New C functions to import a column and a view from a DMS to another DMS
This commit is contained in:
Celine Mercier
321
src/obidms.c
321
src/obidms.c
@ -19,12 +19,13 @@
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#include <sys/types.h>
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#include <dirent.h>
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#include <unistd.h>
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#include <libgen.h> /* <EC> : Addted the 28 july 2017 to include basename */
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#include <libgen.h> /* <EC> : Added July 28th 2017 to include basename */
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#include "obidms.h"
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#include "obierrno.h"
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#include "obidebug.h"
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#include "obidmscolumn.h"
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#include "obiview.h"
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#include "obiblob_indexer.h"
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#include "utils.h"
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#include "obilittlebigman.h"
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@ -770,3 +771,321 @@ DIR* opendir_in_dms(OBIDMS_p dms, const char* path_name)
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return directory;
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}
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// TODO move somewhere else maybe
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// TODO discuss arguments
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obiversion_t obi_import_column(const char* dms_path_1, const char* dms_path_2, const char* column_name, obiversion_t version_number)
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{
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OBIDMS_p dms_1;
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OBIDMS_p dms_2;
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OBIDMS_column_p column_1;
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OBIDMS_column_p column_2;
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OBIDMS_column_header_p header_1;
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OBIDMS_column_header_p header_2;
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int avl_exists;
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const char* avl_name;
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char* new_avl_name;
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obiversion_t new_version;
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int i;
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int avl_count;
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char* avl_name_1;
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char* avl_name_2;
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char* avl_file_path_1;
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char* avl_file_path_2;
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char* avl_data_file_path_1;
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char* avl_data_file_path_2;
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char* complete_avl_name;
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Obi_indexer_p avl_group;
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dms_1 = obi_open_dms(dms_path_1);
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if (dms_1 == NULL)
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{
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obidebug(1, "\nError opening a DMS to import a column from it");
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return -1;
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}
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dms_2 = obi_dms(dms_path_2);
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if (dms_2 == NULL)
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{
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obidebug(1, "\nError opening or creating a DMS to import a column into it");
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return -1;
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}
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column_1 = obi_open_column(dms_1, column_name, version_number);
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if (column_1 == NULL)
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{
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obidebug(1, "\nError opening a column to import in another DMS");
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return -1;
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}
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header_1 = column_1->header;
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// Check if associated indexer exists BEFORE creating the new column as that will automatically create it if it doesn't already exist
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avl_name = header_1->indexer_name;
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avl_exists = obi_indexer_exists(dms_2, avl_name);
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if (avl_exists == -1)
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{
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obidebug(1, "\nError checking if an indexer exists while importing a column");
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return -1;
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}
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if (avl_exists)
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// Use automatic name
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new_avl_name = NULL;
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else
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// Name can stay the same
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new_avl_name = header_1->indexer_name;
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// Create new column
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column_2 = obi_create_column(dms_2, column_name, header_1->returned_data_type, header_1->line_count,
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header_1->nb_elements_per_line, header_1->elements_names, true,
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new_avl_name, (header_1->associated_column).column_name, (header_1->associated_column).version,
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header_1->comments);
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if (column_2 == NULL)
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{
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obidebug(1, "\nError creating the new column while importing a column");
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return -1;
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}
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header_2 = column_2->header;
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// Get the new version to return
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new_version = header_2->version;
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// Copy lines_used informations
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header_2->lines_used = header_1->lines_used;
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// Copy data TODO check how much time and memory that costs, eventually use write() instead
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memcpy(column_2->data, column_1->data, header_1->data_size);
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// Copy the AVL files if there are some (overwriting the automatically created files)
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if ((header_1->returned_data_type == OBI_STR) || (header_1->returned_data_type == OBI_SEQ) || (header_1->returned_data_type == OBI_QUAL))
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{
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avl_name_1 = (char*) malloc((strlen(header_1->indexer_name) + 1) * sizeof(char));
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if (avl_name_1 == NULL)
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{
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obi_set_errno(OBI_MALLOC_ERROR);
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obidebug(1, "\nError allocating memory for an AVL name when importing a column");
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return -1;
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}
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strcpy(avl_name_1, header_1->indexer_name);
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avl_name_2 = (char*) malloc((strlen(header_2->indexer_name) + 1) * sizeof(char));
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if (avl_name_2 == NULL)
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{
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obi_set_errno(OBI_MALLOC_ERROR);
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obidebug(1, "\nError allocating memory for an AVL name when importing a column");
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return -1;
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}
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strcpy(avl_name_2, header_2->indexer_name);
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avl_count = (column_1->indexer->last_avl_idx) + 1;
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// Close column to manipulate AVL files safely (but not multithreading safe) (TODO not sure how important this is, can't find informations about conflicts when using write() on mmapped files)
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if (obi_close_column(column_1) < 0)
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{
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obidebug(1, "\nError closing an imported column");
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return -1;
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}
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if (obi_close_column(column_2) < 0)
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{
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obidebug(1, "\nError closing an imported column");
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return -1;
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}
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for (i=0; i < avl_count; i++)
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{
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avl_file_path_1 = obi_get_full_path_of_avl_file_name(dms_1, avl_name_1, i);
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if (avl_file_path_1 == NULL)
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{
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obidebug(1, "\nError getting an AVL file path while importing a column");
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return -1;
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}
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avl_data_file_path_1 = obi_get_full_path_of_avl_data_file_name(dms_1, avl_name_1, i);
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if (avl_data_file_path_1 == NULL)
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{
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obidebug(1, "\nError getting an AVL file path while importing a column");
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return -1;
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}
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avl_file_path_2 = obi_get_full_path_of_avl_file_name(dms_2, avl_name_2, i);
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if (avl_file_path_2 == NULL)
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{
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obidebug(1, "\nError getting an AVL file path while importing a column");
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return -1;
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}
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avl_data_file_path_2 = obi_get_full_path_of_avl_data_file_name(dms_2, avl_name_2, i);
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if (avl_data_file_path_2 == NULL)
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{
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obidebug(1, "\nError getting an AVL file path while importing a column");
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return -1;
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}
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// Copy AVL file
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if (copy_file(avl_file_path_1, avl_file_path_2) < 0)
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{
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obidebug(1, "\nError copying an AVL file while importing a column");
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return -1;
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}
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// Copy AVL data file
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if (copy_file(avl_data_file_path_1, avl_data_file_path_2) < 0)
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{
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obidebug(1, "\nError copying a data AVL file while importing a column");
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return -1;
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}
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free(avl_file_path_1);
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free(avl_file_path_2);
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free(avl_data_file_path_1);
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free(avl_data_file_path_2);
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}
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// Update AVL names in headers
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avl_group = obi_open_indexer(dms_2, avl_name_2);
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for (i=0; i < avl_count; i++)
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{
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complete_avl_name = obi_build_avl_name_with_idx(avl_name_2, i);
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strcpy((((avl_group->sub_avls)[i])->header)->avl_name, complete_avl_name);
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strcpy(((((avl_group->sub_avls)[i])->data)->header)->avl_name, complete_avl_name);
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free(complete_avl_name);
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}
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free(avl_name_1);
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free(avl_name_2);
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}
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else
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{
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if (obi_close_column(column_1) < 0)
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{
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obidebug(1, "\nError closing an imported column");
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return -1;
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}
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if (obi_close_column(column_2) < 0)
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{
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obidebug(1, "\nError closing an imported column");
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return -1;
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}
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}
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// Copy associated column (update version)
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//new_associated_col_version = import_column(dms_path_1, dms_path_2, header_1->associated_column_name, header_1->associated_column_version);
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// TODO no? because if iterating over all columns in a view etc.... iterate and change associated columns version refs afterwards?
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// Close the DMS
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obi_close_dms(dms_1);
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obi_close_dms(dms_2);
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return new_version;
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}
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// TODO move somewhere else maybe
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// TODO discuss arguments
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int obi_import_view(const char* dms_path_1, const char* dms_path_2, const char* view_name_1, const char* view_name_2)
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{
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OBIDMS_p dms_1;
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OBIDMS_p dms_2;
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Obiview_p view_1;
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Obiview_p view_2;
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obiversion_t new_version;
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int i;
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dms_1 = obi_open_dms(dms_path_1);
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if (dms_1 == NULL)
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{
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obidebug(1, "\nError opening a DMS to import a view from it");
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return -1;
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}
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dms_2 = obi_dms(dms_path_2);
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if (dms_2 == NULL)
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{
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obidebug(1, "\nError opening or creating a DMS to import a view into it");
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return -1;
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}
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// Open view to import
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view_1 = obi_open_view(dms_1, view_name_1);
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// Create new view
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if (strcmp((view_1->infos)->view_type, VIEW_TYPE_NUC_SEQS) == 0)
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view_2 = obi_new_view_nuc_seqs(dms_2, view_name_2, NULL, NULL, (view_1->infos)->comments, false);
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else // Non-typed view
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view_2 = obi_new_view(dms_2, view_name_2, NULL, NULL, (view_1->infos)->comments);
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// Import line count
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view_2->infos->line_count = view_1->infos->line_count;
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// Import the line selection column if there is one
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if (! view_1->infos->all_lines)
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{
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view_2->infos->all_lines = false;
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new_version = obi_import_column(dms_path_1, dms_path_2, ((view_1->infos)->line_selection).column_name, ((view_1->infos)->line_selection).version);
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if (new_version == -1)
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{
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obidebug(1, "\nError importing a line selection column while importing a view");
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return -1;
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}
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strcpy(((view_2->infos)->line_selection).column_name, ((view_1->infos)->line_selection).column_name);
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((view_2->infos)->line_selection).version = new_version;
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view_2->line_selection = obi_open_column(dms_2, ((view_2->infos)->line_selection).column_name, ((view_2->infos)->line_selection).version);
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if (view_2->line_selection == NULL)
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{
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obidebug(1, "\nError opening a line selection column while importing a view");
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return -1;
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}
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}
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// Import each column and update with the new version number
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for (i=0; i < (view_1->infos->column_count); i++)
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{
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new_version = obi_import_column(dms_path_1, dms_path_2, ((((view_1->infos)->column_references)[i]).column_refs).column_name, ((((view_1->infos)->column_references)[i]).column_refs).version);
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if (new_version == -1)
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{
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obidebug(1, "\nError importing a column while importing a view");
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return -1;
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}
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if (obi_view_add_column(view_2,
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((((view_1->infos)->column_references)[i]).column_refs).column_name,
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new_version,
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(((view_1->infos)->column_references)[i]).alias,
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0,
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0,
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0,
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NULL,
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NULL,
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NULL,
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-1,
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NULL,
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false) < 0)
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{
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obidebug(1, "\nError adding a column to a view while importing it");
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return -1;
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}
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}
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// Close the views
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if (obi_save_and_close_view(view_1) < 0)
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{
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obidebug(1, "\nError closing a view after importing from it");
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return -1;
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}
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if (obi_save_and_close_view(view_2) < 0)
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{
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obidebug(1, "\nError closing a view after importing it");
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return -1;
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}
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// Close the DMS
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obi_close_dms(dms_1);
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obi_close_dms(dms_2);
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return 0;
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}
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