Tripal User's Meeting 2019/11/05

Agenda

Community Highlights

Please add anything you would like to highlight about your Tripal-based projects: publications, new extension modules, new collaborations, newly funded grants, project update, etc.  We won't talk about these in the meetings but may tweet them from the Tripal twitter account if you approve!

Agenda

1. Messages from the PMC (Lacey Sanderson, Bradford Condon, Stephen Ficklin)

   • Tripal v4 Update

2. Messages from the TAC Chair (Meg Staton)

   • None at this time.

3. PAG  Workshop & Hackathon Committee (Lacey Sanderson, Jill Wegrzyn, Chris Childers)

   • New Abstract Deadline: November 8

     1. There are still open time slots!

   • Suggestions for Hackathon Working Groups

     1. Tripal 4 (upgrade of Tripal 3 to Drupal 8)

     2. Chado Updates

     3. Tripal file module development

     4. Genome Project/Assembly pages

   • Request for an afternoon for a TAC meeting (perhaps Friday afternoon)

4. File Module Request for Input  (Sean Buehler)

   • Original document

   • Recent document

   • Original Scope

     1. To automatically create download links on data pages.

     2. To provide access to files via web services.

        1. For file access (where are the files and downloading them)

        2. Random access to the file.

     3. To allow for data retrieval from indexed files for data that is not conducive for storage in Chado (e.g. genomic alignments in BAM files).

     4. Provide access control for files.

   • New ideas

     1. To be implemented as a "File" field to be associated with any given bundle type

     2. Manage both local and remote files (HTTP or FTP)

     3. Enable (or provide) file housekeeping

        1. Periodically check that all listed files are available/correct (md5?)

        2. Some kind of version control

     4. Interface with the loaders - when a file is loaded, also gets stored as a flat file

        1. Lacey:  add files uploaded via loaders to be re-used in an "existing files" drop down.

     5. Enforce standards

        1. file organization structure (IE folders) and/or standard file names

        2. file format checking (lightweight)

        3. DOI and licensing for files

5. Training MegaSearch Module (Chun-huai Cheng)

   • Repository: https://gitlab.com/mainlabwsu/tripal_megasearch

   • Supports Drupal 7 (tripal 2 or 3)

   • Allows for download of data from chado and searching

   • You can limit the number of results a user can download

   • There is a single page where the user can choose the data type they are interested in. Then they are given a form specific to that data type that they can use to filter the results

   • Counts of results are shown before download and can be refreshed based on filters

   • You can change the output by selecting different fields

   • Some data types (e.g. genes) offer download of fasta file format. All support tab-delimited (excel).

   • Publication has a dynamic query form which can be built up one field at a time to restrict to results

   • Installation instructions are on the Readme

   • You can either serve data from the chado base tables or from the materialized views distributed with this module.

   • Static forms work best with the materialized views (some predefined with module)

   • If there is no static form available then it will fall back to the dynamic form.

   • There is a configuration form at Mainlab > Tripal MegaSearch

     1. Includes download limits, instruction text, remove duplicates, number of rows, disable view result, etc.

   • You can set up support for custom data types in the module/conf directory

     1. Example with documentation: https://gitlab.com/mainlabwsu/tripal_megasearch/blob/master/conf/tripal_megasearch.mviews.inc#L3-27

     2. Key of definition array matches to the underlying database table. You can then define which fields are available for the user to filter on in the ‘fields’ key. Specifically the key is the column name and the value is the label on the site.

   • Only supports public data. Make sure that the materialized view does not populate with private data