TODO.md

InjectTool TODO

• Data export: How data needs to be exported? How IMAGE metadata works?

  • IMAGE metadata defines fields in .xls used for import. There is a correspondance between IMAGE metadata columns and UID database columns
  • Exporting data in IMAGE metadata excel template, could be useful for data cleaning?
  • if needed, should be implemented using django-rest-framework

• Regarding data submissions

  • implement the sameAs key for already submitted biosamples:

    "sampleRelationships": [
      {
        "relationshipNature": "same as",
        "alias": "502-W-133-4FE274B"
      }
    ]
    

  • Supposing a submission has issues in USI validation. Shuold I track it in validation tables? should I have tables for USI errors, since if the data is validated using image_validation is not a user error?

• NGINX media folder can serve media files (jpg, etc).

  • add subdirs in media folder data_source/ - using a subdir for each template could avoid name collision and visualize the original file name

• Django enhancements

  • all foreign keys in django.admin dropdown lists are rendered in HTML page, and this make the pages bigger. At the moment, pages are rendered using raw_id_fields as described here. Others solutions could be autocomplete fields or using django-salmonella
  • see django_filters and django_tables. For an example tutorial see here
  • django-pgcrypto?

• Regarding Data validation:

  • reloading submission should invalidate validationresults

• Regarding EditSubmissionView

  • search?

• Regarding django 3rd party modules:

  • Install django.contrib.sites (it is useful?)
  • Use django-bootstrap4 to render forms
  • django-braces: it is useful?
  • read about django session
  • django-crispy-forms

• Regarding tests:

  • implement functional testing
  • test each management command, or at least that it works

• Regarding languages, dictionaries and ontology terms:

  • browse by languages, see all synonym in every language (add navigation links)
  • add a custom synonym manually

• Regarding site visualization

  • Token generation could be requested using modals when submitting to biosample, there's no difference from a web page, however, is only aesthetic
  • Add breadcrumb for pages
  • serving all 3rd party modules using CDN when possible
  • Pagination: missing jumping to a particular page function

• Issues relative to UID:

  • display the real name of file for the uploaded file
    • not so easy, maybe: add a CharField for user filename; Create a custom django.forms.fields.FileField or a validation function that track the realfilename and set it to a hidden field. Save to a model.CharField and display that field in DetailViews
    • add the uploaded time for file?
  • Change WAITING in PROCESSING (implies something happening)
  • Submission.message as ArrayField (to store more messages?)

• Relate to templatetags

  • process and render pagination with get parameters. See:
    • https://simpleisbetterthancomplex.com/snippet/2016/08/22/dealing-with-querystring-parameters.html
    • https://gist.github.com/benbacardi/d6cd0fb8c85e1547c3c60f95f5b2d5e1
  • customize queryset
  • Read documentation about advanced templatetags

• Related to CRBanim

  • deal with biosample records