const char* column_name,
-								  OBIType_t type,
-								  size_t nb_lines,
-								  size_t nb_elements_per_line,
-								  const char*  elements_names);
+		                          const char* column_name,
+								  OBIType_t data_type,
+								  index_t nb_lines,
+								  index_t nb_elements_per_line,
+								  const char* elements_names,
+								  const char* array_name);
 
 
 /**
  * @brief Opens a column in read-only mode.
  *
- * @param dms a pointer on an OBIDMS
- * @param column_name the name of the column
- * @param version_number the version of the column that should be opened (if -1, the latest version number is retrieved)
+ * @param dms A pointer on an OBIDMS.
+ * @param column_name The name of the column.
+ * @param version_number The version of the column that should be opened (if -1, the latest version is retrieved).
  *
- * @return a pointer to the opened column
+ * @returns A pointer on the opened column structure.
+ * @retval NULL if an error occurred.
  *
  * @since July 2015
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
@@ -165,12 +207,13 @@ OBIDMS_column_p obi_open_column(OBIDMS_p dms, const char* column_name, obiversio
 /**
  * @brief Clones a column, and returns a pointer to the writable new column.
  *
- * @param dms a pointer on an OBIDMS
- * @param column_name the name of the column to clone
- * @param version_number the version of the column that should be cloned (if -1, the latest version number is retrieved)
- * @param clone_data whether the data should be copied or not
+ * @param dms A pointer on an OBIDMS.
+ * @param column_name The name of the column to clone.
+ * @param version_number The version of the column that should be cloned (if -1, the latest version is retrieved).
+ * @param clone_data Whether the data should be copied or not.
  *
- * @return a pointer to the created column
+ * @returns A pointer to the created column.
+ * @retval NULL if an error occurred.
  *
  * @since August 2015
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
@@ -181,10 +224,10 @@ OBIDMS_column_p obi_clone_column(OBIDMS_p dms, const char* column_name, obiversi
 /**
  * @brief Closes a column.
  *
- * @param column a pointer on an OBIDMS column
+ * @param column A pointer on an OBIDMS column.
  *
- * @return 0 if the operation was successfully completed
- * @return -1 if an error occurred
+ * @retval 0 if the operation was successfully completed.
+ * @retval -1 if an error occurred.
  *
  * @since July 2015
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
@@ -193,12 +236,13 @@ int obi_close_column(OBIDMS_column_p column);
 
 
 /**
- * @brief Truncates a column file to the number of lines used.
+ * @brief Truncates a column file to the number of lines used rounded to the nearest
+ * 		  greater multiple of the page size.
  *
- * @param column a pointer on an OBIDMS column
+ * @param column A pointer on an OBIDMS column.
  *
- * @return 0 if the operation was successfully completed
- * @return -1 if an error occurred
+ * @retval 0 if the operation was successfully completed.
+ * @retval -1 if an error occurred.
  *
  * @since August 2015
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
@@ -209,10 +253,10 @@ int obi_truncate_column_to_lines_used(OBIDMS_column_p column);
 /**
  * @brief Enlarges a column file.
  *
- * @param column a pointer on an OBIDMS column
+ * @param column A pointer on an OBIDMS column.
  *
- * @return 0 if the operation was successfully completed
- * @return -1 if an error occurred
+ * @retval 0 if the operation was successfully completed.
+ * @retval -1 if an error occurred.
  *
  * @since August 2015
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
@@ -221,12 +265,13 @@ int obi_enlarge_column(OBIDMS_column_p column);
 
 
 /**
- * @brief Truncates a column file to the number of lines used and closes it.
+ * @brief Truncates a column file to the number of lines used rounded to the nearest
+ *        greater multiple of the page size and closes it.
  *
- * @param column a pointer on an OBIDMS column
+ * @param column A pointer on an OBIDMS column.
  *
- * @return 0 if the operation was successfully completed
- * @return -1 if an error occurred
+ * @retval 0 if the operation was successfully completed.
+ * @retval -1 if an error occurred.
  *
  * @since August 2015
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
@@ -235,134 +280,75 @@ int obi_truncate_and_close_column(OBIDMS_column_p column);
 
 
 /*
- * @brief Sets the data in a column to the NA value of the data type.
+ * @brief Sets the data in a column to the NA value of the data OBIType.
  *
- * @param column a pointer on an OBIDMS column
- * @param start the first line number of the block that should be set
- * @param nb_lines the number of lines that should be set
+ * @param column A pointer on an OBIDMS column.
+ * @param start The first line number of the block that should be set.
+ * @param nb_lines The number of lines that should be set.
  *
  * @since August 2015
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-void obi_ini_to_NA_values(OBIDMS_column_p column, size_t start, size_t nb_lines);
+void obi_ini_to_NA_values(OBIDMS_column_p column, index_t first_line_nb, index_t nb_lines);	// TO make private?
 
 
 /**
- * @brief Sets the 'writable' header attribute of an OBIDMS column to False.
+ * @brief Recovers the header of an OBIDMS column from the column name.
  *
- * @param column a pointer on an OBIDMS column
+ * @warning The header structure has to be munmapped by the caller.
+ *
+ * @param dms A pointer on an OBIDMS.
+ * @param column_name The name of an OBIDMS column.
+ *
+ * @returns A pointer on the mmapped header of the column.
+ * @retval NULL if an error occurred.
+ *
+ * @since October 2015
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+OBIDMS_column_header_p obi_column_get_header_from_name(OBIDMS_p dms, const char* column_name);
+
+
+/**
+ * @brief Munmap a mmapped header as returned by obi_column_get_header_from_name().
+ *
+ * @param header A pointer on the mmapped header structure.
+ *
+ * @retval 0 if the operation was successfully completed.
+ * @retval -1 if an error occurred.
+ *
+ * @since October 2015
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+int obi_unmap_header(OBIDMS_column_header_p header);
+
+
+/**
+ * @brief Recovers the index of an element in an OBIDMS column from the element's name.
+ *
+ * @param column A pointer on an OBIDMS column.
+ * @param element_name The name of the element.
+ *
+ * @returns The index of the element in a line of the column.
+ * @retval SIZE_MAX if an error occurred.
  *
  * @since July 2015
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-void obi_column_make_unwritable(OBIDMS_column_p column);
+index_t obi_column_get_element_index_from_name(OBIDMS_column_p column, const char* element_name);
 
 
 /**
- * @brief Recovers the line count of an OBIDMS column.
+ * @brief Formats a date in a way that is easy to read.
  *
- * @param column a pointer on an OBIDMS column
+ * @param date A date.
  *
- * @return the line count of the column
+ * @returns The date formatted in a way that is easy to read.
  *
- * @since July 2015
+ * @since October 2015
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-size_t obi_column_get_line_count(OBIDMS_column_p column);
-
-
-/**
- * @brief Recovers the number of lines used in an OBIDMS column.
- *
- * @param column a pointer on an OBIDMS column
- *
- * @return the number of lines used in the column
- *
- * @since August 2015
- * @author Celine Mercier (celine.mercier@metabarcoding.org)
- */
-size_t obi_column_get_nb_lines_used(OBIDMS_column_p column);
-
-
-/**
- * @brief Recovers the data type of an OBIDMS column.
- *
- * @param column a pointer on an OBIDMS column
- *
- * @return the data type of the column
- *
- * @since July 2015
- * @author Celine Mercier (celine.mercier@metabarcoding.org)
- */
-OBIType_t obi_column_get_data_type(OBIDMS_column_p column);
-
-
-/**
- * @brief Recovers the data type of an OBIDMS column from the column name.
- *
- * @param dms a pointer on an OBIDMS
- * @param column_name the name of an OBIDMS column
- *
- * @return the data type of the column
- *
- * @since July 2015
- * @author Celine Mercier (celine.mercier@metabarcoding.org)
- */
-OBIType_t obi_column_get_data_type_from_name(OBIDMS_p dms, const char* column_name);
-
-
-/**
- * @brief Recovers the line count of an OBIDMS column from the column name.
- *
- * @param dms a pointer on an OBIDMS
- * @param column_name the name of an OBIDMS column
- *
- * @return the line count of the column
- *
- * @since September 2015
- * @author Celine Mercier (celine.mercier@metabarcoding.org)
- */
-size_t obi_column_get_line_count_from_name(OBIDMS_p dms, const char* column_name);
-
-
-/**
- * @brief Recovers the elements names of an OBIDMS column.
- *
- * @param column a pointer on an OBIDMS column
- *
- * @return the elements names
- *
- * @since July 2015
- * @author Celine Mercier (celine.mercier@metabarcoding.org)
- */
-const char* obi_column_get_elements_names(OBIDMS_column_p column);
-
-
-/**
- * @brief Recovers the index of an element in an OBIDMS column from its name.
- *
- * @param column a pointer on an OBIDMS column
- * @param element_name the name of the element
- *
- * @return the index of the element in a line of the column
- *
- * @since July 2015
- * @author Celine Mercier (celine.mercier@metabarcoding.org)
- */
-size_t obi_column_get_element_index_from_name(OBIDMS_column_p column, const char* element_name);
-
-
-/**
- * @brief Recovers the number of elements per line in an OBIDMS column.
- *
- * @param column a pointer on an OBIDMS column
- *
- * @return the number of elements per line
- *
- * @since July 2015
- * @author Celine Mercier (celine.mercier@metabarcoding.org)
- */
-size_t obi_column_get_nb_elements_per_line(OBIDMS_column_p column);
+char* obi_column_format_date(time_t date);
 
 
 #endif /* OBIDMSCOLUMN_H_ */

src/obidmscolumn_bool.c

@@ -1,5 +1,5 @@
 /****************************************************************************
- * OBIDMS_column_bool functions                                              *
+ * OBIDMS_column_bool functions                                             *
  ****************************************************************************/
 
 /**
@@ -19,7 +19,7 @@
 #include "obidebug.h"
 
 
-#define DEBUG_LEVEL 0
+#define DEBUG_LEVEL 0	// TODO has to be defined somewhere else (cython compil flag?)
 
 
 /**********************************************************************
@@ -28,7 +28,7 @@
  *
  **********************************************************************/
 
-int obi_column_set_obibool_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx, obibool_t value)
+int obi_column_set_obibool_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx, obibool_t value)
 {
 	// Check that the line number is not greater than the maximum allowed
 	if (line_nb >= MAXIMUM_LINE_COUNT)
@@ -57,7 +57,7 @@ int obi_column_set_obibool_with_elt_idx(OBIDMS_column_p column, size_t line_nb,
 }
 
 
-obibool_t obi_column_get_obibool_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx)
+obibool_t obi_column_get_obibool_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx)
 {
 	if ((line_nb+1) > (column->header)->lines_used)
 	{
@@ -69,56 +69,24 @@ obibool_t obi_column_get_obibool_with_elt_idx(OBIDMS_column_p column, size_t lin
 }
 
 
-int obi_column_set_obibool_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name, obibool_t value)
+int obi_column_set_obibool_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name, obibool_t value)
 {
-	size_t element_idx;
-
-	if (!strcmp(element_name, "\0"))	// element name is empty
-	{
-		if (obi_column_get_nb_elements_per_line(column) == 1)	// check that there is only one element per line
-			element_idx = 0;
-		else													// there is more than one element per line
-		{
-			obi_set_errno(OBICOL_UNKNOWN_ERROR);
-			obidebug(1, "\nAn element name must be specified");
-        	return -1;
-		}
-	}
-    else
-    {
-		element_idx = obi_column_get_element_index_from_name(column, element_name);
-		if (element_idx == -1)
-			return -1;
-    }
-
+	index_t element_idx;
+	element_idx = obi_column_get_element_index_from_name(column, element_name);
+	if (element_idx == OBIIdx_NA)
+		return -1;
 	obi_column_set_obibool_with_elt_idx(column, line_nb, element_idx, value);
-
 	return 0;
 }
 
 
-obibool_t obi_column_get_obibool_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name)
+obibool_t obi_column_get_obibool_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name)
 {
-	size_t element_idx;
-
-	if (!strcmp(element_name, "\0"))	// element name is empty
-	{
-		if (obi_column_get_nb_elements_per_line(column) == 1)	// check that there is only one element per line
-			element_idx = 0;
-		else													// there is more than one element per line
-		{
-			obi_set_errno(OBICOL_UNKNOWN_ERROR);
-			obidebug(1, "\nAn element name must be specified");
-        	return OBIBool_NA;
-		}
-	}
-    else
-    {
-		element_idx = obi_column_get_element_index_from_name(column, element_name);
-		if (element_idx == -1)
-			return OBIBool_NA;
-    }
+	index_t element_idx;
 
+	element_idx = obi_column_get_element_index_from_name(column, element_name);
+	if (element_idx == OBIIdx_NA)
+		return OBIBool_NA;
 	return obi_column_get_obibool_with_elt_idx(column, line_nb, element_idx);
 }
 

src/obidmscolumn_bool.h

@@ -10,6 +10,10 @@
  */
 
 
+#ifndef OBIDMSCOLUMN_BOOL_H_
+#define OBIDMSCOLUMN_BOOL_H_
+
+
 #include <stdlib.h>
 #include <stdio.h>
 
@@ -20,82 +24,76 @@
 /**
  * @brief Sets a value in an OBIDMS column containing data with the type OBI_BOOL, using the index of the element in the line.
  *
- * @param column a pointer as returned by obi_create_column()
  * @warning Pointers returned by obi_open_column() don't allow writing.
  *
- * @param line_nb the number of the line where the value should be set
+ * @param column A pointer as returned by obi_create_column() or obi_clone_column().
+ * @param line_nb The number of the line where the value should be set.
+ * @param element_idx The index of the element that should be set in the line.
+ * @param value The value that should be set.
  *
- * @param element_idx the index of the element that should be set in the line
- *
- * @param value the value that should be set
- *
- * @return an integer value indicating the success of the operation.
- *
- * @retvalue 0 on success
- * @retvalue -1 on failure and the `obi_errno` variable is set.
+ * @returns An integer value indicating the success of the operation.
+ * @retval 0 on success.
+ * @retval -1 if an error occurred.
  *
  * @since July 2015
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-int obi_column_set_obibool_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx, obibool_t value);
+int obi_column_set_obibool_with_elt_idx(OBIDMS_column_p column, index_t line_nb, size_t element_idx, obibool_t value);
 
 
 /**
  * @brief Recovers a value in an OBIDMS column containing data with the type OBI_BOOL.
  *
- * @param column a pointer as returned by obi_create_column()
+ * @param column A pointer as returned by obi_create_column().
+ * @param line_nb The number of the line where the value should be recovered.
+ * @param element_idx The index of the element that should be recovered in the line.
  *
- * @param line_nb the number of the line where the value should be recovered
- *
- * @param element_idx the index of the element that should be recovered in the line
- *
- * @return the recovered value
+ * @returns The recovered value.
+ * @retval OBIBool_NA the NA value of the type if an error occurred and obi_errno is set.
  *
  * @since July 2015
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-obibool_t obi_column_get_obibool_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx);
+obibool_t obi_column_get_obibool_with_elt_idx(OBIDMS_column_p column, index_t line_nb, size_t element_idx);
 
 
 /**
- * @brief Sets a value in an OBIDMS column containing data with the type OBI_BOOL, using the name of the element in the line.
+ * @brief Sets a value in an OBIDMS column containing data with the type OBI_BOOL,
+ *        using the name of the element in the line.
  *
- * @param column a pointer as returned by obi_create_column()
  * @warning Pointers returned by obi_open_column() don't allow writing.
  *
- * @param line_nb the number of the line where the value should be set
+ * @param column A pointer as returned by obi_create_column() or obi_clone_column().
+ * @param line_nb The number of the line where the value should be set.
+ * @param element_name The name of the element that should be set in the line.
+ * @param value The value that should be set.
  *
- * @param element_name the name of the element that should be set in the line
- * If empty, it is checked that there is only one element per line
- *
- * @param value the value that should be set
- *
- * @return an integer value indicating the success of the operation.
- *
- * @retvalue 0 on success
- * @retvalue -1 on failure and the `obi_errno` variable is set.
+ * @returns An integer value indicating the success of the operation.
+ * @retval 0 on success.
+ * @retval -1 if an error occurred.
  *
  * @since August 2015
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-int obi_column_set_obibool_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name, obibool_t value);
+int obi_column_set_obibool_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name, obibool_t value);
 
 
 /**
- * @brief Recovers a value in an OBIDMS column containing data with the type OBI_BOOL, using the name of the element in the line.
+ * @brief Recovers a value in an OBIDMS column containing data with the type OBI_BOOL,
+ *        using the name of the element in the line.
  *
- * @param column a pointer as returned by obi_create_column()
+ * @param column A pointer as returned by obi_create_column() or obi_clone_column().
+ * @param line_nb The number of the line where the value should be recovered.
+ * @param element_name The name of the element that should be recovered in the line.
  *
- * @param line_nb the number of the line where the value should be recovered
- *
- * @param element_name the name of the element that should be recovered in the line
- * If empty, it is checked that there is only one element per line
- *
- * @return the recovered value
- * @retvalue -1 on failure and the `obi_errno` variable is set. TODO an other value must be chosen
+ * @returns The recovered value.
+ * @retval OBIBool_NA the NA value of the type if an error occurred and obi_errno is set.
  *
  * @since August 2015
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-obibool_t obi_column_get_obibool_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name);
+obibool_t obi_column_get_obibool_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name);
+
+
+#endif /* OBIDMSCOLUMN_BOOL_H_ */
 

src/obidmscolumn_char.c

@@ -19,7 +19,7 @@
 #include "obidebug.h"
 
 
-#define DEBUG_LEVEL 0
+#define DEBUG_LEVEL 0	// TODO has to be defined somewhere else (cython compil flag?)
 
 
 /**********************************************************************
@@ -28,7 +28,7 @@
  *
  **********************************************************************/
 
-int obi_column_set_obichar_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx, obichar_t value)
+int obi_column_set_obichar_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx, obichar_t value)
 {
 	// Check that the line number is not greater than the maximum allowed
 	if (line_nb >= MAXIMUM_LINE_COUNT)
@@ -57,7 +57,7 @@ int obi_column_set_obichar_with_elt_idx(OBIDMS_column_p column, size_t line_nb,
 }
 
 
-obichar_t obi_column_get_obichar_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx)
+obichar_t obi_column_get_obichar_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx)
 {
 	if ((line_nb+1) > (column->header)->lines_used)
 	{
@@ -65,61 +65,28 @@ obichar_t obi_column_get_obichar_with_elt_idx(OBIDMS_column_p column, size_t lin
 		obidebug(1, "\nError trying to get a value that is beyond the current number of lines used");
 		return OBIChar_NA;
 	}
-
 	return *(((obichar_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx);
 }
 
 
-int obi_column_set_obichar_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name, obichar_t value)
+int obi_column_set_obichar_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name, obichar_t value)
 {
-	size_t element_idx;
-
-	if (!strcmp(element_name, "\0"))	// element name is empty
-	{
-		if (obi_column_get_nb_elements_per_line(column) == 1)	// check that there is only one element per line
-			element_idx = 0;
-		else													// there is more than one element per line
-		{
-			obi_set_errno(OBICOL_UNKNOWN_ERROR);
-			obidebug(1, "\nAn element name must be specified");
-        	return -1;
-		}
-	}
-    else
-    {
-		element_idx = obi_column_get_element_index_from_name(column, element_name);
-		if (element_idx == -1)
-			return -1;
-    }
-
+	index_t element_idx;
+	element_idx = obi_column_get_element_index_from_name(column, element_name);
+	if (element_idx == OBIIdx_NA)
+		return -1;
 	obi_column_set_obichar_with_elt_idx(column, line_nb, element_idx, value);
-
 	return 0;
 }
 
 
-obichar_t obi_column_get_obichar_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name)
+obichar_t obi_column_get_obichar_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name)
 {
-	size_t element_idx;
-
-	if (!strcmp(element_name, "\0"))	// element name is empty
-	{
-		if (obi_column_get_nb_elements_per_line(column) == 1)	// check that there is only one element per line
-			element_idx = 0;
-		else													// there is more than one element per line
-		{
-			obi_set_errno(OBICOL_UNKNOWN_ERROR);
-			obidebug(1, "\nAn element name must be specified");
-        	return OBIChar_NA;
-		}
-	}
-    else
-    {
-		element_idx = obi_column_get_element_index_from_name(column, element_name);
-		if (element_idx == -1)
-			return OBIChar_NA;
-    }
+	index_t element_idx;
 
+	element_idx = obi_column_get_element_index_from_name(column, element_name);
+	if (element_idx == OBIIdx_NA)
+		return OBIChar_NA;
 	return obi_column_get_obichar_with_elt_idx(column, line_nb, element_idx);
 }
 

src/obidmscolumn_char.h

@@ -10,6 +10,10 @@
  */
 
 
+#ifndef OBIDMSCOLUMN_CHAR_H_
+#define OBIDMSCOLUMN_CHAR_H_
+
+
 #include <stdlib.h>
 #include <stdio.h>
 
@@ -20,82 +24,76 @@
 /**
  * @brief Sets a value in an OBIDMS column containing data with the type OBI_CHAR, using the index of the element in the line.
  *
- * @param column a pointer as returned by obi_create_column()
  * @warning Pointers returned by obi_open_column() don't allow writing.
  *
- * @param line_nb the number of the line where the value should be set
+ * @param column A pointer as returned by obi_create_column() or obi_clone_column().
+ * @param line_nb The number of the line where the value should be set.
+ * @param element_idx The index of the element that should be set in the line.
+ * @param value The value that should be set.
  *
- * @param element_idx the index of the element that should be set in the line
- *
- * @param value the value that should be set
- *
- * @return an integer value indicating the success of the operation.
- *
- * @retvalue 0 on success
- * @retvalue -1 on failure and the `obi_errno` variable is set.
+ * @returns An integer value indicating the success of the operation.
+ * @retval 0 on success.
+ * @retval -1 if an error occurred.
  *
  * @since July 2015
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-int obi_column_set_obichar_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx, obichar_t* value);
+int obi_column_set_obichar_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx, obichar_t value);
 
 
 /**
  * @brief Recovers a value in an OBIDMS column containing data with the type OBI_CHAR.
  *
- * @param column a pointer as returned by obi_create_column()
+ * @param column A pointer as returned by obi_create_column().
+ * @param line_nb The number of the line where the value should be recovered.
+ * @param element_idx The index of the element that should be recovered in the line.
  *
- * @param line_nb the number of the line where the value should be recovered
- *
- * @param element_idx the index of the element that should be recovered in the line
- *
- * @return the recovered value
+ * @returns The recovered value.
+ * @retval OBIBool_NA the NA value of the type if an error occurred and obi_errno is set.
  *
  * @since July 2015
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-obichar_t* obi_column_get_obichar_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx);
+obichar_t obi_column_get_obichar_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx);
 
 
 /**
- * @brief Sets a value in an OBIDMS column containing data with the type OBI_CHAR, using the name of the element in the line.
+ * @brief Sets a value in an OBIDMS column containing data with the type OBI_CHAR,
+ *        using the name of the element in the line.
  *
- * @param column a pointer as returned by obi_create_column()
  * @warning Pointers returned by obi_open_column() don't allow writing.
  *
- * @param line_nb the number of the line where the value should be set
+ * @param column A pointer as returned by obi_create_column() or obi_clone_column().
+ * @param line_nb The number of the line where the value should be set.
+ * @param element_name The name of the element that should be set in the line.
+ * @param value The value that should be set.
  *
- * @param element_name the name of the element that should be set in the line
- * If empty, it is checked that there is only one element per line
- *
- * @param value the value that should be set
- *
- * @return an integer value indicating the success of the operation.
- *
- * @retvalue 0 on success
- * @retvalue -1 on failure and the `obi_errno` variable is set.
+ * @returns An integer value indicating the success of the operation.
+ * @retval 0 on success.
+ * @retval -1 if an error occurred.
  *
  * @since August 2015
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-int obi_column_set_obichar_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name, obichar_t value);
+int obi_column_set_obichar_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name, obichar_t value);
 
 
 /**
- * @brief Recovers a value in an OBIDMS column containing data with the type OBI_CHAR, using the name of the element in the line.
+ * @brief Recovers a value in an OBIDMS column containing data with the type OBI_CHAR,
+ *        using the name of the element in the line.
  *
- * @param column a pointer as returned by obi_create_column()
+ * @param column A pointer as returned by obi_create_column() or obi_clone_column().
+ * @param line_nb The number of the line where the value should be recovered.
+ * @param element_name The name of the element that should be recovered in the line.
  *
- * @param line_nb the number of the line where the value should be recovered
- *
- * @param element_name the name of the element that should be recovered in the line
- * If empty, it is checked that there is only one element per line
- *
- * @return the recovered value
- * @retvalue NULL on failure and the `obi_errno` variable is set. TODO an other value should be chosen maybe
+ * @returns The recovered value.
+ * @retval OBIBool_NA the NA value of the type if an error occurred and obi_errno is set.
  *
  * @since August 2015
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-obichar_t obi_column_get_obichar_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name);
+obichar_t obi_column_get_obichar_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name);
+
+
+#endif /* OBIDMSCOLUMN_CHAR_H_ */
 

src/obidmscolumn_float.c

@@ -19,7 +19,7 @@
 #include "obidebug.h"
 
 
-#define DEBUG_LEVEL 0
+#define DEBUG_LEVEL 0	// TODO has to be defined somewhere else (cython compil flag?)
 
 
 /**********************************************************************
@@ -28,7 +28,7 @@
  *
  **********************************************************************/
 
-int obi_column_set_obifloat_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx, obifloat_t value)
+int obi_column_set_obifloat_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx, obifloat_t value)
 {
 	// Check that the line number is not greater than the maximum allowed
 	if (line_nb >= MAXIMUM_LINE_COUNT)
@@ -57,7 +57,7 @@ int obi_column_set_obifloat_with_elt_idx(OBIDMS_column_p column, size_t line_nb,
 }
 
 
-obifloat_t obi_column_get_obifloat_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx)
+obifloat_t obi_column_get_obifloat_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx)
 {
 	if ((line_nb+1) > (column->header)->lines_used)
 	{
@@ -69,56 +69,24 @@ obifloat_t obi_column_get_obifloat_with_elt_idx(OBIDMS_column_p column, size_t l
 }
 
 
-int obi_column_set_obifloat_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name, obifloat_t value)
+int obi_column_set_obifloat_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name, obifloat_t value)
 {
-	size_t element_idx;
-
-	if (!strcmp(element_name, "\0"))	// element name is empty
-	{
-		if (obi_column_get_nb_elements_per_line(column) == 1)	// check that there is only one element per line
-			element_idx = 0;
-		else													// there is more than one element per line
-		{
-			obi_set_errno(OBICOL_UNKNOWN_ERROR);
-			obidebug(1, "\nAn element name must be specified");
-        	return -1;
-		}
-	}
-    else
-    {
-		element_idx = obi_column_get_element_index_from_name(column, element_name);
-		if (element_idx == -1)
-			return -1;
-    }
-
+	index_t element_idx;
+	element_idx = obi_column_get_element_index_from_name(column, element_name);
+	if (element_idx == OBIIdx_NA)
+		return -1;
 	obi_column_set_obifloat_with_elt_idx(column, line_nb, element_idx, value);
-
 	return 0;
 }
 
 
-obifloat_t obi_column_get_obifloat_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name)
+obifloat_t obi_column_get_obifloat_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name)
 {
-	size_t element_idx;
-
-	if (!strcmp(element_name, "\0"))	// element name is empty
-	{
-		if (obi_column_get_nb_elements_per_line(column) == 1)	// check that there is only one element per line
-			element_idx = 0;
-		else													// there is more than one element per line
-		{
-			obi_set_errno(OBICOL_UNKNOWN_ERROR);
-			obidebug(1, "\nAn element name must be specified");
-        	return OBIFloat_NA;
-		}
-	}
-    else
-    {
-		element_idx = obi_column_get_element_index_from_name(column, element_name);
-		if (element_idx == -1)
-			return OBIFloat_NA;
-    }
+	index_t element_idx;
 
+	element_idx = obi_column_get_element_index_from_name(column, element_name);
+	if (element_idx == OBIIdx_NA)
+		return OBIFloat_NA;
 	return obi_column_get_obifloat_with_elt_idx(column, line_nb, element_idx);
 }
 

src/obidmscolumn_float.h

@@ -10,6 +10,10 @@
  */
 
 
+#ifndef OBIDMSCOLUMN_FLOAT_H_
+#define OBIDMSCOLUMN_FLOAT_H_
+
+
 #include <stdlib.h>
 #include <stdio.h>
 
@@ -20,82 +24,76 @@
 /**
  * @brief Sets a value in an OBIDMS column containing data with the type OBI_FLOAT, using the index of the element in the line.
  *
- * @param column a pointer as returned by obi_create_column()
  * @warning Pointers returned by obi_open_column() don't allow writing.
  *
- * @param line_nb the number of the line where the value should be set
+ * @param column A pointer as returned by obi_create_column() or obi_clone_column().
+ * @param line_nb The number of the line where the value should be set.
+ * @param element_idx The index of the element that should be set in the line.
+ * @param value The value that should be set.
  *
- * @param element_idx the index of the element that should be set in the line
- *
- * @param value the value that should be set
- *
- * @return an integer value indicating the success of the operation.
- *
- * @retvalue 0 on success
- * @retvalue -1 on failure and the `obi_errno` variable is set.
+ * @returns An integer value indicating the success of the operation.
+ * @retval 0 on success.
+ * @retval -1 if an error occurred.
  *
  * @since July 2015
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-int obi_column_set_obifloat_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx, obifloat_t value);
+int obi_column_set_obifloat_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx, obifloat_t value);
 
 
 /**
  * @brief Recovers a value in an OBIDMS column containing data with the type OBI_FLOAT.
  *
- * @param column a pointer as returned by obi_create_column()
+ * @param column A pointer as returned by obi_create_column().
+ * @param line_nb The number of the line where the value should be recovered.
+ * @param element_idx The index of the element that should be recovered in the line.
  *
- * @param line_nb the number of the line where the value should be recovered
- *
- * @param element_idx the index of the element that should be recovered in the line
- *
- * @return the recovered value
+ * @returns The recovered value.
+ * @retval OBIBool_NA the NA value of the type if an error occurred and obi_errno is set.
  *
  * @since July 2015
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-obifloat_t obi_column_get_obifloat_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx);
+obifloat_t obi_column_get_obifloat_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx);
 
 
 /**
- * @brief Sets a value in an OBIDMS column containing data with the type OBI_FLOAT, using the name of the element in the line.
+ * @brief Sets a value in an OBIDMS column containing data with the type OBI_FLOAT,
+ *        using the name of the element in the line.
  *
- * @param column a pointer as returned by obi_create_column()
  * @warning Pointers returned by obi_open_column() don't allow writing.
  *
- * @param line_nb the number of the line where the value should be set
+ * @param column A pointer as returned by obi_create_column() or obi_clone_column().
+ * @param line_nb The number of the line where the value should be set.
+ * @param element_name The name of the element that should be set in the line.
+ * @param value The value that should be set.
  *
- * @param element_name the name of the element that should be set in the line
- * If empty, it is checked that there is only one element per line
- *
- * @param value the value that should be set
- *
- * @return an integer value indicating the success of the operation.
- *
- * @retvalue 0 on success
- * @retvalue -1 on failure and the `obi_errno` variable is set.
+ * @returns An integer value indicating the success of the operation.
+ * @retval 0 on success.
+ * @retval -1 if an error occurred.
  *
  * @since August 2015
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-int obi_column_set_obifloat_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name, obifloat_t value);
+int obi_column_set_obifloat_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name, obifloat_t value);
 
 
 /**
- * @brief Recovers a value in an OBIDMS column containing data with the type OBI_FLOAT, using the name of the element in the line.
+ * @brief Recovers a value in an OBIDMS column containing data with the type OBI_FLOAT,
+ *        using the name of the element in the line.
  *
- * @param column a pointer as returned by obi_create_column()
+ * @param column A pointer as returned by obi_create_column() or obi_clone_column().
+ * @param line_nb The number of the line where the value should be recovered.
+ * @param element_name The name of the element that should be recovered in the line.
  *
- * @param line_nb the number of the line where the value should be recovered
- *
- * @param element_name the name of the element that should be recovered in the line
- * If empty, it is checked that there is only one element per line
- *
- * @return the recovered value
- * @retvalue -1 on failure and the `obi_errno` variable is set. TODO an other value must be chosen
+ * @returns The recovered value.
+ * @retval OBIBool_NA the NA value of the type if an error occurred and obi_errno is set.
  *
  * @since August 2015
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-obifloat_t obi_column_get_obifloat_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name);
+obifloat_t obi_column_get_obifloat_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name);
+
+
+#endif /* OBIDMSCOLUMN_FLOAT_H_ */
 

src/obidmscolumn_idx.c

@@ -1,124 +0,0 @@
-/****************************************************************************
- * OBIDMS_column_idx functions                                              *
- ****************************************************************************/
-
-/**
- * @file obidsmcolumn_idx.c
- * @author Celine Mercier
- * @date August 10th 2015
- * @brief Functions handling OBIColumns containing data with the OBIType OBI_IDX.
- */
-
-
-#include <stdlib.h>
-#include <stdio.h>
-
-#include "obidmscolumn.h"
-#include "obitypes.h"
-#include "obierrno.h"
-#include "obidebug.h"
-
-
-#define DEBUG_LEVEL 0
-
-
-/**********************************************************************
- *
- * D E F I N I T I O N   O F   T H E   P U B L I C   F U N C T I O N S
- *
- **********************************************************************/
-
-int obi_column_set_obiidx_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx, obiidx_t value)
-{
-	// Check that the line number is not greater than the maximum allowed
-	if (line_nb >= MAXIMUM_LINE_COUNT)
-	{
-		obi_set_errno(OBICOL_UNKNOWN_ERROR);
-		obidebug(1, "\nError trying to set a value at a line number greater than the maximum allowed");
-    	return -1;
-	}
-
-	// Check if the file needs to be enlarged
-	while ((line_nb+1) > (column->header)->line_count)
-	{
-		// Enlarge the file
-		if (obi_enlarge_column(column) < 0)
-	    	return -1;
-	}
-
-	// Update lines used
-	if ((line_nb+1) > (column->header)->lines_used)
-		(column->header)->lines_used = line_nb+1;
-
-	// Set the value
-	*(((obiidx_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx) = value;
-
-	return 0;
-}
-
-
-obiidx_t obi_column_get_obiidx_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx)
-{
-	if ((line_nb+1) > (column->header)->lines_used)
-	{
-		obi_set_errno(OBICOL_UNKNOWN_ERROR);
-		obidebug(1, "\nError trying to get a value that is beyond the current number of lines used");
-		return OBIIdx_NA;
-	}
-	return *(((obiidx_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx);
-}
-
-
-int obi_column_set_obiidx_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name, obiidx_t value)
-{
-	size_t element_idx;
-
-	if (!strcmp(element_name, "\0"))	// element name is empty
-	{
-		if (obi_column_get_nb_elements_per_line(column) == 1)	// check that there is only one element per line
-			element_idx = 0;
-		else													// there is more than one element per line
-		{
-			obi_set_errno(OBICOL_UNKNOWN_ERROR);
-			obidebug(1, "\nAn element name must be specified");
-        	return -1;
-		}
-	}
-    else
-    {
-		element_idx = obi_column_get_element_index_from_name(column, element_name);
-		if (element_idx == -1)
-			return -1;
-    }
-
-	obi_column_set_obiidx_with_elt_idx(column, line_nb, element_idx, value);
-
-	return 0;
-}
-
-
-obiidx_t obi_column_get_obiidx_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name)
-{
-	size_t element_idx;
-
-	if (!strcmp(element_name, "\0"))	// element name is empty
-	{
-		if (obi_column_get_nb_elements_per_line(column) == 1)	// check that there is only one element per line
-			element_idx = 0;
-		else													// there is more than one element per line
-		{
-			obi_set_errno(OBICOL_UNKNOWN_ERROR);
-			obidebug(1, "\nAn element name must be specified");
-        	return OBIIdx_NA;
-		}
-	}
-    else
-    {
-		element_idx = obi_column_get_element_index_from_name(column, element_name);
-		if (element_idx == -1)
-			return OBIIdx_NA;
-    }
-
-	return obi_column_get_obiidx_with_elt_idx(column, line_nb, element_idx);
-}
-

src/obidmscolumn_idx.h

@@ -1,101 +0,0 @@
-/****************************************************************************
- * OBIDMS_column_idx header file                                            *
- ****************************************************************************/
-
-/**
- * @file obidsmcolumn_idx.h
- * @author Celine Mercier
- * @date August 10th 2015
- * @brief Header file for the functions handling OBIColumns containing data with the OBIType OBI_IDX.
- */
-
-
-#include <stdlib.h>
-#include <stdio.h>
-
-#include "obidmscolumn.h"
-#include "obitypes.h"
-
-
-/**
- * @brief Sets a value in an OBIDMS column containing data with the type OBI_IDX, using the index of the element in the line.
- *
- * @param column a pointer as returned by obi_create_column()
- * @warning Pointers returned by obi_open_column() don't allow writing.
- *
- * @param line_nb the number of the line where the value should be set
- *
- * @param element_idx the index of the element that should be set in the line
- *
- * @param value the value that should be set
- *
- * @return an integer value indicating the success of the operation.
- *
- * @retvalue 0 on success
- * @retvalue -1 on failure and the `obi_errno` variable is set.
- *
- * @since July 2015
- * @author Celine Mercier (celine.mercier@metabarcoding.org)
- */
-int obi_column_set_obiidx_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx, obiidx_t value);
-
-
-/**
- * @brief Recovers a value in an OBIDMS column containing data with the type OBI_IDX.
- *
- * @param column a pointer as returned by obi_create_column()
- *
- * @param line_nb the number of the line where the value should be recovered
- *
- * @param element_idx the index of the element that should be recovered in the line
- *
- * @return the recovered value
- *
- * @since July 2015
- * @author Celine Mercier (celine.mercier@metabarcoding.org)
- */
-obiidx_t obi_column_get_obiidx_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx);
-
-
-/**
- * @brief Sets a value in an OBIDMS column containing data with the type OBI_IDX, using the name of the element in the line.
- *
- * @param column a pointer as returned by obi_create_column()
- * @warning Pointers returned by obi_open_column() don't allow writing.
- *
- * @param line_nb the number of the line where the value should be set
- *
- * @param element_name the name of the element that should be set in the line
- * If empty, it is checked that there is only one element per line
- *
- * @param value the value that should be set
- *
- * @return an integer value indicating the success of the operation.
- *
- * @retvalue 0 on success
- * @retvalue -1 on failure and the `obi_errno` variable is set.
- *
- * @since August 2015
- * @author Celine Mercier (celine.mercier@metabarcoding.org)
- */
-int obi_column_set_obiidx_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name, obiidx_t value);
-
-
-/**
- * @brief Recovers a value in an OBIDMS column containing data with the type OBI_IDX, using the name of the element in the line.
- *
- * @param column a pointer as returned by obi_create_column()
- *
- * @param line_nb the number of the line where the value should be recovered
- *
- * @param element_name the name of the element that should be recovered in the line
- * If empty, it is checked that there is only one element per line
- *
- * @return the recovered value
- * @retvalue -1 on failure and the `obi_errno` variable is set. TODO an other value must be chosen
- *
- * @since August 2015
- * @author Celine Mercier (celine.mercier@metabarcoding.org)
- */
-obiidx_t obi_column_get_obiidx_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name);
-

src/obidmscolumn_int.c

@@ -19,7 +19,7 @@
 #include "obidebug.h"
 
 
-#define DEBUG_LEVEL 0
+#define DEBUG_LEVEL 0	// TODO has to be defined somewhere else (cython compil flag?)
 
 
 /**********************************************************************
@@ -28,7 +28,7 @@
  *
  **********************************************************************/
 
-int obi_column_set_obiint_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx, obiint_t value)
+int obi_column_set_obiint_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx, obiint_t value)
 {
 	// Check that the line number is not greater than the maximum allowed
 	if (line_nb >= MAXIMUM_LINE_COUNT)
@@ -57,7 +57,7 @@ int obi_column_set_obiint_with_elt_idx(OBIDMS_column_p column, size_t line_nb, s
 }
 
 
-obiint_t obi_column_get_obiint_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx)
+obiint_t obi_column_get_obiint_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx)
 {
 	if ((line_nb+1) > (column->header)->lines_used)
 	{
@@ -69,56 +69,24 @@ obiint_t obi_column_get_obiint_with_elt_idx(OBIDMS_column_p column, size_t line_
 }
 
 
-int obi_column_set_obiint_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name, obiint_t value)
+int obi_column_set_obiint_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name, obiint_t value)
 {
-	size_t element_idx;
-
-	if (!strcmp(element_name, "\0"))	// element name is empty
-	{
-		if (obi_column_get_nb_elements_per_line(column) == 1)	// check that there is only one element per line
-			element_idx = 0;
-		else													// there is more than one element per line
-		{
-			obi_set_errno(OBICOL_UNKNOWN_ERROR);
-			obidebug(1, "\nAn element name must be specified");
-        	return -1;
-		}
-	}
-    else
-    {
-		element_idx = obi_column_get_element_index_from_name(column, element_name);
-		if (element_idx == -1)
-			return -1;
-    }
-
+	index_t element_idx;
+	element_idx = obi_column_get_element_index_from_name(column, element_name);
+	if (element_idx == OBIIdx_NA)
+		return -1;
 	obi_column_set_obiint_with_elt_idx(column, line_nb, element_idx, value);
-
 	return 0;
 }
 
 
-obiint_t obi_column_get_obiint_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name)
+obiint_t obi_column_get_obiint_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name)
 {
-	size_t element_idx;
-
-	if (!strcmp(element_name, "\0"))	// element name is empty
-	{
-		if (obi_column_get_nb_elements_per_line(column) == 1)	// check that there is only one element per line
-			element_idx = 0;
-		else													// there is more than one element per line
-		{
-			obi_set_errno(OBICOL_UNKNOWN_ERROR);
-			obidebug(1, "\nAn element name must be specified");
-        	return OBIInt_NA;
-		}
-	}
-    else
-    {
-		element_idx = obi_column_get_element_index_from_name(column, element_name);
-		if (element_idx == -1)
-			return OBIInt_NA;
-    }
+	index_t element_idx;
 
+	element_idx = obi_column_get_element_index_from_name(column, element_name);
+	if (element_idx == OBIIdx_NA)
+		return OBIInt_NA;
 	return obi_column_get_obiint_with_elt_idx(column, line_nb, element_idx);
 }
 

src/obidmscolumn_int.h

@@ -5,11 +5,15 @@
 /**
  * @file obidsmcolumn_int.h
  * @author Celine Mercier
- * @date July 21st 2015
+ * @date August 10th 2015
  * @brief Header file for the functions handling OBIColumns containing data with the OBIType OBI_INT.
  */
 
 
+#ifndef OBIDMSCOLUMN_INT_H_
+#define OBIDMSCOLUMN_INT_H_
+
+
 #include <stdlib.h>
 #include <stdio.h>
 
@@ -20,82 +24,76 @@
 /**
  * @brief Sets a value in an OBIDMS column containing data with the type OBI_INT, using the index of the element in the line.
  *
- * @param column a pointer as returned by obi_create_column()
  * @warning Pointers returned by obi_open_column() don't allow writing.
  *
- * @param line_nb the number of the line where the value should be set
+ * @param column A pointer as returned by obi_create_column() or obi_clone_column().
+ * @param line_nb The number of the line where the value should be set.
+ * @param element_idx The index of the element that should be set in the line.
+ * @param value The value that should be set.
  *
- * @param element_idx the index of the element that should be set in the line
- *
- * @param value the value that should be set
- *
- * @return an integer value indicating the success of the operation.
- *
- * @retvalue 0 on success
- * @retvalue -1 on failure and the `obi_errno` variable is set.
+ * @returns An integer value indicating the success of the operation.
+ * @retval 0 on success.
+ * @retval -1 if an error occurred.
  *
  * @since July 2015
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-int obi_column_set_obiint_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx, obiint_t value);
+int obi_column_set_obiint_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx, obiint_t value);
 
 
 /**
  * @brief Recovers a value in an OBIDMS column containing data with the type OBI_INT.
  *
- * @param column a pointer as returned by obi_create_column()
+ * @param column A pointer as returned by obi_create_column().
+ * @param line_nb The number of the line where the value should be recovered.
+ * @param element_idx The index of the element that should be recovered in the line.
  *
- * @param line_nb the number of the line where the value should be recovered
- *
- * @param element_idx the index of the element that should be recovered in the line
- *
- * @return the recovered value
+ * @returns The recovered value.
+ * @retval OBIBool_NA the NA value of the type if an error occurred and obi_errno is set.
  *
  * @since July 2015
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-obiint_t obi_column_get_obiint_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx);
+obiint_t obi_column_get_obiint_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx);
 
 
 /**
- * @brief Sets a value in an OBIDMS column containing data with the type OBI_INT, using the name of the element in the line.
+ * @brief Sets a value in an OBIDMS column containing data with the type OBI_INT,
+ *        using the name of the element in the line.
  *
- * @param column a pointer as returned by obi_create_column()
  * @warning Pointers returned by obi_open_column() don't allow writing.
  *
- * @param line_nb the number of the line where the value should be set
+ * @param column A pointer as returned by obi_create_column() or obi_clone_column().
+ * @param line_nb The number of the line where the value should be set.
+ * @param element_name The name of the element that should be set in the line.
+ * @param value The value that should be set.
  *
- * @param element_name the name of the element that should be set in the line
- * If empty, it is checked that there is only one element per line
- *
- * @param value the value that should be set
- *
- * @return an integer value indicating the success of the operation.
- *
- * @retvalue 0 on success
- * @retvalue -1 on failure and the `obi_errno` variable is set.
+ * @returns An integer value indicating the success of the operation.
+ * @retval 0 on success.
+ * @retval -1 if an error occurred.
  *
  * @since August 2015
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-int obi_column_set_obiint_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name, obiint_t value);
+int obi_column_set_obiint_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name, obiint_t value);
 
 
 /**
- * @brief Recovers a value in an OBIDMS column containing data with the type OBI_INT, using the name of the element in the line.
+ * @brief Recovers a value in an OBIDMS column containing data with the type OBI_INT,
+ *        using the name of the element in the line.
  *
- * @param column a pointer as returned by obi_create_column()
+ * @param column A pointer as returned by obi_create_column() or obi_clone_column().
+ * @param line_nb The number of the line where the value should be recovered.
+ * @param element_name The name of the element that should be recovered in the line.
  *
- * @param line_nb the number of the line where the value should be recovered
- *
- * @param element_name the name of the element that should be recovered in the line
- * If empty, it is checked that there is only one element per line
- *
- * @return the recovered value
- * @retvalue -1 on failure and the `obi_errno` variable is set. TODO an other value must be chosen
+ * @returns The recovered value.
+ * @retval OBIBool_NA the NA value of the type if an error occurred and obi_errno is set.
  *
  * @since August 2015
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-obiint_t obi_column_get_obiint_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name);
+obiint_t obi_column_get_obiint_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name);
+
+
+#endif /* OBIDMSCOLUMN_INT_H_ */
 

src/obidmscolumn_str.c

@@ -0,0 +1,120 @@
+/****************************************************************************
+ * OBIDMS_column_str functions                                              *
+ ****************************************************************************/
+
+/**
+ * @file obidsmcolumn_str.c
+ * @author Celine Mercier
+ * @date October 28th 2015
+ * @brief Functions handling OBIColumns containing data in the form of indices referring to character strings.
+ */
+
+
+#include <stdlib.h>
+#include <stdio.h>
+
+#include "obidmscolumn.h"
+#include "obitypes.h"
+#include "obierrno.h"
+#include "obidebug.h"
+#include "obiarray.h"
+
+
+#define DEBUG_LEVEL 0	// TODO has to be defined somewhere else (cython compil flag?)
+
+
+/**********************************************************************
+ *
+ * D E F I N I T I O N   O F   T H E   P U B L I C   F U N C T I O N S
+ *
+ **********************************************************************/
+
+int obi_column_set_obistr_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx, char* value)
+{
+	byte_t* value_b;
+	index_t idx;
+
+	// Check that the line number is not greater than the maximum allowed
+	if (line_nb >= MAXIMUM_LINE_COUNT)
+	{
+		obi_set_errno(OBICOL_UNKNOWN_ERROR);
+		obidebug(1, "\nError trying to set a value at a line number greater than the maximum allowed");
+    	return -1;
+	}
+
+	// Check if the file needs to be enlarged
+	while ((line_nb+1) > (column->header)->line_count)
+	{
+		// Enlarge the file
+		if (obi_enlarge_column(column) < 0)
+	    	return -1;
+	}
+
+	// Update lines used
+	if ((line_nb+1) > (column->header)->lines_used)
+		(column->header)->lines_used = line_nb+1;
+
+	// Encode the value on a byte array with a header
+	value_b = obi_str_to_obibytes(value);
+	if (value_b == NULL)
+		return -1;
+
+	// Add in the obiarray
+	idx = obi_array_add(column->array, value_b);
+	if (idx == -1)
+		return -1;
+
+	// Add the value's index in the column
+	*(((index_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx) = idx;
+
+	free(value_b);
+
+	return 0;
+}
+
+
+const char* obi_column_get_obistr_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx)
+{
+	index_t idx;
+	byte_t* value_b;
+
+	if ((line_nb+1) > (column->header)->lines_used)
+	{
+		obi_set_errno(OBICOL_UNKNOWN_ERROR);
+		obidebug(1, "\nError trying to get a value that is beyond the current number of lines used");
+		return "\0";		// TODO
+	}
+
+	idx = *(((index_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx);
+
+	// Check NA
+	if (idx == OBIIdx_NA)
+		return "\0";		// TODO
+
+	value_b = obi_array_get(column->array, idx);
+	return obi_obibytes_to_str(value_b);
+}
+
+
+int obi_column_set_obistr_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name, char* value)
+{
+	index_t element_idx;
+	element_idx = obi_column_get_element_index_from_name(column, element_name);
+	if (element_idx == OBIIdx_NA)
+		return -1;
+	if (obi_column_set_obistr_with_elt_idx(column, line_nb, element_idx, value) < 0)
+		return -1;
+	return 0;
+}
+
+
+const char* obi_column_get_obistr_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name)
+{
+	index_t element_idx;
+
+	element_idx = obi_column_get_element_index_from_name(column, element_name);
+	if (element_idx == OBIIdx_NA)
+		return "\0";
+	return obi_column_get_obistr_with_elt_idx(column, line_nb, element_idx);
+}
+

src/obidmscolumn_str.h

@@ -0,0 +1,101 @@
+/****************************************************************************
+ * OBIDMS_column_str header file                                            *
+ ****************************************************************************/
+
+/**
+ * @file obidsmcolumn_str.h
+ * @author Celine Mercier
+ * @date October 28th 2015
+ * @brief Header file for the functions handling OBIColumns containing data in the form of indices referring to character strings.
+ */
+
+
+#ifndef OBIDMSCOLUMN_STR_H_
+#define OBIDMSCOLUMN_STR_H_
+
+
+#include <stdlib.h>
+#include <stdio.h>
+
+#include "obidmscolumn.h"
+#include "obitypes.h"
+
+
+/**
+ * @brief Sets a value in an OBIDMS column containing data in the form of indices referring
+ * to character strings in an obiarray, using the index of the element in the line.
+ *
+ * @warning Pointers returned by obi_open_column() don't allow writing.
+ *
+ * @param column A pointer as returned by obi_create_column() or obi_clone_column().
+ * @param line_nb The number of the line where the value should be set.
+ * @param element_idx The index of the element that should be set in the line.
+ * @param value The value that should be set.
+ *
+ * @returns An integer value indicating the success of the operation.
+ * @retval 0 on success.
+ * @retval -1 if an error occurred.
+ *
+ * @since October 2015
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+int obi_column_set_obistr_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx, char* value);
+
+
+/**
+ * @brief Recovers a value in an OBIDMS column containing data in the form of indices referring
+ * to character strings in an obiarray, using the index of the element in the line.
+ *
+ * @param column A pointer as returned by obi_create_column().
+ * @param line_nb The number of the line where the value should be recovered.
+ * @param element_idx The index of the element that should be recovered in the line.
+ *
+ * @returns The recovered value.
+ * @retval '\0' the NA value of the type if an error occurred and obi_errno is set.
+ *
+ * @since October 2015
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+const char* obi_column_get_obistr_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx);
+
+
+/**
+ * @brief Sets a value in an OBIDMS column containing data in the form of indices referring
+ * to character strings in an obiarray, using the name of the element in the line.
+ *
+ * @warning Pointers returned by obi_open_column() don't allow writing.
+ *
+ * @param column A pointer as returned by obi_create_column() or obi_clone_column().
+ * @param line_nb The number of the line where the value should be set.
+ * @param element_name The name of the element that should be set in the line.
+ * @param value The value that should be set.
+ *
+ * @returns An integer value indicating the success of the operation.
+ * @retval 0 on success.
+ * @retval -1 if an error occurred.
+ *
+ * @since October 2015
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+int obi_column_set_obistr_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name, char* value);
+
+
+/**
+ * @brief Recovers a value in an OBIDMS column containing data in the form of indices referring
+ * to character strings in an obiarray, using the name of the element in the line.
+ *
+ * @param column A pointer as returned by obi_create_column() or obi_clone_column().
+ * @param line_nb The number of the line where the value should be recovered.
+ * @param element_name The name of the element that should be recovered in the line.
+ *
+ * @returns The recovered value.
+ * @retval '\0' the NA value of the type if an error occurred and obi_errno is set.
+ *
+ * @since October 2015
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+const char* obi_column_get_obistr_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name);
+
+
+#endif /* OBIDMSCOLUMN_IDX_H_ */
+

src/obidmscolumndir.c

@@ -4,7 +4,7 @@
 
 /**
  * @file obidmscolumndir.c
- * @author Celine Mercier
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
  * @date 18 June 2015
  * @brief Functions for OBIDMS column directories.
  */
@@ -25,7 +25,7 @@
 #include "obidebug.h"
 
 
-#define DEBUG_LEVEL 0
+#define DEBUG_LEVEL 0	// TODO has to be defined somewhere else (cython compil flag?)
 
 
 /**************************************************************************
@@ -43,15 +43,10 @@
  *
  * @warning The returned pointer has to be freed by the caller.
  *
- * @param column_name the name of the OBIDMS column
+ * @param column_name The name of the OBIDMS column.
  *
- * @return a pointer to the OBIDMS column directory name
- * @retvalue <column_directory_name> if everything is ok
- * @retvalue NULL if an error occurs
- *
- * ###Error values
- * 		- OBIDMS_MEMORY_ERROR    : something wrong occurred during memory allocation.
- * 		- OBIDMS_LONG_NAME_ERROR : the database name exceeds the limit.
+ * @returns A pointer to the OBIDMS column directory name.
+ * @retval NULL if an error occurred.
  *
  * @since June 2015
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
@@ -78,10 +73,10 @@ static char* build_column_directory_name(const char* column_name)
 	}
 
 	// Test if the database name is not too long
-	if (strlen(column_directory_name) >= OBIDMS_COLUMN_DIR_MAX_NAME)
+	if (strlen(column_directory_name) >= OBIDMS_COLUMN_MAX_NAME)
 	{
 		obi_set_errno(OBICOLDIR_LONG_NAME_ERROR);
-		obidebug(1, "\nError building a column directory name");
+		obidebug(1, "\nError due to column name too long");
 		free(column_directory_name);
 		return NULL;
 	}

src/obidmscolumndir.h

@@ -6,57 +6,56 @@
  * @file obidmscolumndir.h
  * @author Celine Mercier
  * @date 18 June 2015
- * @brief Header file for OBIDMS column directories.
+ * @brief Header file for the OBIDMS column directories structures and functions.
  */
 
+
 #ifndef OBIDMSCOLUMNGROUP_H_
 #define OBIDMSCOLUMNGROUP_H_
 
+
 #include <stdlib.h>
 #include <stdio.h>
 #include <dirent.h>
 
 #include "obidms.h"
 
-#define OBIDMS_MAX_COLNAME (128) /**< The maximum length of an OBIDMS column name
-                                  */
 
-#define OBIDMS_COLUMN_DIR_MAX_NAME (2048) 	/**< The maximum length of an OBIDMS column directory name
-                                		 */
+#define OBIDMS_COLUMN_MAX_NAME (2048) /**< The maximum length of an OBIDMS column name.
+                                       */
 
-/** @brief A structure describing an OBIDMS column directory instance
+
+/**
+ * @brief A structure describing an OBIDMS column directory instance.
  *
  * A pointer to this structure is returned on creation
  * and opening of an OBIDMS column directory.
  */
-
 typedef struct OBIDMS_column_directory {
-	OBIDMS_p	dms;	 										/**< A pointer to a DMS instance.
+	OBIDMS_p	dms;	 										 /**< A pointer to a DMS instance.
      	 	 	 	 	 	 	 	 	 	 	 	 		 	 */
-	char 		column_name[OBIDMS_MAX_COLNAME+1];				/**< The name of the column
-																 *   contained in the directory.
+	char 		column_name[OBIDMS_COLUMN_MAX_NAME+1];		     /**< The name of the column
+																 *    contained in the directory.
 																 */
-	char		directory_name[OBIDMS_COLUMN_DIR_MAX_NAME+1];	/**< The name of the directory
-	                                     	 	 	 	 	 	 *   containing the column.
+	char		directory_name[OBIDMS_COLUMN_MAX_NAME+1];	     /**< The name of the directory
+	                                     	 	 	 	 	 	 *    containing the column.
 	                                     	 	 	 	 	 	 */
-	DIR*		directory;										/**< A directory entry usable to
-										 	 	 	 	 	 	 *   refer and scan the database directory.
+	DIR*		directory;										 /**< A directory entry usable to
+										 	 	 	 	 	 	 *    refer and scan the database directory.
 										 	 	 	 	 	 	 */
 } OBIDMS_column_directory_t, *OBIDMS_column_directory_p;
 
 
-/*@
- * @brief Checks if an OBIDMS column directory exists
+/**
+ * @brief Checks if an OBIDMS column directory exists.
  *
- * @param dms a pointer to an OBIDMS as returned by obi_create_dms() or obi_open_dms()
- * @param column_name a pointer to a C string containing the name of the column.
- *                    The actual directory name used to store the column is
- *                    `<column_name>.obicol`.
+ * @param dms A pointer to an OBIDMS as returned by obi_create_dms() or obi_open_dms().
+ * @param column_name A pointer to a C string containing the name of the column.
  *
- * @return an integer value indicating the status of the column directory
- * @retvalue 1 the directory exist
- * @retvalue 0 the directory does not exist
- * @retvalue -1 an error occurred
+ * @returns An integer value indicating the status of the column directory.
+ * @retval 1 if the directory exists.
+ * @retval 0 if the directory does not exist.
+ * @retval -1 if an error occurred.
  *
  * @see obi_close_column_directory()
  * @since June 2015
@@ -72,17 +71,14 @@ int obi_column_directory_exists(OBIDMS_p dms, const char* column_name);
  * if a directory with this name does not already exist
  * before creating the new column directory.
  *
- * @param dms a pointer to an OBIDMS as returned by obi_create_dms() or obi_open_dms()
- * @param column_name a pointer to a C string containing the name of the column.
+ * @param dms A pointer to an OBIDMS as returned by obi_create_dms() or obi_open_dms().
+ * @param column_name A pointer to a C string containing the name of the column.
  *                    The actual directory name used to store the column will be
  *                    `<column_name>.obicol`.
  *
- * @return a pointer to an OBIDMS column directory structure describing the newly created
- * 		   directory
- * @retval NULL on error and the `obi_errno` variable is set.
- *
- * ###Error values
- * 		- OBIDMS_COL_DIR_EXIST_ERROR     : xxxxx a database with the same name already exists.
+ * @returns A pointer to an OBIDMS column directory structure describing the newly created
+ * 		    directory.
+ * @retval NULL if an error occurred.
  *
  * @see obi_close_column_directory()
  * @since June 2015
@@ -94,16 +90,13 @@ OBIDMS_column_directory_p obi_create_column_directory(OBIDMS_p dms, const char*
 /**
  * @brief Opens an existing OBIDMS column directory instance.
  *
- * @param dms a pointer to an OBIDMS as returned by obi_create_dms() or obi_open_dms()
- * @param column_name a pointer to a C string containing the name of the column.
+ * @param dms A pointer to an OBIDMS as returned by obi_create_dms() or obi_open_dms().
+ * @param column_name A pointer to a C string containing the name of the column.
  *                    The actual directory name used to store the column is
  *                    `<column_name>.obicol`.
  *
- * @return a pointer to the OBIDMS column directory structure describing the directory
- * @retval NULL on error and the `obi_errno`variable is set.
- *
- * ###Error values
- * 		- OBIDMS_COL_DIR_ERROR     : xxxxx a database with the same name already exists.
+ * @returns A pointer to the OBIDMS column directory structure describing the directory.
+ * @retval NULL if an error occurred.
  *
  * @see obi_close_column_directory()
  * @since June 2015
@@ -118,17 +111,13 @@ OBIDMS_column_directory_p obi_open_column_directory(OBIDMS_p dms, const char* co
  * If the directory already exists, this function opens it, otherwise it
  * creates a new column directory.
  *
- * @param dms a pointer to an OBIDMS as returned by obi_create_dms() or obi_open_dms()
- * @param column_name a pointer to a C string containing the name of the column.
+ * @param dms A pointer to an OBIDMS as returned by obi_create_dms() or obi_open_dms().
+ * @param column_name A pointer to a C string containing the name of the column.
  *                    The actual directory name used to store the column is
  *                    `<column_name>.obicol`.
  *
- * @return a pointer to the OBIDMS column directory structure describing the directory
- * @retval NULL on error and the `obi_errno`variable is set.
- *
- * ###Error values
- * 		- OBIDMS_LONG_NAME_ERROR : the database name exceeds the limit.
- * 		- OBIDMS_MEMORY_ERROR    : something wrong occurred during memory allocation.
+ * @returns A pointer to the OBIDMS column directory structure describing the directory.
+ * @retval NULL if an error occurred.
  *
  * @since June 2015
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
@@ -139,13 +128,13 @@ OBIDMS_column_directory_p obi_column_directory(OBIDMS_p dms, const char* column_
 /**
  * @brief Closes an opened OBIDMS column directory instance.
  *
- * @param column_directory a pointer to an OBIDMS column directory as returned by
- * obi_create_column_directory() or obi_open_column_directory()
+ * @param column_directory A pointer to an OBIDMS column directory as returned by
+ *                         obi_create_column_directory() or obi_open_column_directory().
  *
- * @return an integer value indicating the success of the operation. Even on
- * 		   error, the `OBIDMS_column_directory` structure is freed
- * @retvalue 0 on success
- * @retvalue -1 on failure and the `obi_errno` variable is set.
+ * @returns An integer value indicating the success of the operation. Even on
+ * 		    error, the `OBIDMS_column_directory` structure is freed.
+ * @retval 0 on success.
+ * @retval -1 if an error occurred.
  *
  * @see obi_create_column_directory()
  * @see obi_open_column_directory()

src/obierrno.c

@@ -1,10 +1,14 @@
-/*
- * obierrno.c
- *
- *  Created on: 23 mai 2015
- *      Author: coissac
+/****************************************************************************
+ * Code for obi errnos                                                      *
+ ****************************************************************************/
+
+/**
+ * @file obierrno.c
+ * @author Eric Coissac (eric.coissac@metabarcoding.org)
+ * @date 23 May 2015
+ * @brief Code for obi errnos.
  */
 
 
-int obi_errno;
+int obi_errno = 0;
 

src/obierrno.h

@@ -1,20 +1,26 @@
-/*
- * obierrno.h
- *
- *  Created on: 23 mai 2015
- *      Author: coissac
+/****************************************************************************
+ * Header file for obi errnos                                               *
+ ****************************************************************************/
+
+/**
+ * @file obierrno.h
+ * @author Eric Coissac (eric.coissac@metabarcoding.org)
+ * @date 23 May 2015
+ * @brief Header file for obi errnos.
  */
 
+
 #ifndef OBIERRNO_H_
 #define OBIERRNO_H_
 
+
 /**
  * @brief The declaration of the external variable `obi_errno`.
  *
  * `obi_errno` is an equivalent of `errno` for the system level error,
- * but for errors generated by the C layer of the OBITools framework.
+ * but for errors generated by the C layer of the OBITools3 framework.
  *
- * @todo We have to look into defining this variable as thread specific.
+ * @TODO We have to look into defining this variable as thread specific.
  */
 extern int obi_errno;
 
@@ -24,8 +30,8 @@ extern int obi_errno;
  *        the specified `err` code
  *
  * This function is defined as a macro to reduce the risk
- * of increasing the problem generating the error by calling
- * a new function.
+ * of increasing the problem by generating another error by calling
+ * another function.
  *
  * @param err The error code as an integer value.
  *
@@ -41,6 +47,8 @@ extern int obi_errno;
  * Error codes set in errno following an error related
  * to the manipulation of an OBIDMS.
  *
+ * @TODO
+ *
  * @{
  */
 #define OBIDMS_EXIST_ERROR     		(1) 	/**< Trying to create an OBIDMS with a name
@@ -90,6 +98,8 @@ extern int obi_errno;
                                     	 	 */
 #define OBICOL_ACCESS_ERROR    		(19) 	/**< Permission error trying to access an OBIDSM column directory
                                     		 */
+#define OBI_ARRAY_ERROR				(20)    /** Error while handling an array
+											 */
 /**@}*/
 
 #endif /* OBIERRNO_H_ */

src/obilittlebigman.c

@@ -1,8 +1,12 @@
-/*
- * littlebigman.c
- *
- *  Created on: 23 mai 2015
- *      Author: coissac
+/****************************************************************************
+ * Code for endianness checking                                             *
+ ****************************************************************************/
+
+/**
+ * @file obilittlebigman.c
+ * @author Eric Coissac (eric.coissac@metabarcoding.org)
+ * @date 23 May 2015
+ * @brief Code endianness checking.
  */
 
 #include "obilittlebigman.h"

src/obilittlebigman.h

@@ -1,15 +1,22 @@
-/*
- * littlebigman.h
- *
- *  Created on: 23 mai 2015
- *      Author: coissac
+/****************************************************************************
+ * Header file for endianness checking                                      *
+ ****************************************************************************/
+
+/**
+ * @file obilittlebigman.h
+ * @author Eric Coissac (eric.coissac@metabarcoding.org)
+ * @date 23 May 2015
+ * @brief Header file for endianness checking.
  */
 
+
 #ifndef OBILITTLEBIGMAN_H_
 #define OBILITTLEBIGMAN_H_
 
+
 #include <stdbool.h>
 
+
 /**
  * Test if the architecture of the processor is little endian.
  *
@@ -41,7 +48,7 @@
  *  In this architecture, the last address is
  *  used to store the byte of lighter weight (LITTLE ENDian)
  *
- * @return a `bool` value:
+ * @returns a `bool` value:
  * 		- `true`  if the architecture is little endian
  * 		- `false` if the architecture is big endian
  *

src/obitypes.c

@@ -1,8 +1,12 @@
-/*
- * obitypes.c
- *
- *  Created on: 23 mai 2015
- *      Author: coissac
+/****************************************************************************
+ * OBITypes functions                                                       *
+ ****************************************************************************/
+
+/**
+ * @file obitypes.h
+ * @author Eric Coissac (eric.coissac@metabarcoding.org)
+ * @date 23 May 2015
+ * @brief Functions for the handling of OBITypes.
  */
 
 
@@ -13,7 +17,7 @@
 #include "obierrno.h"
 
 
-#define DEBUG_LEVEL 0
+#define DEBUG_LEVEL 0	// TODO has to be defined somewhere else (cython compil flag?)
 
 
 size_t obi_sizeof(OBIType_t type)
@@ -36,7 +40,7 @@ size_t obi_sizeof(OBIType_t type)
 	case OBI_CHAR:  size = sizeof(obichar_t);
 					break;
 
-	case OBI_IDX:   size = sizeof(obiidx_t);
+	case OBI_IDX:   size = sizeof(index_t);
 					break;
 
 	default:        size = 0;
@@ -46,7 +50,7 @@ size_t obi_sizeof(OBIType_t type)
 }
 
 
-size_t obi_array_sizeof(OBIType_t type, size_t nb_lines, size_t nb_elements_per_line)
+size_t obi_array_sizeof(OBIType_t type, index_t nb_lines, index_t nb_elements_per_line)
 {
 	size_t size;
 	size_t rsize;

src/obitypes.h

@@ -1,10 +1,15 @@
+/****************************************************************************
+ * Header file for OBITypes                                                 *
+ ****************************************************************************/
+
 /**
  * @file obitypes.h
- * @author Celine Mercier
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
  * @date 18 May 2015
- * @brief Header file for the OBITypes.
+ * @brief Header file for the handling of OBITypes.
  */
 
+
 #ifndef OBITYPES_H_
 #define OBITYPES_H_
 
@@ -13,10 +18,11 @@
 #include <stdint.h>
 
 
-#define OBIInt_NA (INT32_MIN)
-#define OBIIdx_NA (SIZE_MAX)
-#define OBIFloat_NA (float_NA())
-#define OBIChar_NA (0)				// TODO not sure about this one as it can be impossible to distinguish from uninitialized values
+#define OBIInt_NA (INT32_MIN)		/**< NA value for the type OBI_INT */
+#define OBIIdx_NA (INT64_MIN)		/**< NA value for indices */
+#define OBIFloat_NA (float_NA())	/**< NA value for the type OBI_FLOAT */
+#define OBIChar_NA (0)				/**< NA value for the type OBI_CHAR */
+										 // TODO not sure about this one as it can be impossible to distinguish from uninitialized values
 
 
 /**
@@ -38,16 +44,19 @@ typedef enum OBIType {
 	OBI_FLOAT,					/**< a floating value (C type : double) */
 	OBI_BOOL,					/**< a boolean true/false value, see obibool_t enum */
 	OBI_CHAR,					/**< a character (C type : char) */
-	OBI_IDX					    /**< an index in a data structure (C type : size_t) */
+	OBI_IDX					    /**< an index in a data structure (C type : int64_t) */
 } OBIType_t, *OBIType_p;
 
 
+typedef int64_t index_t;
 typedef int32_t obiint_t;
 typedef double obifloat_t;
 typedef char obichar_t;
-typedef size_t obiidx_t;
 
 
+/**
+ * @brief Union used to compute the NA value of the OBI_FLOAT OBIType.
+ */
 typedef union
 {
     double value;
@@ -55,7 +64,11 @@ typedef union
 } ieee_double;
 
 
-static double float_NA(void)	// as defined in R
+/**
+ * @brief Returns the NA value of the OBI_FLOAT OBIType.
+ * This value corresponds to the float NA value as defined in R.
+ */
+static double float_NA(void)
 {
     volatile ieee_double x;
     x.word[0] = 0x7ff00000;
@@ -65,12 +78,12 @@ static double float_NA(void)	// as defined in R
 
 
 /**
- * @brief returns the memory size in bytes of an OBIType
+ * @brief Returns the memory size in bytes of an OBIType.
  *
- * @param type the OBIType code used as query
+ * @param type The OBIType code used as query.
  *
- * @return the size in bytes of the type
- * @retval 0 on error (unknown type)
+ * @returns The size in bytes of the type.
+ * @retval 0 if an error occurred (unknown type).
  *
  * @since May 2015
  * @author Eric Coissac (eric.coissac@metabarcoding.org)
@@ -79,31 +92,32 @@ size_t obi_sizeof(OBIType_t type);
 
 
 /**
- * @brief returns the size requested to store an array of OBIType
+ * @brief Returns the size required to store an array of elements with an OBIType.
  *
- * The returned size is large enough to store an array of size nbelement
- * but rounded at a multiple of the memory page size.
+ * The returned size is large enough to store an array large enough
+ * to store all the elements but rounded at a multiple of the memory page size.				// TODO this might be redundant but still a good thing
  *
- * @param type the OBIType code used as query
- * @param nbelement the number of elements to be stored
+ * @param data_type The OBIType of the elements.
+ * @param nb_lines The number of lines to be stored.
+ * @param nb_elements_per_line The number of elements per line.
  *
- * @return the size in bytes of the array
- * @retval 0 on error (unknown type)
+ * @returns The size in bytes of the array.
+ * @retval 0 if an error occurred (unknown type).
  *
  * @since May 2015
  * @author Eric Coissac (eric.coissac@metabarcoding.org)
  */
-size_t obi_array_sizeof(OBIType_t type, size_t nbelements, size_t nb_elements_per_line);
+size_t obi_array_sizeof(OBIType_t data_type, index_t nb_lines, index_t nb_elements_per_line);
 
 
 /**
- * @brief returns the name in the form of a character string of an OBIType
+ * @brief Returns the name in the form of a character string of an OBIType.
  *
  *
- * @param data_type the OBIType code used as query
+ * @param data_type The OBIType code used as query.
  *
- * @return the name of the OBIType
- * @retval NULL on error (unknown type or error allocating the memory for the character string)
+ * @returns The name of the OBIType.
+ * @retval NULL if an error occurred (unknown type or error allocating the memory for the character string).
  *
  * @since August 2015
  * @author Celine Mercier (celine.mercier@metabarcoding.org)

src/private_at_functions.c

@@ -3,8 +3,8 @@
  ****************************************************************************/
 
 /**
- * @file private_at_functions.h
- * @author Celine Mercier
+ * @file private_at_functions.c
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
  * @date 15 June 2015
  * @brief Private replacement functions for *at functions.
  */
@@ -23,14 +23,7 @@
 #include "obierrno.h"
 
 
-#define DEBUG_LEVEL 0
-
-
-/**********************************************************************
- *
- * D E F I N I T I O N   O F   T H E   P U B L I C   F U N C T I O N S
- *
- **********************************************************************/
+#define DEBUG_LEVEL 0	// TODO has to be defined somewhere else (cython compil flag?)
 
 
 char* get_full_path(int directory_file_descriptor, const char* path_name)
@@ -50,7 +43,7 @@ char* get_full_path(int directory_file_descriptor, const char* path_name)
 		return NULL;
 	}
 
-	// TODO check errors
+	// TODO check errors?
 	strlcat(full_path, "/", MAX_PATH_LEN);
 	strlcat(full_path, path_name, MAX_PATH_LEN);
 
@@ -77,39 +70,3 @@ DIR* private_opendirat(int directory_file_descriptor, const char* path_name)
 }
 
 
-//int private_openat(int directory_file_descriptor, const char* path_name, int flags)
-//{
-//	char* full_path;
-//	int file_descriptor;
-//
-//	full_path = get_full_path(directory_file_descriptor, path_name);
-//	if (full_path == NULL)
-//		return -1;
-//
-//	file_descriptor = open(full_path, flags);
-//
-//	free(full_path);
-//
-//	return file_descriptor;
-//}
-//
-//
-//int private_mkdirat(int directory_file_descriptor, const char* path_name, mode_t mode)
-//{
-//	char* full_path;
-//
-//	full_path = get_full_path(directory_file_descriptor, path_name);
-//	if (full_path == NULL)
-//		return -1;
-//
-//	if (mkdir(full_path, mode) < 0)
-//	{
-//		free(full_path);
-//		return -1;
-//	}
-//
-//	free(full_path);
-//
-//	return 0;
-//}
-

src/private_at_functions.h

@@ -1,10 +1,15 @@
+/****************************************************************************
+ * Header file for private *at functions                                    *
+ ****************************************************************************/
+
 /**
- * @file private_openat.h
- * @author Celine Mercier
+ * @file private_at_functions.h
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
  * @date 15 June 2015
- * @brief Header file for the replacement *at function.
+ * @brief Header file for the private replacement functions for *at functions.
  */
 
+
 #ifndef PRIVATE_OPENAT_H_
 #define PRIVATE_OPENAT_H_
 
@@ -12,27 +17,22 @@
 #include <sys/stat.h>
 
 
-#define MAX_PATH_LEN 4096
+#define MAX_PATH_LEN 4096	/**< Maximum length for the character string defining a
+ 	 	 	 	 	 	 	 	 file or directory path */
 
 
 /**
- * Internal function getting the full path of a file or a directory from its
- * path relative to a directory file descriptor.
- *
+ * @brief Internal function getting the full path of a file or a directory from its
+ *        path relative to a directory file descriptor.
  *
  * @warning The returned pointer has to be freed by the caller.
  *
- * @param directory_file_descriptor the file descriptor for the directory to which
- * 									path_name is relative
- * @param path_name the path name for the file or directory, relative to directory_file_descriptor
+ * @param directory_file_descriptor The file descriptor for the directory to which
+ * 									path_name is relative.
+ * @param path_name The path name for the file or directory, relative to directory_file_descriptor.
  *
- * @return a pointer to the full path
- * @retvalue <full_path> if everything is ok
- * @retvalue NULL if an error occurs
- *
- * ###Error values
- * 		- OBIDMS_MEMORY_ERROR    : something wrong occurred during memory allocation.
- * 		- OBIDMS_LONG_NAME_ERROR : the database name exceeds the limit.
+ * @returns A pointer to the full path.
+ * @retval NULL if an error occurred.
  *
  * @since June 2015
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
@@ -43,10 +43,11 @@ char* get_full_path(int directory_file_descriptor, const char* path_name);
 /**
  * @brief Replacement function for opendirat() : open a directory relative to a directory file descriptor.
  *
- * @param directory_file_descriptor the file descriptor for the directory in which the directory should be opened
- * @param path_name the path name for the directory to be opened, relative to directory_file_descriptor
+ * @param directory_file_descriptor The file descriptor for the directory in which the directory should be opened.
+ * @param path_name The path name for the directory to be opened, relative to directory_file_descriptor.
  *
- * @return the file descriptor of the opened directory
+ * @returns The file descriptor of the opened directory.
+ * @retval NULL if an error occurred.
  *
  * @since June 2015
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
@@ -54,34 +55,4 @@ char* get_full_path(int directory_file_descriptor, const char* path_name);
 DIR* private_opendirat(int directory_file_descriptor, const char* path_name);
 
 
-///**
-// * @brief Replacement function for openat() : open a file relative to a directory file descriptor.
-// *
-// * @param directory_file_descriptor the file descriptor for the directory in which the file should be opened
-// * @param path_name the path name for the file, relative to directory_file_descriptor
-// * @param flags the access modes
-// *
-// * @return the file descriptor of the opened file
-// *
-// * @since June 2015
-// * @author Celine Mercier (celine.mercier@metabarcoding.org)
-// */
-//int private_openat(int directory_file_descriptor, const char* path_name, int flags);
-//
-//
-///**
-// * @brief Replacement function for mkdirat() : create a directory relative to a directory file descriptor.
-// *
-// * @param directory_file_descriptor the file descriptor for the directory in which the directory should be created
-// * @param path_name the path name for the new directory, relative to directory_file_descriptor
-// * @param mode the access mode
-// *
-// * @return the file descriptor of the created directory
-// *
-// * @since June 2015
-// * @author Celine Mercier (celine.mercier@metabarcoding.org)
-// */
-//int private_mkdirat(int directory_file_descriptor, const char* path_name, mode_t mode);
-
-
 #endif /* PRIVATEOPENAT_H_ */