Germplasm Cross Importer: Available documentation!¶

Features¶

Germplasm Cross Importer is developed following Tripal Developer’s Guide » Creating Custom Data Loaders. This module is developed for bulk load germplasm crosses into database.

File Upload¶

Format requirements for upload files can be found easily in UI while using this module.

Prefix and Organism¶

Organism must be selected from dropdown menu before upload. Prefix text box is optional to fill in and default the value is ‘GERM’. The uniquename for each germplasm will be ‘GERM’ followed by it’s stock id but user can give a unique prefix to replace ‘GERM’.

Bulk load germplasm crosses¶

As Chado is the data store for Tripal, germplasm data will be saved in five chado tables: cv, cvterm, stock, stockprop, and stock_relationship in this module.

required control vocabularies (CVs) and CV terms will be checked before data loading

germplasm crosses will be loaded into table stock

properties for each germplasm will be loaded into table stockprop

relationships with parents for each germplasm will be loaded into table stock_relationship

Note

CVs and CV terms used in this module is customized for our database. Users can check their own database and modify CVs and CV terms accordingly.

PHP UnitTest¶

PHP UnitTest is created to guarantee the integrity of data insertion.

Installation¶

Note

It is recommended to clear cashes regularly in this installation processes.

Download Module¶

The module is available as one repository for Pulse Bioinformatics, University of Saskatchewan on GitHub. Recommended method of downloading and installation is using git:

cd [your drupal root]/sites/all/modules

git clone https://github.com/UofS-Pulse-Binfo/tripal_germplasm_importer.git

Germplasm Cross Importer should be installed by now and the status of this module can be checked in “Home » Administration » Tripal » Modules”.

_images/install.1.tripal_module_page.png

Enable Module¶

The module can be enabled in “Home » Administration » Tripal » Modules” by select the checkbox under “ENABLED” column (as shown in above image) and then click on “Save Configuration” button by the bottom of page.

Another method that can enable our module is using drush:

drush pm-enable tripal_germplasm_importer

Use Module¶

After Germplasm Cross Importer is installed and enabled, it should be ready to use in “Home » Administration » Tripal » Data Loader”.