Closes issue #47 by storing each view in a separate file named with the

view's name and created upon view creation.

python/obitools3/obidms/_obidms.pxd

@@ -91,5 +91,5 @@ cdef class OBIDMS:
     cpdef OBIView open_view(self, str view_name)
     cpdef OBIView new_view(self, str view_name, object view_to_clone=*, list line_selection=*, str view_type=*, str comments=*)
     cpdef dict read_view_infos(self, str view_name)
-    cpdef dict read_views(self)
+#    cpdef dict read_views(self)    TODO
 

python/obitools3/obidms/_obidms.pyx

@@ -54,16 +54,15 @@ from ._obidmscolumn_seq cimport OBIDMS_column_seq, \
                                 OBIDMS_column_multi_elts_seq
 
 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_view_map_file, \
+                           obi_view_unmap_file, \
                            obi_open_view,  \
-                           obi_read_view_infos, \
-                           obi_close_view_infos, \
                            obi_view_delete_column, \
                            obi_view_add_column, \
                            obi_view_get_column, \
@@ -291,11 +290,11 @@ cdef class OBIView :
             raise Exception("Error creating/opening a view")
 
         self.pointer = view
-        self.name = bytes2str(view.name)
+        self.name = bytes2str(view.infos.name)
         
         # Go through columns to build list of corresponding python instances
         self.columns = {}
-        for i in range(view.column_count) :
+        for i in range(view.infos.column_count) :
             column_p               = <OBIDMS_column_p> (view.columns)[i]
             header                 = (column_p).header
             col_name               = bytes2str(header.name)         
@@ -305,7 +304,7 @@ cdef class OBIView :
 
     def __repr__(self) :
         cdef str s
-        s = str(self.name) + ", " + str(self.comments) + ", " + str(self.pointer.line_count) + " lines\n" 
+        s = str(self.name) + ", " + str(self.comments) + ", " + str(self.pointer.infos.line_count) + " lines\n" 
         for column_name in self.columns :
             s = s + self.columns[column_name].__repr__() + '\n'
         return s
@@ -402,7 +401,7 @@ cdef class OBIView :
         cdef OBIView_line line          # TODO Check that this works for NUC SEQ views
         
         # Yield each line
-        lines_used = (self.pointer).line_count
+        lines_used = self.pointer.infos.line_count
         
         for line_nb in range(lines_used) :
             line = self[line_nb]
@@ -486,12 +485,12 @@ cdef class OBIView_NUC_SEQS(OBIView):
             raise Exception("Error creating/opening view")
 
         self.pointer = view
-        self.name = bytes2str(view.name)
+        self.name = bytes2str(view.infos.name)
-        self.comments = bytes2str(view.comments)
+        self.comments = bytes2str(view.infos.comments)
         
         # Go through columns to build list of corresponding python instances
         self.columns = {}
-        for i in range(view.column_count) :
+        for i in range(view.infos.column_count) :
             column_p               = <OBIDMS_column_p> (view.columns)[i]
             header                 = (column_p).header
             col_name               = bytes2str(header.name)         
@@ -621,54 +620,84 @@ cdef class OBIDMS :
 
 
     cpdef dict read_view_infos(self, str view_name) :
-        all_views = self.read_views()
-        return all_views[view_name]
         
-
+        cdef Obiview_infos_p      view_infos_p
-    cpdef dict read_views(self) :    # TODO function that prints the dic nicely and function that prints 1 view nicely. Add column type in col ref
+        cdef dict                 view_infos_d
-        
-        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 = {}
+        view_infos_p = obi_view_map_file(self.pointer, str2bytes(view_name))
-        all_views_p = obi_read_view_infos(self.pointer)
+        view_infos_d = {}
-        if all_views_p == NULL :
+        view_infos_d["name"] = bytes2str(view_infos_p.name)
-            raise Exception("No views to read")
+        view_infos_d["comments"] = bytes2str(view_infos_p.comments)
-        nb_views = <int> (all_views_p.header).view_count
+        view_infos_d["view_type"] = bytes2str(view_infos_p.view_type)
-        for i in range(nb_views) :
+        view_infos_d["column_count"] = <int> view_infos_p.column_count
-            view_p = (<Obiview_infos_p> (all_views_p.view_infos)) + i
+        view_infos_d["line_count"] = <int> view_infos_p.line_count
-            view_name = bytes2str(view_p.name)
+        view_infos_d["created_from"] = bytes2str(view_infos_p.created_from)
-            views[view_name] = {}
+        view_infos_d["creation_date"] = bytes2str(obi_format_date(view_infos_p.creation_date))
-            views[view_name]["comments"] = bytes2str(view_p.comments)
+        if (view_infos_p.all_lines) :
-            views[view_name]["view_type"] = bytes2str(view_p.view_type)
+            view_infos_d["line_selection"] = None
-            views[view_name]["column_count"] = <int> view_p.column_count
+        else :
-            views[view_name]["line_count"] = <int> view_p.line_count
+            view_infos_d["line_selection"] = {}
-            views[view_name]["view_number"] = <int> view_p.view_number
+            view_infos_d["line_selection"]["column_name"] = bytes2str((view_infos_p.line_selection).column_name)
-            views[view_name]["created_from"] = bytes2str(view_p.created_from)
+            view_infos_d["line_selection"]["version"] = <int> (view_infos_p.line_selection).version
-            views[view_name]["creation_date"] = bytes2str(obi_format_date(view_p.creation_date))
+        view_infos_d["column_references"] = {}
-            if (view_p.all_lines) :
+        column_refs = view_infos_p.column_references
-                views[view_name]["line_selection"] = None
+        for j in range(view_infos_d["column_count"]) :
-            else :
+            column_name = bytes2str((column_refs[j]).column_name)
-                views[view_name]["line_selection"] = {}
+            view_infos_d["column_references"][column_name] = {}
-                views[view_name]["line_selection"]["column_name"] = bytes2str((view_p.line_selection).column_name)
+            view_infos_d["column_references"][column_name]["version"] = column_refs[j].version
-                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
         
-        obi_close_view_infos(all_views_p);
+        obi_view_unmap_file(self.pointer, view_infos_p)
 
-        return views
+        return view_infos_d
+
+
+#     cpdef dict read_views(self) :    # TODO function that prints the dic nicely and function that prints 1 view nicely. 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_view_infos(self.pointer)
+#         if all_views_p == NULL :
+#             raise Exception("No views to read")
+#         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]["comments"] = bytes2str(view_p.comments)
+#             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_format_date(view_p.creation_date))
+#             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
+#         
+#         obi_close_view_infos(all_views_p);
+#         
+#         return views
     
     
     

python/obitools3/obidms/capi/obiview.pxd

@@ -23,21 +23,6 @@ cdef extern from "obiview.h" nogil:
     extern const_char_p DEFINITION_COLUMN
     extern const_char_p QUALITY_COLUMN
 
-    struct Obiview_t :
-        OBIDMS_p            dms
-        const_char_p        name
-        const_char_p        created_from
-        const_char_p        view_type
-        bint                read_only
-        OBIDMS_column_p     line_selection
-        OBIDMS_column_p     new_line_selection
-        index_t             line_count
-        int                 column_count
-        OBIDMS_column_p     columns
-        const_char_p        comments
-
-    ctypedef Obiview_t* Obiview_p
-
 
     struct Column_reference_t :
         const_char_p  column_name
@@ -47,7 +32,6 @@ cdef extern from "obiview.h" nogil:
 
 
     struct Obiview_infos_t :
-        int                 view_number
         time_t              creation_date
         const_char_p        name
         const_char_p        created_from
@@ -62,19 +46,15 @@ cdef extern from "obiview.h" nogil:
     ctypedef Obiview_infos_t* Obiview_infos_p
 
 
-    struct Obiviews_header_t :
+    struct Obiview_t :
-        size_t header_size
+        Obiview_infos_p     infos
-        size_t views_size
+        OBIDMS_p            dms
-        int    view_count
+        bint                read_only
+        OBIDMS_column_p     line_selection
+        OBIDMS_column_p     new_line_selection
+        OBIDMS_column_p     columns
 
-    ctypedef Obiviews_header_t* Obiviews_header_p
+    ctypedef Obiview_t* Obiview_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, const_char_p comments)
@@ -85,6 +65,10 @@ cdef extern from "obiview.h" nogil:
 
     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, const_char_p comments)
               
+    Obiview_infos_p obi_view_map_file(OBIDMS_p dms, const char* view_name)
+
+    int obi_view_unmap_file(OBIDMS_p dms, Obiview_infos_p view_infos)
+
     Obiview_p obi_open_view(OBIDMS_p dms, const_char_p view_name)
     
     int obi_view_add_column(Obiview_p view,
@@ -114,10 +98,6 @@ cdef extern from "obiview.h" nogil:
     
     int obi_save_and_close_view(Obiview_p view)
 
-    Obiviews_infos_all_p obi_read_view_infos(OBIDMS_p dms)
-
-    int obi_close_view_infos(Obiviews_infos_all_p views)
-
     int obi_column_set_obiint_with_elt_name_in_view(Obiview_p view,
                                                     OBIDMS_column_p column, 
                                                     index_t line_nb, 

src/obidms.c

@@ -252,7 +252,7 @@ OBIDMS_p obi_create_dms(const char* dms_path)
 		return NULL;
 	}
 
-	// Get file descriptor of DMS directory to create the indexer directory
+	// Get file descriptor of DMS directory to create other directories
 	dms_dir = opendir(directory_name);
 	if (dms_dir == NULL)
 	{
@@ -280,6 +280,14 @@ OBIDMS_p obi_create_dms(const char* dms_path)
 		return NULL;
 	}
 
+	// Create the view directory
+	if (mkdirat(dms_file_descriptor, VIEW_DIR_NAME, 00777) < 0)
+	{
+		obi_set_errno(OBIVIEW_ERROR);
+		obidebug(1, "\nProblem creating a view directory");
+		return NULL;
+	}
+
 	// Isolate the dms name
 	j = 0;
 	for (i=0; i<strlen(dms_path); i++)
@@ -447,6 +455,30 @@ OBIDMS_p obi_open_dms(const char* dms_path)
 		return NULL;
 	}
 
+	// Open the view directory
+	dms->view_directory = opendir_in_dms(dms, VIEW_DIR_NAME);
+	if (dms->view_directory == NULL)
+	{
+		obi_set_errno(OBIDMS_UNKNOWN_ERROR);
+		obidebug(1, "\nError opening the view directory");
+		closedir(dms->indexer_directory);
+		closedir(dms->directory);
+		free(dms);
+		return NULL;
+	}
+
+	// Store the view directory's file descriptor
+	dms->view_dir_fd = dirfd(dms->view_directory);
+	if (dms->view_dir_fd < 0)
+	{
+		obi_set_errno(OBIDMS_UNKNOWN_ERROR);
+		obidebug(1, "\nError getting the file descriptor of the view directory");
+		closedir(dms->view_directory);
+		closedir(dms->directory);
+		free(dms);
+		return NULL;
+	}
+
 	// Initialize the list of opened columns
 	dms->opened_columns = (Opened_columns_list_p) malloc(sizeof(Opened_columns_list_t));
 	(dms->opened_columns)->nb_opened_columns = 0;
@@ -486,7 +518,7 @@ int obi_close_dms(OBIDMS_p dms)
 		while ((dms->opened_columns)->nb_opened_columns > 0)
 			obi_close_column(*((dms->opened_columns)->columns));
 
-		// Close dms and indexer directories
+		// Close dms, and view and indexer directories
 		if (closedir(dms->directory) < 0)
 		{
 			obi_set_errno(OBIDMS_MEMORY_ERROR);
@@ -501,6 +533,13 @@ int obi_close_dms(OBIDMS_p dms)
 			free(dms);
 			return -1;
 		}
+		if (closedir(dms->view_directory) < 0)
+		{
+			obi_set_errno(OBIVIEW_ERROR);
+			obidebug(1, "\nError closing a view directory");
+			free(dms);
+			return -1;
+		}
 		free(dms);
 	}
 

src/obidms.h

@@ -30,6 +30,8 @@
  	 	 	 	 	 	 	 	 	 	 	 	 */
 #define INDEXER_DIR_NAME "OBIBLOB_INDEXERS"  	/**< The name of the Obiblob indexer directory.
                                 	 	 	 	 */
+#define VIEW_DIR_NAME "VIEWS"					/**< The name of the view directory.
+												 */
 #define TAXONOMY_DIR_NAME "TAXONOMY"    		/**< The name of the taxonomy directory.
                                 	 	 	 	 */
 #define MAX_NB_OPENED_COLUMNS (100) 			/**< The maximum number of columns open at the same time.
@@ -98,6 +100,12 @@ typedef struct OBIDMS {
 	int						indexer_dir_fd;						/**< The file descriptor of the directory entry
 																 *   usable to refer and scan the indexer directory.
 																 */
+	DIR*					view_directory;						/**< A directory entry usable to
+																 *   refer and scan the view directory.
+																 */
+	int						view_dir_fd;						/**< The file descriptor of the directory entry
+																 *   usable to refer and scan the view directory.
+																 */
 	bool					little_endian;						/**< Endianness of the database.
 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 */
 	Opened_columns_list_p 	opened_columns;						/**< List of opened columns.

src/obiview.h

@@ -34,8 +34,6 @@
                                 	 	  	  	 */
 #define VIEW_TYPE_MAX_LENGTH (1024)   			/**< The maximum length of the type name of a view.
                                 	 	  	  	 */
-#define OBIVIEW_FILE_NAME "obiviews"   			/**< The default name of a view file.
-                                	 	  	  	 */
 #define LINES_COLUMN_NAME "LINES"				/**< The name of the column containing the line selections
  	 	 	 	 	 	 	 	 	 	 	 	 *   in all views.
                                 	 	  	  	 */
@@ -56,45 +54,6 @@
                                 	 	  	  	 */
 
 
-/**
- * @brief Structure for an opened view.
- */
-typedef struct Obiview {
-
-	OBIDMS_p         	dms;    									/**< A pointer on the DMS to which the view belongs.
-	 	 	    													 */
-	char   				name[OBIVIEW_NAME_MAX_LENGTH+1];    		/**< Name of the view.
-	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 */
-	char				created_from[OBIVIEW_NAME_MAX_LENGTH+1];    /**< Name of the view from which that view was cloned if the view was cloned.
- 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 */
-	char				view_type[VIEW_TYPE_MAX_LENGTH+1];			/**< Type of the view if there is one.
-																	 *   Types existing: NUC_SEQS_VIEW.
- 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 */
-	bool             	read_only;    								/**< Whether the view is read-only or can be modified.
-																	 */
-	OBIDMS_column_p  	line_selection;    							/**< A pointer on the column containing the line selection
-																	 *   associated with the view if there is one.
-																	 *   This line selection is read-only, and when a line from the view is read,
-																	 *   it is this line selection that is used.
-	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 */
-	OBIDMS_column_p  	new_line_selection;    						/**< A pointer on the column containing the new line selection being built
-	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 *   to associate with the view, if there is one.
-	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 *   When a line is selected with obi_select_line() or obi_select_lines(),
-	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 *   it is recorded in this line selection.
-	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 */
-	index_t			 	line_count;    								/**< The number of lines in the view. Refers to the number of lines in each
-	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 *   column of the view if line_selection is NULL, or to the line count of
-	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 *   line_selection if it is not NULL.
- 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 */
-	int    			 	column_count;    							/**< The number of columns in the view.
- 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 */
-	OBIDMS_column_p  	columns[MAX_NB_OPENED_COLUMNS];    			/**< Array of pointers on all the columns of the view.
-	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 */
-	char 				comments[OBIVIEW_COMMENTS_MAX_LENGTH+1];	/**< Comments, additional informations on the view.
-	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 */
-} Obiview_t, *Obiview_p;
-
-
 /**
  * @brief Structure referencing a column by its name and its version.
  */
@@ -112,8 +71,6 @@ typedef struct Column_reference {
  * 		  Once a view has been written in the view file, it can not be modified and can only be read.
  */
 typedef struct Obiview_infos {
-	int					view_number;    							/**< Number of the view in the view file.
-	 	 	    													 */
 	time_t 		 		creation_date;    							/**< Time at which the view was written in the view file.
 		 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 */
 	char   				name[OBIVIEW_NAME_MAX_LENGTH+1];    		/**< Name of the view, used to identify it.
@@ -138,7 +95,29 @@ typedef struct Obiview_infos {
 } Obiview_infos_t, *Obiview_infos_p;
 
 
-// TODO : Combine the common elements of the Obiview_infos and Obiview structures in one structure used by both?
+/**
+ * @brief Structure for an opened view.
+ */
+typedef struct Obiview {
+	Obiview_infos_p     infos;										/**< A pointer on the mapped view informations.
+		 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 */
+	OBIDMS_p         	dms;    									/**< A pointer on the DMS to which the view belongs.
+	 	 	    													 */
+	bool             	read_only;    								/**< Whether the view is read-only or can be modified.
+																	 */
+	OBIDMS_column_p  	line_selection;    							/**< A pointer on the column containing the line selection
+																	 *   associated with the view if there is one.
+																	 *   This line selection is read-only, and when a line from the view is read,
+																	 *   it is this line selection that is used.
+	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 */
+	OBIDMS_column_p  	new_line_selection;    						/**< A pointer on the column containing the new line selection being built
+	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 *   to associate with the view, if there is one.
+	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 *   When a line is selected with obi_select_line() or obi_select_lines(),
+	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 *   it is recorded in this line selection.
+	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 */
+	OBIDMS_column_p  	columns[MAX_NB_OPENED_COLUMNS];    			/**< Array of pointers on all the columns of the view.
+	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 */
+} Obiview_t, *Obiview_p;
 
 
 /**
@@ -269,6 +248,37 @@ Obiview_p obi_new_view_nuc_seqs(OBIDMS_p dms, const char* view_name, Obiview_p v
 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, const char* comments);
 
 
+/**
+ * @brief Maps a view file and returns the mapped structure stored in it.
+ *
+ * @param dms A pointer on the OBIDMS.
+ * @param view_name The unique name identifying the view.
+ *
+ * @returns A pointer on the mapped view infos structure.
+ * @retval NULL if an error occurred.
+ *
+ * @since June 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+Obiview_infos_p obi_view_map_file(OBIDMS_p dms, const char* view_name);
+
+
+/**
+ * @brief Unmaps a view file.
+ *
+ * @param dms A pointer on the OBIDMS.
+ * @param view_infos A pointer on the mapped view infos structure.
+ *
+ * @returns A value indicating the success of the operation.
+ * @retval 0 if the operation was successfully completed.
+ * @retval -1 if an error occurred.
+ *
+ * @since June 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+int obi_view_unmap_file(OBIDMS_p dms, Obiview_infos_p view_infos);
+
+
 /**
  * @brief Opens a view identified by its name stored in the view file.
  *