Fixed issue #2027111

tripal_analysis/includes/tripal_analysis.chado_node.inc

@@ -123,9 +123,9 @@ function chado_analysis_form($node, &$form_state) {
     $sourceuri      = $form_state['input']['sourceuri'];
     $timeexecuted   = $form_state['input']['timeexecuted'];
     $description    = $form_state['input']['description'];
-    $d_removed      = $form_state['input']['removed'];
-    $num_new        = $form_state['input']['num_new'] ? $form_state['input']['num_new'] : 0;
-    $analysis_type  = $form_state['input']['analysis_type'];
+    $d_removed      = isset($form_state['input']['removed']) ? $form_state['input']['removed'] : array();
+    $num_new        = isset($form_state['input']['num_new']) ? $form_state['input']['num_new'] : 0;
+    $analysis_type  = isset($form_state['input']['analysis_type']) ? $form_state['input']['analysis_type'] : '';
   }
 
   $form['title']= array(

tripal_cv/includes/tripal_cv.charts.inc

@@ -1,256 +0,0 @@
-<?php
-/**
- * @file
- * Tripal API for generating a Google Chart of count data
- */
-
-/**
- * Generates JSON used for generating a Google chart of count data associated
- * with a controlled vocabulary.  An example would be features assigned to
- * Gene Ontology terms.
- *
- * To generate a chart, the progammer must first create a materialized view that
- * will generate count data for a given controlled vocabulary.  For example, the Tripal
- * Analysis GO creates a materialized view for counting Gene Ontology assignments
- * to features.  This view is created on install of the module and is named
- * 'go_count_analysis'.
- *
- * Next, an HTML 'div' box must be added to the desired page
- * with a class name of 'tripal_cv_chart', and an id of the following format:
- *
- *  tripal_[module_name]_cv_chart_[unique id]
- *
- * where [module_name] is the name of the tripal module (e.g. tripal_analyisis_go)
- * and [unique id] is some unique identifier that the contolling module
- * recognizes. This string is the $chart_id variable passed as the first argument
- * to the function.  For example, the Tripal GO Analysis module generates
- * chart ids of the form:
- *
- *  tripal_analysis_go_cv_chart_10_2_bp
- *
- * In this case the module that will manage this chart is identified as 'tripal_analysis_go' and within
- * the [unique id] portion contains the
- * organism_id (e.g. 10), analysis_id (e.g. 2) and chart type (bp = biological process).
- *
- * Second, the programmer must then define a hook in the controlling module for setting
- * some options used to build the chart.  The hook has the form:  hook_cv_chart($chart_id).
- * This hook should accept the full $chart_id as the single parameter.  For the Tripal
- * Analysis GO module the hook is named:  tripal_analysis_go_cv_chart.
- *
- * The array returned by this hook must have the following fields:
- *  - count_mview
- *      the name of the materialized view that contains the count data
- *      this materialized view must have at least two columns, one with the cvterm_id
- *      for each term and a second column containing the counts
- *  - cvterm_id_column
- *      the column name in the materialized view that contains
- *      the cvterm_ids
- *  - count_column
- *      the column name in the materialized view that contains the
- *      counts
- *  - filter
- *      an SQL compatible WHERE clause string (whithout the word 'WHERE')
- *      that can be used for filtering the records in the materialized view.
- *  - title
- *      the title for the chart
- *  - type
- *      the type of chart to create (see Google Charts documenation). Leave
- *      blank for a pie chart.
- *  - size
- *      the dimensions of the chart in pixels (see Google Charts documenations
- *      for exact size limitations).
- *
- * Example from the tripal_analysis_go module:
- * @code
- *  function tripal_analysis_go_cv_chart($chart_id) {
- *
- *    // The CV module will create the JSON array necessary for buillding a
- *    // pie chart using jgChart and Google Charts.  We have to pass to it
- *    // a table that contains count information, tell it which column
- *    // contains the cvterm_id and provide a filter for getting the
- *    // results we want from the table.
- *    $organism_id = preg_replace("/^tripal_analysis_go_cv_chart_(\d+)-(\d+)_(bp|cc|mf)$/","$1",$chart_id);
- *    $analysis_id = preg_replace("/^tripal_analysis_go_cv_chart_(\d+)-(\d+)_(bp|cc|mf)$/","$2",$chart_id);
- *    $type        = preg_replace("/^tripal_analysis_go_cv_chart_(\d+)-(\d+)_(bp|cc|mf)$/","$3",$chart_id);
- *
- *    $sql = "SELECT * FROM {analysis} WHERE analysis_id = :analysis_id";
- *    $analysis = chado_query($sql, array(':analysis_id' => $analysis_id))->fetchObject();
- *
- *    if (strcmp($type,'mf')==0) {
- *       $class = 'molecular_function';
- *       $title = "Number of Molecular Function Terms From $analysis->name Analysis";
- *    }
- *    if (strcmp($type,'cc')==0) {
- *       $class = 'cellular_component';
- *       $title = "Number of Cellular Component Terms From $analysis->name Analysis";
- *    }
- *    if (strcmp($type,'bp')==0) {
- *       $class = 'biological_process';
- *       $title = "Number of Biological Process Terms From $analysis->name Analysis";
- *    }
- *    $options = array(
- *       count_mview      => 'go_count_analysis',
- *       cvterm_id_column => 'cvterm_id',
- *       count_column     => 'feature_count',
- *       filter           => "
- *          CNT.organism_id = $organism_id AND
- *          CNT.analysis_id = $analysis_id AND
- *          CNT.cvterm_id IN (
- *            SELECT CVTR.subject_id
- *            FROM {cvterm_relationship} CVTR
- *              INNER JOIN {CVTerm} CVT on CVTR.object_id = CVT.cvterm_id
- *              INNER JOIN {CV} on CVT.cv_id = CV.cv_id
- *            WHERE CVT.name = '$class' AND
- *                   CV.name = '$class'
- *          )
- *       ",
- *       type             => 'p',
- *       size             => '550x175',
- *       title            => $title,
- *    );
- *    return $options;
- *  }
- *
- * @endcode
- *
- * @param $chart_id
- *   The unique identifier for the chart
- *
- * @return
- *   JSON array needed for the js caller
- *
- * With these three components (materialized view, a 'div' box with proper CSS class and ID, and a hook_cv_chart)
- * a chart will be created on the page.  There is no need to call this function directly.
- *
- * @ingroup tripal_cv_api
- */
-function tripal_cv_chart($chart_id) {
-  // parse out the tripal module name from the chart_id to find out
-  // which Tripal "hook" to call:
-  $tripal_mod = preg_replace("/^(tripal_.+?)_cv_chart_(.+)$/", "$1", $chart_id);
-  $callback = $tripal_mod . "_cv_chart";
-
-  // now call the function in the module responsible for the chart to fill out
-  // an options array needed by the tripal_cv_count_chart call below.
-  $opt = call_user_func_array($callback, array($chart_id));
-
-  // build the JSON array to return to the javascript caller
-  $json_arr = tripal_cv_count_chart(
-    $opt['count_mview'],
-    $opt['cvterm_id_column'],
-    $opt['count_column'],
-    $opt['filter'],
-    $opt['title'],
-    $opt['type'],
-    $opt['size']
-  );
-  $json_arr[] = $chart_id;  // add the chart_id back into the json array
-
-  return drupal_json($json_arr);
-
-}
-
- /**
-  * This function generates an array with fields compatible with Google charts used
-  * for generating pie charts of counts associated with terms in
-  * a controlled vocabulary.  An example would be counts of features assigned
-  * to terms in the Sequence Ontology.
-  *
-  * @param $cnt_table
-  *   The name of the table (most likely a materialized view) that
-  *   contains count data for each term.  The table must have at least
-  *   two columns, one with the cvterm_id for each term, and a second
-  *   column with the count (i.e. features assigned the term).
-  * @param $fk_column
-  *   This is the name of the column in the $cnt_table that holds the
-  *   cvterm_id for each term.
-  * @param $cnt_column
-  *   The name of the column in the $cnt_table containing the counts
-  * @param $filter
-  *   An SQL compatible 'where' clause (without the word 'WHERE') used
-  *   to filter the records in the $cnt_table
-  * @param $title
-  *   The title of the chart to be rendered.
-  * @param $type
-  *   The type of chart to be rendered. The value used here is the same as
-  *   the type names for Google charts. Default is p3 (pie chart).
-  * @param $size
-  *   The size in pixels of the chart to be rendered. Default is 300x75. The
-  *   size of the chart is constrained by Google charts.  See the Google
-  *   chart documentation for exact limitations.
-  *
-  * @return
-  *   An array that has the settings needed for Google Charts to creat the chart.
-  *
-  * @ingroup tripal_cv_api
-  */
-function tripal_cv_count_chart($cnt_table, $fk_column,
-  $cnt_column, $filter = NULL, $title = '', $type = 'p3', $size='300x75') {
-
-  if (!$type) {
-    $type = 'p3';
-  }
-
-  if (!$size) {
-    $size = '300x75';
-  }
-
-  if (!$filter) {
-    $filter = '(1=1)';
-  }
-
-  $is_pie = 0;
-  if (strcmp($type, 'p') == 0 or strcmp($type, 'p3') == 0) {
-    $is_pie = 1;
-  }
-  $sql = "
-    SELECT CVT.name, CVT.cvterm_id, CNT.$cnt_column as num_items
-    FROM {$cnt_table} CNT
-     INNER JOIN {cvterm} CVT on CNT.$fk_column = CVT.cvterm_id
-    WHERE $filter
-  ";
-
-  $features = array();
-  $results = chado_query($sql);
-  $data = array();
-  $axis = array();
-  $legend = array();
-  $total = 0;
-  $max = 0;
-  $i = 1;
-  while ($term = db_fetch_object($results)) {
-
-    if ($is_pie) {
-      $axis[] = "$term->name (" . number_format($term->num_items) . ")";
-      $data[] = array($term->num_items, 0, 0);
-    }
-    else {
-      $axis[] = "$term->name (" . number_format($term->num_items) . ")";
-      $data[] = array($term->num_items);
-      //$legend[] = "$term->name (" . number_format($term->num_items) . ")";
-    }
-    if ($term->num_items > $max) {
-      $max = $term->num_items;
-    }
-    $total += $term->num_items;
-    $i++;
-  }
-  // convert numerical values into percentages
-  foreach ($data as &$set) {
-    $set[0] = ($set[0] / $total) * 100;
-  }
-  $opt[] = array(
-    data => $data,
-    axis_labels => $axis,
-    legend => $legend,
-    size => $size,
-    type => $type,
-
-    bar_width     => 10,
-    bar_spacing   => 0,
-    title         => $title
-  );
-  //   $opt[] = $sql;
-
-  return $opt;
-}

tripal_cv/includes/tripal_cv.trees.inc

@@ -1,468 +0,0 @@
-<?php
-/**
- * @file
- * Functions for rendering term tree's
- */
-
-/**
- * Renders the cv_list form
- *
- * @ingroup tripal_cv
- */
-function tripal_cv_show_browser() {
-
-  $content = drupal_get_form('tripal_cv_list_form');
-  $content .= "
-    <div id=\"cv_browser\"></div>
-  ";
-
-  return $content;
-}
-
-
-/**
- * Generates JSON used for generating an exapandable tree of terms from
- * a controlled vocabulary that has associated counts.
- *
- * The progammer must first create a materialized view that
- * will generate count data for a given controlled vocabulary.  For example, the Tripal
- * Analysis GO creates a materialized view for counting Gene Ontology assignments
- * to features.  This view is created on install of the module and is named
- * 'go_count_analysis'.
- *
- * Second, the progammer must add an HTML 'div' box to the desired page
- * with a class name of 'tripal_cv_tree', and an id of the following format:
- *
- *  tripal_[module_name]_cv_tree_[unique id]
- *
- * where [module_name] is the name of the tripal module (e.g. tripal_analyisis_go)
- * and [unique id] is some unique identifier that the contolling module
- * recognizes. This string is the $tree_id variable passed as the first argument
- * to the function.  For example, the Tripal GO Analysis module generates
- * tree ids of the form:
- *
- *  tripal_analysis_go_cv_tree_10-2_bp
- *
- * In this case the module that will manage this tree is identified as 'tripal_analysis_go' and within
- * the [unique id] portion contains the
- * organism_id (e.g. 10), analysis_id (e.g. 2) and tree type (bp = biological process).
- *
- * Second, the programmer must then define a hook in the controlling module for setting
- * some options used to build the chart.  The hook has the form:  hook_cv_tree($tree_id).
- * This hook should accept the full $tree_id as the single parameter.  For the Tripal
- * Analysis GO module the hook is named:  tripal_analysis_go_cv_tree.
- *
- * The array returned by this hook must have the following fields:
- *  - cv_id
- *      the cv_id for the controlled vocabulary
- *  - count_mview
- *      the name of the materialized view that contains the count data
- *      this materialized view must have at least two columns, one with the cvterm_id
- *      for each term and a second column containing the counts. The tree will only
- *      be expanded to include child terms that have counts.
- *  - cvterm_id_column
- *      the column name in the materialized view that contains
- *      the cvterm_ids
- *  - count_column
- *      the column name in the materialized view that contains the
- *      counts
- *  - filter
- *      an SQL compatible WHERE clause string (whithout the word 'WHERE')
- *      that can be used for filtering the records in the materialized view.
- *  - label
- *      the title for the tree
- *
- * Example from the tripal_analysis_go module:
- * @code
- *  function tripal_analysis_go_cv_tree($tree_id) {
- *
- *   $organism_id = preg_replace("/^tripal_analysis_go_cv_tree_(\d+)-(\d+)_(bp|cc|mf)$/","$1",$tree_id);
- *   $analysis_id = preg_replace("/^tripal_analysis_go_cv_tree_(\d+)-(\d+)_(bp|cc|mf)$/","$2",$tree_id);
- *   $type        = preg_replace("/^tripal_analysis_go_cv_tree_(\d+)-(\d+)_(bp|cc|mf)$/","$3",$tree_id);
- *
- *   if(strcmp($type,'mf')==0) {
- *      $class = 'molecular_function';
- *   }
- *   if(strcmp($type,'cc')==0) {
- *      $class = 'cellular_component';
- *   }
- *   if(strcmp($type,'bp')==0) {
- *      $class = 'biological_process';
- *   }
- *
- *   $options = array(
- *      cv_id            => tripal_cv_get_cv_id($class),
- *      count_mview      => 'go_count_analysis',
- *      cvterm_id_column => 'cvterm_id',
- *      count_column     => 'feature_count',
- *      filter           => "CNT.organism_id = $organism_id AND CNT.analysis_id = $analysis_id",
- *      label            => 'Features',
- *   );
- *   return $options;
- * }
- *
- * @endcode
- *
- * @param $tree_id
- *   The unique identifier for the tree
- *
- * @return
- *   JSON array needed for the jsTree package for generating expandable trees.
- *
- * With these three components (materialized view, a 'div' box with proper CSS class and ID, and a hook_cv_tree)
- * a tree will be created on the page.  There is no need to call this function directly.
- *
- * @ingroup tripal_cv_api
- */
-function tripal_cv_tree($tree_id) {
-  // parse out the tripal module name from the chart_id to find out
-  // which Tripal "hook" to call:
-  $tripal_mod = preg_replace("/^(tripal_.+?)_cv_tree_(.+)$/", "$1", $tree_id);
-  if ($tripal_mod) {
-    $callback = $tripal_mod . "_cv_tree";
-
-    // now call the function in the module responsible for the tree.  This
-    // should call the tripal_cv_init_cv with the proper parameters set for
-    // getting the cv_id of the vocabulary to use
-    $opt = call_user_func_array($callback, array($tree_id));
-
-    // we only need to return the cv_id for this function call.
-    $json_array[] = $opt['cv_id'];
-  }
-
-  $json_array[] = $tree_id;
-  return drupal_json($json_array);
-}
-
-/**
- * Update the JSON tree describing a tree
- *
- * @ingroup tripal_cv
- */
-function tripal_cv_update_tree() {
-  $content = array();
-  $ontology = 'sequence';
-
-  // get the id of the term to look up
-  $cv = check_plain($_REQUEST['cv']);
-  $term = check_plain($_REQUEST['term']);
-  $tree_id = check_plain($_REQUEST['tree_id']);
-
-  // get the options needed for this tree from the tripal module that
-  // wants to create the tree
-  $tripal_mod = preg_replace("/^(tripal_.+?)_cv_tree_(.+)$/", "$1", $tree_id);
-  if ($tripal_mod) {
-    $callback = $tripal_mod . "_cv_tree";
-    $opt = call_user_func_array($callback, array($tree_id));
-  }
-
-  // get the CV root terms
-  if (strcmp($term, 'root')==0) {
-    if (!$cv) {
-      $cv = $opt['cv_id'];
-    }
-    $content = tripal_cv_init_tree($cv, $opt['count_mview'],
-      $opt['cvterm_id_column'], $opt['count_column'], $opt['filter'], $opt['label']);
-
-  // get the children terms
-  }
-  else {
-    $content = tripal_cv_get_term_children($term, $opt['count_mview'],
-      $opt['cvterm_id_column'], $opt['count_column'], $opt['filter'], $opt['label']);
-  }
-
-  drupal_json($content);
-}
-
-/**
- * Generates JSON needed for jsTree Root-level Branches
- *
- * This function returns the JSON array for the jsTree
- *    jQuery code that builds a tree for browsing the ontology.  This function
- *    should be called to generate the root level branches of the tree.
- *
- * @ingroup tripal_cv
- */
-function tripal_cv_init_tree($cv_id, $cnt_table = NULL, $fk_column = NULL,
-  $cnt_column = NULL, $filter = NULL, $label = NULL) {
-
-  // get the list of root terms for the provided CV
-  $sql = "
-    SELECT *
-    FROM {cv_root_mview} CRM
-    WHERE cv_id = :cv_id
-  ";
-  $results = chado_query($sql, array(':cv_id' => $cv_id));
-
-  // prepare the SQL statement that will allow us to pull out count
-  // information for each term in the tree.
-  if ($cnt_table) {
-    if (!$filter) {
-      $filter = '(1=1)';
-    }
-    $cnt_sql = "
-       SELECT CVT.name, CVT.cvterm_id, CNT.$cnt_column as num_items
-       FROM {$cnt_table} CNT
-        INNER JOIN {cvterm} CVT on CNT.$fk_column = CVT.cvterm_id
-       WHERE $filter AND CVT.cvterm_id = :cvterm_id
-       ORDER BY $cnt_column desc
-    ";
-  }
-
-  foreach ($results as $term) {
-    $name = $term->name;
-    $count = 0;
-    if ($cnt_table) {
-      $cnt_results = chado_query($cnt_sql, array(':cvterm_id' => $term->cvterm_id));
-      foreach ($cnt_results as $cnt) {
-        $count += $cnt->cnt;
-      }
-      if ($count > 0) {
-        $name .= " ($count $label(s))";
-      }
-    }
-    $content[] = array(
-      'attributes' => array(
-        'id' => $term->cvterm_id,
-      ),
-      'state' => 'closed',
-      'data' => $name,
-      'children' => array(),
-    );
-  }
-
-  return $content;
-
-}
-
-/**
- *  Generates JSON needed for jsTree -expanding a term to view children
- *
- *  This function returns the JSON array for the jsTree
- *    jQuery code when expanding a term to view it's children.
- *
- * @ingroup tripal_cv_api
- */
-function tripal_cv_get_term_children($cvterm_id, $cnt_table = NULL,
-  $fk_column = NULL, $cnt_column = NULL, $filter = NULL, $label = NULL) {
-
-  // get the children for the term provided
-  $sql = "
-    SELECT CVTR.cvterm_relationship_id,CVTR.subject_id,
-       CVT1.name as subject_name, CVT3.name as type_name, CVTR.type_id,
-       CVT2.name as object_name,CVTR.object_id
-    FROM {cvterm_relationship} CVTR
-       INNER JOIN {CVTerm} CVT1 on CVTR.subject_id = CVT1.cvterm_id
-       INNER JOIN {CVTerm} CVT2 on CVTR.object_id = CVT2.cvterm_id
-       INNER JOIN {CVTerm} CVT3 on CVTR.type_id = CVT3.cvterm_id
-       INNER JOIN {CV} on CV.cv_id = CVT1.cv_id
-    WHERE CVTR.object_id = :cvterm_id
-    ORDER BY CVT1.name
-  ";
-  $results = chado_query($sql, array(':cvterm_id' => $cvterm_id));
-
-  // prepare the SQL statement that will allow us to pull out count
-  // information for each term in the tree.
-  if ($cnt_table) {
-    if (!$filter) {
-      $filter = '(1=1)';
-    }
-    $cnt_sql = "
-       SELECT CVT.name, CVT.cvterm_id, CNT.$cnt_column as num_items
-       FROM {$cnt_table} CNT
-        INNER JOIN {cvterm} CVT on CNT.$fk_column = CVT.cvterm_id
-       WHERE $filter AND CVT.cvterm_id = :cvterm_id
-       ORDER BY $cnt_column desc
-    ";
-  }
-
-  // populate the JSON content array
-  foreach ($results as $term) {
-    // count the number of items per term if requested
-    $name = $term->subject_name;
-    $count = 0;
-    if ($cnt_table) {
-      $cnt_results = chado_query($cnt_sql, array(':cvterm_id' => $term->subject_id));
-      foreach ($cnt_results as $cnt) {
-        $count += $cnt->num_items;
-      }
-      if ($count > 0) {
-        $name .= " (" . number_format($count) . " $label)";
-
-        // check if we have any children if so then set the value
-        $children = chado_query($sql, array(':cvterm_id' => $term->subject_id))->fetchObject();
-        $state = 'leaf';
-        if ($children) {
-          $state = 'closed';
-        }
-        $content[] = array(
-          'attributes' => array(
-            'id' => $term->subject_id,
-          ),
-          'state' => $state,
-          'data' => $name,
-          'children' => array(),
-        );
-      }
-    }
-    else {
-      // check if we have any children if so then set the value
-      $children = chado_query($sql, array(':cvterm_id' => $term->subject_id))->fetchObject();
-      $state = 'leaf';
-      if ($children) {
-        $state = 'closed';
-      }
-      $content[] = array(
-        'attributes' => array(
-           'id' => $term->subject_id,
-        ),
-        'state' => $state,
-        'data' => $name,
-        'children' => array(),
-      );
-    }
-  }
-  $content[] = $cnt_sql;
-
-  return $content;
-}
-
-/**
- * Initilizes term tree browser
- *
- * @ingroup tripal_cv
- */
-function tripal_cv_init_browser($cv_id) {
-
-  $content = "
-    <div id=\"tripal_cv_cvterm_info_box\">
-      <a href=\"#\" onclick=\"$('#tripal_cv_cvterm_info_box').hide()\" style=\"float: right\">Close [X]</a>
-      <h3>Term Information</h3>
-      <div id=\"tripal_cv_cvterm_info\"></div>
-    </div>
-    <div id=\"tripal_ajaxLoading\" style=\"display:none\">
-      <div id=\"loadingText\">Loading...</div>
-      <img src=\"$url\">
-    </div>
-    <h3>Tree Browser</h3>
-    <div id=\"browser\"</div>
-    </div>
-  ";
-
-  drupal_json(array('update' => "$content"));
-
-}
-
-/**
- * Describe a cvterm (Rendered)
- *
- * @ingroup tripal_cv
- */
-function tripal_cv_cvterm_info($cvterm_id) {
-
-  // get the id of the term to look up
-  $cv = check_plain($_REQUEST['cv']);
-  $tree_id = check_plain($_REQUEST['tree_id']);
-
-  // first get any additional information to add to the cvterm
-  if (strcmp($tree_id, 'undefined') != 0) {
-    $tripal_mod = preg_replace("/^(tripal_.+?)_cv_tree_(.+)$/", "$1", $tree_id);
-    if ($tripal_mod) {
-      $callback = $tripal_mod . "_cvterm_add";
-      $opt = call_user_func_array($callback, array($cvterm_id, $tree_id));
-    }
-  }
-
-  $sql = "
-    SELECT CVT.name as cvtermname, CVT.definition, CV.name as cvname,
-       DBX.accession,DB.urlprefix,DB.db_id,DB.name as dbname
-    FROM {CVTerm} CVT
-      INNER JOIN {CV} on CVT.cv_id = CV.cv_id
-      INNER JOIN {dbxref} DBX on CVT.dbxref_id = DBX.dbxref_id
-      INNER JOIN {DB} on DBX.db_id = DB.db_id
-    WHERE CVT.cvterm_id = :cvterm_id
-  ";
-  $cvterm = chado_query($sql, array(':cvterm_id' => $cvterm_id))->fetchObject();
-
-  $sql = "
-    SELECT CVTS.synonym, CVT.name as cvname
-    FROM {cvtermsynonym} CVTS
-      INNER JOIN {cvterm} CVT on CVTS.type_id = CVT.cvterm_id
-    WHERE CVTS.cvterm_id = :cvterm_id
-
-  ";
-  $results = chado_query($sql, array(':cvterm_id' => $cvterm_id));
-  foreach ($results as $synonym) {
-    $synonym_rows .= "<b>$synonym->cvname:</b>  $synonym->synonym<br />";
-  }
-
-  $accession = $cvterm->accession;
-  if ($cvterm->urlprefix) {
-    $accession = "<a href=\"$cvterm->urlprefix$cvterm->accession\">$cvterm->accession</a>";
-  }
-
-  $content = "
-    <div id=\"cvterm\">
-    <table>
-      <tr><th>Term</th><td>$cvterm->cvtermname</td></tr>
-      <tr><th>Accession</th><td>$accession</td></tr>
-      <tr><th>Ontology</th><td>$cvterm->cvname</td></tr>
-      <tr><th>Definition</th><td>$cvterm->definition</td></tr>
-      <tr><th>Synonyms</th><td>$synonym_rows</td></tr>
-      <tr><th>Internal ID</th><td>$cvterm_id</td></tr>
-  ";
-
-  // now add in any additional options from a hook
-  if ($opt) {
-    foreach ($opt as $key => $value) {
-      $content .= "<tr><th>$key</th><td>$value</td>";
-    }
-  }
-
-  // close out the information table
-  $content .= "
-    </table>
-    </div>
-  ";
-  drupal_json(array('update' => $content));
-}
-
-/**
- * Form listing CVs
- *
- * @ingroup tripal_cv
- */
-function tripal_cv_list_form($form, &$form_state) {
-
-  // get a list of db from chado for user to choose
-  $sql = "
-    SELECT DISTINCT CV.name,CV.cv_id
-    FROM {cvterm_relationship} CVTR
-       INNER JOIN {cvterm} CVT on CVTR.object_id = CVT.cvterm_id
-       INNER JOIN {CV} on CV.cv_id = CVT.cv_id
-  ";
-  $results = chado_query($sql);
-
-  $blastdbs = array();
-  $cvs[''] = '';
-  foreach ($results as $cv) {
-    $cvs[$cv->cv_id] = $cv->name;
-  }
-
-  $form['db_options'] = array(
-    '#type' => 'value',
-    '#value' => $cvs
-  );
-
-  $form['cv_list'] = array(
-    '#title' => t('CVs with relationships'),
-    '#type' => 'select',
-    '#description' => t('Choose the controlled vocabulary to browse'),
-    '#options' => $form['db_options']['#value'],
-    '#attributes' => array(
-      'onChange' => "return tripal_cv_init_browser(this)",
-    )
-  );
-
-  return $form;
-}

tripal_cv/tripal_cv.module

@@ -19,8 +19,6 @@ require_once 'api/tripal_cv.schema.api.inc';
 require_once 'api/tripal_cv.DEPRECATED.inc';
 
 require_once 'includes/tripal_cv.admin.inc';
-require_once 'includes/tripal_cv.charts.inc';
-require_once 'includes/tripal_cv.trees.inc';
 require_once 'includes/tripal_cv.obo_loader.inc';
 require_once 'includes/tripal_cv.cv_form.inc';
 require_once 'includes/tripal_cv.cvterm_form.inc';