GitLab

Fixed LOVD light

- This view is currently not linked to from LOVD+, unless public variants are present, but it's always reachable.

- Don't define in multiple places that VOT columns aren't shared for LOVD+ and LOVD light.
- Also, LOVD+'s method of removing columns for all when turning off the public flag, should not be introduced in LOVD light.

- It was false when the variants VL should only be shown per chromosome.

- VOT columns aren't shared in LOVD light!

Fixed bug; HGNC IDs weren't handled well in the submission API.

- ctype_digit() doesn't work always on integers.
- Closes #492.

Added links to Orphanet from the gene homepages.

- Removed Orphanet links from the 2Do.
- Fixed typo in changelog.
- Updated copyright to 2021 in template.

- Version bump to 3.0-25c.

Fixed query error.

- We require HTTPS now on the live site.

Fixed bug; VOT's updateAll() didn't handle numeric column like updateEntry() does, resulting in query errors for empty fields.
- These fields should have been caught and transformed into NULL values.

Automatically add the Entrez ID and OMIM ID to genes when editing them.

When a gene has no Entrez ID or no OMIM ID but the HGNC does know these IDs now, LOVD will add them when the gene is edited.
- The gene must be created or last edited at least one week ago for LOVD to check for these IDs.
- Closes #483.

Attempt to fix test timeouts.

- Let the test continue to the full download test, so I can see which gene stopped working.

- This should print the progress of the process every 5 seconds for one minute, so we can see if it actually gets stuck or if it is just terribly slow.

Attempt to fix repeated random failures of the tests by re-clicking a button when the previous click didn't seem to do anything.

Fixed missing proper checks on select field values.

Removed Conversion variant type.

- Extended matching of delins variants, allowing for positions.
- These positions actually require c. or g. when a reference sequence in included.
- Removed some verification of the "con" variant type, it's rejected for HGVS checks (but still supported for getting positions).

// See: http://varnomen.hgvs.org/bg-material/consultation/svd-wg009/

Change 'Ter' amino acid to '*'.