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Feature/postgres database #523
Commits on Mar 8, 2019
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changed database connection type; playhouse.postgres_ext requires Pos…
…tgresqlExtDatabase
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other_names for a gene is now in a separate table
Import changes done according to planned DB schema changes.
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Skip lines with non-standard rsid
This should probably be handled more carefully
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feat: Change mysql database to postgres database
This removes the MySQL schema and replaces it with postgres schemas, as well as updating the test dummy data.
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feat: Rewrite travis tests to use postgres
Replaces mysql tests with postgres tests. No new tests are added, the old tests are just rewriten for postgres.
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Save sampleCount in sample_sets, add parameter to import script
Information from `NS` or header in vcf gets saved to data.sample_sets.sample_size (No changes to db schemas needed anymore!)
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Add parameters for assembly_id and beacon_description
assembly_id sets data.dataset_versions.var_call_ref (remember to update beacon schema) beacon_description sets data.datasets.beacon_description sampleset_size sets a cusom sampleset size set_vcf_sampleset_size sets the sampleset size according to the vcf
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use beacon fix for A[NC] for all datasets without A[NC]_adj. Also che…
…ck that gene identifiers contain ENSG
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feat: Add option to specify settings file
Martin Norling committedMar 8, 2019 Configuration menu - View commit details
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Commits on Mar 14, 2019
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Commits on Mar 15, 2019
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Commits on Mar 18, 2019
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feat: Remove dbSNP and OMIM data
Removes dbSNP and OMIM data, as we felt that they did not contribute enough to the system.
Martin Norling committedMar 18, 2019 Configuration menu - View commit details
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feat: Adapt beacon schemat to schema changes
Adds indexes to beacon schema, changes views to work with changes in the data schema, and adds beacon schema to docker-compose.
Martin Norling committedMar 18, 2019 Configuration menu - View commit details
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use minimal representation for variants
Also avoid recalculation of identical data structure
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Merge pull request #527 from NBISweden/hot_fix/bug_fix
Attempt to get code to work: don't reference data before it is created
Linus Östberg authoredMar 18, 2019 Configuration menu - View commit details
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Commits on Mar 19, 2019
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test: Fix travis tests for postgres update
Martin Norling committedMar 19, 2019 Configuration menu - View commit details
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Commits on Mar 20, 2019
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a few fixes for batch management
- check batch size using >= - check if batch: instead of if len(batch): - no need to reset batch at end - a few formatting changes
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Commits on Mar 21, 2019
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Commits on Mar 22, 2019
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