Comments (2)
Keeping this open as the blastx, tblastn, blastp forms still need their advanced options and the ability to upload files is also broken. That said, I think the functionality that is there does work 🤔 although it's hard to tell because the result page and the blast submission job itself are broken 🙈
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More detail for how to finish the upgrade of these forms:
For each of the forms,
- Copy the form elements from the Tripal 3 version. The form elements are in the tripal_blast/includes/blast_ui.form_advanced_options.inc file, function matching the pattern blast_ui_BLASTPROGRAM_advanced_options_form where you replace BLASTPROGRAM with one of the three to be upgraded.
- Paste them into the $form_alter array in the formOptions() function of the associated Tripal 4 service. These services are found in the src/Services/ directory and include the Blast Program in their name.
- Go to the page for that blast program in your Tripal site where the code changes were made and confirm that they show up similarly to how they did in Tripal 3.
Notes
- The validate and submit will also need to be transferred over but we will wait to do this until later as currently it is hard to confirm that has been done without error.
- The blastn program has already been done so that can be used as an example.
- The Tripal 3 code can be found here: tripal_blast/includes/blast_ui.form_advanced_options.inc
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Related Issues (20)
- Tripal Blast doesn't show up in the Extensions listing
- Blast Overview Javascript issues
- Current Documentation HOT 1
- Unable to install via Composer
- Undefined array key "cvitjs_location" in blast_ui HOT 2
- 'File is not accessible' issue in tripal blast (related to sites/default/files/tripal_blast/ or /tmp?) HOT 2
- Error - "File is not accessible" HOT 2
- max_target_seqs parameter HOT 3
- Overly aggressive regex to remove database extension in api/blast_ui.api.inc HOT 1
- Undefined variable HOT 1
- Trimming of input sequence HOT 1
- Issues with online docs HOT 2
- Blast analyses failed: "We encountered an error and are unable to load your BLAST results" HOT 4
- Upgrade to Tripal 4 + Drupal 9 HOT 10
- Progressive Display Controls HOT 1
- PHP8 Deprecation warnings HOT 1
- PHP8 catches mismatched parameter names HOT 1
- Tripal blast not run smoothly when using 'drush trp-run-jobs' command line HOT 4
- Modify queue priority of BLAST jobs
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