Added Obiviews specialized for the handling of nucleotide sequences

python/obitools3/obidms/_obidms.pxd

@@ -64,6 +64,15 @@ cdef class OBIView:
     cpdef save_and_close(self)
 
 
+cdef class OBIView_NUC_SEQS(OBIView):
+
+    cdef OBIDMS_column ids
+    cdef OBIDMS_column sequences
+    cdef OBIDMS_column descriptions
+    
+    cpdef delete_column(self, str column_name)
+    
+
 cdef class OBIView_line :
 
     cdef index_t index
@@ -77,5 +86,7 @@ cdef class OBIDMS:
     
     cpdef close(self)
     cpdef OBIView open_view(self, str view_name)
-    cpdef OBIView new_view(self, str view_name, object view_to_clone=*, list line_selection=*)
+    cpdef OBIView new_view(self, str view_name, object view_to_clone=*, list line_selection=*, str view_type=*)
+    cpdef dict read_view_infos(self, str view_name)
+    cpdef dict read_views(self)
 

python/obitools3/obidms/_obidms.pyx

@@ -48,16 +48,26 @@ from ._obidmscolumn_seq cimport OBIDMS_column_seq, \
 from ._obidms cimport OBIView, OBIView_line
 
 from .capi.obiview cimport Obiview_p, \
+                           Obiviews_infos_all_p, \
+                           Obiview_infos_p, \
+                           Column_reference_p, \
+                           obi_new_view_nuc_seqs, \
                            obi_new_view, \
                            obi_new_view_cloned_from_name, \
+                           obi_new_view_nuc_seqs_cloned_from_name, \
                            obi_open_view,  \
+                           obi_read_views, \
                            obi_view_delete_column, \
                            obi_view_add_column, \
                            obi_view_get_column, \
                            obi_view_get_pointer_on_column_in_view, \
                            obi_select_line, \
                            obi_select_lines, \
-                           obi_save_and_close_view
+                           obi_save_and_close_view, \
+                           VIEW_TYPE_NUC_SEQS, \
+                           NUC_SEQUENCE_COLUMN, \
+                           ID_COLUMN, \
+                           DESCRIPTION_COLUMN
                            
 from libc.stdlib cimport malloc
 from cpython.pycapsule cimport PyCapsule_New, PyCapsule_GetPointer
@@ -380,7 +390,6 @@ cdef class OBIView :
             raise Exception("Problem adding a column in a view")
         
         # Store the column pointer
-        
         column_pp = obi_view_get_pointer_on_column_in_view(self.pointer, column_name_b)
         if column_pp == NULL :
             raise Exception("Problem getting a column in a view")
@@ -451,6 +460,112 @@ cdef class OBIView :
 
 #############################################
 
+cdef class OBIView_NUC_SEQS(OBIView):
+    
+    def __init__(self, OBIDMS dms, str view_name, bint new=False, object view_to_clone=None, list line_selection=None): 
+        
+        cdef Obiview_p view = NULL
+        cdef int i
+        cdef list col_list
+        cdef str col_name
+        cdef OBIDMS_column column
+        cdef OBIDMS_column_p column_p
+        cdef OBIDMS_column_p* column_pp
+        cdef OBIDMS_column_header_p header
+        cdef index_t* line_selection_p
+                
+        self.dms = dms
+        
+        if line_selection is not None :
+            line_selection_p = <index_t*> malloc((len(line_selection) + 1) * sizeof(index_t))
+            for i in range(len(line_selection)) :
+                line_selection_p[i] = line_selection[i]     # TODO type problem?
+            line_selection_p[len(line_selection)] = -1
+        else :
+            line_selection_p = NULL
+       
+        if new :
+            if view_to_clone is not None :
+                if type(view_to_clone) == str :
+                    view = obi_new_view_nuc_seqs_cloned_from_name(dms.pointer, str2bytes(view_name), str2bytes(view_to_clone), line_selection_p)
+                else :
+                    view = obi_new_view_nuc_seqs(dms.pointer, str2bytes(view_name), (<OBIView> view_to_clone).pointer, line_selection_p)
+            elif view_to_clone is None :
+                view = obi_new_view_nuc_seqs(dms.pointer, str2bytes(view_name), NULL, line_selection_p)
+        elif not new :
+            if view_name is not None :
+                view = obi_open_view(dms.pointer, str2bytes(view_name))
+            elif view_name is None :
+                view = obi_open_view(dms.pointer, NULL)
+        
+        if view == NULL :
+            raise Exception("Error creating/opening view")
+
+        self.pointer = view
+        self.name = bytes2str(view.name)
+        
+        # go through columns to build list and open python object (TODO make separate function?)
+        self.columns = {}
+        self.columns_pp = {}
+                
+        i = 0
+        while i < view.column_count :
+            column_pp = <OBIDMS_column_p*> ((view.columns)+i)
+            column_p = <OBIDMS_column_p> (view.columns)[i]
+            header = (column_p).header
+            
+            col_name = bytes2str(header.name)
+            col_capsule = PyCapsule_New(column_pp, NULL, NULL)   # TODO discuss
+            (self.columns_pp)[col_name] = col_capsule
+            
+            subclass = OBIDMS_column.get_subclass_type(column_p)
+            self.columns[col_name] = subclass(self, col_name)
+            
+            i+=1
+        
+        self.ids = self.columns[bytes2str(ID_COLUMN)]
+        self.sequences = self.columns[bytes2str(NUC_SEQUENCE_COLUMN)]
+        self.descriptions = self.columns[bytes2str(DESCRIPTION_COLUMN)]
+
+
+    cpdef delete_column(self, str column_name) :
+        
+        cdef int i
+        cdef Obiview_p view
+        cdef OBIDMS_column column
+        cdef OBIDMS_column_p column_p
+        cdef OBIDMS_column_p* column_pp
+        cdef OBIDMS_column_header_p header
+        cdef str column_n
+ 
+        if ((column_name == bytes2str(ID_COLUMN)) or (column_name == bytes2str(NUC_SEQUENCE_COLUMN)) or (column_name == bytes2str(DESCRIPTION_COLUMN))) :
+            raise Exception("Can't delete an obligatory column from a NUC_SEQS view")
+        
+        view = self.pointer
+ 
+        if obi_view_delete_column(view, str2bytes(column_name)) < 0 :
+            raise Exception("Problem deleting a column from a view")
+        
+        # Update the dictionaries of column pointers and column objects, and update pointers in column objects (make function?):
+        (self.columns).pop(column_name)
+        (self.columns_pp).pop(column_name)
+        
+        i = 0
+        while i < view.column_count :
+            column_pp = <OBIDMS_column_p*> ((view.columns)+i)
+            column_p = <OBIDMS_column_p> (view.columns)[i]
+            header = (column_p).header
+            col_name = bytes2str(header.name)
+            col_capsule = PyCapsule_New(column_pp, NULL, NULL)
+            (self.columns_pp)[col_name] = col_capsule
+            i+=1
+
+        for column_n in self.columns :
+            (self.columns[column_n]).update_pointer()
+
+
+#############################################
+
 cdef class OBIView_line :
 
     def __init__(self, OBIView view, index_t line_nb) :
@@ -520,12 +635,81 @@ cdef class OBIDMS :
     cpdef close(self) :
         if (obi_close_dms(self.pointer)) < 0 :
             raise Exception("Problem closing an OBIDMS")
-     
-    
-    cpdef OBIView open_view(self, str view_name) :
-        return OBIView(self, view_name)
-  
-  
-    cpdef OBIView new_view(self, str view_name, object view_to_clone=None, list line_selection=None) :
-        return OBIView(self, view_name, new=True, view_to_clone=view_to_clone, line_selection=line_selection)
 
+
+    cpdef OBIView open_view(self, str view_name) :
+        
+        cdef object view_class
+        cdef dict view_infos
+        
+        view_infos = self.read_view_infos(view_name)
+        
+        if view_infos["view_type"] == bytes2str(VIEW_TYPE_NUC_SEQS) :   # TODO not gonna work
+            view_class = OBIView_NUC_SEQS
+        else :
+            view_class = OBIView
+        
+        return view_class(self, view_name)
+    
+
+    cpdef OBIView new_view(self, str view_name, object view_to_clone=None, list line_selection=None, str view_type=None) :
+        
+        cdef object view_class
+        
+        if view_type is not None :
+            if view_type == bytes2str(VIEW_TYPE_NUC_SEQS) : # TODO not gonna work
+                view_class = OBIView_NUC_SEQS
+        else :
+            view_class = OBIView
+        
+        return view_class(self, view_name, new=True, view_to_clone=view_to_clone, line_selection=line_selection)
+
+
+    cpdef dict read_view_infos(self, str view_name) :
+        all_views = self.read_views()
+        return all_views[view_name]
+
+
+    cpdef dict read_views(self) :    # TODO function that gets 1 view with name, function that prints the dic and function that prints 1 view. Add column type in col ref
+        
+        cdef Obiviews_infos_all_p all_views_p
+        cdef Obiview_infos_p view_p
+        cdef Column_reference_p column_refs
+        cdef int nb_views
+        cdef int i, j
+        cdef str view_name
+        cdef str column_name
+        cdef dict views
+        cdef bytes name_b
+        
+        views = {}
+        all_views_p = obi_read_views(self.pointer)
+        nb_views = <int> (all_views_p.header).view_count
+        for i in range(nb_views) :
+            view_p = (<Obiview_infos_p> (all_views_p.view_infos)) + i
+            view_name = bytes2str(view_p.name)
+            views[view_name] = {}
+            views[view_name]["view_type"] = bytes2str(view_p.view_type)
+            views[view_name]["column_count"] = <int> view_p.column_count
+            views[view_name]["line_count"] = <int> view_p.line_count
+            views[view_name]["view_number"] = <int> view_p.view_number
+            views[view_name]["created_from"] = bytes2str(view_p.created_from)
+            views[view_name]["creation_date"] = bytes2str(obi_column_format_date(view_p.creation_date))     # TODO move this function in utils or somethings
+            if (view_p.all_lines) :
+                views[view_name]["line_selection"] = None
+            else :
+                views[view_name]["line_selection"] = {}
+                views[view_name]["line_selection"]["column_name"] = bytes2str((view_p.line_selection).column_name)
+                views[view_name]["line_selection"]["version"] = <int> (view_p.line_selection).version
+            views[view_name]["column_references"] = {}
+            column_refs = view_p.column_references
+            for j in range(views[view_name]["column_count"]) :
+                column_name = bytes2str((column_refs[j]).column_name)
+                views[view_name]["column_references"][column_name] = {}
+                views[view_name]["column_references"][column_name]["version"] = column_refs[j].version
+        
+        return views
+    
+    
+    
+    

python/obitools3/obidms/capi/obiview.pxd

@@ -3,15 +3,21 @@
 from .obitypes           cimport const_char_p, \
                                  OBIType_t, \
                                  obiversion_t, \
-                                 index_t
+                                 index_t, \
+                                 time_t
 from ..capi.obidms       cimport OBIDMS_p
 from ..capi.obidmscolumn cimport OBIDMS_column_p
 
 
 cdef extern from "obiview.h" nogil:
 
+    extern const_char_p VIEW_TYPE_NUC_SEQS
+    extern const_char_p NUC_SEQUENCE_COLUMN
+    extern const_char_p ID_COLUMN
+    extern const_char_p DESCRIPTION_COLUMN
+
     struct Column_reference_t :
-        char          column_name
+        const_char_p  column_name
         obiversion_t  version
     
     ctypedef Column_reference_t* Column_reference_p
@@ -31,12 +37,48 @@ cdef extern from "obiview.h" nogil:
     ctypedef Obiview_t* Obiview_p
 
 
+    struct Obiview_infos_t :
+        int                 view_number
+        int                 column_count
+        index_t             line_count
+        const_char_p        name
+        const_char_p        created_from
+        time_t              creation_date
+        bint                all_lines
+        Column_reference_t  line_selection
+        Column_reference_p  column_references
+        const_char_p        view_type
+
+    ctypedef Obiview_infos_t* Obiview_infos_p
+
+
+    struct Obiviews_header_t :
+        size_t header_size
+        size_t views_size
+        int    view_count
+    
+    ctypedef Obiviews_header_t* Obiviews_header_p
+
+
+    struct Obiviews_infos_all_t :
+        Obiviews_header_p    header
+        Obiview_infos_p      view_infos
+
+    ctypedef Obiviews_infos_all_t* Obiviews_infos_all_p
+
+
+    Obiview_p obi_new_view_nuc_seqs(OBIDMS_p dms, const_char_p view_name, Obiview_p view_to_clone, index_t* line_selection)
+
     Obiview_p obi_new_view(OBIDMS_p dms, const_char_p view_name, Obiview_p view_to_clone, index_t* line_selection)
     
-    Obiview_p obi_new_view_cloned_from_name(OBIDMS_p dms, const char* view_name, const char* view_to_clone_name, index_t* line_selection)
+    Obiview_p obi_new_view_cloned_from_name(OBIDMS_p dms, const_char_p view_name, const_char_p view_to_clone_name, index_t* line_selection)
 
+    Obiview_p obi_new_view_nuc_seqs_cloned_from_name(OBIDMS_p dms, const_char_p view_name, const_char_p view_to_clone_name, index_t* line_selection)
+              
     Obiview_p obi_open_view(OBIDMS_p dms, const_char_p view_name)
     
+    Obiviews_infos_all_p obi_read_views(OBIDMS_p dms)
+
     int obi_view_add_column(Obiview_p view,
                             const_char_p column_name,
                             obiversion_t version_number,

src/obiview.c

@@ -209,6 +209,50 @@ int create_obiview_file(int dms_file_descriptor)
  **********************************************************************/
 
 
+Obiview_p obi_new_view_nuc_seqs(OBIDMS_p dms, const char* view_name, Obiview_p view_to_clone, index_t* line_selection)
+{
+	Obiview_p view;
+
+	if (view_to_clone != NULL)
+	{ // TODO check that the view to clone is already a NUC_SEQS view (discuss possibility of transforming type of a view)
+		if (strcmp(view_to_clone->view_type, VIEW_TYPE_NUC_SEQS))
+		{
+			obi_set_errno(OBIVIEW_ERROR);
+			obidebug(1, "Trying to clone a non-NUC SEQS view to create a NUC SEQS view");
+			return NULL;
+		}
+	}
+
+	view = obi_new_view(dms, view_name, view_to_clone, line_selection);
+
+	strcpy(view->view_type, VIEW_TYPE_NUC_SEQS);
+
+	if (view_to_clone == NULL)
+	{
+		// Adding sequence column
+		if (obi_view_add_column(view, NUC_SEQUENCE_COLUMN, -1, OBI_SEQ, 0, 1, NUC_SEQUENCE_COLUMN, NUC_SEQUENCE_AVL, "Nucleotide sequences", true) < 0)
+		{
+			obidebug(1, "Error adding an obligatory column in a nucleotide sequences view");
+			return NULL;
+		}
+		// Adding id column
+		if (obi_view_add_column(view, ID_COLUMN, -1, OBI_STR, 0, 1, ID_COLUMN, ID_AVL, "Ids", true) < 0)
+		{
+			obidebug(1, "Error adding an obligatory column in a nucleotide sequences view");
+			return NULL;
+		}
+		// Adding description column
+		if (obi_view_add_column(view, DESCRIPTION_COLUMN, -1, OBI_STR, 0, 1, DESCRIPTION_COLUMN, DESCRIPTION_AVL, "Descriptions", true) < 0)
+		{
+			obidebug(1, "Error adding an obligatory column in a nucleotide sequences view");
+			return NULL;
+		}
+	}
+
+	return view;
+}
+
+
 Obiview_p obi_new_view(OBIDMS_p dms, const char* view_name, Obiview_p view_to_clone, index_t* line_selection)
 {
 	Obiview_p view;
@@ -297,6 +341,7 @@ Obiview_p obi_new_view(OBIDMS_p dms, const char* view_name, Obiview_p view_to_cl
 			}
 		}
 
+		strcpy(view->view_type, view_to_clone->view_type);
 		strcpy(view->created_from, view_to_clone->name);
 		view->new_line_selection = NULL;
 	}
@@ -308,8 +353,9 @@ Obiview_p obi_new_view(OBIDMS_p dms, const char* view_name, Obiview_p view_to_cl
 		view->line_count         = 0;
 		view->line_selection     = NULL;
 		view->new_line_selection = NULL;
-		(view->created_from)[0]    = '\0';
+		(view->created_from)[0]  = '\0';
-		//view->columns            = NULL; TODO
+		(view->view_type)[0]     = '\0';
+		//view->columns          = NULL; TODO
 	}
 
 	strcpy(view->name, view_name);
@@ -328,6 +374,25 @@ Obiview_p obi_new_view_cloned_from_name(OBIDMS_p dms, const char* view_name, con
 	if (view_to_clone == NULL)
 		return NULL;
 	view = obi_new_view(dms, view_name, view_to_clone, line_selection);
+
+	obi_close_view(view_to_clone);
+
+	return view;
+}
+
+
+Obiview_p obi_new_view_nuc_seqs_cloned_from_name(OBIDMS_p dms, const char* view_name, const char* view_to_clone_name, index_t* line_selection)
+{
+	Obiview_p view;
+	Obiview_p view_to_clone;
+
+	view_to_clone = obi_open_view(dms, view_to_clone_name);
+	if (view_to_clone == NULL)
+		return NULL;
+	view = obi_new_view_nuc_seqs(dms, view_name, view_to_clone, line_selection);
+
+	obi_close_view(view_to_clone);
+
 	return view;
 }
 
@@ -466,6 +531,7 @@ Obiview_p obi_open_view(OBIDMS_p dms, const char* view_name)
 	view->line_count = view_infos->line_count;
 	strcpy(view->created_from, view_infos->created_from);
 	strcpy(view->name, view_infos->name);
+	strcpy(view->view_type, view_infos->view_type);
 
 	// Open the columns to read
 	for (i=0; i<(view_infos->column_count); i++)
@@ -493,6 +559,91 @@ Obiview_p obi_open_view(OBIDMS_p dms, const char* view_name)
 }
 
 
+Obiviews_infos_all_p obi_read_views(OBIDMS_p dms)
+{
+	char*       		 view_file_name;
+	int 				 obiview_file_descriptor;
+	size_t  			 header_size;
+	Obiviews_header_p 	 header;
+	Obiview_infos_p 	 view_infos;
+	Obiviews_infos_all_p views;
+
+	view_file_name = build_obiview_file_name();
+	if (view_file_name == NULL)
+		return NULL;
+
+	// Open view file, read header size and map header and views
+	obiview_file_descriptor = openat(dms->dir_fd, view_file_name, O_RDWR, 0777);
+	if (obiview_file_descriptor < 0)
+	{	// No views yet
+		free(view_file_name);
+		return NULL;
+	}
+
+	free(view_file_name);
+
+	// Read the header size
+	if (read(obiview_file_descriptor, &header_size, sizeof(size_t)) < ((ssize_t) sizeof(size_t)))
+	{
+		obi_set_errno(OBIVIEW_ERROR);
+		obidebug(1, "\nError reading the header size of an obiview file (trying to open a view when there are none?)");
+		close(obiview_file_descriptor);
+		return NULL;
+	}
+
+	// Map the header
+	header = mmap(NULL,
+				  header_size,
+				  PROT_READ | PROT_WRITE,
+				  MAP_SHARED,
+				  obiview_file_descriptor,
+				  0
+ 	 	   	   	 );
+	if (header == MAP_FAILED)
+	{
+		obi_set_errno(OBIVIEW_ERROR);
+		obidebug(1, "\nError mmapping an obiview file header");
+		close(obiview_file_descriptor);
+		return NULL;
+	}
+
+	// Map the views
+	view_infos = mmap(NULL,
+				 header->views_size,
+				 PROT_READ | PROT_WRITE,
+				 MAP_SHARED,
+				 obiview_file_descriptor,
+				 header_size
+ 	 	   	   	);
+	if (view_infos == MAP_FAILED)
+	{
+		obi_set_errno(OBIVIEW_ERROR);
+		obidebug(1, "\nError mmapping the views from an obiview file");
+		munmap(header, header_size);
+		close(obiview_file_descriptor);
+		return NULL;
+	}
+
+	views = (Obiviews_infos_all_p) malloc(sizeof(Obiviews_infos_all_t));
+	if (views == NULL)
+	{
+		obi_set_errno(OBIVIEW_ERROR);
+		obidebug(1, "\nError mmapping the views from an obiview file");
+		munmap(view_infos, header->views_size);
+		munmap(header, header_size);
+		close(obiview_file_descriptor);
+		return NULL;
+	}
+
+	views->header = header;
+	views->view_infos = view_infos;
+
+	close(obiview_file_descriptor);
+
+	return views;
+}
+
+
 int obi_view_add_column(Obiview_p view,
 						const char* column_name,
 						obiversion_t version_number,
@@ -605,6 +756,8 @@ int obi_view_delete_column(Obiview_p view, const char* column_name)
 	int  i;
 	bool found;
 
+	// TODO check that not deleting an obligatory column?
+
 	// Check that the view is not read-only
 	if (view->read_only)
 	{
@@ -879,6 +1032,8 @@ int obi_save_view(Obiview_p view)
 	view_infos->creation_date = time(NULL);
 	strcpy(view_infos->created_from, view->created_from);
 	strcpy(view_infos->name, view->name);
+	strcpy(view_infos->view_type, view->view_type);
+
 	// Store reference for the line selection associated with that view
 	if (view->new_line_selection != NULL)
 	{

src/obiview.h

@@ -30,6 +30,19 @@
                                 	 	   */
 #define OBIVIEW_FILE_NAME "obiviews"
 
+#define VIEW_TYPE_MAX_NAME (1024)
+
+#define VIEW_TYPE_NUC_SEQS "NUC_SEQS_VIEW"
+
+#define NUC_SEQUENCE_COLUMN "NUC_SEQ"
+#define NUC_SEQUENCE_AVL "NUC_SEQ_AVL"
+
+#define ID_COLUMN "ID"
+#define ID_AVL "ID_AVL"
+
+#define DESCRIPTION_COLUMN "DESCRIPTION"
+#define DESCRIPTION_AVL "DESCRIPTION_AVL"
+
 #define LINES_COLUMN_NAME "LINES"
 
 
@@ -69,6 +82,8 @@ typedef struct Obiview {
 
 	int					view_number;
 
+	char				view_type[VIEW_TYPE_MAX_NAME+1];
+
 } Obiview_t, *Obiview_p;
 
 
@@ -94,6 +109,8 @@ typedef struct Obiview_infos {
 
 	Column_reference_t	column_references[MAX_NB_OPENED_COLUMNS];
 
+	char				view_type[VIEW_TYPE_MAX_NAME+1];
+
 } Obiview_infos_t, *Obiview_infos_p;
 
 
@@ -110,20 +127,26 @@ typedef struct Obiviews_header {
 /**
  * @brief .
  */
-typedef struct Obiviews {	// not used
+typedef struct Obiviews_infos_all {
 	Obiviews_header_p	header;
 
-	Obiview_infos_p 	views;
+	Obiview_infos_p 	view_infos;
 
-} Obiviews_t, *Obiviews_p;
+} Obiviews_infos_all_t, *Obiviews_infos_all_p;
 
 
+Obiview_p obi_new_view_nuc_seqs(OBIDMS_p dms, const char* view_name, Obiview_p view_to_clone, index_t* line_selection);
+
 Obiview_p obi_new_view(OBIDMS_p dms, const char* view_name, Obiview_p view_to_clone, index_t* line_selection);
 
 Obiview_p obi_new_view_cloned_from_name(OBIDMS_p dms, const char* view_name, const char* view_to_clone_name, index_t* line_selection);
 
+Obiview_p obi_new_view_nuc_seqs_cloned_from_name(OBIDMS_p dms, const char* view_name, const char* view_to_clone_name, index_t* line_selection);
+
 Obiview_p obi_open_view(OBIDMS_p dms, const char* view_name);
 
+Obiviews_infos_all_p obi_read_views(OBIDMS_p dms);
+
 int obi_view_add_column(Obiview_p view,
 						const char* column_name,
 						obiversion_t version_number,