C sources modified to add the handling of OBIDM columns with the type

OBI_INT, and the handling of multiple types in general

src/obidms.c

@@ -14,6 +14,10 @@
 
 #include "obidms.h"
 #include "obierrno.h"
+#include "obidebug.h"
+#include "obidmscolumn.h"
+
+#define DEBUG_LEVEL 0
 
 
 /**************************************************************************
@@ -148,6 +152,7 @@ OBIDMS_p obi_open_dms(const char* dms_name)
 	directory = opendir(directory_name);
 	if (directory == NULL)
 	{
+		obidebug(1, "Can't open DMS");
 		switch (errno)
 		{
 			case ENOENT:
@@ -206,6 +211,49 @@ OBIDMS_p obi_dms(const char* dms_name)
 }
 
 
+int obi_list_columns(OBIDMS_p dms)
+{
+  DIR           *d;
+  struct dirent *dir;
+  char*			dir_name;
+  char*			extension;
+  OBIType_t     data_type;
+  obiversion_t	latest_version;
+
+  d = dms->directory;
+
+  dir = readdir(d);
+
+  fprintf(stderr, "Column name\tData type\tLatest version");
+
+  while (dir != NULL)
+  {
+	  dir_name  = strdup(dir->d_name);
+	  if (dir_name == NULL)
+	  {
+		  obidebug(1, "\nError strdup-ing a directory name");
+		  return -1;
+	  }
+
+	  dir_name  = strtok(dir_name, ".");
+	  extension = strtok(NULL, ".");
+
+	  if ((extension != NULL) && (strcmp("obicol", extension) == 0))
+	  // Found a column directory
+	  {
+		  data_type = obi_column_get_data_type_from_name(dms, dir_name);
+		  latest_version = obi_column_get_latest_version_from_name(dms, dir_name);
+		  fprintf(stderr, "\n%s\t%d\t%d", dir_name, data_type, latest_version);
+	  }
+	  dir = readdir(d);
+  }
+
+  rewinddir(d);
+
+  return(0);
+}
+
+
 int obi_close_dms(OBIDMS_p dms)
 {
 	if (dms != NULL)

src/obidms.h

@@ -126,6 +126,23 @@ OBIDMS_p obi_open_dms(const char *dms_name);
 OBIDMS_p obi_dms(const char *dms_name);
 
 
+/**
+ * @brief Lists all the column directories in the OBIDMS, their data type and
+ * their latest version.
+ *
+ * @param dms a pointer as returned by obi_create_dms() or obi_open_dms().
+ *
+ * @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_list_columns(OBIDMS_p dms);
+
+
 /**
  * @brief Closes an opened OBITools Data Management instance (OBIDMS).
  *

src/obidmscolumn.c

@@ -3,7 +3,7 @@
  ****************************************************************************/
 
 /**
- * @file OBIDMS_column.h
+ * @file obidmscolumn.c
  * @author Celine Mercier
  * @date 22 May 2015
  * @brief Functions for the shared elements of all the OBIColumn structures.
@@ -12,6 +12,7 @@
 
 #include <stdlib.h>
 #include <stdio.h>
+#include <string.h>
 #include <sys/types.h>
 #include <dirent.h>
 #include <unistd.h>
@@ -27,6 +28,11 @@
 #include "obidebug.h"
 #include "obilittlebigman.h"
 
+#include "obidmscolumn_int.h"
+
+
+#define DEBUG_LEVEL 0
+
 
 /**************************************************************************
  *
@@ -115,13 +121,28 @@ static obiversion_t obi_get_new_version_number(OBIDMS_column_directory_p column_
 static int 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.
+ *
+ * @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
+ *
+ * @since July 2015
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+int obi_column_set_elements_names(OBIDMS_column_p column, const char* elements_names);
+
+
 /************************************************************************
  *
  * D E F I N I T I O N   O F   T H E   P R I V A T E   F U N C T I O N S
  *
  ************************************************************************/
 
-#define DEBUG_LEVEL 0
 
 static char *build_column_file_name(const char *column_name, obiversion_t version_number)
 {
@@ -423,6 +444,16 @@ static int create_version_file(OBIDMS_column_directory_p column_directory)
 }
 
 
+int obi_column_set_elements_names(OBIDMS_column_p column, const char* elements_names)
+{
+	(column->header)->elements_names = malloc(strlen(elements_names)*sizeof(char) + 1);
+	if ((column->header)->elements_names == NULL)
+		return -1;
+	strcpy((column->header)->elements_names, elements_names);
+	return 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
@@ -521,6 +552,32 @@ obiversion_t obi_get_latest_version_number(OBIDMS_column_directory_p column_dire
 }
 
 
+obiversion_t obi_column_get_latest_version_from_name(OBIDMS_p dms, const char* column_name)
+{
+	OBIDMS_column_directory_p	column_directory;
+	obiversion_t	   			latest_version;
+
+	// Get the column directory structure associated to the column
+	column_directory = obi_open_column_directory(dms, column_name);
+	if (column_directory == NULL)
+	{
+		obidebug(1, "\nProblem opening column directory");
+		return -1;
+	}
+
+	// Get the latest version number
+	latest_version = obi_get_latest_version_number(column_directory);
+	if (latest_version < 0)
+	{
+		obidebug(1, "\nProblem getting the latest version number");
+		obi_close_column_directory(column_directory);
+		return -1;
+	}
+
+	return latest_version;
+}
+
+
 size_t obi_get_platform_header_size()
 {
 	return getpagesize() * 1;
@@ -547,6 +604,8 @@ OBIDMS_column_p obi_create_column(OBIDMS_p dms,
 
 	new_column = NULL;
 
+	// TODO check that informations are not NULL/invalid
+
 	// Get the column directory structure associated to the column
 	column_directory = obi_column_directory(dms, column_name);
 	if (column_directory == NULL)
@@ -673,8 +732,7 @@ OBIDMS_column_p obi_create_column(OBIDMS_p dms,
 	header->version       		 = version_number;
 	header->comments[0]   		 = 0x0;
 
-	header->elements_names = malloc(strlen(elements_names)*sizeof(char) + 1);
-	strcpy(header->elements_names, elements_names);
+	obi_column_set_elements_names(new_column, elements_names);
 
 	strncpy(header->name, column_name, OBIDMS_MAX_COLNAME);
 
@@ -683,3 +741,316 @@ OBIDMS_column_p obi_create_column(OBIDMS_p dms,
 
 	return new_column;
 }
+
+
+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;
+	char* 						column_file_name;
+	int 						column_file_descriptor;
+	int							column_dir_file_descriptor;
+	size_t 						header_size;
+	size_t 						data_size;
+
+	column = NULL;
+
+	// Get the column directory structure associated to the column
+	column_directory = obi_open_column_directory(dms, column_name);
+	if (column_directory == NULL)
+	{
+		obidebug(1, "\nProblem opening column directory");
+		return NULL;
+	}
+
+	// Get the file descriptor associated to the column directory
+	column_dir_file_descriptor = dirfd(column_directory->directory);
+	if (column_dir_file_descriptor < 0)
+	{
+		obidebug(1, "\nProblem opening column directory");
+		obi_set_errno(OBICOLDIR_UNKNOWN_ERROR);
+		obi_close_column_directory(column_directory);
+		return NULL;
+	}
+
+	// Calculate the header size
+	header_size = obi_get_platform_header_size();
+
+	// Get the latest version number if it has the value -1 (not given by user)
+	if (version_number == -1)
+	{
+		version_number = obi_get_latest_version_number(column_directory);
+		if (version_number < 0)
+		{
+			obidebug(1, "\nProblem getting the latest version number");
+			obi_close_column_directory(column_directory);
+			close(column_dir_file_descriptor);
+			return NULL;
+		}
+	}
+
+	// Get the column file name
+	column_file_name = build_column_file_name(column_name, version_number);
+	if (column_file_name == NULL)
+	{
+		obidebug(1, "Problem building column file name");
+		obi_close_column_directory(column_directory);
+		close(column_dir_file_descriptor);
+		return NULL;
+	}
+
+	// Open the column file, ALWAYS READ-ONLY
+	column_file_descriptor = openat(column_dir_file_descriptor, column_file_name, O_RDONLY);
+	if (column_file_descriptor < 0)
+	{
+		obidebug(1, "\nCan't open column file");
+		obi_set_errno(OBICOL_UNKNOWN_ERROR);
+		obi_close_column_directory(column_directory);
+		close(column_dir_file_descriptor);
+		free(column_file_name);
+		return NULL;
+	}
+
+	// Allocate the memory for the column structure
+	column = (OBIDMS_column_p) malloc(sizeof(OBIDMS_column_t));
+	if (column == NULL)
+	{
+		obi_set_errno(OBICOL_UNKNOWN_ERROR);
+		obi_close_column_directory(column_directory);
+		close(column_dir_file_descriptor);
+		close(column_file_descriptor);
+		free(column_file_name);
+		return NULL;
+	}
+
+	// Fill the column structure
+	column->dms    			 = dms;
+	column->column_directory = column_directory;
+	column->header 			 = mmap(NULL,
+			                  	  	header_size,
+			                  	  	PROT_READ,
+			                  	  	MAP_SHARED,
+			                  	  	column_file_descriptor,
+			                  	  	0
+			                 	 	);
+
+	if (column->header == MAP_FAILED)
+	{
+		obi_set_errno(OBICOL_UNKNOWN_ERROR);
+		obi_close_column_directory(column_directory);
+		close(column_dir_file_descriptor);
+		close(column_file_descriptor);
+		free(column_file_name);
+		free(column);
+		return NULL;
+	}
+
+	// Check endianness?
+
+	// Compute data size from the informations in the header
+	data_size = ((column->header)->line_count) * sizeof((column->header)->data_type);	// TODO line_count for tests, change to lines_used later
+
+	column->data   			 = mmap(NULL,
+			                 	 	data_size,
+			                 	 	PROT_READ,
+			                 	 	MAP_SHARED,
+			                 	 	column_file_descriptor,
+			                 	 	header_size
+			                	    );
+
+	if (column->data == MAP_FAILED)
+	{
+		munmap(column->header, header_size);
+		obi_set_errno(OBICOL_UNKNOWN_ERROR);
+		obi_close_column_directory(column_directory);
+		close(column_dir_file_descriptor);
+		close(column_file_descriptor);
+		free(column_file_name);
+		free(column);
+		return NULL;
+	}
+
+	column->writable  = false;
+
+	free(column_file_name);
+	close(column_file_descriptor);
+
+	return column;
+}
+
+
+int obi_close_column(OBIDMS_column_p column)
+{
+	//munmap?
+	free(column);
+	return 0;
+}
+
+
+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;
+}
+
+
+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 		header;
+	OBIDMS_column_directory_p	column_directory;
+	char* 						column_file_name;
+	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
+	column_directory = obi_open_column_directory(dms, column_name);
+	if (column_directory == NULL)
+	{
+		obidebug(1, "\nProblem opening column directory");
+		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)
+	{
+		obidebug(1, "\nProblem opening column directory");
+		obi_set_errno(OBICOLDIR_UNKNOWN_ERROR);
+		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, "\nProblem getting the latest version number");
+		obi_close_column_directory(column_directory);
+		close(column_dir_file_descriptor);
+		return -1;
+	}
+
+	// Get the column file name
+	column_file_name = build_column_file_name(column_name, version_number);
+	if (column_file_name == NULL)
+	{
+		obidebug(1, "Problem building column file name");
+		obi_close_column_directory(column_directory);
+		close(column_dir_file_descriptor);
+		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, "\nCan't open column file");
+		obi_set_errno(OBICOL_UNKNOWN_ERROR);
+		obi_close_column_directory(column_directory);
+		close(column_dir_file_descriptor);
+		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)
+	{
+		obi_set_errno(OBICOL_UNKNOWN_ERROR);
+		obi_close_column_directory(column_directory);
+		close(column_dir_file_descriptor);
+		close(column_file_descriptor);
+		free(column_file_name);
+		free(header);
+		return -1;
+	}
+
+	// Check endianness?
+
+	data_type = header->data_type;
+
+	free(column_file_name);
+	close(column_file_descriptor);
+	munmap(header, header_size);
+	return data_type;
+}
+
+
+const char* obi_column_get_elements_names(OBIDMS_column_p column)
+{
+	return (column->header)->elements_names;
+}
+
+
+// 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)
+{
+	char* elements_names;
+	char* name;
+	size_t element_index;
+
+	elements_names = strdup((column->header)->elements_names);
+	if (elements_names == NULL)
+	{
+		obidebug(1, "\nError strdup-ing the elements names");
+		return -1;
+	}
+
+	element_index = 0;
+
+	name = strtok (elements_names, ";");	// not thread safe, see strtok_r maybe
+	if (strcmp(element_name, name) == 0)
+	{
+		free(elements_names);
+		return element_index;
+	}
+	element_index++;
+
+	while (name != NULL)
+	{
+		name = strtok (NULL, ";");			// not thread safe, see strtok_r maybe
+		if (strcmp(element_name, name) == 0)
+		{
+			free(elements_names);
+			return element_index;
+		}
+		element_index++;
+	}
+
+	obidebug(1, "\nCan't find element name");
+	free(elements_names);
+	return -1;
+}
+
+
+size_t obi_column_get_nb_elements_per_line(OBIDMS_column_p column)
+{
+	return (column->header)->nb_elements_per_line;
+}
+
+
+

src/obidmscolumn.h

@@ -86,6 +86,28 @@ typedef struct OBIDMS_column {
 } OBIDMS_column_t, *OBIDMS_column_p;
 
 
+/**
+ * @brief Returns the latest version of a column in a column directory
+ *
+ * @param column_directory
+ *
+ * @return the latest version number kept in the version file
+ * @return -1 if an error occurred
+ */
+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
+ *
+ * @param column_name
+ *
+ * @return the latest version number kept in the version file
+ * @return -1 if an error occurred
+ */
+obiversion_t obi_column_get_latest_version_from_name(OBIDMS_p dms, const char* column_name);
+
+
 /**
  * @brief Returns the header size in bytes of a column on this platform.
  *
@@ -103,7 +125,7 @@ size_t obi_get_platform_header_size();
 /**
  * @brief Creates a column.
  *
- * @param dms a pointer on an OBIDMS 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_elements the number of elements to be stored
@@ -120,15 +142,123 @@ OBIDMS_column_p obi_create_column(OBIDMS_p dms,
 
 
 /**
- * @brief Returns the latest column version in the `dms` database
+ * @brief Opens a column in read-only mode.
  *
- * @param dms a pointer as returned by obi_create_dms() or obi_open_dms()
+ * @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
+ *
+ * @return a pointer to the opened column
  *
- * @return the bigger version number used for this column
- * @return -1 if the column does not exist
+ * @since July 2015
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-obiversion_t obi_get_latest_version_number(OBIDMS_column_directory_p column_directory);
+OBIDMS_column_p obi_open_column(OBIDMS_p dms, const char* column_name, obiversion_t version_number);
+
+
+/**
+ * @brief Closes a column.
+ *
+ * @param column a pointer on an OBIDMS column
+ *
+ * @return 0 if the operation was successfully completed
+ * @return -1 if an error occurred
+ *
+ * @since July 2015
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+int obi_close_column(OBIDMS_column_p column);
+
+
+/**
+ * @brief Sets the 'writable' header attribute of an OBIDMS column to False.
+ *
+ * @param column a pointer on an OBIDMS column
+ *
+ * @since July 2015
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+void obi_column_make_unwritable(OBIDMS_column_p column);
+
+
+/**
+ * @brief Recovers the line count of an OBIDMS column.
+ *
+ * @param column a pointer on an OBIDMS column
+ *
+ * @return the line count of the column
+ *
+ * @since July 2015
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+size_t obi_column_get_line_count(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);
+