New OBIDMS method to list the columns of an OBIDMS

python/obitools3/obidms/capidms.pxd

@@ -1,3 +1,4 @@
+
 cdef extern from *:
     ctypedef char* const_char_p "const char*"
 
@@ -14,7 +15,10 @@ cdef extern from "obidms.h" nogil:
     OBIDMS_p obi_open_dms(const_char_p dms_name)
     OBIDMS_p obi_dms(const_char_p dms_name)
     int obi_close_dms(OBIDMS_p dms)
-    int obi_list_columns(OBIDMS_p dms)
+
+from obitools3.obidms.obidmscolumn.capidmscolumn cimport *
+
 
 cdef class OBIDMS:
     cdef OBIDMS_p pointer
+    cdef str dms_name

python/obitools3/obidms/capidms.pyx

@@ -1,15 +1,34 @@
 #cython: language_level=3
 
+from pathlib import Path
+
 from .capidms cimport *
 
+
 cdef class OBIDMS :
     
     def __init__(self, dms_name) :
         dms_name_b = dms_name.encode(encoding='UTF-8')
+        self.dms_name = dms_name
         self.pointer = obi_dms(dms_name_b)
         
 #    def __del__(self) :
 #        obi_close_dms(self.pointer)
 
     def list(self):
-        obi_list_columns(self.pointer)
+        p = Path(self.dms_name+'.obidms')
+        #dms = {}
+        print("{:<25} {:<25} {:<25} {:<25}".format('-Column name-','-Data type-','-Latest version number-', '-Line count of latest version-'))
+        for entry in p.iterdir():
+            if entry.suffix == ".obicol":
+                column_name = entry.stem
+                column_name_b = column_name.encode('utf-8')
+                #dms[column_name] = {}
+                data_type = (name_data_type(obi_column_get_data_type_from_name(self.pointer, column_name_b))).decode('utf-8')
+                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))
+                

python/obitools3/obidms/obidmscolumn/capidmscolumn.pxd

@@ -35,6 +35,9 @@ cdef extern from "obidmscolumn.h" nogil:
     OBIType_t obi_column_get_data_type_from_name(OBIDMS_p dms, const char* column_name)
     OBIDMS_column_p obi_clone_column(OBIDMS_p dms, const char* column_name, obiversion_t version_number, bint clone_data)
     int obi_truncate_and_close_column(OBIDMS_column_p column)
+    obiversion_t obi_column_get_latest_version_from_name(OBIDMS_p dms, const char* column_name)
+    OBIType_t obi_column_get_data_type_from_name(OBIDMS_p dms, const char* column_name)
+    size_t obi_column_get_line_count_from_name(OBIDMS_p dms, const char* column_name)
 
 
 cdef class OBIDMS_column:

src/obidms.c

@@ -216,54 +216,6 @@ 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);
-  if (dir == NULL)
-  {
-	  obidebug(1, "\nError reading in the OBIDMS directory");
-	  return -1;
-  }
-
-  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

@@ -126,23 +126,6 @@ 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

@@ -1347,13 +1347,99 @@ OBIType_t obi_column_get_data_type_from_name(OBIDMS_p dms, const char* column_na
 }
 
 
+size_t obi_column_get_line_count_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;
+	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)
+	{
+		obi_set_errno(OBICOL_UNKNOWN_ERROR);
+		obidebug(1, "\nError mmapping the header of a column");
+		close(column_file_descriptor);
+		free(column_file_name);
+		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;
 }
 
 
-// to be rewritten in an optimized and safe way
+// 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)
 {
 	char* elements_names;

src/obidmscolumn.h

@@ -312,6 +312,20 @@ OBIType_t obi_column_get_data_type(OBIDMS_column_p column);
 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.
  *