- 08 Aug, 2019 2 commits
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Fokkema authored
- Can now also handle DOIs. - Added support for {PMID:PubMed 2019 abstract:12345678} format. The script will fetch the paper's author and year using eutils and rewrite the reference to {PMID:Author et al (Year):12345678}. - Implemented a cache to make sure eutils doesn't get the same question twice. - Updated lovd_callJSONService() to be able to return an array instead of an object.
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Fokkema authored
Reverted ONLY_FULL_GROUP_BY changes.
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- 07 Aug, 2019 3 commits
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Fokkema authored
- It makes no sense to order on something, if we do a GROUP BY on the PK that we also do a WHERE on. Only one line will be returned anyway. - Added sorting to the GROUP_CONCAT() so that the gene symbols will be sorted in the email's subject. - Don't overcomplicate the query for fetching curators.
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Fokkema authored
- Don't pull out extra fields out of the database, just because we're sorting on it. - Don't sort on a field alias if you can sort on the actual fields.
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Fokkema authored
- Genes are assumed to be in sense when at least one transcript is in sense.
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- 06 Aug, 2019 4 commits
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Fokkema authored
- Also simplified SELECTs whereever possible. - Custom VLs with VOG as the first table (Variant VL on Screenings VE and Individual VE) no longer show the minimal VOT's effectid, but instead the VOG's effectid, which makes much more sense. - These changes might also lead to some speedups.
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Fokkema authored
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Fokkema authored
- Reviewed all MIN()/MAX() uses. - For BED files, always return the mapping on the earliest transcript. - For the genes list, assume the gene is in sense when at least one transcript is in sense.
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Fokkema authored
Fix `variants/in_gene` view.
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- 05 Aug, 2019 1 commit
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Fokkema authored
- Removed more min() and max() calls.
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- 01 Aug, 2019 4 commits
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Fokkema authored
- This speeds up the query quite a lot. - Also, rename LEFT JOINs to LEFT OUTER JOINs to make more clear what they are.
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Fokkema authored
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Fokkema authored
- Even if we try to play nice, the totally unnecessary MIN() and MAX() calls slow down queries a lot. - See #386.
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Fokkema authored
Fixed some problems with the DOI view.
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- 31 Jul, 2019 3 commits
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Fokkema authored
- Pagination was off, but especially if you're searching by journal you need pagination. - Fixed the journal search; DOIs can also contain slashes and journal names can contain dots. - Cleaned up the code a bit.
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Fokkema authored
Allow for publisher and journal-specific queries using the DOI reference search.
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Fokkema authored
Enlarge the DNA and protein fields to support longer insertions.
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- 30 Jul, 2019 5 commits
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Fokkema authored
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Fokkema authored
- Normally DOI reference searches are on the full DOI only (like 10.1002/humu.21438). Now, also allow for searches using the journal's DOI, like 10.1002/humu. - Implements #257.
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Fokkema authored
- This allows for larger insertions to be stored. - LOVD+ is using the same size, so this also removes one difference between LOVD3 and LOVD+.
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Fokkema authored
- This allows for larger insertions to be stored. - LOVD+ is using the same sizes, so this also reduces one difference between LOVD3 and LOVD+.
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Fokkema authored
Multiple bug fixes.
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- 29 Jul, 2019 1 commit
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Fokkema authored
Updated the ReadingFrameChecker; it now provides the correct (new) HGVS nomenclature.
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- 25 Jul, 2019 9 commits
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Fokkema authored
The public gene-specific downloads now have these non-public columns removed from the Phenotype object as well.
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Fokkema authored
- Selected user's IDs where stored in both userid and id. Since the latter is visible, part of this selection could be influenced. Now only userid is used, making the filtering of the VL complete invisible to the user. - Also, when selecting users as curators/collaborators, their ID wasn't added to their name, like with previously selected users.
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Fokkema authored
- The dropdown became too large on large databases. - The VL is much better equipped to handle large datasets. - The output is restricted for curators in case they curate 25 genes or less. - The currently selected gene is highlighted.
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Fokkema authored
A download will now no longer show inactive Phenotype and VOT columns, if filters are active for Diseases or Genes, respectively. - This cleans up the file a lot for single-gene downloads. - It reports a warning for Phenotype data, since it's possible that data is selected unrelated to the selected Disease(s).
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Fokkema authored
The public gene-specific downloads had some non-public columns included, like status, created_by, created_date, etc. - These are now removed. They're not damaging to be shared, but they're not shown on VLs or VEs, so they should remain hidden in the download as well.
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Fokkema authored
- Now, it'll take the VOG's effectid and it'll copy it.
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Fokkema authored
- The old notation (c.154-?_295+?del) was not correct anymore. - The new notation is c.(153+1_154-1)_(295+1_296-1)del.
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Fokkema authored
Allow LOVD3 to nicely display JSON data in fields.
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Fokkema authored
Fixed bug; lovd_getVariantInfo() didn't recognize delins variants.
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- 24 Jul, 2019 2 commits
- 28 Feb, 2019 1 commit
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Fokkema authored
Fix optimizer for complex queries.
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- 18 Feb, 2019 3 commits
- 15 Feb, 2019 2 commits