608 lines
23 KiB
C
Executable File
608 lines
23 KiB
C
Executable File
/****************************************************************************
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* OBIDMS columns header file *
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****************************************************************************/
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/**
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* @file obidmscolumn.h
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* @author Celine Mercier (celine.mercier@metabarcoding.org)
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* @date 12 May 2015
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* @brief Header file for the functions and structures shared by all the OBIDMS columns.
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*/
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#ifndef OBIDMSCOLUMN_H_
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#define OBIDMSCOLUMN_H_
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#include <stdio.h>
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#include <sys/types.h>
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#include <unistd.h>
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#include <stdbool.h>
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#include <time.h>
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#include <stdbool.h>
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#include "obidms.h"
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#include "obitypes.h"
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#include "obierrno.h"
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#include "obilittlebigman.h"
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#include "obidmscolumndir.h"
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#include "obiblob_indexer.h"
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// TODO delete useless ones, add default nb?
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#define ELEMENTS_NAMES_MAX (1000000) /**< The maximum length of the list of elements names. // TODO Discuss
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*/
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#define NB_ELTS_MAX_IF_DEFAULT_NAME (1000000) /**< The maximum number of elements per line if the default element names
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* are used ("0\01\02\0...\0n"), considering ELEMENTS_NAMES_MAX. // TODO not up to date
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*/
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#define COLUMN_GROWTH_FACTOR (2) /**< The growth factor when a column is enlarged.
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*/
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#define MAXIMUM_LINE_COUNT (1000000000) /**< The maximum line count for the data of a column (1E9). //TODO
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*/
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#define COMMENTS_MAX_LENGTH (4096) /**< The maximum length for comments.
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*/
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#define FORMATTED_ELT_NAMES_SEPARATOR '\0' /**< The separator between elements names once formatted to be stored in columns.
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*/
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#define NOT_FORMATTED_ELT_NAMES_SEPARATOR ';' /**< The separator between elements names before being formatted to be stored in columns (e.g. as sent by the upper layer).
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*/
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/**
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* @brief Structure referencing a column by its name and its version.
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*/
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typedef struct Column_reference {
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char column_name[OBIDMS_COLUMN_MAX_NAME+1]; /**< Name of the column.
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*/
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obiversion_t version; /**< Version of the column.
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*/
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} Column_reference_t, *Column_reference_p;
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/**
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* @brief OBIDMS column header structure.
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*/
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typedef struct OBIDMS_column_header {
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size_t header_size; /**< Size of the header in bytes.
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*/
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size_t data_size; /**< Size of the data in bytes.
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*/
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index_t line_count; /**< Number of lines of data allocated.
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*/
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index_t lines_used; /**< Number of lines of data used (the highest index where data has been entered + 1).
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*/
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index_t nb_elements_per_line; /**< Number of elements per line.
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*/
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OBIType_t returned_data_type; /**< Type of the data that is returned when getting an
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* element from the column.
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*/
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OBIType_t stored_data_type; /**< Type of the data that is actually stored in the data
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* part of the column.
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*/
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bool dict_column; /**< Whether the column contains dictionary-like values.
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*/
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bool tuples; /**< A boolean indicating whether the column contains indices referring to indexed tuples.
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*/
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bool to_eval; /**< A boolean indicating whether the column contains expressions that should be evaluated
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* (typically OBI_STR columns containing character strings to be evaluated by Python).
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*/
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time_t creation_date; /**< Date of creation of the file.
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*/
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obiversion_t version; /**< Version of the column.
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*/
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obiversion_t cloned_from; /**< Version of the column from which this column
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* was cloned from (-1 if it was not created by cloning
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* another column).
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*/
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char name[OBIDMS_COLUMN_MAX_NAME+1]; /**< The column name as a NULL terminated string.
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*/
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char indexer_name[INDEXER_MAX_NAME+1]; /**< If there is one, the indexer name as a NULL terminated string.
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*/
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Column_reference_t associated_column; /**< If there is one, the reference to the associated column.
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*/
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bool finished; /**< A boolean indicating whether the column was properly closed by the view that created it.
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*/
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char comments[COMMENTS_MAX_LENGTH+1]; /**< Comments stored as a classical zero end C string.
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*/
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int64_t elements_names_length; /**< Length of the character array where the elements names are stored.
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*/
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char* elements_names; /**< Pointer in mem_arnea on the names of the line elements with '\0' as separator
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* and '\0\0' as terminal flag.
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* (default are the indices: "0\01\02\0...\0n\0\0").
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*/
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int64_t* elements_names_idx; /**< Pointer in mem_arena on the index for the start of each element name in elements_names.
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*/
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int64_t* sorted_elements_idx; /**< Index for the sorted element names in elements_names_idx.
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*/
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byte_t mem_arena[]; /**< Memory array where the elements names, the elements names index and the sorted elements index are stored.
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*/
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} OBIDMS_column_header_t, *OBIDMS_column_header_p;
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/**
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* @brief OBIDMS column structure.
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*
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* A data structure of this type is returned by the functions
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* creating, opening or cloning an OBIDMS column.
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*/
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typedef struct OBIDMS_column {
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OBIDMS_p dms; /**< A pointer to the OBIDMS structure to
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* which the column belongs.
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*/
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OBIDMS_column_directory_p column_directory; /**< A pointer to the OBIDMS column directory
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* structure to which the column belongs.
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*/
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OBIDMS_column_header_p header; /**< A pointer to the header of the column.
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*/
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Obi_indexer_p indexer; /**< A pointer to the blob indexer associated
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* with the column if there is one.
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*/
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void* data; /**< A `void` pointer to the beginning of the data.
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*
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* @warning Never use this member directly outside
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* of the code of the low level functions
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* of the OBIDMS.
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*/
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bool writable; /**< Indicates if the column is writable or not.
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* - `true` the column is writable
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* - `false` the column is read-only
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*
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* A column is writable only by its creator
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* until it closes it.
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*/
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size_t counter; /**< Indicates by how many threads/programs
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* (TODO) the column is used.
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*/
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} OBIDMS_column_t, *OBIDMS_column_p;
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/**
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* @brief Function building the full path to the version file of a column in an OBIDMS.
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*
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* @warning The returned pointer has to be freed by the caller.
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*
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* @param dms A pointer on the OBIDMS.
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* @param column_name The name of the OBIDMS column file.
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*
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* @returns A pointer to the version file name.
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* @retval NULL if an error occurred.
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*
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* @since October 2017
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* @author Celine Mercier (celine.mercier@metabarcoding.org)
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*/
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char* obi_version_file_full_path(OBIDMS_p dms, const char* column_name);
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/**
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* @brief Function building the full path to the version file of a column in an OBIDMS.
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*
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* @warning The returned pointer has to be freed by the caller.
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*
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* @param dms A pointer on the OBIDMS.
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* @param column_name The name of the OBIDMS column file.
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* @param version_number The version number of the OBIDMS column file.
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*
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* @returns A pointer to the version file name.
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* @retval NULL if an error occurred.
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*
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* @since October 2017
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* @author Celine Mercier (celine.mercier@metabarcoding.org)
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*/
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char* obi_column_full_path(OBIDMS_p dms, const char* column_name, obiversion_t version_number);
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/**
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* @brief Returns the latest version number of a column in a column directory using the column directory structure.
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*
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* @param column_directory A pointer as returned by obi_create_column_directory() or obi_open_column_directory().
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*
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* @returns The latest version number kept in the version file.
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* @retval -1 if an error occurred.
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*
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* @since May 2015
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* @author Eric Coissac (eric.coissac@metabarcoding.org)
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*/
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obiversion_t obi_get_latest_version_number(OBIDMS_column_directory_p column_directory);
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/**
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* @brief Returns the latest version of a column in a column directory using the column name.
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*
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* @param dms A pointer on an OBIDMS.
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* @param column_name The column name.
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*
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* @returns The latest version number kept in the version file.
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* @retval -1 if an error occurred.
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*
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* @since May 2015
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* @author Eric Coissac (eric.coissac@metabarcoding.org)
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*/
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obiversion_t obi_column_get_latest_version_from_name(OBIDMS_p dms, const char* column_name);
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/**
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* @brief Returns the header size in bytes of a column.
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*
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* The header size is rounded to a multiple of the memory page size.
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*
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* @param nb_elements_per_line The number of elements per line.
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* @param elts_names_length The length of elements_names including the two terminal '\0's.
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*
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* @returns The header size in bytes.
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*
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* @since May 2015
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* @author Celine Mercier (celine.mercier@metabarcoding.org)
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*/
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size_t obi_calculate_header_size(index_t nb_elements_per_line, int64_t elts_names_length);
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/**
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* @brief Creates a column.
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*
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* The minimum data size allocated is one memory page, and the data is initialized to the NA value of the OBIType.
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* If there is an indexer associated with the column, it is opened or created if it does not already exist.
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*
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* @warning If there is one element per line, elements_names should be equal to column_name. // TODO change this condition?
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*
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* @param dms A pointer on an OBIDMS.
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* @param column_name The name of the new column.
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* @param data_type The OBIType code of the data.
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* @param nb_lines The number of lines to be stored (can be 0 if not known).
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* @param nb_elements_per_line The number of elements per line.
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* @param elements_names The names of the elements with ';' as separator (no terminal ';'),
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* NULL or "" if the default names are to be used ("0\01\02\0...\0n").
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* @param elt_names_formatted Whether the separator for the elements names is ';' (false), or '\0' (true, as formatted by format_elements_names()).
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* @param dict_column A boolean indicating whether the column should contain dictionary-like values.
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* @param tuples A boolean indicating whether the column should contain indices referring to indexed tuples.
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* @param to_eval A boolean indicating whether the column contains expressions that should be evaluated
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* (typically OBI_STR columns containing character strings to be evaluated by Python).
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* @param indexer_name The name of the indexer if there is one associated with the column.
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* If NULL or "", the indexer name is set as the column name.
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* @param associated_column_name The name of the associated column if there is one (otherwise NULL or "").
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* @param associated_column_version The version of the associated column if there is one (otherwise -1).
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* @param comments Optional comments associated with the column in JSON format (NULL, "" or "{}" if no comments associated).
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*
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* @returns A pointer on the newly created column structure.
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* @retval NULL if an error occurred.
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*
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* @since May 2015
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* @author Celine Mercier (celine.mercier@metabarcoding.org)
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*/
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OBIDMS_column_p obi_create_column(OBIDMS_p dms,
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const char* column_name,
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OBIType_t data_type,
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index_t nb_lines,
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index_t nb_elements_per_line,
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char* elements_names,
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bool elt_names_formatted,
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bool dict_column,
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bool tuples,
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bool to_eval,
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const char* indexer_name,
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const char* associated_column_name,
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obiversion_t associated_column_version,
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const char* comments
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);
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/**
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* @brief Opens a column in read-only mode.
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*
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* @param dms A pointer on an OBIDMS.
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* @param column_name The name of the column.
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* @param version_number The version of the column that should be opened (if -1, the latest version is retrieved).
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*
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* @returns A pointer on the opened column structure.
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* @retval NULL if an error occurred.
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*
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* @since July 2015
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* @author Celine Mercier (celine.mercier@metabarcoding.org)
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*/
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OBIDMS_column_p obi_open_column(OBIDMS_p dms, const char* column_name, obiversion_t version_number);
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/**
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* @brief Clones a column, and returns a pointer to the writable new column.
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*
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* @param dms A pointer on an OBIDMS.
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* @param column_name The name of the column to clone.
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* @param version_number The version of the column that should be cloned (if -1, the latest version is retrieved).
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* @param clone_data Whether the data should be copied or not.
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*
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* @returns A pointer to the created column.
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* @retval NULL if an error occurred.
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*
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* @since August 2015
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* @author Celine Mercier (celine.mercier@metabarcoding.org)
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*/
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OBIDMS_column_p obi_clone_column(OBIDMS_p dms, OBIDMS_column_p line_selection, const char* column_name, obiversion_t version_number, bool clone_data);
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/**
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* @brief Clones a column indexer to have it writable.
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*
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* @param column A pointer on an OBIDMS column.
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*
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* @retval 0 if the operation was successfully completed.
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* @retval -1 if an error occurred.
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*
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* @since November 2016
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* @author Celine Mercier (celine.mercier@metabarcoding.org)
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*/
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int obi_clone_column_indexer(OBIDMS_column_p column);
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/**
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* @brief Truncates a column to the number of lines used if it is not read-only and closes it.
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*
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* @warning This function does not flag the column as finished, only finish_view() in the obiview source file does that.
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*
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* @param column A pointer on an OBIDMS column.
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*
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* @retval 0 if the operation was successfully completed.
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* @retval -1 if an error occurred.
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*
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* @since July 2015
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* @author Celine Mercier (celine.mercier@metabarcoding.org)
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*/
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int obi_close_column(OBIDMS_column_p column);
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/**
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* @brief Truncates a column file to the number of lines used rounded to the nearest
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* greater multiple of the page size.
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*
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* @param column A pointer on an OBIDMS column.
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*
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* @retval 0 if the operation was successfully completed.
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* @retval -1 if an error occurred.
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*
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* @since August 2015
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* @author Celine Mercier (celine.mercier@metabarcoding.org)
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*/
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int obi_truncate_column(OBIDMS_column_p column);
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/**
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* @brief Enlarges a column file.
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*
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* @param column A pointer on an OBIDMS column.
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*
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* @retval 0 if the operation was successfully completed.
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* @retval -1 if an error occurred.
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*
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* @since August 2015
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* @author Celine Mercier (celine.mercier@metabarcoding.org)
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*/
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int obi_enlarge_column(OBIDMS_column_p column);
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/**
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* @brief Writes comments to a column file.
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*
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* @warning This overwrites any other previous comments.
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*
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* @param column A pointer on an OBIDMS column.
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* @param comments A character string containing the comments.
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*
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* @retval 0 if the operation was successfully completed.
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* @retval -1 if an error occurred.
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*
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* @since August 2018
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* @author Celine Mercier (celine.mercier@metabarcoding.org)
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*/
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int obi_column_write_comments(OBIDMS_column_p column, const char* comments);
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/**
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* @brief Adds comments to a column file.
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*
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* This reads the comments in the JSON format and adds the key value pair.
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* If the key already exists, the value format is turned to array and the new value is appended
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* if it is not already in the array.
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*
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* @param column A pointer on an OBIDMS column.
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* @param key The key.
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* @param value The value associated with the key.
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*
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* @retval 0 if the operation was successfully completed.
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* @retval -1 if an error occurred.
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*
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* @since August 2018
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* @author Celine Mercier (celine.mercier@metabarcoding.org)
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*/
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int obi_column_add_comment(OBIDMS_column_p column, const char* key, const char* value);
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/*
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* @brief Sets the data in a column to the specified value.
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*
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* @warning The specified value should be the atomic value effectively stored in the column (i.e. it can not be a character string for example).
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*
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* @param column A pointer on an OBIDMS column.
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* @param start The first line number of the block that should be set.
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* @param nb_lines The number of lines that should be set.
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* @param value_p A pointer on the value to which the column should be set.
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*
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* @since May 2018
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* @author Celine Mercier (celine.mercier@metabarcoding.org)
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*/
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void obi_set_column_to_value(OBIDMS_column_p column,
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index_t first_line_nb,
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index_t nb_lines,
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void* value_p);
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/*
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* @brief Sets the data in a column to the NA value of the data OBIType.
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*
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* @param column A pointer on an OBIDMS column.
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* @param start The first line number of the block that should be set.
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* @param nb_lines The number of lines that should be set.
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*
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* @since August 2015
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* @author Celine Mercier (celine.mercier@metabarcoding.org)
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*/
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void obi_ini_to_NA_values(OBIDMS_column_p column, index_t first_line_nb, index_t nb_lines); // TODO make private?
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/**
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* @brief Recovers the header of an OBIDMS column from the column name.
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*
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* @warning The header structure has to be munmapped by the caller.
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*
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* @param dms A pointer on an OBIDMS.
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* @param column_name The name of an OBIDMS column.
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* @param version_number The version of the column from which the header should be
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* retrieved (-1: latest version).
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*
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* @returns A pointer on the mmapped header of the column.
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* @retval NULL if an error occurred.
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*
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* @since October 2015
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* @author Celine Mercier (celine.mercier@metabarcoding.org)
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*/
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OBIDMS_column_header_p obi_column_get_header_from_name(OBIDMS_p dms, const char* column_name, obiversion_t version_number);
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/**
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* @brief Munmap a mmapped header as returned by obi_column_get_header_from_name().
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*
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* @param header A pointer on the mmapped header structure.
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*
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* @retval 0 if the operation was successfully completed.
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* @retval -1 if an error occurred.
|
|
*
|
|
* @since October 2015
|
|
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
|
*/
|
|
int obi_close_header(OBIDMS_column_header_p header);
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|
|
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/**
|
|
* @brief Recovers the index of an element in an OBIDMS column from the element's name.
|
|
*
|
|
* @param column A pointer on an OBIDMS column.
|
|
* @param element_name The name of the element.
|
|
*
|
|
* @returns The index of the element in a line of the column.
|
|
* @retval OBIIdx_NA if an error occurred.
|
|
*
|
|
* @since July 2015
|
|
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
|
*/
|
|
index_t obi_column_get_element_index_from_name(OBIDMS_column_p column, const char* element_name);
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/**
|
|
* @brief Recovers the elements names of the lines of a column, with ';' as separator (i.e. "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 January 2017
|
|
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
|
*/
|
|
char* obi_get_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);
|
|
|
|
|
|
/**
|
|
* @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);
|
|
|
|
|
|
/**
|
|
* @brief Prepares a column to set a value.
|
|
*
|
|
* @param column A pointer on an OBIDMS column.
|
|
* @param line_nb The number of the line at which the value will be set.
|
|
*
|
|
* @retval 0 if the operation was successfully completed.
|
|
* @retval -1 if an error occurred.
|
|
*
|
|
* @since April 2016
|
|
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
|
*/
|
|
int obi_column_prepare_to_set_value(OBIDMS_column_p column, index_t line_nb, index_t elt_idx);
|
|
|
|
|
|
/**
|
|
* @brief Prepares a column to recover a value.
|
|
*
|
|
* @param column A pointer on an OBIDMS column.
|
|
* @param line_nb The number of the line at which the value will be recovered.
|
|
*
|
|
* @retval 0 if the operation was successfully completed.
|
|
* @retval -1 if an error occurred.
|
|
*
|
|
* @since April 2016
|
|
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
|
*/
|
|
int obi_column_prepare_to_get_value(OBIDMS_column_p column, index_t line_nb);
|
|
|
|
|
|
/**
|
|
* @brief Goes through all the column files of a DMS and checks for views that have
|
|
* not been flagged as finished (done by the finish_view() function in the
|
|
* obiview source file).
|
|
*
|
|
* @param dms A pointer on an OBIDMS.
|
|
*
|
|
* @returns A boolean indicating whether unfinished views were found.
|
|
*
|
|
* @since September 2019
|
|
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
|
*/
|
|
int obi_dms_has_unfinished_columns(OBIDMS_p dms);
|
|
|
|
|
|
/**
|
|
* @brief Goes through all the column files of a DMS and deletes columns that have
|
|
* not been flagged as finished (done by the finish_view() function in the
|
|
* obiview source file).
|
|
*
|
|
* @param dms A pointer on an OBIDMS.
|
|
*
|
|
* @returns A value indicating the success of the operation.
|
|
* @retval 0 if the operation was successfully completed.
|
|
* @retval -1 if an error occurred.
|
|
*
|
|
* @since October 2017
|
|
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
|
*/
|
|
int obi_clean_unfinished_columns(OBIDMS_p dms);
|
|
|
|
|
|
#endif /* OBIDMSCOLUMN_H_ */
|