Commit 38718320 by Celine Mercier

First version for the association of one column to another. Closes #55

parent 8ee85c30
......@@ -527,14 +527,16 @@ size_t obi_get_platform_header_size()
}
OBIDMS_column_p obi_create_column(OBIDMS_p dms,
const char* column_name,
OBIType_t data_type,
index_t nb_lines,
index_t nb_elements_per_line,
const char* elements_names,
const char* indexer_name,
const char* comments
OBIDMS_column_p obi_create_column(OBIDMS_p dms,
const char* column_name,
OBIType_t data_type,
index_t nb_lines,
index_t nb_elements_per_line,
const char* elements_names,
const char* indexer_name,
const char* associated_column_name,
obiversion_t associated_column_version,
const char* comments
)
{
OBIDMS_column_p new_column;
......@@ -750,6 +752,30 @@ OBIDMS_column_p obi_create_column(OBIDMS_p dms,
if (comments != NULL)
strncpy(header->comments, comments, COMMENTS_MAX_LENGTH);
// Store the associated column reference if needed // TODO discuss cases
if (data_type == OBI_QUAL)
{
if (associated_column_name == NULL)
{
obidebug(1, "\nError: The name of the associated column when creating a new column is NULL");
munmap(new_column->header, header_size);
close(column_file_descriptor);
free(new_column);
return NULL;
}
strcpy((header->associated_column).column_name, associated_column_name);
if (associated_column_version == -1)
{
obidebug(1, "\nError: The version of the associated column when creating a new column is not defined");
munmap(new_column->header, header_size);
close(column_file_descriptor);
free(new_column);
return NULL;
}
(header->associated_column).version = associated_column_version;
}
// If the data type is OBI_STR, OBI_SEQ or OBI_QUAL, the associated obi_indexer is opened or created
if ((returned_data_type == OBI_STR) || (returned_data_type == OBI_SEQ) || (returned_data_type == OBI_QUAL))
{
......@@ -964,6 +990,8 @@ OBIDMS_column_p obi_clone_column(OBIDMS_p dms,
nb_elements_per_line,
(column_to_clone->header)->elements_names,
(column_to_clone->header)->indexer_name,
((column_to_clone->header)->associated_column).column_name,
((column_to_clone->header)->associated_column).version,
(column_to_clone->header)->comments
);
......
......@@ -39,42 +39,55 @@
/**
* @brief Structure referencing a column by its name and its version.
*/
typedef struct Column_reference {
char column_name[OBIDMS_COLUMN_MAX_NAME+1]; /**< Name of the column.
*/
obiversion_t version; /**< Version of the column.
*/
} Column_reference_t, *Column_reference_p;
/**
* @brief OBIDMS column header structure.
*/
typedef struct OBIDMS_column_header {
size_t header_size; /**< Size of the header in bytes.
*/
size_t data_size; /**< Size of the data in bytes.
*/
index_t line_count; /**< Number of lines of data allocated.
*/
index_t lines_used; /**< Number of lines of data used.
*/
index_t nb_elements_per_line; /**< Number of elements per line.
*/
char elements_names[ELEMENTS_NAMES_MAX+1]; /**< Names of the line elements with ';' as separator
* (should be the column name if one element per line).
*/
OBIType_t returned_data_type; /**< Type of the data that is returned when getting an
* element from the column.
*/
OBIType_t stored_data_type; /**< Type of the data that is actually stored in the data
* part of the column.
*/
time_t creation_date; /**< Date of creation of the file.
*/
obiversion_t version; /**< Version of the column.
*/
obiversion_t cloned_from; /**< Version of the column from which this column
* was cloned from (-1 if it was not created by cloning
* another column).
*/
char name[OBIDMS_COLUMN_MAX_NAME+1]; /**< The column name as a NULL terminated string.
*/
char indexer_name[INDEXER_MAX_NAME+1]; /**< If there is one, the indexer name as a NULL terminated string.
*/
char comments[COMMENTS_MAX_LENGTH+1]; /**< Comments stored as a classical zero end C string.
*/
size_t header_size; /**< Size of the header in bytes.
*/
size_t data_size; /**< Size of the data in bytes.
*/
index_t line_count; /**< Number of lines of data allocated.
*/
index_t lines_used; /**< Number of lines of data used.
*/
index_t nb_elements_per_line; /**< Number of elements per line.
*/
char elements_names[ELEMENTS_NAMES_MAX+1]; /**< Names of the line elements with ';' as separator
* (should be the column name if one element per line).
*/
OBIType_t returned_data_type; /**< Type of the data that is returned when getting an
* element from the column.
*/
OBIType_t stored_data_type; /**< Type of the data that is actually stored in the data
* part of the column.
*/
time_t creation_date; /**< Date of creation of the file.
*/
obiversion_t version; /**< Version of the column.
*/
obiversion_t cloned_from; /**< Version of the column from which this column
* was cloned from (-1 if it was not created by cloning
* another column).
*/
char name[OBIDMS_COLUMN_MAX_NAME+1]; /**< The column name as a NULL terminated string.
*/
char indexer_name[INDEXER_MAX_NAME+1]; /**< If there is one, the indexer name as a NULL terminated string.
*/
Column_reference_t associated_column; /**< If there is one, the reference to the associated column.
*/
char comments[COMMENTS_MAX_LENGTH+1]; /**< Comments stored as a classical zero end C string.
*/
} OBIDMS_column_header_t, *OBIDMS_column_header_p;
......@@ -168,13 +181,15 @@ size_t obi_get_platform_header_size();
* @param nb_elements_per_line The number of elements per line. // TODO talk about default values
* @param elements_names The names of the elements with ';' as separator.
* @param indexer_name The name of the indexer if there is one associated with the column.
* @param associated_column_name The name of the associated column if there is one.
* @param associated_column_version The version of the associated column if there is one.
* @param comments Optional comments associated with the column.
*
* @returns A pointer on the newly created column structure.
* @retval NULL if an error occurred.
*
* @since May 2015
* @author Eric Coissac (eric.coissac@metabarcoding.org)
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
OBIDMS_column_p obi_create_column(OBIDMS_p dms,
const char* column_name,
......@@ -183,6 +198,8 @@ OBIDMS_column_p obi_create_column(OBIDMS_p dms,
index_t nb_elements_per_line,
const char* elements_names,
const char* indexer_name,
const char* associated_column_name,
obiversion_t associated_column_version,
const char* comments
);
......
......@@ -582,7 +582,11 @@ bool view_check_quality_matches_seq_column(Obiview_p view) // TODO Print error i
if (qual_column == NULL)
return false;
seq_column = obi_view_get_column(view, NUC_SEQUENCE_COLUMN); // TODO Get associated nuc column
seq_column = obi_view_get_column(view, ((qual_column->header)->associated_column).column_name);
//seq_column = obi_open_column(view->dms, ((qual_column->header)->associated_column).column_name, ((qual_column->header)->associated_column).version);
// TODO discuss the fact that it's opened outside of the context of the view or not
// TODO if outside of view, make function that opens a column from a column reference structure?
if (seq_column == NULL)
return false;
......@@ -608,6 +612,9 @@ bool view_check_quality_matches_seq_column(Obiview_p view) // TODO Print error i
return false;
}
}
//obi_close_column(seq_column);
return true;
}
......@@ -714,7 +721,7 @@ Obiview_p obi_new_view(OBIDMS_p dms, const char* view_name, Obiview_p view_to_cl
// If there is a new line selection, build it by combining it with the one from the view to clone if there is one
else if (line_selection != NULL)
{
view->line_selection = obi_create_column(view->dms, LINES_COLUMN_NAME, OBI_IDX, 0, 1, LINES_COLUMN_NAME, NULL, NULL);
view->line_selection = obi_create_column(view->dms, LINES_COLUMN_NAME, OBI_IDX, 0, 1, LINES_COLUMN_NAME, NULL, NULL, -1, NULL);
if ((view->line_selection) == NULL)
{
obidebug(1, "\nError creating a column corresponding to a line selection");
......@@ -836,7 +843,8 @@ Obiview_p obi_new_view_cloned_from_name(OBIDMS_p dms, const char* view_name, con
Obiview_p obi_new_view_nuc_seqs(OBIDMS_p dms, const char* view_name, Obiview_p view_to_clone, index_t* line_selection, const char* comments)
{
Obiview_p view;
Obiview_p view;
OBIDMS_column_p associated_nuc_column;
if (view_to_clone != NULL)
{ // Check that the view to clone is already a NUC_SEQS view (TODO discuss possibility of transforming type of a view)
......@@ -857,25 +865,26 @@ Obiview_p obi_new_view_nuc_seqs(OBIDMS_p dms, const char* view_name, Obiview_p v
if (view_to_clone == NULL)
{
// Adding sequence column
if (obi_view_add_column(view, NUC_SEQUENCE_COLUMN, -1, OBI_SEQ, 0, 1, NUC_SEQUENCE_COLUMN, "", "Nucleotide sequences", true) < 0)
if (obi_view_add_column(view, NUC_SEQUENCE_COLUMN, -1, OBI_SEQ, 0, 1, NUC_SEQUENCE_COLUMN, "", NULL, -1, "Nucleotide sequences", true) < 0)
{
obidebug(1, "Error adding an obligatory column in a nucleotide sequences view");
return NULL;
}
// Adding id column
if (obi_view_add_column(view, ID_COLUMN, -1, OBI_STR, 0, 1, ID_COLUMN, "", "Ids", true) < 0)
if (obi_view_add_column(view, ID_COLUMN, -1, OBI_STR, 0, 1, ID_COLUMN, "", NULL, -1, "Ids", true) < 0)
{
obidebug(1, "Error adding an obligatory column in a nucleotide sequences view");
return NULL;
}
// Adding definition column
if (obi_view_add_column(view, DEFINITION_COLUMN, -1, OBI_STR, 0, 1, DEFINITION_COLUMN, "", "Definitions", true) < 0)
if (obi_view_add_column(view, DEFINITION_COLUMN, -1, OBI_STR, 0, 1, DEFINITION_COLUMN, "", NULL, -1, "Definitions", true) < 0)
{
obidebug(1, "Error adding an obligatory column in a nucleotide sequences view");
return NULL;
}
// Adding quality column
if (obi_view_add_column(view, QUALITY_COLUMN, -1, OBI_QUAL, 0, 1, QUALITY_COLUMN, "", "Sequence qualities", true) < 0)
associated_nuc_column = obi_view_get_column(view, NUC_SEQUENCE_COLUMN);
if (obi_view_add_column(view, QUALITY_COLUMN, -1, OBI_QUAL, 0, 1, QUALITY_COLUMN, "", (associated_nuc_column->header)->name, (associated_nuc_column->header)->version, "Sequence qualities", true) < 0) // TODO discuss automatic association
{
obidebug(1, "Error adding an obligatory column in a nucleotide sequences view");
return NULL;
......@@ -1062,6 +1071,8 @@ int obi_view_add_column(Obiview_p view,
index_t nb_elements_per_line,
const char* elements_names,
const char* indexer_name,
const char* associated_column_name,
obiversion_t associated_column_version,
const char* comments,
bool create) // all infos for creation or open
{
......@@ -1131,7 +1142,7 @@ int obi_view_add_column(Obiview_p view,
// Open or create the column
if (create)
{ // Create column
column = obi_create_column(view->dms, column_name, data_type, nb_lines, nb_elements_per_line, elements_names, indexer_name, comments);
column = obi_create_column(view->dms, column_name, data_type, nb_lines, nb_elements_per_line, elements_names, indexer_name, associated_column_name, associated_column_version, comments);
}
else
{ // Open column
......@@ -1241,7 +1252,7 @@ int obi_select_line(Obiview_p view, index_t line_nb)
// If the column for line selection doesn't already exists, create it and store its informations
if ((view->new_line_selection) == NULL)
{
view->new_line_selection = obi_create_column(view->dms, LINES_COLUMN_NAME, OBI_IDX, 0, 1, LINES_COLUMN_NAME, NULL, NULL);
view->new_line_selection = obi_create_column(view->dms, LINES_COLUMN_NAME, OBI_IDX, 0, 1, LINES_COLUMN_NAME, NULL, NULL, -1, NULL);
if ((view->new_line_selection) == NULL)
{
obidebug(1, "\nError creating a column corresponding to a line selection");
......@@ -1276,7 +1287,7 @@ int obi_select_lines(Obiview_p view, index_t* line_nbs)
// If column for line selection doesn't already exists, create it and store its informations
if ((view->new_line_selection) == NULL)
{
view->new_line_selection = obi_create_column(view->dms, LINES_COLUMN_NAME, OBI_IDX, 0, 1, LINES_COLUMN_NAME, NULL, NULL);
view->new_line_selection = obi_create_column(view->dms, LINES_COLUMN_NAME, OBI_IDX, 0, 1, LINES_COLUMN_NAME, NULL, NULL, -1, NULL);
if ((view->new_line_selection) == NULL)
{
obidebug(1, "\nError creating a column corresponding to a line selection");
......
......@@ -55,17 +55,6 @@
/**
* @brief Structure referencing a column by its name and its version.
*/
typedef struct Column_reference {
char column_name[OBIDMS_COLUMN_MAX_NAME+1]; /**< Name of the column.
*/
obiversion_t version; /**< Version of the column.
*/
} Column_reference_t, *Column_reference_p;
/**
* @brief Structure for a closed view stored in the view file.
* Views are identified by their name.
* Once a view has been written in the view file, it can not be modified and can only be read.
......@@ -333,6 +322,8 @@ int obi_view_add_column(Obiview_p view,
index_t nb_elements_per_line,
const char* elements_names,
const char* indexer_name,
const char* associated_column_name,
obiversion_t associated_column_version,
const char* comments,
bool create);
......
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