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bradfordcondon / tripal_cvb

Tripal CV Browser extension.

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Tripal CV Browser Extension Module

CONTENTS OF THIS FILE

  • Introduction
  • Requirements
  • Installation
  • Configuration
  • Actions
  • Q & A
  • Maintainers

INTRODUCTION

This module can be used to display and browse a hierachical tree representation of any controlled vocabulary (CV) stored into Chado (cvterm table). The vocabulary to browse must have relationships stored into the cvterm_relationship table where the children term is the subject (subject_id) and the parent term is the object (object_id). Circular relationships and network relationships are not an issue since the tree is not generated nor loaded when the CV browser page is accessed; Only root elements are displayed and each first level of a subtree is loaded (ajax) when the used click on the parent node.

A generic CV browser page can be used to browse any CV from CV root term(s) or from user-selected terms. The URL of the page can be constructed this way: 'tripal/cvbrowser/' + <either 'cv' or 'cvterm', depending on the type of identifiers provided after> + <CV or CV term identifier(s) or name(s) (separated by "+" signs if more than on value is provided)>. Examples:

  • tripal/cvbrowser/cv/biological_process+molecular_function+cellular_component
  • tripal/cvbrowser/cvterm/1234

REQUIREMENTS

This module requires the following:

INSTALLATION

CONFIGURATION

  • Configure the CV browser in "Administration > Tripal > Extensions > Tripal CV Browser > Settings" (/admin/tripal/extension/tripal_cvb).

  • Configure user permissions in "Administration > People > Permissions" (/admin/people/permissions):

    • "Use tripal cv browser page": allows users to access to the generic CV browser page. With this permission, any CV or CV term can be browsed as the user only needs to know the CV name or CV cv_id or CV term name or CV term cvterm_id in order to use it in the browser page URL. If you want to restrict CV browsing, then do not give this permission to your users.

    • "Administer Tripal CV Browser": allows users to access to the CV browser administration pages and see the administration help page.

  • After creating custom CV browser(s), place them on your site using the block configuration page in "Administration > Structure > Blocks" (admin/structure/block). You can also configure access permission and block visibility for each block using their "configuration" link. If you prefer to have your browsers displayed as a page instead of a block, you can use the Drupal path 'tripal/cvbrowser/browser/' + the CV browser machine name. In this case, access are managed using the "Use tripal cv browser page" permission.

ACTIONS

Actions are operations that can be performed automatically or by a user click on a term of a CV browser. There are several types of actions:

  • View: it uses a display of a Drupal view to render something given a "cvterm_id" as parameter. The "use Ajax" setting of the view display must be turned on.

  • Path: it uses a Drupal path and append a given "cvterm_id" to it as parameter in order to display the associated page content if no other pattern has been specified in the path. Otherwise, the "%" character will be replaced by the "cvterm_id". It is also possible to use the following replacement patterns:

    • "!cvterm_id": will be replaced by the Chado "cvterm_id"; ex.: "41"
    • "!cvterm": will be replaced by the CV term name; ex.: "organelle inheritance"
    • "!dbxref_id": will be replaced by the Chado "dbxref_id"; ex.: "46"
    • "!accession": will be replaced by the CV term accession (identfier) on the database it comes from; ex.: "0048308"
    • "!cv": will be replaced by the CV name; ex.: "biological_process"
    • "!cv_id": will be replaced by the Chado "cv_id"; ex.: "15"
    • "!db": will be replaced by the database name the CV term comes from. ex.: "GO" ex.: "admin/tripal/chado/tripal_cv/cv/15/cvterm/edit" would become "admin/tripal/chado/tripal_cv/cv/15/cvterm/edit/41" and "admin/tripal/chado/tripal_cv/cv/!cv_id/cvterm/edit/!cvterm_id" would become "admin/tripal/chado/tripal_cv/cv/15/cvterm/edit/41"

  • External URL: it displays a link to an external site page. Several parameters can be replaced in that URL if you use the following placeholders:

  • Javascript: it executes the given javascript function name given it a "cvterm" object as only argument. This object has the following properties:

    • "name": the CV term name; ex.: "organelle inheritance"
    • "cv": the CV term CV name; ex.: "biological_process"
    • "definition": the CV term definition; ex.: "The partitioning of organelles between daughter cells at cell division. [GOC:jid]"
    • "db": the CV term database of origin name; ex.: "GO"
    • "urlprefix": the CV term database URL prefix; ex.: "http://amigo.geneontology.org/amigo/term/GO:"
    • "dbxref": the CV term database accession; ex.: "0048308"
    • "is_obsolete": the CV term "obsolete" status (boolean "0" or "1"); ex.: "0"
    • "is_relationshiptype": the CV term "relationship type" status (boolean "0" or "1"); ex.: "0"
    • "relationship": the name of the relationship between the CV term and its parent term; ex.: "is_a"
    • "children_count": the number of children of the CV term; ex.: "7"
    • "cvterm_id": Chado cvterm_id; ex.: "41"
    • "cv_id": Chado cv_id; ex.: "15"
    • "dbxref_id": Chado dbxref_id. ex.: "46" ex.: "Drupal.tripal_cvb.cvtermDump" (this is a function provided by this module) which prototype is ("Drupal" is a predefinied variable): "Drupal.tripal_cvb.cvtermDump = function (cvterm) { ... };"

Action field (ie. action to use) content depends on the type of action. For "View", it must contain "the view machine name" + colon + "the display id" but the user interface separate these parameters into 2 dedicated fields for convenience. For "Path", it must be the Drupal path with or without ending slash. For "External URL", it must be the full URL (replacement patterns were described in previous paragraph). And finally, for "Javascript", it must be the function name without parenthesis or any other piece of code.

"Link label" is the label of the action that is displayed before the action has been executed.

The Auto-run checkbox setup if the action should be executed when the page is loaded or when the user clicks on the action link. This setting is ignored by the "External URL" type of action.

The target defines where the output of the action should be displayed (setting ignored by External URL and Javascript). There are 3 types of targets:

  • Term line: it will be displayed on the same line as the CV term on the CV browser tree.

  • Theme region: it will be displayed on a region of the current Drupal theme.

  • DOM object identifier: it will be displayed in the HTML element matching the given identifier (it is based on jQuery selectors). By default, it will be the CV term element.

The target identifier is used to identify the corresponding target according to its type: it is ignored for the Term line, it is the region machine name for the Theme region and it is a jQuery selector for the DOM object identifier.

The last setting is the insertion method: "Replace" will replace the content of the corresponding target and "Append" will add the content to the given target. Note: the target settings are ignored for the "External URL" type of action.

Q & A

Q: How can I remove the "[is a]" and "[part of]" prefix on my browser? A: You have to override the CSS styles: .tripal-cvb-relationship-is_a >.tripal-cvb-cvterm:before and .tripal-cvb-relationship-part_of >.tripal-cvb-cvterm:before

For instance: .tripal-cvb-relationship-is_a >.tripal-cvb-cvterm:before, .tripal-cvb-relationship-part_of >.tripal-cvb-cvterm:before { color: inherit; content: "" !important; padding-right: 0; }

Q: Can I customize the tree nodes according to their parental relationship? A: Yes, use CSS class names of the form: "tripal-cvb-relationship-" + relationship name with groups of non-word characters replaced by a single "". ex.: "part of" becomes "tripal-cvb-relationship-part_of". "weird 'relationship'" becomes "tripal-cvb-relationship-weird_relationship".

MAINTAINERS

Current maintainers:

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Tripal CV Browser extension.

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