tripal_stock_help.tpl.php 10.0 KB

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  1. <h3>Tripal Stock Quick Links</h3>
  2. <ul>
  3. <li><?php print l(t('Configuration'), 'admin/tripal/tripal_stock/configuration') ?></li>
  4. <li><?php print l(t('Stock Listing'), 'stocks') ?></li>
  5. </ul>
  6. <br>
  7. <h3>Module Description:</h3>
  8. <p>The Tripal Stock Module provides functionality for adding, editing, deleting and accessing chado stocks. The stock module was designed to store information about stock collections in a laboratory. What is called a stock could also be called a strain or an accession. There is a lot in common between a Drosophila stock and a Saccharomyces strain and an Arabidopsis line. They all come from some taxon, have genotypes, physical locations in the lab, some conceivable relationship with a publication, some conceivable relationship with a sequence feature (such as a transgene), and could be described by some ontology term. For more information about the chado Stock Module <a href="http://gmod.org/wiki/Chado_Stock_Module">see the GMOD Wiki Page</a></p>
  9. <h3>Setup Instructions:</h3>
  10. <ul>
  11. <li><p><b>Set Permissions</b>: By default only the site administrator account has access to create, edit, delete
  12. or administer analyses. Navigate to the <?php print l('permissions page', 'admin/user/permissions')?> and set the
  13. permissions under the 'tripal_stock' section as appropriate for your site. For a simple setup, allow anonymous
  14. users access to view content and create a special role for creating, editing and other administrative tasks.</p></li>
  15. <li><p><b>Set Ontologies</b>: Since at the time of this modules developement there is no accepted ontology for
  16. describing stocks, their properties and relationships, this module allows you to select the controlled
  17. vocabularies (CVs) in your Chado Database you would like to govern these data. To Set the Controlled Vocabularies for Stocks:
  18. First, ensure your Controlled Vocabulary is in Chado. This can be done by either loading an existing Ontology into Chado using
  19. the <a href="tripal_cv/ontology_loader">Tripal Ontology Loader</a> OR create your ontology from scratch by first
  20. <a href="tripal_cv/add_cv">creating a controlled vocabulary</a> and then <a href="tripal_cv/add_cvterm">adding terms to it</a>.
  21. Then go to the <a href="tripal_stock/configuration">Configuration Page for Stocks</a> and, in the "Set Stock Controlled Vocabularies" Fieldset,
  22. select the Controlled Vocaulary name for Stock Types, Stock Properties and Stock Relationship Types.</p>
  23. <ol type="i">
  24. <li>Stock Types: When you are creating stocks, the type of each stock must be indicated. This might include "DNA extraction", "Individual Plant/Animal" or even "Progeny Population".</li>
  25. <li>Stock Properties: This module also allows you to assign properties to any stock. Each property has a type and a value where type is required an value is not. Therefore, if you want to say that a stock was grown at 23 degrees Celcius then the Type would be "temperature grown at" and the value would be 23 degrees Celcius. As such the Stock Properties controlled vocabulary might include "temperature grown at", "diet", "extraction date", "stock location", etc.</li>
  26. <li>Stock Relationship Types: You can also specify relationships between stocks. For example, a stock of type="DNA extraction" (Stock 1a) is related to the stock of type="Individual Plant/Animal" (Stock 1) that it was extracted from. Thus you might specify the relationship Stock 1 is the source material for Stock 1a where the relationship type is "is the source material for". As such Stock Relationship Types might include "is the source material for", "is maternal parent of", "is individual of population", etc.</li>
  27. </ol>
  28. </li>
  29. <li><p><b>Set Permissions</b>: The stock module supports the Drupal user permissions interface for
  30. controlling access to stock content and functions. These permissions include viewing,
  31. creating, editing or administering of
  32. stock content. The default is that only the original site administrator has these
  33. permissions. You can <a href="<?php url('admin/user/roles') ?>">add roles</a> for classifying users,
  34. <a href="<?php url('admin/user/user') ?>">assign users to roles</a> and
  35. <a href="<?php url('admin/user/permissions') ?>">assign permissions</a> for the stock content to
  36. those roles. For a simple setup, allow anonymous users access to view organism content and
  37. allow the site administrator all other permissions.</p></li>
  38. <li><p><b>Sync Stocks</b>: if you chado database already contains stocks, they need to be sync'd with Drupal.
  39. This creates Drupal Content including detail pages for each stock (known as nodes in Drupal). To sync' Chado
  40. with Drupal simply go to the <?php print l('stock configuration page', 'admin/tripal/tripal_stock/configuration') ?>
  41. and in the "Sync Stocks" Fieldset select the Organisms whose associated stocks you would like
  42. to sync. If this list doesn't contain an organism which you know is in Chado go to the
  43. Organism Configuration Page and make sure it is sync'd with Drupal.</p></li>
  44. </ul>
  45. <h3>Features of this Module:</h3>
  46. <ul>
  47. <li><p><b><a href="../../node/add/chado_stock">Create a Generic Stock:</a></b>
  48. This allows you to create content in your drupal and chado for a stock (only the unique stock identifier
  49. is duplicated). A Generic Stock must have a unique name, a type and an organism. In addition, you can
  50. optionally supply a more human-readable name, a primary database reference and even a short description.
  51. The Create Generic Stock form is a multistep form with the first step creating the Basic stock (stored
  52. in the stock table). All the remaining steps are optional and descriptions of each follow:</p>
  53. <ol type="i">
  54. <li>The Next Step is to Add Properties to the newly created stock. Properties allow you to specify
  55. additional details about a given stock. Since the types of properties you can add are goverened by
  56. a controlled vocaulary that you can create, you have complete control over what additional properties
  57. you want to allow.</li>
  58. <li>Then you can Add External Database References. A Database Reference can be thought of as a
  59. synonym for the current stock where you want to specify a source for that synonym. The source
  60. would then be thought of as the database where a database can either be online and provide automatic
  61. linking out to the synonymous record or offline and simply be a text name of the source. To create a
  62. database reference with a given source you must first add the database to
  63. chado <?php print l('here', 'admin/tripal/tripal_db/')?><a href="tadmin/tripal/tripal_db/add_db">here</a>.</li>
  64. <li>Finally you can Add Relationships between Stocks. This allows you to specify, for example, the source
  65. material of a stock or one of it's parents. To create a relationship between your newly added stock and
  66. another stock, the other stock must first be created as this one was. Also, since the types of
  67. relationships is governed by a controlled vocabulary, just like with properties you have complete
  68. control over which relationships you want to allow. Once you click "Finish" you will be re-directed
  69. to the Details Page of the new Stock.</li>
  70. </ol>
  71. </li>
  72. <li><p><b>Details Page of a Stock:</b> Each stock get's it's own page on this website. This page is meant
  73. to give an overall picture of
  74. the stock including listing the basic details, as well as, all properties, database references and
  75. relationships. To understand where it is -All page content in Drupal is known as a node and is given
  76. a unique identifier or nid. Thus every drupal page has a path of node/[nid]. You can get to the
  77. Details page for a given stock from either of the stock listings described below.
  78. If you want to customize the look of the stock Details page simply copy the PHP/HTML template
  79. node-chado_stock.tpl.php from theme_tripal to the base theme you are currently using. Then edit it
  80. as desired. There are plans to integrate this details page with Drupal Panels which will provide a
  81. much more user-friendly and no-programming-needed method to customize this page.</p></li>
  82. <li><p><b>Adding/Updating/Deleting Stocks and their Properties, Database References and Relationships:</b>
  83. The Stock Details Page also acts as a landing pad for updating/deleting stocks.</p>
  84. <p>To <b>update a stock</b>,
  85. go to the stocks details page and click on the Edit tab near the top of the page. This tab will only be
  86. visable if you have permission to edit chado stock content (See post installation steps above for
  87. information on setting user permissions). </p>
  88. <p>To <b>delete a stock</b>, click the Edit tab and
  89. then near the bottom of the form, click the Delete button. This will delete the entire stock including
  90. it's properties, database references and any relationships including it.</p>
  91. <p>To <b>update/delete a given property of a stock</b>, click the "Edit Properties" Tab near the top of
  92. the stock details page. This form provides a listing of all existing properties for the given stock with
  93. form elements allowing you to change their value. After editing the properties you wanted to, simply click
  94. the "Update Properties" button to update all the properties for that stock. To delete a given property
  95. simply click the "Delete" Button beside the property you want to delete. You cannot undo this action!</p>
  96. <p>To <b>add a property to the given stock</b> simply fill out the "Add Property" form at the bottom of
  97. the "Edit Properties" Tab.</p>
  98. <p>For <b>Adding, updating and deleting Database References and Relationships</b> for a given stock is
  99. exactly the same as the method for properties. To edit Database References, click the "Edit DB References"
  100. tab and to add/edit/update stock relationships, click the "Edit Relationships" tab.</p>
  101. </li>
  102. </ul>