obi ls: now done in C (preparing things for R packages to read DMS) and

switch to version 3.0.0b36

src/obidms.c

@@ -1409,6 +1409,107 @@ DIR* opendir_in_dms(OBIDMS_p dms, const char* path_name)
 }
 
 
+char* obi_dms_formatted_infos(OBIDMS_p dms, bool detailed)
+{
+	char*          dms_infos = NULL;
+	char*   	   view_infos = NULL;
+	char*          view_name = NULL;
+	char*          tax_name = NULL;
+	char*          all_tax_dir_path = NULL;
+	int            i;
+	struct dirent* dp;
+	Obiview_p      view;
+
+	// DMS name
+	dms_infos = (char*) malloc((strlen("# DMS name: ")+strlen(dms->dms_name)+strlen("\n# Views:\n")+1) * sizeof(char));
+	if (dms_infos == NULL)
+	{
+		obidebug(1, "\nError allocating memory for DMS formatted infos");
+		return NULL;
+	}
+	strcpy(dms_infos, "# DMS name: ");
+	strcat(dms_infos, dms->dms_name);
+	strcat(dms_infos, "\n# Views:\n");
+
+	// Go through views and get their infos
+	rewinddir(dms->view_directory);
+	while ((dp = readdir(dms->view_directory)) != NULL)
+	{
+		if ((dp->d_name)[0] == '.')
+			continue;
+		i=0;
+		while ((dp->d_name)[i] != '.')
+			i++;
+		view_name = (char*) malloc((i+1) * sizeof(char));
+		if (view_name == NULL)
+		{
+			obi_set_errno(OBI_MALLOC_ERROR);
+			obidebug(1, "\nError allocating memory for a view name when getting formatted DMS infos: file %s", dp->d_name);
+			return NULL;
+		}
+		strncpy(view_name, dp->d_name, i);
+		view_name[i] = '\0';
+		view = obi_open_view(dms, view_name);
+		if (view == NULL)
+		{
+			obidebug(1, "\nError opening a view to get DMS formatted infos");
+			return NULL;
+		}
+		if (detailed)
+			view_infos = obi_view_formatted_infos(view, detailed);
+		else
+			view_infos = obi_view_formatted_infos_one_line(view);
+		if (view_infos == NULL)
+		{
+			obidebug(1, "\nError getting a view infos to get DMS formatted infos");
+			return NULL;
+		}
+		dms_infos = realloc(dms_infos, (strlen(dms_infos)+strlen(view_infos)+1) * sizeof(char));
+		if (dms_infos == NULL)
+		{
+			obidebug(1, "\nError reallocating memory for DMS formatted infos");
+			return NULL;
+		}
+		strcat(dms_infos, view_infos);
+		if (obi_save_and_close_view(view) < 0)
+		{
+			obidebug(1, "\nError closing view while getting DMS formatted infos");
+			return NULL;
+		}
+		if (detailed)
+		{
+			dms_infos = realloc(dms_infos, (strlen(dms_infos)+2) * sizeof(char));
+			strcat(dms_infos, "\n");
+		}
+	}
+
+	// Add taxonomies
+	dms_infos = realloc(dms_infos, (strlen(dms_infos)+strlen("\n# Taxonomies:\n")+1) * sizeof(char));
+	if (dms_infos == NULL)
+	{
+		obidebug(1, "\nError reallocating memory for DMS formatted infos");
+		return NULL;
+	}
+	strcat(dms_infos, "# Taxonomies:\n");
+	rewinddir(dms->tax_directory);
+	while ((dp = readdir(dms->tax_directory)) != NULL)
+	{
+		if ((dp->d_name)[0] == '.')
+			continue;
+		tax_name = dp->d_name;
+		dms_infos = realloc(dms_infos, (strlen(dms_infos)+strlen("  # ")+strlen(view_infos)+1) * sizeof(char));
+		if (dms_infos == NULL)
+		{
+			obidebug(1, "\nError reallocating memory for DMS formatted infos");
+			return NULL;
+		}
+		strcat(dms_infos, "  # ");
+		strcat(dms_infos, tax_name);
+	}
+	return dms_infos;
+}
+
+
 // TODO move somewhere else maybe
 // TODO discuss arguments
 obiversion_t obi_import_column(const char* dms_path_1, const char* dms_path_2, const char* column_name, obiversion_t version_number)

src/obidms.h

@@ -459,6 +459,23 @@ char* obi_dms_get_full_path(OBIDMS_p dms, const char* path_name);
 DIR* opendir_in_dms(OBIDMS_p dms, const char* path_name);
 
 
+/**
+ * @brief Returns the informations of a DMS with a human readable format (dms name, taxonomies and view infos).
+ *
+ * @warning The returned pointer has to be freed by the caller.
+ *
+ * @param column A pointer on a DMS.
+ * @param detailed Whether the informations should contain detailed view infos.
+ *
+ * @returns A pointer on a character array where the formatted DMS informations are stored.
+ * @retval NULL if an error occurred.
+ *
+ * @since September 2020
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+char* obi_dms_formatted_infos(OBIDMS_p dms, bool detailed);
+
+
 /**
  * @brief Imports a column, copying it from a DMS to another DMS, and returns the version of the column in the destination DMS.
  *

src/obidmscolumn.c

@@ -2435,17 +2435,77 @@ char* obi_column_formatted_infos(OBIDMS_column_p column, bool detailed)
 {
 	char* column_infos = NULL;
 	char* elt_names = NULL;
-	char* column_name = NULL;
-	 // should be in view.c because alias exists in the context of view
-	column_infos = malloc(2048 * sizeof(char)); // TODO
+	char* data_type_str = NULL;
+	char* comments = NULL;
 
+	// Get element names informations
 	elt_names = obi_get_formatted_elements_names(column);
+	if (elt_names == NULL)
+	{
+		obidebug(1, "\nError getting formatted elements names for formatted columns infos");
+		return NULL;
+	}
 
+	// Get data type informations
+	data_type_str = name_data_type((column->header)->returned_data_type);
+	if (data_type_str == NULL)
+	{
+		obidebug(1, "\nError getting formatted data type for formatted columns infos");
+		return NULL;
+	}
 
-//  "column_name, data type: OBI_TYPE, element names: [formatted element names](, all comments)"
+	// Get commments if detailed informations required
+	if (detailed)
+		comments = (column->header)->comments;
 
+	// Build the string of formatted infos, allocating memory as needed
+
+	// Data type
+	column_infos = (char*) malloc((strlen("data type: ")+strlen(data_type_str)+1) * sizeof(char));
+	if (column_infos == NULL)
+	{
+		obi_set_errno(OBI_MALLOC_ERROR);
+		obidebug(1, "\nError allocating memory for formatted column infos");
+		return NULL;
+	}
+
+	strcpy(column_infos, "data type: ");
+	strcat(column_infos, data_type_str);
+
+	// Element names if more than 1
+	if ((column->header)->nb_elements_per_line > 1)
+	{
+		column_infos = realloc(column_infos, (strlen(column_infos)+strlen(", elements: ")+strlen(elt_names)+1) * sizeof(char));
+		if (column_infos == NULL)
+		{
+			obi_set_errno(OBI_MALLOC_ERROR);
+			obidebug(1, "\nError allocating memory for formatted column infos");
+			return NULL;
+		}
+
+		strcat(column_infos, ", elements: ");
+		strcat(column_infos, elt_names);
+	}
+
+	if (detailed && (strlen(comments)>2)) // Add all comments if required and not empty
+	{
+		column_infos = realloc(column_infos, (strlen(column_infos)+strlen("\nComments:\n")+strlen(comments)+1) * sizeof(char));
+		if (column_infos == NULL)
+		{
+			obi_set_errno(OBI_MALLOC_ERROR);
+			obidebug(1, "\nError allocating memory for formatted column infos");
+			return NULL;
+		}
+
+		strcat(column_infos, "\nComments:\n");
+		strcat(column_infos, comments);
+	}
+
+//  "data type: OBI_TYPE, element names: [formatted element names](, all comments)"
 
 	free(elt_names);
+	free(data_type_str);
+
 	return column_infos;
 }
 
@@ -2492,7 +2552,6 @@ int obi_column_prepare_to_set_value(OBIDMS_column_p column, index_t line_nb, ind
 }
 
 
-
 int obi_column_prepare_to_get_value(OBIDMS_column_p column, index_t line_nb)
 {
 	if ((line_nb+1) > ((column->header)->line_count))

src/obidmscolumn.h

@@ -505,12 +505,37 @@ index_t obi_column_get_element_index_from_name(OBIDMS_column_p column, const cha
 char* obi_get_elements_names(OBIDMS_column_p column);
 
 
-// TODO
-//char* obi_get_formatted_elements_names(OBIDMS_column_p column);
+/**
+ * @brief Recovers the elements names of the lines of a column with a human readable format ("0; 1; 2; ...; n\0").
+ *
+ * @warning The returned pointer has to be freed by the caller.
+ *
+ * @param column A pointer on an OBIDMS column.
+ *
+ * @returns A pointer on a character array where the elements names are stored.
+ * @retval NULL if an error occurred.
+ *
+ * @since September 2020
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+char* obi_get_formatted_elements_names(OBIDMS_column_p column);
 
 
-// TODO
-//char* obi_column_formatted_infos(OBIDMS_column_p column);
+/**
+ * @brief Returns the informations of a column with a human readable format (data type, element names, comments).
+ *
+ * @warning The returned pointer has to be freed by the caller.
+ *
+ * @param column A pointer on an OBIDMS column.
+ * @param detailed Whether the informations should contain column comments or just data type and element names.
+ *
+ * @returns A pointer on a character array where the formatted column informations are stored.
+ * @retval NULL if an error occurred.
+ *
+ * @since September 2020
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+char* obi_column_formatted_infos(OBIDMS_column_p column, bool detailed);
 
 
 /**

src/obiview.c

@@ -17,6 +17,7 @@
 #include <sys/mman.h>
 #include <inttypes.h>
 #include <math.h>
+#include <time.h>
 //#include <ctype.h>
 
 #include "obiview.h"
@@ -1185,6 +1186,7 @@ static int close_view(Obiview_p view)
 			obidebug(1, "\nError getting a column to close from the linked list of column pointers of a view");
 			return -1;
 		}
+
 		if (obi_close_column(column) < 0)
 		{
 			obidebug(1, "\nError closing a column while closing a view");
@@ -2603,6 +2605,144 @@ int obi_view_create_column_alias(Obiview_p view, const char* current_name, const
 }
 
 
+char* obi_view_formatted_infos(Obiview_p view, bool detailed)
+{
+	int             i;
+	char*   		view_infos = NULL;
+	char*   		view_name = NULL;
+	time_t  		creation_date = NULL;
+	char*			creation_date_str = NULL;
+	index_t 		line_count;
+	char    		line_count_str[256];
+	OBIDMS_column_p column;
+	char*			column_alias = NULL;
+	char*   		column_infos = NULL;
+	char*			comments = NULL;
+
+	// View name
+	view_name = (view->infos)->name;
+	view_infos = (char*) malloc((strlen("# View name:\n")+strlen(view_name)+1) * sizeof(char));
+	strcpy(view_infos, "# View name:\n");
+	strcat(view_infos, view_name);
+
+	// Date created
+	if (view->read_only) // Date not saved until view is finished writing
+	{
+		creation_date = (view->infos)->creation_date;
+		creation_date_str = ctime(&creation_date);
+		view_infos = realloc(view_infos, (strlen(view_infos)+strlen("\n# Date created:\n")+strlen(creation_date_str)+1) * sizeof(char));
+		strcat(view_infos, "\n# Date created:\n");
+		strcat(view_infos, creation_date_str);
+	}
+
+	// Line count
+	line_count = (view->infos)->line_count;
+	snprintf(line_count_str, sizeof line_count_str, "%zu", line_count);
+	view_infos = realloc(view_infos, (strlen(view_infos)+strlen("\n# Line count:\n")+strlen(line_count_str)+1) * sizeof(char));
+	strcat(view_infos, "# Line count:\n");
+	strcat(view_infos, line_count_str);
+
+	// Columns: go through each, print their alias then their infos
+	view_infos = realloc(view_infos, (strlen(view_infos)+strlen("\n# Columns:")+1) * sizeof(char));
+	strcat(view_infos, "\n# Columns:");
+	for (i=0; i<((view->infos)->column_count); i++)
+	{
+		column = *((OBIDMS_column_p*)ll_get(view->columns, i));
+		if (column == NULL)
+		{
+			obidebug(1, "\nError getting a column from the linked list of column pointers of a view to format view infos");
+			return NULL;
+		}
+
+		// Column alias
+		column_alias = (((view->infos)->column_references)[i]).alias;
+		view_infos = realloc(view_infos, (strlen(view_infos)+strlen("\n")+strlen(column_alias)+strlen(", ")+1) * sizeof(char));
+		strcat(view_infos, "\n");
+		strcat(view_infos, column_alias);
+		strcat(view_infos, ", ");
+
+		// Column infos
+		column_infos = obi_column_formatted_infos(column, detailed);
+		if (column_infos == NULL)
+		{
+			obidebug(1, "\nError getting column infos to format view infos");
+			return NULL;
+		}
+
+		view_infos = realloc(view_infos, (strlen(view_infos)+strlen(column_infos)+1) * sizeof(char));
+		strcat(view_infos, column_infos);
+		free(column_infos);
+	}
+
+	// Get commments if detailed informations required
+	if (detailed)
+	{
+		comments = (view->infos)->comments;
+		if (strlen(comments)>2) // Add all comments if not empty
+		{
+			view_infos = realloc(view_infos, (strlen(view_infos)+strlen("\n# Comments:\n")+strlen(comments)+1) * sizeof(char));
+			if (view_infos == NULL)
+			{
+				obi_set_errno(OBI_MALLOC_ERROR);
+				obidebug(1, "\nError allocating memory for formatted view infos");
+				return NULL;
+			}
+
+			strcat(view_infos, "\n# Comments:\n");
+			strcat(view_infos, comments);
+		}
+	}
+
+	view_infos = realloc(view_infos, (strlen(view_infos)+2) * sizeof(char));
+	strcat(view_infos, "\n");
+
+	return view_infos;
+}
+
+
+char* obi_view_formatted_infos_one_line(Obiview_p view)
+{
+	int             i;
+	char*   		view_infos = NULL;
+	char*   		view_name = NULL;
+	time_t  		creation_date = NULL;
+	char*			creation_date_str = NULL;
+	index_t 		line_count;
+	char    		line_count_str[256];
+
+	// View name
+	view_name = (view->infos)->name;
+	view_infos = (char*) malloc((strlen("  # ")+strlen(view_name)+2) * sizeof(char));
+	strcpy(view_infos, "  # ");
+	strcat(view_infos, view_name);
+	strcat(view_infos, ":");
+
+	// Date created
+	if (view->read_only) // Date not saved until view is finished writing
+	{
+		creation_date = (view->infos)->creation_date;
+		creation_date_str = ctime(&creation_date);
+		// Delete \n added by ctime
+		creation_date_str[strlen(creation_date_str)-1] = '\0';
+		view_infos = realloc(view_infos, (strlen(view_infos)+strlen(" Date created: ")+strlen(creation_date_str)+1) * sizeof(char));
+		strcat(view_infos, " Date created: ");
+		strcat(view_infos, creation_date_str);
+	}
+
+	// Line count
+	line_count = (view->infos)->line_count;
+	snprintf(line_count_str, sizeof line_count_str, "%zu", line_count);
+	view_infos = realloc(view_infos, (strlen(view_infos)+strlen(" ; Line count: ")+strlen(line_count_str)+1) * sizeof(char));
+	strcat(view_infos, " ; Line count: ");
+	strcat(view_infos, line_count_str);
+
+	view_infos = realloc(view_infos, (strlen(view_infos)+2) * sizeof(char));
+	strcat(view_infos, "\n");
+
+	return view_infos;
+}
+
+
 int obi_view_write_comments(Obiview_p view, const char* comments)
 {
 	size_t new_size;

src/obiview.h

@@ -519,6 +519,39 @@ OBIDMS_column_p* obi_view_get_pointer_on_column_in_view(Obiview_p view, const ch
 int obi_view_create_column_alias(Obiview_p view, const char* current_name, const char* alias);
 
 
+/**
+ * @brief Returns the informations of a view with a human readable format (view name, date created, line count, column informations, comments).
+ *
+ * @warning The returned pointer has to be freed by the caller.
+ *
+ * @param column A pointer on a view.
+ * @param detailed Whether the informations should contain view comments.
+ *
+ * @returns A pointer on a character array where the formatted view informations are stored.
+ * @retval NULL if an error occurred.
+ *
+ * @since September 2020
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+char* obi_view_formatted_infos(Obiview_p view, bool detailed);
+
+
+/**
+ * @brief Returns the informations of a view with a human readable format on one line (view name, date created, line count).
+ *
+ * @warning The returned pointer has to be freed by the caller.
+ *
+ * @param column A pointer on a view.
+ *
+ * @returns A pointer on a character array where the formatted view informations are stored.
+ * @retval NULL if an error occurred.
+ *
+ * @since September 2020
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+char* obi_view_formatted_infos_one_line(Obiview_p view);
+
+
 /**
  * @brief Internal function writing new comments in a view file.
  *