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@@ -3,7 +3,7 @@
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/**
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* Purpose: Provide Guidance to new Tripal Admin
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*
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- * @return
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+ * @return
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* HTML Formatted text
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*
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* @ingroup tripal_feature
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@@ -12,31 +12,31 @@ function tripal_feature_module_description_page() {
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$text .= '<h3>Tripal Feature Administrative Tools Quick Links:</h3>';
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$text .= "<ul>
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- <li><a href=\"".url("admin/tripal/tripal_feature/configuration") . "\">Feature Configuration</a></li>
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- <li><a href=\"".url("admin/tripal/tripal_feature/fasta_loader"). "\">Import a multi-FASTA file</a></li>
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- <li><a href=\"".url("admin/tripal/tripal_feature/gff3_load"). "\">Import a GFF3 file</a></li>
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- <li><a href=\"".url("admin/tripal/tripal_feature/sync") . "\">Sync Features</a></li>
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- <li><a href=\"".url("admin/tripal/tripal_feature/delete") . "\">Delete Features</a></li>
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+ <li><a href=\"" . url("admin/tripal/tripal_feature/configuration") . "\">Feature Configuration</a></li>
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+ <li><a href=\"" . url("admin/tripal/tripal_feature/fasta_loader") . "\">Import a multi-FASTA file</a></li>
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+ <li><a href=\"" . url("admin/tripal/tripal_feature/gff3_load") . "\">Import a GFF3 file</a></li>
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+ <li><a href=\"" . url("admin/tripal/tripal_feature/sync") . "\">Sync Features</a></li>
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+ <li><a href=\"" . url("admin/tripal/tripal_feature/delete") . "\">Delete Features</a></li>
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</ul>";
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-# <li><a href=\"".url("admin/tripal/tripal_feature/aggregate"). "\">Feature Relationship Aggegators</a></li>
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+# <li><a href=\"".url("admin/tripal/tripal_feature/aggregate"). "\">Feature Relationship Aggegators</a></li>
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$text .= '<h3>Module Description:</h3>';
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$text .= '<p>This module provides an interface for the Chado feature module which stores information
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related to genomic features. This module provides support for bulk loading of data in
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- FASTA or GFF format, visualization of "feature" pages, editing and updating.
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+ FASTA or GFF format, visualization of "feature" pages, editing and updating.
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</p>';
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$text .= '<h3>Setup Instructions:</h3>';
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$text .= '<p>After installation of the feature module. The following tasks should be performed
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<ol>
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- <li><p><b>Set Permissions</b>: The feature module supports the Drupal user permissions interface for
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- controlling access to feature content and functions. These permissions include viewing,
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+ <li><p><b>Set Permissions</b>: The feature module supports the Drupal user permissions interface for
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+ controlling access to feature content and functions. These permissions include viewing,
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creating, editing or administering of
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- feature content. The default is that only the original site administrator has these
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- permissions. You can <a href="'.url('admin/user/roles').'">add roles</a> for classifying users,
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- <a href="'.url('admin/user/user').'">assign users to roles</a> and
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- <a href="'.url('admin/user/permissions').'">assign permissions</a> for the feature content to
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- those roles. For a simple setup, allow anonymous users access to view organism content and
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+ feature content. The default is that only the original site administrator has these
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+ permissions. You can <a href="' . url('admin/user/roles') . '">add roles</a> for classifying users,
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+ <a href="' . url('admin/user/user') . '">assign users to roles</a> and
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+ <a href="' . url('admin/user/permissions') . '">assign permissions</a> for the feature content to
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+ those roles. For a simple setup, allow anonymous users access to view organism content and
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allow the site administrator all other permissions.</p></li>
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<li><p><b>Themeing</b>: Before content from Chado can be visualized the Tripal base theme must
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@@ -46,8 +46,8 @@ function tripal_feature_module_description_page() {
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<li><p><b>Loading of Ontologies</b>: If you
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used Tripal to create the Chado database, then you must load ontologies before proceeding. Visit the
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- page to <a href="'.url('admin/tripal/tripal_cv/obo_loader').'">load ontologies</a> and load at
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- least the following ontologies:
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+ page to <a href="' . url('admin/tripal/tripal_cv/obo_loader') . '">load ontologies</a> and load at
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+ least the following ontologies:
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<ul>
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<li>Chado Feature Properties</li>
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<li>Relationship Ontology</li>
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@@ -55,80 +55,80 @@ function tripal_feature_module_description_page() {
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<li>Gene Ontology (if loading GO terms for features)</li>
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</ul></p></li>
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- <li><p><b>Create Organisms</b>: Before adding feature data you must already have the
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- organisms loaded in the database. See the
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- <a href="'.url('admin/tripal/tripal_organism').'">Tripal Organism Admin page</a> for
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+ <li><p><b>Create Organisms</b>: Before adding feature data you must already have the
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+ organisms loaded in the database. See the
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+ <a href="' . url('admin/tripal/tripal_organism') . '">Tripal Organism Admin page</a> for
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instructions for adding and Syncing organisms.</p></li>
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<li><p><b>Create Analysis</b>: Tripal requires that feature data loaded using the Tripal loaders
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be associated with an analyis. This provides a grouping for the feature data and can be used
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later to visualize data pipelines. Before loading feature data through the FASTA or GFF loaders
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- you will need to <a href="'.url('node/add').'">create an analysis</a> for the data.</p></li>
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+ you will need to <a href="' . url('node/add') . '">create an analysis</a> for the data.</p></li>
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- <li><p><b>Create Referring Database Entries</b>: If you would like to associate your feature data with an
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- external reference database, check to ensure that the <a href="'.url('admin/tripal/tripal_db/edit_db').'">
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- database record already exists</a>. If not you should <a href="'.url('admin/tripal/tripal_db/add_db').'">add a new database record</a> before importing
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+ <li><p><b>Create Referring Database Entries</b>: If you would like to associate your feature data with an
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+ external reference database, check to ensure that the <a href="' . url('admin/tripal/tripal_db/edit_db') . '">
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+ database record already exists</a>. If not you should <a href="' . url('admin/tripal/tripal_db/add_db') . '">add a new database record</a> before importing
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feature data.</p></li>
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- <li><p><b>Data Import</b>: if you do not already have an existing Chado database with preloaded data
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+ <li><p><b>Data Import</b>: if you do not already have an existing Chado database with preloaded data
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then you will want
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- to import data. You can do so using the Chado perl scripts that come with the normal
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- <a href="http://gmod.org/wiki/Chado">distribution of Chado</a> or you can use the <a href="'.url('admin/tripal/tripal_feature/fasta_loader').'">FASTA loader</a> and
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- <a href="'.url('admin/tripal/tripal_feature/gff3_load').'">GFF loader</a> provided here. If you
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+ to import data. You can do so using the Chado perl scripts that come with the normal
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+ <a href="http://gmod.org/wiki/Chado">distribution of Chado</a> or you can use the <a href="' . url('admin/tripal/tripal_feature/fasta_loader') . '">FASTA loader</a> and
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+ <a href="' . url('admin/tripal/tripal_feature/gff3_load') . '">GFF loader</a> provided here. If you
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created the Chado database using Tripal then you\'ll most likely want to use the Tripal loaders. If your data
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- is not condusive for loading with these loaders you may have to write your own loaders.
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+ is not condusive for loading with these loaders you may have to write your own loaders.
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</p></li>
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<li><p><b>Sync Features</b>: After data is loaded you need to sync features. This process is what
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creates the pages for viewing online. Not all features need be synced. For instance, if you
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have loaded whole genome sequence with fully defined gene models with several features to define
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a gene and its products (e.g. gene, mRNA, CDS, 5\'UTR, 3\'UTR, etc) you probably only want to create
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- pages for genes or genes and mRNA. You probably do not want a page for a 5\'UTR.
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- Using the <a href="'.url('admin/tripal/tripal_feature/configuration/sync').'">Feature Sync page</a>
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+ pages for genes or genes and mRNA. You probably do not want a page for a 5\'UTR.
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+ Using the <a href="' . url('admin/tripal/tripal_feature/configuration/sync') . '">Feature Sync page</a>
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you can sync (or create pages) for the desired feature types. </p></li>
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- <li><p><b>Set Feature URL</b>: It is often convenient to have a simple URL for each feature page.
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+ <li><p><b>Set Feature URL</b>: It is often convenient to have a simple URL for each feature page.
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For example, http://www.mygenomesite.org/[feature], where [feature] is a unique identifier for a feature page.
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- With this, people can easily include links to feature pages of interest. Use the
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- <a href="'.url('admin/tripal/tripal_feature/configuration').'">Feature Configuration page</a>
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+ With this, people can easily include links to feature pages of interest. Use the
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+ <a href="' . url('admin/tripal/tripal_feature/configuration') . '">Feature Configuration page</a>
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to specify whether to use the feature name, unique name or internal ID as the [feature] portion of the
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URL. Select the one that will guarantee a unique identifier for feature pages.</p></li>
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<li><p><b>Indexing</b>: Once all data has been loaded (including analysis data--e.g. blast, interpro, etc.)
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- you can index all feature pages for searching if you want to ues the Drupal default search mechanism.
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- Use the <a href="'.url('admin/tripal/tripal_feature/configuration').'">Feature Configuration page</a>
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+ you can index all feature pages for searching if you want to ues the Drupal default search mechanism.
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+ Use the <a href="' . url('admin/tripal/tripal_feature/configuration') . '">Feature Configuration page</a>
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to either Index (for the first time) or "Reindex" (after adding new data)
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the feature pages for searching. Once the site is 100% indexed the pages will be searchable using Drupal\'s
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- full text searching. You can find the percent indexed for the entire site by visiting the
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- <a href="'.url('admin/settings/search').'">Search settings page</a>. Indexing
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+ full text searching. You can find the percent indexed for the entire site by visiting the
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+ <a href="' . url('admin/settings/search') . '">Search settings page</a>. Indexing
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can take quite a while if you have a lot of data</p></li>
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- <li><p><b>Set Taxonomy</b>: Drupal provides a mechanism for categorizing content to allow
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- for advanced searching. Drupal calls this "Taxonomy", but is essentially categorizing the pages.
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- You can categorize feature pages by their type (e.g. gene, mRNA, contig, EST, etc.) and by the
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- organism to which they belong. This allows for filtering of search results by organism and feature type.
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- Use the <a href="'.url('admin/tripal/tripal_feature/configuration').'">Feature Configuration page</a> to
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+ <li><p><b>Set Taxonomy</b>: Drupal provides a mechanism for categorizing content to allow
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+ for advanced searching. Drupal calls this "Taxonomy", but is essentially categorizing the pages.
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+ You can categorize feature pages by their type (e.g. gene, mRNA, contig, EST, etc.) and by the
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+ organism to which they belong. This allows for filtering of search results by organism and feature type.
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+ Use the <a href="' . url('admin/tripal/tripal_feature/configuration') . '">Feature Configuration page</a> to
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set the Taxonomy.</p></li>
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</ol>
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</p>';
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-
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-
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+
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+
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$text .= '<h3>Features of this Module:</h3>';
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- $text .= '<p>Aside from data loading and feature page setup (as described in the Setup section above),
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+ $text .= '<p>Aside from data loading and feature page setup (as described in the Setup section above),
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The Tripal feature module also provides the following functionality
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<ul>
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- <li><p><b>Feature Browser:</b> The feature browser is a tabular list of features with links to their
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- feature pages which appears on the organism
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+ <li><p><b>Feature Browser:</b> The feature browser is a tabular list of features with links to their
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+ feature pages which appears on the organism
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page. It was created to provide a mechanism to allow site visitors to quickly
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accesss feature pages when they do not know what to search for. For sites with large numbers of features, this
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- method for finding a specific pages is inadequate, but may still be included to aid new site
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- visitors. This browser can be toggled on or off using the
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- <a href="'.url('admin/tripal/tripal_feature/configuration').'">Feature Configuration page</a></p></li>
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-
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+ method for finding a specific pages is inadequate, but may still be included to aid new site
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+ visitors. This browser can be toggled on or off using the
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+ <a href="' . url('admin/tripal/tripal_feature/configuration') . '">Feature Configuration page</a></p></li>
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+
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<li><p><b>Feature Summary Report:</b> The feature summary report is a pie chart that indicates the types and quantities
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- of feature types (Sequence Ontology terms) that are loaded in the database. It appears on the organism
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- page. The summary can be toggled on or off using the
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- <a href="'.url('admin/tripal/tripal_feature/configuration').'">Feature Configuration page</a></p></li>
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+ of feature types (Sequence Ontology terms) that are loaded in the database. It appears on the organism
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+ page. The summary can be toggled on or off using the
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+ <a href="' . url('admin/tripal/tripal_feature/configuration') . '">Feature Configuration page</a></p></li>
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<li><p><b>Integration with Drupal Views</b>: <a href="http://drupal.org/project/views">Drupal Views</a> is
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a powerful tool that allows the site administrator to create lists or basic searching forms of Chado content.
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@@ -136,56 +136,56 @@ function tripal_feature_module_description_page() {
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and create custom lists without PHP programming or customization of Tripal source code. Views can also
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be created to filter content that has not yet been synced with Druapl in order to protect access to non
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published data (only works if Chado was installed using Tripal). You can see a list of available pre-existing
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- Views <a href="'.url('admin/build/views/').'">here</a>, as well as create your own. </p></li>
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+ Views <a href="' . url('admin/build/views/') . '">here</a>, as well as create your own. </p></li>
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- <li><p><b>Basic Feature Lookup View</b>: This module provides a basic <a href="'.url('features').'">feature search
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+ <li><p><b>Basic Feature Lookup View</b>: This module provides a basic <a href="' . url('features') . '">feature search
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tool</a> for finding or listing features in Chado. It does not require indexing for Drupal searching but relies
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- on Drupal Views. <a href="http://drupal.org/project/views">Drupal Views</a> must be installed. </p></li>
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+ on Drupal Views. <a href="http://drupal.org/project/views">Drupal Views</a> must be installed. </p></li>
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- <li><p><b>Delete Features</b>: This module provides a <a href="'.url('admin/tripal/tripal_feature/delete').'">Delete Feature page</a>
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+ <li><p><b>Delete Features</b>: This module provides a <a href="' . url('admin/tripal/tripal_feature/delete') . '">Delete Feature page</a>
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for bulk deltions of features. You may delete features using a list of feature names, or for a specific organism
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- or for a specific feature type.</p></li>
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+ or for a specific feature type.</p></li>
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</ul>
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</p>';
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$text .= '<h3>Page Customizations</h3>';
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- $text .= '<p>There are several ways to customize the look-and-feel for the way Chado data is presented through Tripal.
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+ $text .= '<p>There are several ways to customize the look-and-feel for the way Chado data is presented through Tripal.
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Below is a description of several methods. These methods may be used in conjunction with one another to
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- provide fine-grained control.
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+ provide fine-grained control.
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<ul>
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- <li><p><b>Integration with Drupal Panels</b>: <a href="http://drupal.org/project/views">Drupal Panels</a>
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- allows for customization of a page layout if you don\'t want to do PHP/Javascript/CSS programming. Tripal comes with pre-set layouts for feature pages. However,
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+ <li><p><b>Integration with Drupal Panels</b>: <a href="http://drupal.org/project/views">Drupal Panels</a>
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+ allows for customization of a page layout if you don\'t want to do PHP/Javascript/CSS programming. Tripal comes with pre-set layouts for feature pages. However,
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Panels become useful if you prefer a layout that is different from the pre-set layouts. Chado content
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- is provided to Panels in the form of Drupal "blocks" which you can then place anywhere on a page using the
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+ is provided to Panels in the form of Drupal "blocks" which you can then place anywhere on a page using the
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Panel\'s GUI.</p></li>
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- <li><p><b>Drupal\'s Content Construction Kit (CCK)</b>: the
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+ <li><p><b>Drupal\'s Content Construction Kit (CCK)</b>: the
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<a href="http://drupal.org/project/cck">Content Construction Kit (CCK) </a> is a powerful way to add non-Chado content
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to any page without need to edit template files or knowing PHP. You must first download and install CCK.
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With CCK, the site administartor can create a new field to appear on the page. For example, currently,
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- the Chado publication module is not yet supported by Tripal. Therefore, the site administrator can add a text
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+ the Chado publication module is not yet supported by Tripal. Therefore, the site administrator can add a text
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field to the feature pages. This content is not stored in Chado, but will appear on the feature page. A field
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added by CCK will also appear in the form when editing a feature to allow users to manually enter the appropriate
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text. If the default pre-set layout and themeing for Tripal is used, it is better to create the CCK element,
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- indicate that it is not to be shown (using the CCK interface), then manually add the new content type
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+ indicate that it is not to be shown (using the CCK interface), then manually add the new content type
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where desired by editing the templates (as described below). If using Panels, the CCK field can be added to the
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location desired using the Panels interface.</p></li>
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<li><p><b>Drupal Node Templates</b>: The Tripal packages comes with a "theme_tripal" directory that contains the
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themeing for Chado content. The feature module has a template file for feature "nodes" (Tripal feature pages). This file
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is named "node-chado_feature.tpl.php", and provides javascript, HTML and PHP code for display of the feature
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- pages. You can edit this file to control which types of information (or which feature "blocks") are displayed for features. Be sure to
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+ pages. You can edit this file to control which types of information (or which feature "blocks") are displayed for features. Be sure to
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copy these template to your primary theme directory for editing. Do not edit them in the "theme_tripal" directory as
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future Tripal updates may overwrite your customizations. See the <a href="http://tripal.sourceforge.net/">Tripal website </a>
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for instructions on how to access variables and other Chado content within the template file.</p></li>
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<li><p><b>Feature "Block" Templates</b>: In the "theme_tripal" directory is a subdirectory named "tripal_feature".
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Inside this directory is a set of templates that control distinct types of information for features. For example,
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- there is a "base" template for displaying of data directly from the Chado feature table, and a "references"
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+ there is a "base" template for displaying of data directly from the Chado feature table, and a "references"
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template for showing external site references for a feature (data from the feature_dbxref table). These templates are used both by Drupal blocks
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- for use in Drupal Panels (as described above) or for use in the default pre-set layout that the node template
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+ for use in Drupal Panels (as described above) or for use in the default pre-set layout that the node template
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provides (also desribed above). You can customize this template as you desire. Be sure to copy the
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template to your primary theme directory for editing. Do not edit them in the "theme_tripal" directory as
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future Tripal updates may overwrite your customizations. See the <a href="http://tripal.sourceforge.net/">Tripal website </a>
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@@ -194,9 +194,9 @@ function tripal_feature_module_description_page() {
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<li><p><b>Adding Links to the "Resources" Sidebar</b>: If you use the pre-set default Tripal layout for theming, you
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will see a "Resources" sidebar on each page. The links that appear on the sidebar are automatically generated
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- using Javascript for all of the feature "Blocks" that appear on the page. If you want to add additional links
|
|
|
- (e.g. a dynamic link to GBrowse for the feature) and you want that link to appear in the
|
|
|
- "Resources" sidebar, simply edit the Drupal Node Template (as described above) and add the link to the
|
|
|
+ using Javascript for all of the feature "Blocks" that appear on the page. If you want to add additional links
|
|
|
+ (e.g. a dynamic link to GBrowse for the feature) and you want that link to appear in the
|
|
|
+ "Resources" sidebar, simply edit the Drupal Node Template (as described above) and add the link to the
|
|
|
section at the bottom of the template file where the resources section is found.</p></li>
|
|
|
|
|
|
</ul>
|
|
|
@@ -210,16 +210,16 @@ function tripal_feature_module_description_page() {
|
|
|
*
|
|
|
* @ingroup tripal_feature
|
|
|
*/
|
|
|
-function tripal_feature_admin () {
|
|
|
+function tripal_feature_admin() {
|
|
|
|
|
|
// before proceeding check to see if we have any
|
|
|
// currently processing jobs. If so, we don't want
|
|
|
// to give the opportunity to sync libraries
|
|
|
$active_jobs = FALSE;
|
|
|
- if(tripal_get_module_active_jobs('tripal_feature')){
|
|
|
+ if (tripal_get_module_active_jobs('tripal_feature')) {
|
|
|
$active_jobs = TRUE;
|
|
|
}
|
|
|
- if(!$active_jobs){
|
|
|
+ if (!$active_jobs) {
|
|
|
|
|
|
get_tripal_feature_admin_form_url_set($form);
|
|
|
|
|
|
@@ -229,7 +229,7 @@ function tripal_feature_admin () {
|
|
|
'#collapsible' => 1,
|
|
|
'#collapsed' => 1 ,
|
|
|
);
|
|
|
- $allowedoptions1 = array (
|
|
|
+ $allowedoptions1 = array(
|
|
|
'show_feature_browser' => "Show the feature browser on the organism page. The browser loads when page loads. This may be slow for large sites.",
|
|
|
'hide_feature_browser' => "Hide the feature browser on the organism page. Disables the feature browser completely.",
|
|
|
);
|
|
|
@@ -237,7 +237,7 @@ function tripal_feature_admin () {
|
|
|
|
|
|
$form['browser']['browser_desc'] = array(
|
|
|
'#type' => 'markup',
|
|
|
- '#value' => 'A feature browser can be added to an organism page to allow users to quickly '.
|
|
|
+ '#value' => 'A feature browser can be added to an organism page to allow users to quickly '.
|
|
|
'access a feature. This will most likely not be the ideal mechanism for accessing feature '.
|
|
|
'information, especially for large sites, but it will alow users exploring the site (such '.
|
|
|
'as students) to better understand the data types available on the site.',
|
|
|
@@ -246,9 +246,9 @@ function tripal_feature_admin () {
|
|
|
$form['browser']['feature_types'] = array(
|
|
|
'#title' => t('Feature Types'),
|
|
|
'#type' => 'textarea',
|
|
|
- '#description' => t("Enter the Sequence Ontology (SO) terms for the feature types that ".
|
|
|
+ '#description' => t("Enter the Sequence Ontology (SO) terms for the feature types that " .
|
|
|
"will be shown in the feature browser."),
|
|
|
- '#default_value' => variable_get('chado_browser_feature_types','gene contig'),
|
|
|
+ '#default_value' => variable_get('chado_browser_feature_types', 'gene contig'),
|
|
|
);
|
|
|
|
|
|
|
|
|
@@ -256,9 +256,9 @@ function tripal_feature_admin () {
|
|
|
'#title' => 'Feature Browser on Organism Page',
|
|
|
'#type' => 'radios',
|
|
|
'#options' => $allowedoptions1,
|
|
|
- '#default_value'=>variable_get('tripal_feature_browse_setting', 'show_feature_browser'),
|
|
|
+ '#default_value' => variable_get('tripal_feature_browse_setting', 'show_feature_browser'),
|
|
|
);
|
|
|
-
|
|
|
+
|
|
|
$form['browser']['browse_features_library'] = array(
|
|
|
'#title' => 'Feature Browser on Library Page',
|
|
|
'#type' => 'radios',
|
|
|
@@ -266,7 +266,7 @@ function tripal_feature_admin () {
|
|
|
'show_feature_browser' => "Show the feature browse on the library page. The browser loads when page loads. This may be slow for large sites.",
|
|
|
'hide_feature_browser' => "Hide the feature browser on the library page. Disables the feature browser completely.",
|
|
|
),
|
|
|
- '#default_value'=>variable_get('tripal_library_feature_browse_setting', 'show_feature_browser'),
|
|
|
+ '#default_value' => variable_get('tripal_library_feature_browse_setting', 'show_feature_browser'),
|
|
|
);
|
|
|
|
|
|
$form['browser']['browse_features_analysis'] = array(
|
|
|
@@ -276,9 +276,9 @@ function tripal_feature_admin () {
|
|
|
'show_feature_browser' => "Show the feature browse on the analysis page. The browser loads when page loads. This may be slow for large sites.",
|
|
|
'hide_feature_browser' => "Hide the feature browser on the analysis page. Disables the feature browser completely.",
|
|
|
),
|
|
|
- '#default_value'=>variable_get('tripal_analysis_feature_browse_setting', 'show_feature_browser'),
|
|
|
+ '#default_value' => variable_get('tripal_analysis_feature_browse_setting', 'show_feature_browser'),
|
|
|
);
|
|
|
-
|
|
|
+
|
|
|
$form['browser']['set_browse_button'] = array(
|
|
|
'#type' => 'submit',
|
|
|
'#value' => t('Set Browser'),
|
|
|
@@ -305,7 +305,7 @@ function tripal_feature_admin () {
|
|
|
'#title' => t('Feature Types'),
|
|
|
'#type' => 'textarea',
|
|
|
'#description' => t("Enter the Sequence Ontology (SO) terms for the allowed feature types when creating or editing features."),
|
|
|
- '#default_value' => variable_get('chado_edit_feature_types','gene contig EST mRNA'),
|
|
|
+ '#default_value' => variable_get('chado_edit_feature_types', 'gene contig EST mRNA'),
|
|
|
);
|
|
|
|
|
|
$form['feature_edit']['set_feature_types'] = array(
|
|
|
@@ -328,7 +328,7 @@ function tripal_feature_admin () {
|
|
|
'type and quantity of features available for the organism.',
|
|
|
'#type' => 'radios',
|
|
|
'#options' => $allowedoptions2,
|
|
|
- '#default_value'=>variable_get('tripal_feature_summary_setting', 'show_feature_summary'),
|
|
|
+ '#default_value' => variable_get('tripal_feature_summary_setting', 'show_feature_summary'),
|
|
|
);
|
|
|
$form['summary']['feature_mapping'] = array(
|
|
|
'#title' => 'Map feature types',
|
|
|
@@ -339,7 +339,7 @@ function tripal_feature_admin () {
|
|
|
'SO term to be more human readable form, use an \'=\' sign after the SO term (e.g. \'polypeptide = Protein\')'),
|
|
|
'#type' => 'textarea',
|
|
|
'#rows' => 15,
|
|
|
- '#default_value'=>variable_get('tripal_feature_summary_report_mapping', ''),
|
|
|
+ '#default_value' => variable_get('tripal_feature_summary_report_mapping', ''),
|
|
|
);
|
|
|
$form['summary']['set_summary_button'] = array(
|
|
|
'#type' => 'submit',
|
|
|
@@ -350,7 +350,8 @@ function tripal_feature_admin () {
|
|
|
get_tripal_feature_admin_form_taxonomy_set($form);
|
|
|
get_tripal_feature_admin_form_reindex_set($form);
|
|
|
get_tripal_feature_admin_form_cleanup_set($form);
|
|
|
- } else {
|
|
|
+ }
|
|
|
+ else {
|
|
|
$form['notice'] = array(
|
|
|
'#type' => 'fieldset',
|
|
|
'#title' => t('Feature Management Temporarily Unavailable')
|
|
|
@@ -375,51 +376,51 @@ function tripal_feature_admin_validate($form, &$form_state) {
|
|
|
global $user; // we need access to the user info
|
|
|
$job_args = array();
|
|
|
|
|
|
- variable_set('chado_browser_feature_types',$form_state['values']['feature_types']);
|
|
|
+ variable_set('chado_browser_feature_types', $form_state['values']['feature_types']);
|
|
|
|
|
|
// if the user wants to sync up the chado features then
|
|
|
// add the job to the management queue
|
|
|
- switch ($form_state['values']['op']){
|
|
|
+ switch ($form_state['values']['op']) {
|
|
|
|
|
|
case t('Sync all Features') :
|
|
|
- tripal_add_job('Sync all features','tripal_feature',
|
|
|
- 'tripal_feature_sync_features',$job_args,$user->uid);
|
|
|
+ tripal_add_job('Sync all features', 'tripal_feature',
|
|
|
+ 'tripal_feature_sync_features', $job_args, $user->uid);
|
|
|
break;
|
|
|
|
|
|
case t('Set/Reset Taxonomy for all feature nodes') :
|
|
|
- tripal_add_job('Set all feature taxonomy','tripal_feature',
|
|
|
- 'tripal_features_set_taxonomy',$job_args,$user->uid);
|
|
|
+ tripal_add_job('Set all feature taxonomy', 'tripal_feature',
|
|
|
+ 'tripal_features_set_taxonomy', $job_args, $user->uid);
|
|
|
break;
|
|
|
|
|
|
case t('Reindex all feature nodes') :
|
|
|
- tripal_add_job('Reindex all features','tripal_feature',
|
|
|
- 'tripal_features_reindex',$job_args,$user->uid);
|
|
|
+ tripal_add_job('Reindex all features', 'tripal_feature',
|
|
|
+ 'tripal_features_reindex', $job_args, $user->uid);
|
|
|
break;
|
|
|
|
|
|
case t('Clean up orphaned features') :
|
|
|
- tripal_add_job('Cleanup orphaned features','tripal_feature',
|
|
|
- 'tripal_features_cleanup',$job_args,$user->uid);
|
|
|
+ tripal_add_job('Cleanup orphaned features', 'tripal_feature',
|
|
|
+ 'tripal_features_cleanup', $job_args, $user->uid);
|
|
|
break;
|
|
|
|
|
|
case t('Set Browser') :
|
|
|
- variable_set('tripal_feature_browse_setting',$form_state['values']['browse_features']);
|
|
|
+ variable_set('tripal_feature_browse_setting', $form_state['values']['browse_features']);
|
|
|
variable_set('tripal_library_feature_browse_setting', $form_state['values']['browse_features_library']);
|
|
|
variable_set('tripal_analysis_feature_browse_setting', $form_state['values']['browse_features_analysis']);
|
|
|
break;
|
|
|
|
|
|
case t('Set Feature Types') :
|
|
|
- variable_set('tripal_feature_type_setting',$form_state['values']['feature_edit_types']);
|
|
|
+ variable_set('tripal_feature_type_setting', $form_state['values']['feature_edit_types']);
|
|
|
break;
|
|
|
|
|
|
case t('Set Summary') :
|
|
|
- variable_set('tripal_feature_summary_setting',$form_state['values']['feature_summary']);
|
|
|
- variable_set('tripal_feature_summary_report_mapping',$form_state['values']['feature_mapping']);
|
|
|
+ variable_set('tripal_feature_summary_setting', $form_state['values']['feature_summary']);
|
|
|
+ variable_set('tripal_feature_summary_report_mapping', $form_state['values']['feature_mapping']);
|
|
|
break;
|
|
|
|
|
|
case t('Set Feature URLs') :
|
|
|
- variable_set('chado_feature_url',$form_state['values']['feature_url']);
|
|
|
- tripal_add_job('Set Feature URLs','tripal_feature',
|
|
|
- 'tripal_feature_set_urls',$job_args,$user->uid);
|
|
|
+ variable_set('chado_feature_url', $form_state['values']['feature_url']);
|
|
|
+ tripal_add_job('Set Feature URLs', 'tripal_feature',
|
|
|
+ 'tripal_feature_set_urls', $job_args, $user->uid);
|
|
|
break;
|
|
|
}
|
|
|
}
|
|
|
@@ -488,7 +489,7 @@ function get_tripal_feature_admin_form_reindex_set(&$form) {
|
|
|
*
|
|
|
* @ingroup tripal_feature
|
|
|
*/
|
|
|
-function get_tripal_feature_admin_form_taxonomy_set (&$form) {
|
|
|
+function get_tripal_feature_admin_form_taxonomy_set(&$form) {
|
|
|
|
|
|
|
|
|
$form['taxonomy'] = array(
|
|
|
@@ -505,13 +506,13 @@ function get_tripal_feature_admin_form_taxonomy_set (&$form) {
|
|
|
"filtering during searching."),
|
|
|
'#weight' => 1,
|
|
|
);
|
|
|
- $tax_options = array (
|
|
|
+ $tax_options = array(
|
|
|
'organism' => t('Organism name'),
|
|
|
'feature_type' => t('Feature Type (e.g. EST, mRNA, etc.)'),
|
|
|
'analysis' => t('Analysis Name'),
|
|
|
'library' => t('Library Name'),
|
|
|
);
|
|
|
- $form['taxonomy']['tax_classes'] = array (
|
|
|
+ $form['taxonomy']['tax_classes'] = array(
|
|
|
'#title' => t('Available Taxonomic Classes'),
|
|
|
'#type' => t('checkboxes'),
|
|
|
'#description' => t("Please select the class of terms to assign to ".
|
|
|
@@ -521,7 +522,7 @@ function get_tripal_feature_admin_form_taxonomy_set (&$form) {
|
|
|
'#suffix' => '</div>',
|
|
|
'#options' => $tax_options,
|
|
|
'#weight' => 2,
|
|
|
- '#default_value' => variable_get('tax_classes',''),
|
|
|
+ '#default_value' => variable_get('tax_classes', ''),
|
|
|
);
|
|
|
$form['taxonomy']['button'] = array(
|
|
|
'#type' => 'submit',
|
|
|
@@ -531,13 +532,13 @@ function get_tripal_feature_admin_form_taxonomy_set (&$form) {
|
|
|
|
|
|
}
|
|
|
|
|
|
-function get_tripal_feature_admin_form_url_set (&$form) {
|
|
|
+function get_tripal_feature_admin_form_url_set(&$form) {
|
|
|
|
|
|
$form['url'] = array(
|
|
|
'#type' => 'fieldset',
|
|
|
'#title' => t('Feature URL Path')
|
|
|
);
|
|
|
- $form['url']['desc'] = array (
|
|
|
+ $form['url']['desc'] = array(
|
|
|
'#type' => 'markup',
|
|
|
'#value' => t('Each synced feature will have a unique URL which consists of '.
|
|
|
'the site domain followed by a unique identifer: for '.
|
|
|
@@ -557,19 +558,19 @@ function get_tripal_feature_admin_form_url_set (&$form) {
|
|
|
'It only need be unique among the synced dataset.'),
|
|
|
'#required' => FALSE,
|
|
|
'#options' => array('internal ID' => 'internal ID (Chado feature_id)',
|
|
|
- 'feature unique name' => 'feature unique name',
|
|
|
+ 'feature unique name' => 'feature unique name',
|
|
|
'feature name' => 'feature name'),
|
|
|
- '#default_value' => variable_get('chado_feature_url','internal ID'),
|
|
|
+ '#default_value' => variable_get('chado_feature_url', 'internal ID'),
|
|
|
);
|
|
|
|
|
|
- $form['url']['chado_feature_accession_prefix'] = array (
|
|
|
+ $form['url']['chado_feature_accession_prefix'] = array(
|
|
|
'#title' => t('ID Prefix'),
|
|
|
'#type' => t('textfield'),
|
|
|
'#description' => t("If you choose an Internal ID above you must also enter an ID prefix.".
|
|
|
"this prefix will be prepended to the internal ID number (e.g. ID38294). ".
|
|
|
"if you chose to use the feature name or unique name then this prfix is not used"),
|
|
|
'#required' => TRUE,
|
|
|
- '#default_value' => variable_get('chado_feature_accession_prefix','ID'),
|
|
|
+ '#default_value' => variable_get('chado_feature_accession_prefix', 'ID'),
|
|
|
);
|
|
|
|
|
|
$form['url']['button'] = array(
|
|
|
@@ -583,9 +584,9 @@ function get_tripal_feature_admin_form_url_set (&$form) {
|
|
|
*
|
|
|
* @ingroup tripal_feature
|
|
|
*/
|
|
|
-function tripal_feature_aggregator_page(){
|
|
|
+function tripal_feature_aggregator_page() {
|
|
|
$add_url = url("admin/tripal/tripal_feature/aggregate/new");
|
|
|
- $output = "<a href=\"$add_url\">Add a new aggregator</a>";
|
|
|
+ $output = "<a href=\"$add_url\">Add a new aggregator</a>";
|
|
|
$output .= drupal_get_form('tripal_feature_aggregator_select_form');
|
|
|
$output .= '<div id="db-edit-div">Please select an aggregator base type to view or edit</div>';
|
|
|
return $output;
|
|
|
@@ -596,23 +597,23 @@ function tripal_feature_aggregator_page(){
|
|
|
*
|
|
|
* @ingroup tripal_feature
|
|
|
*/
|
|
|
-function tripal_feature_aggregator_select_form(){
|
|
|
+function tripal_feature_aggregator_select_form() {
|
|
|
+
|
|
|
+ // get a list of base terms from chado for user to choose
|
|
|
+ $sql = "SELECT DISTINCT type_id FROM {tripal_feature_relagg} ORDER BY type_id ";
|
|
|
+ $results = db_query($sql);
|
|
|
|
|
|
- // get a list of base terms from chado for user to choose
|
|
|
- $sql = "SELECT DISTINCT type_id FROM {tripal_feature_relagg} ORDER BY type_id ";
|
|
|
- $results = db_query ($sql);
|
|
|
-
|
|
|
$sql = "SELECT * FROM {cvterm} WHERE cvterm_id = %d";
|
|
|
$previous_db = tripal_db_set_active('chado');
|
|
|
- $types = array();
|
|
|
+ $types = array();
|
|
|
$types[] = '';
|
|
|
- while($base = db_fetch_object($results)){
|
|
|
- $term = db_fetch_object(db_query($sql,$base->type_id));
|
|
|
- $types[$base->type_id] = $term->name;
|
|
|
+ while ($base = db_fetch_object($results)) {
|
|
|
+ $term = db_fetch_object(db_query($sql, $base->type_id));
|
|
|
+ $types[$base->type_id] = $term->name;
|
|
|
}
|
|
|
tripal_db_set_active($previous_db);
|
|
|
|
|
|
- $form['type_id'] = array(
|
|
|
+ $form['type_id'] = array(
|
|
|
'#title' => t('Aggregator Base Type'),
|
|
|
'#type' => 'select',
|
|
|
'#options' => $types,
|
|
|
@@ -623,7 +624,7 @@ function tripal_feature_aggregator_select_form(){
|
|
|
'event' => 'change',
|
|
|
'method' => 'replace',
|
|
|
),
|
|
|
- );
|
|
|
+ );
|
|
|
|
|
|
return $form;
|
|
|
}
|
|
|
@@ -633,28 +634,29 @@ function tripal_feature_aggregator_select_form(){
|
|
|
*
|
|
|
* @ingroup tripal_feature
|
|
|
*/
|
|
|
-function tripal_feature_aggregator_form(&$form_state = NULL,$type_id = NULL){
|
|
|
+function tripal_feature_aggregator_form(&$form_state = NULL, $type_id = NULL) {
|
|
|
|
|
|
// get this requested database
|
|
|
- if($type_id){
|
|
|
+ if ($type_id) {
|
|
|
$sql = "SELECT * FROM {tripal_feature_relagg} WHERE type_id = %d ";
|
|
|
$tsql = "SELECT * FROM {cvterm} WHERE cvterm_id = %d ";
|
|
|
|
|
|
// get the default list of terms
|
|
|
- $results = db_query($sql,$type_id);
|
|
|
- while($type = db_fetch_object($results)){
|
|
|
+ $results = db_query($sql, $type_id);
|
|
|
+ while ($type = db_fetch_object($results)) {
|
|
|
$previous_db = tripal_db_set_active('chado');
|
|
|
- $term = db_fetch_object(db_query($tsql,$type->rel_type_id));
|
|
|
+ $term = db_fetch_object(db_query($tsql, $type->rel_type_id));
|
|
|
tripal_db_set_active($previous_db);
|
|
|
$default_others .= $term->name . " ";
|
|
|
}
|
|
|
- $default_base = $base->name;
|
|
|
+ $default_base = $base->name;
|
|
|
$action = 'Update';
|
|
|
$form['type_id'] = array(
|
|
|
'#type' => 'hidden',
|
|
|
'#value' => $type_id
|
|
|
);
|
|
|
- } else {
|
|
|
+ }
|
|
|
+ else {
|
|
|
$action = 'Add';
|
|
|
$form['base']= array(
|
|
|
'#type' => 'textfield',
|
|
|
@@ -674,22 +676,23 @@ function tripal_feature_aggregator_form(&$form_state = NULL,$type_id = NULL){
|
|
|
'#required' => TRUE,
|
|
|
'#weight' => 2
|
|
|
);
|
|
|
-
|
|
|
- if(strcmp($action,'Update')==0){
|
|
|
- $form['update'] = array (
|
|
|
+
|
|
|
+ if (strcmp($action, 'Update')==0) {
|
|
|
+ $form['update'] = array(
|
|
|
'#type' => 'submit',
|
|
|
'#value' => t('Update'),
|
|
|
'#weight' => 5,
|
|
|
'#executes_submit_callback' => TRUE,
|
|
|
);
|
|
|
- $form['delete'] = array (
|
|
|
+ $form['delete'] = array(
|
|
|
'#type' => 'submit',
|
|
|
'#value' => t('Delete'),
|
|
|
'#weight' => 6,
|
|
|
'#executes_submit_callback' => TRUE,
|
|
|
);
|
|
|
- } else {
|
|
|
- $form['add'] = array (
|
|
|
+ }
|
|
|
+ else {
|
|
|
+ $form['add'] = array(
|
|
|
'#type' => 'submit',
|
|
|
'#value' => t('Add'),
|
|
|
'#weight' => 5,
|
|
|
@@ -707,49 +710,49 @@ function tripal_feature_aggregator_form(&$form_state = NULL,$type_id = NULL){
|
|
|
*
|
|
|
* @ingroup tripal_feature
|
|
|
*/
|
|
|
-function tripal_feature_aggregator_form_validate($form, &$form_state){
|
|
|
+function tripal_feature_aggregator_form_validate($form, &$form_state) {
|
|
|
$type_id = $form_state['values']['type_id'];
|
|
|
$base = $form_state['values']['base'];
|
|
|
$others = $form_state['values']['others'];
|
|
|
$op = $form_state['values']['op'];
|
|
|
|
|
|
// split apart the feature types to be aggregated
|
|
|
- $types = preg_split('/\s+/',$others);
|
|
|
+ $types = preg_split('/\s+/', $others);
|
|
|
|
|
|
// the SQL for finding the term
|
|
|
$tsql = "
|
|
|
- SELECT *
|
|
|
- FROM {cvterm} CVT
|
|
|
- INNER JOIN {cv} CV on CVT.cv_id = CV.cv_id
|
|
|
+ SELECT *
|
|
|
+ FROM {cvterm} CVT
|
|
|
+ INNER JOIN {cv} CV on CVT.cv_id = CV.cv_id
|
|
|
WHERE CVT.name = '%s' and CV.name = 'sequence'";
|
|
|
|
|
|
|
|
|
// make sure the base type exists
|
|
|
- if($base){
|
|
|
+ if ($base) {
|
|
|
$previous_db = tripal_db_set_active('chado');
|
|
|
- $term = db_fetch_object(db_query($tsql,$base));
|
|
|
+ $term = db_fetch_object(db_query($tsql, $base));
|
|
|
tripal_db_set_active($previous_db);
|
|
|
- if(!$term){
|
|
|
- form_set_error('base',t('The specified base type is not a valid SO term'));
|
|
|
+ if (!$term) {
|
|
|
+ form_set_error('base', t('The specified base type is not a valid SO term'));
|
|
|
}
|
|
|
|
|
|
// make sure this type doesn't already in the table
|
|
|
$sql = "SELECT * FROM {tripal_feature_relagg} WHERE type_id = %d ";
|
|
|
- $agg = db_fetch_object(db_query($sql,$term->cvterm_id));
|
|
|
- if($agg){
|
|
|
- form_set_error('base',t('The specified base type is already used as a base type for another aggregator and cannot be readded.'));
|
|
|
- }
|
|
|
+ $agg = db_fetch_object(db_query($sql, $term->cvterm_id));
|
|
|
+ if ($agg) {
|
|
|
+ form_set_error('base', t('The specified base type is already used as a base type for another aggregator and cannot be readded.'));
|
|
|
+ }
|
|
|
}
|
|
|
|
|
|
// iterate through each type to be aggregated and make sure they are valid
|
|
|
- foreach($types as $type){
|
|
|
+ foreach ($types as $type) {
|
|
|
$previous_db = tripal_db_set_active('chado');
|
|
|
- $term = db_fetch_object(db_query($tsql,$type));
|
|
|
+ $term = db_fetch_object(db_query($tsql, $type));
|
|
|
tripal_db_set_active($previous_db);
|
|
|
- if(!$term){
|
|
|
- form_set_error('others',t('The specified type ') . $type . t(' is not a valid SO term'));
|
|
|
+ if (!$term) {
|
|
|
+ form_set_error('others', t('The specified type ') . $type . t(' is not a valid SO term'));
|
|
|
}
|
|
|
- }
|
|
|
+ }
|
|
|
}
|
|
|
|
|
|
/**
|
|
|
@@ -757,7 +760,7 @@ function tripal_feature_aggregator_form_validate($form, &$form_state){
|
|
|
*
|
|
|
* @ingroup tripal_feature
|
|
|
*/
|
|
|
-function tripal_feature_aggregator_form_submit($form, &$form_state){
|
|
|
+function tripal_feature_aggregator_form_submit($form, &$form_state) {
|
|
|
|
|
|
$type_id = $form_state['values']['type_id'];
|
|
|
$base = $form_state['values']['base'];
|
|
|
@@ -765,13 +768,13 @@ function tripal_feature_aggregator_form_submit($form, &$form_state){
|
|
|
$op = $form_state['values']['op'];
|
|
|
|
|
|
// split apart the feature types to be aggregated
|
|
|
- $types = preg_split('/\s+/',$others);
|
|
|
+ $types = preg_split('/\s+/', $others);
|
|
|
|
|
|
// the SQL for finding the term
|
|
|
$tsql = "
|
|
|
- SELECT *
|
|
|
- FROM {cvterm} CVT
|
|
|
- INNER JOIN {cv} CV on CVT.cv_id = CV.cv_id
|
|
|
+ SELECT *
|
|
|
+ FROM {cvterm} CVT
|
|
|
+ INNER JOIN {cv} CV on CVT.cv_id = CV.cv_id
|
|
|
WHERE CVT.name = '%s' and CV.name = 'sequence'";
|
|
|
|
|
|
// the SQL for deleting an aggregator
|
|
|
@@ -782,43 +785,44 @@ function tripal_feature_aggregator_form_submit($form, &$form_state){
|
|
|
|
|
|
// if this is an insert then we have a base type name. We
|
|
|
// need to get the corresponding term id
|
|
|
- if($base){
|
|
|
+ if ($base) {
|
|
|
$previous_db = tripal_db_set_active('chado');
|
|
|
- $term = db_fetch_object(db_query($tsql,$base));
|
|
|
+ $term = db_fetch_object(db_query($tsql, $base));
|
|
|
tripal_db_set_active($previous_db);
|
|
|
$type_id = $term->cvterm_id;
|
|
|
}
|
|
|
|
|
|
- if(strcmp($op,'Delete')==0){
|
|
|
- $result = db_query($dsql,$type_id);
|
|
|
- if($result){
|
|
|
+ if (strcmp($op, 'Delete')==0) {
|
|
|
+ $result = db_query($dsql, $type_id);
|
|
|
+ if ($result) {
|
|
|
drupal_set_message("Aggregator deleted");
|
|
|
- } else {
|
|
|
+ }
|
|
|
+ else {
|
|
|
drupal_set_message("Failed to delete mailing list.");
|
|
|
}
|
|
|
}
|
|
|
else {
|
|
|
// for an update, first remove all the current aggregator settings
|
|
|
// and we'll add them again
|
|
|
- $result = db_query($dsql,$type_id);
|
|
|
+ $result = db_query($dsql, $type_id);
|
|
|
|
|
|
// the SQL for inserting the aggregated types
|
|
|
$isql = "
|
|
|
INSERT INTO {tripal_feature_relagg}
|
|
|
(type_id,rel_type_id)
|
|
|
- VALUES
|
|
|
+ VALUES
|
|
|
(%d,%d)
|
|
|
";
|
|
|
|
|
|
// iterate through each type to be aggregated and add an entry in the table
|
|
|
- foreach($types as $type){
|
|
|
+ foreach ($types as $type) {
|
|
|
$previous_db = tripal_db_set_active('chado');
|
|
|
- $term = db_fetch_object(db_query($tsql,$type));
|
|
|
+ $term = db_fetch_object(db_query($tsql, $type));
|
|
|
tripal_db_set_active($previous_db);
|
|
|
- $result = db_query($isql,$type_id,$term->cvterm_id);
|
|
|
+ $result = db_query($isql, $type_id, $term->cvterm_id);
|
|
|
}
|
|
|
drupal_set_message("Aggregator added");
|
|
|
- }
|
|
|
+ }
|
|
|
return '';
|
|
|
}
|
|
|
|
|
|
@@ -827,9 +831,9 @@ function tripal_feature_aggregator_form_submit($form, &$form_state){
|
|
|
*
|
|
|
* @ingroup tripal_feature
|
|
|
*/
|
|
|
-function tripal_feature_aggregator_ajax_edit (){
|
|
|
+function tripal_feature_aggregator_ajax_edit() {
|
|
|
// get the database id, build the form and then return the JSON object
|
|
|
$type_id = $_POST['type_id'];
|
|
|
- $form = drupal_get_form('tripal_feature_aggregator_form',$type_id);
|
|
|
+ $form = drupal_get_form('tripal_feature_aggregator_form', $type_id);
|
|
|
drupal_json(array('status' => TRUE, 'data' => $form));
|
|
|
}
|
Pubudu Basnayaka