tripal/legacy/tripal_stock/theme/templates/tripal_stock_help.tpl.php

<h3>Tripal Stock Quick Links</h3>
<ul>
    <li><?php print l(t('Configuration'), 'admin/tripal/tripal_stock/configuration') ?></li>
    <li><?php print l(t('Stock Listing'), 'stocks') ?></li>
</ul>
<br>
<h3>Module Description:</h3>
<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>

<h3>Setup Instructions:</h3>
<ul>
    <li><p><b>Set Permissions</b>: By default only the site administrator
            account has access to create, edit, delete
            or administer analyses. Navigate to
            the <?php print l('permissions page', 'admin/user/permissions') ?>
            and set the
            permissions under the 'tripal_stock' section as appropriate for your
            site. For a simple setup, allow anonymous
            users access to view content and create a special role for creating,
            editing and other administrative tasks.</p></li>

    <li><p><b>Set Ontologies</b>: Since at the time of this modules developement
            there is no accepted ontology for
            describing stocks, their properties and relationships, this module
            allows you to select the controlled
            vocabularies (CVs) in your Chado Database you would like to govern
            these data. To Set the Controlled Vocabularies for Stocks:
            First, ensure your Controlled Vocabulary is in Chado. This can be
            done by either loading an existing Ontology into Chado using
            the <a href="tripal_cv/ontology_loader">Tripal Ontology Loader</a>
            OR create your ontology from scratch by first
            <a href="tripal_cv/add_cv">creating a controlled vocabulary</a> and
            then <a href="tripal_cv/add_cvterm">adding terms to it</a>.
            Then go to the <a href="tripal_stock/configuration">Configuration
                Page for Stocks</a> and, in the "Set Stock Controlled
            Vocabularies" Fieldset,
            select the Controlled Vocaulary name for Stock Types, Stock
            Properties and Stock Relationship Types.</p>
        <ol type="i">
            <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>
            <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>
            <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>
        </ol>
    </li>

    <li><p><b>Set Permissions</b>: The stock module supports the Drupal user
            permissions interface for
            controlling access to stock content and functions. These permissions
            include viewing,
            creating, editing or administering of
            stock content. The default is that only the original site
            administrator has these
            permissions. You can <a href="<?php url('admin/user/roles') ?>">add
                roles</a> for classifying users,
            <a href="<?php url('admin/user/user') ?>">assign users to roles</a>
            and
            <a href="<?php url('admin/user/permissions') ?>">assign
                permissions</a> for the stock content to
            those roles. For a simple setup, allow anonymous users access to
            view organism content and
            allow the site administrator all other permissions.</p></li>
    <li><p><b>Sync Stocks</b>: if you chado database already contains stocks,
            they need to be sync'd with Drupal.
            This creates Drupal Content including detail pages for each stock
            (known as nodes in Drupal). To sync' Chado
            with Drupal simply go to
            the <?php print l('stock configuration page', 'admin/tripal/tripal_stock/configuration') ?>
            and in the "Sync Stocks" Fieldset select the Organisms whose
            associated stocks you would like
            to sync. If this list doesn't contain an organism which you know is
            in Chado go to the
            Organism Configuration Page and make sure it is sync'd with Drupal.
        </p></li>
</ul>
<h3>Features of this Module:</h3>
<ul>
    <li><p><b><a href="../../node/add/chado_stock">Create a Generic
                    Stock:</a></b>
            This allows you to create content in your drupal and chado for a
            stock (only the unique stock identifier
            is duplicated). A Generic Stock must have a unique name, a type and
            an organism. In addition, you can
            optionally supply a more human-readable name, a primary database
            reference and even a short description.
            The Create Generic Stock form is a multistep form with the first
            step creating the Basic stock (stored
            in the stock table). All the remaining steps are optional and
            descriptions of each follow:</p>
        <ol type="i">
            <li>The Next Step is to Add Properties to the newly created stock.
                Properties allow you to specify
                additional details about a given stock. Since the types of
                properties you can add are goverened by
                a controlled vocaulary that you can create, you have complete
                control over what additional properties
                you want to allow.
            </li>
            <li>Then you can Add External Database References. A Database
                Reference can be thought of as a
                synonym for the current stock where you want to specify a source
                for that synonym. The source
                would then be thought of as the database where a database can
                either be online and provide automatic
                linking out to the synonymous record or offline and simply be a
                text name of the source. To create a
                database reference with a given source you must first add the
                database to
                chado <?php print l('here', 'admin/tripal/tripal_db/') ?><a
                        href="tadmin/tripal/tripal_db/add_db">here</a>.
            </li>
            <li>Finally you can Add Relationships between Stocks. This allows
                you to specify, for example, the source
                material of a stock or one of it's parents. To create a
                relationship between your newly added stock and
                another stock, the other stock must first be created as this one
                was. Also, since the types of
                relationships is governed by a controlled vocabulary, just like
                with properties you have complete
                control over which relationships you want to allow. Once you
                click "Finish" you will be re-directed
                to the Details Page of the new Stock.
            </li>
        </ol>
    </li>

    <li><p><b>Details Page of a Stock:</b> Each stock get's it's own page on
            this website. This page is meant
            to give an overall picture of
            the stock including listing the basic details, as well as, all
            properties, database references and
            relationships. To understand where it is -All page content in Drupal
            is known as a node and is given
            a unique identifier or nid. Thus every drupal page has a path of
            node/[nid]. You can get to the
            Details page for a given stock from either of the stock listings
            described below.
            If you want to customize the look of the stock Details page simply
            copy the PHP/HTML template
            node-chado_stock.tpl.php from theme_tripal to the base theme you are
            currently using. Then edit it
            as desired. There are plans to integrate this details page with
            Drupal Panels which will provide a
            much more user-friendly and no-programming-needed method to
            customize this page.</p></li>

    <li><p><b>Adding/Updating/Deleting Stocks and their Properties, Database
                References and Relationships:</b>
            The Stock Details Page also acts as a landing pad for
            updating/deleting stocks.</p>
        <p>To <b>update a stock</b>,
            go to the stocks details page and click on the Edit tab near the top
            of the page. This tab will only be
            visable if you have permission to edit chado stock content (See post
            installation steps above for
            information on setting user permissions). </p>
        <p>To <b>delete a stock</b>, click the Edit tab and
            then near the bottom of the form, click the Delete button. This will
            delete the entire stock including
            it's properties, database references and any relationships including
            it.</p>
        <p>To <b>update/delete a given property of a stock</b>, click the "Edit
            Properties" Tab near the top of
            the stock details page. This form provides a listing of all existing
            properties for the given stock with
            form elements allowing you to change their value. After editing the
            properties you wanted to, simply click
            the "Update Properties" button to update all the properties for that
            stock. To delete a given property
            simply click the "Delete" Button beside the property you want to
            delete. You cannot undo this action!</p>
        <p>To <b>add a property to the given stock</b> simply fill out the "Add
            Property" form at the bottom of
            the "Edit Properties" Tab.</p>
        <p>For <b>Adding, updating and deleting Database References and
                Relationships</b> for a given stock is
            exactly the same as the method for properties. To edit Database
            References, click the "Edit DB References"
            tab and to add/edit/update stock relationships, click the "Edit
            Relationships" tab.</p>
    </li>
</ul>