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@@ -1,491 +0,0 @@
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-<?php
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-
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-/*************************************************************************
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-*
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-*/
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-function tripal_core_bulk_loader_create (){
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-
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- return drupal_get_form('tripal_core_bulk_loader_create_form');
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-}
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-/*************************************************************************
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-*
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-*/
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-function tripal_core_bulk_loader_create_form (&$form_state = NULL){
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- $form = array();
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-
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- // get the step used by this multistep form
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- $step = 1;
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- if(isset($form_state['storage'])){
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- $step = (int)$form_state['storage']['step'];
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- }
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-
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- $form = array();
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- if($step == 1){
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- tripal_core_bulk_loader_create_form_step1 ($form,$form_state);
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- $form_state['storage']['step'] = $step + 1;
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- }
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- if($step == 2){
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- tripal_core_bulk_loader_create_form_step2 ($form,$form_state);
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- }
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-
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- return $form;
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-}
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-/*************************************************************************
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-*
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-*/
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-function tripal_core_bulk_loader_create_form_validate ($form,&$form_state) {
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-
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-
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-}
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-/*************************************************************************
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-*
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-*/
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-function tripal_core_bulk_loader_create_form_submit ($form,&$form_state) {
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- if($form_State['storage']['step'] < 4){
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- return;
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- }
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-}
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-
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-/*************************************************************************
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-*
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-*/
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-function tripal_core_bulk_loader_create_form_step2 (&$form,$form_state){
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-
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- if(isset($form_state['values']['columns'])){
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- $form_state['storage']['columns'] = $form_state['values']['columns'];
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- }
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-
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- $form['bulk_loader'] = array(
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- '#type' => 'fieldset',
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- '#title' => t('Step 2: Define the columns of the file'),
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- );
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-
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- $columns = $form_state['storage']['columns'];
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-// $form['debug']= array(
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-// '#value' => "Columns: $columns",
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-// '#weight' => -1
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-// );
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-
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- $fields = array();
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- $fields[''] = '';
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-/*
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- $form_fields = array(
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- 'Feature details' => array (
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- 'name' => array(
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- 'description' => 'Feature Name (human readable)',
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- 'table' => array(
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- 'table name' => 'feature',
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- 'fields' => array('name'),
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- ),
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- ),
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- 'uniquename' => array(
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- 'description' => 'Unique Name (must be unique for this organism and feature type)',
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- 'table' => array(
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- 'table name' => 'feature',
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- 'fields' => array('uniquename'),
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- ),
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- ),
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- 'type_id' => array(
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- 'description' => 'Feature type (must be a valid SO term',
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- 'table' => array(
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- 'table name' => 'feature',
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- 'fields' => array('uniquename'),
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- ),
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- ),
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- 'residues' => array(
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- 'description' => 'Residues',
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- 'table' => array(
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- 'table name' => 'feature',
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- 'fields' => array('residues'),
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- ),
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- ),
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- ),
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- 'Organism specification' => array (
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- 'organism_id' => array(
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- 'description' => 'Organism ID number',
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- 'table' => array(
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- 'table name' => 'organism',
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- 'fields' => array('organism_id'),
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- ),
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- ),
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- 'genus' => array(
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- 'description' => 'Genus',
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- 'table' => array(
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- 'table name' => 'organism',
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- 'fields' => array('genus'),
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- ),
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- 'valid values' => 'this'
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- ),
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- 'species' => array(
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- 'description' => 'Species',
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- 'table' => array(
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- 'table name' => 'organism',
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- 'fields' => array('species'),
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- ),
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- ),
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- 'full_name' => array(
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- 'description' => 'Scientific Name (genus + species)',
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- 'table' => array(
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- 'table name' => 'organism',
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- 'fields' => array('genus','species'),
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- 'parser' => '/^(.*?)\s+(.*?)$/',
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- ),
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- ),
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- 'common_name' => array(
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- 'description' => 'Common Name',
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- 'table' => array(
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- 'table name' => 'organism',
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- 'fields' => array('common_name'),
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- ),
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- ),
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- ),
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-1. allow the user to specify the term from a specific vocabulary
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-2. allow the user to specify the vocabulary to choose from
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-3.
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- 'Feature Property' => array (
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- 'property' => array(
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- 'description' => 'Feature property value',
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- 'table' => array(
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- 'table name' => 'featureprop',
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- 'fields' => array('value'),
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- 'check' => array(
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- 'type_id' => {
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- ),
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- ).
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- ),
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- ),
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- );
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-
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-*/
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- // these fields correspond with the columns of the feature table and
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- // the foreign key contraints for the feature table.
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- $fields = array(
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- '' => '',
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- 'ignore' => 'Ignore this column',
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- 'Feature details' => array (
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- 'name' => 'Feature Name (human readable)',
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- 'uniquename' => 'Unique Feature Name',
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- 'type' => 'Feature type (must be a valid SO term)',
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- 'alt_type' => 'Additional ontology term',
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- 'residues' => 'Residues',
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- ),
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- 'Organism specification' => array (
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- 'organism_id' => 'Organism ID number',
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- 'genus' => 'Genus',
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- 'species' => 'Species',
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- 'full_name' => 'Scientific Name (genus + species)',
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- 'common_name' => 'Common Name',
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- ),
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- 'External Database Cross-Reference' => array(
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- 'db_id' => 'Database ID number',
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- 'db_name' => 'Database name (must exists in the database)',
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- 'accession' => 'Accession',
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- ),
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- 'Feature Relationship' => array (
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- 'rel_type' => 'Relationship Type (must be a valid relationship term)',
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- 'parent' => 'Parent unique name',
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- 'parent type' => 'Parent Type (must be a valid SO term)',
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- ),
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- 'Feature Location' => array (
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- 'srcfeature' => 'Reference feature (must already exist in the database)',
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- 'srcfeature_type' => 'Reference feature type (must be a valid SO term)',
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- 'fmin' => 'Start position',
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- 'fmax' => 'Stop position',
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- 'strand' => 'Strand (valid values: 0,-1,+1)',
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- 'phase' => 'Phase (valid values: (+,-,.)',
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- ),
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- 'Feature Property' => array (
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- 'property' => 'Feature property value',
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- ),
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- 'Feature Synonym' => array (
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- 'syn_name' => 'Synonym name',
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- ),
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- 'Library specification' => array (
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- 'library_id' => 'Library ID number',
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- 'library_name' => 'Library name',
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- ),
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- 'Analysis specification' => array (
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- 'analysis_id' => 'Analysis ID number',
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- 'analysis_source' => 'Analysis identifying name (sourcename column in Chado)',
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- 'analysis_desc' => 'Analysis description',
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- 'analysis_program' => 'Analysis program',
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- 'analysis_program_version' => 'Analysis program version'
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- ),
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- );
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-
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- // organism foreign key identifies. These are used to find the organism
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- // for which the feature belongs.
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- $form['columns'] = array(
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- '#type' => 'hidden',
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- '#value' => $columns,
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- );
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-
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-
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- // get the list of organisms
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- $sql = "SELECT * FROM {organism} ORDER BY genus, species";
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- $previous_db = tripal_db_set_active('chado'); // use chado database
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- $org_rset = db_query($sql);
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- tripal_db_set_active($previous_db); // now use drupal database
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- $organisms = array();
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- $genus = array();
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- $species = array();
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- $common_names = array();
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- $genera[''] = '';
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- $species[''] = '';
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- $common_names[''] = '';
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- $full_names[''] = '';
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- while($organism = db_fetch_object($org_rset)){
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- $full_names["$organism->genus $organism->species"] = "$organism->genus $organism->species";
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- $genera[$organism->genus] = "$organism->genus";
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- $species[$organism->species] = "$organism->species";
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- $common_names[$organism->common_name] = "$organism->common_name";
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- }
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-
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- for($i = 1; $i <= $columns; $i++){
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- $form['bulk_loader']["col_$i"] = array(
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- '#type' => 'fieldset',
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- '#title' => t("Column $i of the input file"),
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- );
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- $form['bulk_loader']["col_$i"]["col_type_$i"] = array(
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- '#title' => t('Field Selection'),
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- '#type' => 'select',
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- '#options' => $fields,
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- '#weight' => 0,
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- // this field will use AJAX to populate and information needed
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- // for specific types, such as for feature properties. It
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- // calls the step2_get_type URL and passes the column ($i).
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- // the return value is additional form items or text
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- '#ahah' => array(
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- 'event' => 'change',
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- 'wrapper' => "type_cols_$i",
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- 'path' => "/admin/tripal/bulk_load/step2_get_type/$i",
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- 'effect' => 'fade',
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- 'method' => 'replace'
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- ),
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- );
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-
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- // these next fields are hidden (access = false) and will be shown
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- // if the user selects the feature property type in the drop down
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- // above.
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-
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-
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- //-------------------------------------------------------------------------
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- // default text box for allowed values
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- $form['bulk_loader']["col_$i"]["col_prop_valid_$i"] = array(
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- '#title' => t('Allowed Values'),
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- '#type' => 'textarea',
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- '#weight' => 0,
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- '#description' => 'Please provide a list of allowed values for this field. Separate these values with a space. Leave blank to allow any value',
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- '#access' => FALSE
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- );
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-
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- //-------------------------------------------------------------------------
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- // Organism allowed values
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- $form['bulk_loader']["col_$i"]["col_prop_genera_$i"] = array (
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- '#title' => t('Allowed Values'),
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- '#type' => t('select'),
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- '#description' => t("Choose all allowed genera values for this column (ctrl+click to select multiple values). Select none to allow all"),
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- '#required' => FALSE,
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- '#options' => $genera,
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- '#weight' => 2,
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- '#multiple' => TRUE,
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- '#size' => 10,
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- '#access' => FALSE
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- );
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- $form['bulk_loader']["col_$i"]["col_prop_species_$i"] = array (
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- '#title' => t('Allowed Values'),
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- '#type' => t('select'),
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- '#description' => t("Choose all allowed species values for this column (ctrl+click to select multiple values). Select none to allow all"),
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- '#required' => FALSE,
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- '#options' => $species,
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- '#weight' => 2,
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- '#multiple' => TRUE,
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- '#size' => 10,
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- '#access' => FALSE
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- );
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- $form['bulk_loader']["col_$i"]["col_prop_common_name_$i"] = array (
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- '#title' => t('Allowed Values'),
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- '#type' => t('select'),
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- '#description' => t("Choose all allowed values for this column (ctrl+click to select multiple values). Select none to allow all"),
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- '#required' => FALSE,
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- '#options' => $common_names,
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- '#weight' => 2,
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- '#multiple' => TRUE,
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- '#size' => 10,
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- '#access' => FALSE
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- );
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- $form['bulk_loader']["col_$i"]["col_prop_full_name_$i"] = array (
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- '#title' => t('Allowed Values'),
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- '#type' => t('select'),
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- '#description' => t("Choose all allowed values for this column (shift+click to select multiple values). Select none to allow all"),
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- '#required' => FALSE,
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- '#options' => $full_names,
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- '#weight' => 2,
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- '#multiple' => TRUE,
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- '#size' => 10,
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- '#access' => FALSE
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- );
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-
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-
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- //-------------------------------------------------------------------------
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- // feature property fields
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- $form['bulk_loader']["col_$i"]["col_prop_name_$i"] = array(
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- '#title' => t('Property Name'),
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- '#type' => 'textfield',
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- '#weight' => 1,
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- '#description' => 'Please provide a name for this property. It should be a single
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- word with only alphanumeric characters and underscores. If this
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- name exists as a CV term in Chado already it will be reused, otherwise
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- a new CV term with this name will be added.',
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- '#required' => TRUE,
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- '#access' => FALSE
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- );
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- $form['bulk_loader']["col_$i"]["col_prop_full_name_$i"] = array(
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- '#title' => t('Property Full Name'),
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- '#type' => 'textfield',
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- '#weight' => 3,
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- '#description' => 'Please provide a human readable name for this property. This will be used when
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- displaying the property title',
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- '#access' => FALSE
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- );
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- $form['bulk_loader']["col_$i"]["col_prop_desc_$i"] = array(
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- '#title' => t('Property Description'),
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- '#type' => 'textarea',
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- '#weight' => 4,
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- '#description' => 'Please provide a description of this property.',
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- '#access' => FALSE
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- );
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-
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- // this is an empty div box that gets put on the form. This is the
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- // box where the hidden form elements will be rendered when the
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- // AJAX call returns
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- $form['bulk_loader']["col_$i"]["type_wrap_$i"] = array(
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- '#prefix' => "<div class=\"clear-block\" id=\"type_cols_$i\">",
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- '#value' => ' ',
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- '#suffix' => '</div>',
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- );
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- }
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-
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-
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- $form['submit'] = array (
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- '#type' => 'submit',
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- '#value' => t('Next'),
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- '#weight' => 5,
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- '#executes_submit_callback' => TRUE,
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- );
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-}
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-/*************************************************************************
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-*
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-*/
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-
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-function tripal_core_bulk_loader_ahah_step2_feature_type($column){
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-
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-
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- // create a form_state array to hold the form variables
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- $form_state = array('storage' => NULL, 'submitted' => FALSE);
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- $form_state['storage']['step'] = 2;
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-
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- // retreive the form from the cache
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- $form_build_id = $_POST['form_build_id'];
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- $form = form_get_cache($form_build_id, $form_state);
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-
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- // get the form name
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- $args = $form['#parameters'];
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- $form_id = array_shift($args);
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-
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- // add the post variables to the form and set a few other items
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- $form['#post'] = $_POST;
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- $form['#redirect'] = FALSE;
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- $form['#programmed'] = FALSE;
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- $form_state['post'] = $_POST;
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-
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- drupal_process_form($form_id, $form, $form_state);
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- $form = drupal_rebuild_form($form_id, $form_state, $args, $form_build_id);
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-
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- // get the column
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- $i = $column;
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-
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- // check to see what type of field has been selected and provide the
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- // additional fields as appropriate
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|
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- $type = $form_state["post"]["col_type_$i"];
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|
|
- if(strcmp($type,'genus')==0){
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- $propform['bulk_loader']["col_$i"]["col_prop_genera_$i"] = $form['bulk_loader']["col_$i"]["col_prop_genera_$i"];
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- $propform['bulk_loader']["col_$i"]["col_prop_genera_$i"]['#access'] = TRUE;
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-
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- }
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|
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- elseif(strcmp($type,'species')==0){
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- $propform['bulk_loader']["col_$i"]["col_prop_species_$i"] = $form['bulk_loader']["col_$i"]["col_prop_species_$i"];
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- $propform['bulk_loader']["col_$i"]["col_prop_species_$i"]['#access'] = TRUE;
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-
|
|
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- }
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|
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- elseif(strcmp($type,'common_name')==0){
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|
- $propform['bulk_loader']["col_$i"]["col_prop_common_name_$i"] = $form['bulk_loader']["col_$i"]["col_prop_common_name_$i"];
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- $propform['bulk_loader']["col_$i"]["col_prop_common_name_$i"]['#access'] = TRUE;
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|
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-
|
|
|
- }
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|
|
- elseif(strcmp($type,'full_name')==0){
|
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|
- $propform['bulk_loader']["col_$i"]["col_prop_full_name_$i"] = $form['bulk_loader']["col_$i"]["col_prop_full_name_$i"];
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- $propform['bulk_loader']["col_$i"]["col_prop_full_name_$i"]['#access'] = TRUE;
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|
|
-
|
|
|
- }
|
|
|
- elseif(strcmp($type,'property')==0){
|
|
|
- // we just want to render the property fields that were previously not visible
|
|
|
- $propform['bulk_loader']["col_$i"]["col_prop_name_$i"] = $form['bulk_loader']["col_$i"]["col_prop_name_$i"];
|
|
|
- $propform['bulk_loader']["col_$i"]["col_prop_full_name_$i"] = $form['bulk_loader']["col_$i"]["col_prop_full_name_$i"];
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|
- $propform['bulk_loader']["col_$i"]["col_prop_desc_$i"] = $form['bulk_loader']["col_$i"]["col_prop_desc_$i"];
|
|
|
- $propform['bulk_loader']["col_$i"]["col_prop_name_$i"]['#access'] = TRUE;
|
|
|
- $propform['bulk_loader']["col_$i"]["col_prop_full_name_$i"]['#access'] = TRUE;
|
|
|
- $propform['bulk_loader']["col_$i"]["col_prop_desc_$i"]['#access'] = TRUE;
|
|
|
- }
|
|
|
- else {
|
|
|
- // use a default valid values textbox if we have no special needs for the type
|
|
|
- $propform['bulk_loader']["col_$i"]["col_prop_valid_$i"] = $form['bulk_loader']["col_$i"]["col_prop_valid_$i"];
|
|
|
- $propform['bulk_loader']["col_$i"]["col_prop_valid_$i"]['#access'] = TRUE;
|
|
|
- }
|
|
|
-
|
|
|
- $output = theme('status_messages') . drupal_render($propform);
|
|
|
-
|
|
|
- // Final rendering callback.
|
|
|
- drupal_json(array('status' => TRUE, 'data' => $output));
|
|
|
-}
|
|
|
-/*************************************************************************
|
|
|
-*
|
|
|
-*/
|
|
|
-function tripal_core_bulk_loader_create_form_step1 (&$form,$form_state){
|
|
|
- $modules = array();
|
|
|
- $modules['feature'] = 'Feature';
|
|
|
- $modules['organism'] = 'Organism';
|
|
|
- $modules['library'] = 'Library';
|
|
|
- $modules['analysis'] = 'Analysis';
|
|
|
-
|
|
|
-
|
|
|
- // set the fieldset title to indicate the step
|
|
|
- $form['bulk_loader'] = array(
|
|
|
- '#type' => 'fieldset',
|
|
|
- '#title' => t('Step 1: Select the Chado module'),
|
|
|
- );
|
|
|
-
|
|
|
- $form['bulk_loader']['chado_module'] = array(
|
|
|
- '#title' => t('Chado Module'),
|
|
|
- '#description' => t('Please select the module for which you would like to create an importer'),
|
|
|
- '#type' => 'select',
|
|
|
- '#options' => $modules,
|
|
|
- '#weight' => 0,
|
|
|
- '#required' => TRUE
|
|
|
- );
|
|
|
-
|
|
|
- $form['bulk_loader']['columns']= array(
|
|
|
- '#type' => 'textfield',
|
|
|
- '#title' => t('Number of Columns'),
|
|
|
- '#description' => t('Please specify the number of columns in the input file.'),
|
|
|
- '#weight' => 2,
|
|
|
- '#required' => TRUE
|
|
|
- );
|
|
|
-
|
|
|
- $form['submit'] = array (
|
|
|
- '#type' => 'submit',
|
|
|
- '#value' => t('Next'),
|
|
|
- '#weight' => 5,
|
|
|
- '#executes_submit_callback' => TRUE,
|
|
|
- );
|
|
|
-}
|
laceysanderson