Phenotypic Data Importer

[laceysanderson]

Metadata

• Issue #97

• [x] I feel this PR is ready to be merged.
• [x] This PR is dependent upon https://github.com/tripal/tripal/pull/955

Documentation:

• [x] My code follows the code style of this project.
• [x] My change requires a change to the documentation.
• [x] I have updated the documentation accordingly.

Description

This PR creates a Phenotypic Data Importer which uses the TripalImporter class. This was done to

• move away from the drag and drop element to the more standle tripal html5
• allow us to take advantage of file quotas, etc. provided by the Tripal API
• adhere to Tripal standards

This PR is being made before the loader is complete to meet a loading deadline. See the following:

Known Issues

1. Does not support photos
2. Does not support crop ontology term mapping
3. When validation errors are encountered in step 3 the theme is altered.

None of these issues impact the loading of core phenotypic data with this importer.

Testing?

• [x] I tested on a generic Tripal Site
• [ ] I tested on a KnowPulse Clone
• [ ] This PR includes automated testing

PREP: Create a project and organism. See here for more including how to insert germplasm for testing and check database results.

1. Go to Admin > Tripal > Data Loaders > Phenotypic Data Importer
2. Upload a file, select an existing project and genus.
3. Clicking next should execute basic validation (file type, column header).
4. Run the tripal job for step 2 which should do more extensive checking including germplasm existing ahead of time.
5. Fill out the trait information on step 3 and submit the job.

Example files in analyzedphenotypes/tests/example_files.

[laceysanderson]

Okay, your problems were twofold:

1. Because you had the crop ontology set it triggered code I hadn't tested. The most recent commit comments out that code and removes the error you recieved.
2. The import button showed up when it shouldn't have. This was due to this PR being dependent upon https://github.com/tripal/tripal/pull/955. Please switch to this branch for Tripal

[carolyncaron]

Thanks Lacey!

There are a few issues I ran into that don't necessarily impact the functionality (I think), but addressing them would greatly improve the experience for the user.

• Double quotes prevent certain values from being inserted into the database and no error is given on the page, although a PDO Exception occurs at the end of the Tripal job (after 100% loading complete) regarding not null constraints. I've confirmed that Method Name and Unit have this issue. Location does not, and the quotes are stripped upon db insert.
  • I also noticed that when the quotes were present in the method and/or unit, the summary table rendered as empty. Once I removed the quotes, the summary was there.
• On Stage 3, at one point my Unit contained brackets. I was unable to submit the form because of this and the error was descriptive, but there was no way to change my unit text as the text field was greyed out, so I was forced to change my file and start again. I imagine this to be extremely frustrating during a scenario where there is multiple traits, and the user is not notified of the issue until they try to submit.
• Once I submit the form in Stage 3 (the button reads as "Next Step" which is misleading as there are no more steps), I am immediately redirected to Stage 1 which was very disorientating.

[laceysanderson]

The suggestions brought up by @carolyncaron and the known issues mentioned in the description have been moved to issue #101. I also removed the old uploader so as not to cause confusion.