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2020-11-14SPARQLplayground: Adding additional examplelltommy
2020-11-14Adding an additional example to the SPARQL playgroundlltommy
2020-11-13fix check date sra scriptAndreaGuarracino
2020-11-13generation of dates a little more robustAndreaGuarracino
2020-11-13to not create YAML files with date before 2019 DecemberAndreaGuarracino
2020-11-13there can be two specimen termsAndreaGuarracino
2020-11-13Initial commit: SPARQL playground, which replaces the demo page. Some ↵lltommy
queries have to be adjusted once changed metadata schema is live
2020-11-13Yaml and ShEx changeslltommy
2020-11-13fix in the ids to considerAndreaGuarracino
2020-11-13added ids-to-consider option to the NCBI scriptAndreaGuarracino
2020-11-12added closed shapesAndreaGuarracino
2020-11-12added missing _type: "@id" to the assembly_method field in the schemaAndreaGuarracino
2020-11-12managed the assembly_method in the scripts, doc, and the example templatesAndreaGuarracino
2020-11-12updated alignment_protocol field in the script, doc, and the example templatesAndreaGuarracino
2020-11-12Trying to fix the submitter shape, shex and yamllltommy
2020-11-12Proposed new technology shape/yaml structurelltommy
2020-11-11Support uploading new metadata onlyPeter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-11-11Merge branch 'master' of https://github.com/arvados/bh20-seq-resourcelltommy
2020-11-11Adding GPS coordinates and contitent membership for Memphis and Canadalltommy
2020-11-11Make collect-seqs skip bad inputs.Peter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-11-11Documenting and QC of YAML. Some conflicts discovered that need reviewlltommy
2020-11-11Fix resolving permalinks such as ↵Pjotr Prins
http://covid19.genenetwork.org/resource/MT326090.1
2020-11-11NotesPjotr Prins
2020-11-11Conflict in guix-deployPjotr Prins
2020-11-11DeployPubSeq webserver
2020-11-11DeploymentPjotr Prins
2020-11-11Move files to correct folderlltommy
2020-11-11Merge branch 'master' of https://github.com/arvados/bh20-seq-resourcelltommy
2020-11-11Adding covid death and covid cases per country as additional background ↵lltommy
information
2020-11-11create_sra_metadata script doesn't trick the quality control about missing ↵AndreaGuarracino
date aymore
2020-11-11Merge branch 'master' of https://github.com/arvados/bh20-seq-resourcelltommy
2020-11-11restricting specimen_source to obo:NCIT which would have prevented the ncbi ↵lltommy
taxon bug
2020-11-10Valid uploads with sequence_label in PubSeq replaces old one.Peter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-11-10Merge pull request #116 from arvados/uuid-for-resourcePeter Amstutz
Use arvados uuids for RDF subjects.
2020-11-10Use arvados uuids for RDF subjects.uuid-for-resourcePeter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-11-10Merge pull request #114 from BonfaceKilz/feature/add-twitter-feedPjotr Prins
Feature/add twitter feed
2020-11-10Demo links to permalink for countriesPjotr Prins
2020-11-10Delete unused endpointBonfaceKilz
* bh20simplewebuploader/main.py (feed): Remove it.
2020-11-10Fetch tweets from the correct redis queueBonfaceKilz
* bh20simplewebuploader/main.py (send_home): Replace "gn2-tweet-score" with "bh20-tweet-score".
2020-11-10virtuoso: no-cachePjotr Prins
2020-11-10virtuoso: header changePjotr Prins
2020-11-10Virtuoso: run scriptPjotr Prins
2020-11-10Document Arvados runnerPjotr Prins
2020-11-10virtuoso: Added a --no-cache optionPjotr Prins
2020-11-10Add tweet feedBonfaceKilz
* bh20simplewebuploader/main.py (send_home): Fetch tweets from Redis. * bh20simplewebuploader/static/main.css: Add styles for tweets * bh20simplewebuploader/templates/home.html: Add tweet section in frontpage.
2020-11-09Merge pull request #105 from arvados/fasta-subset-from-queryPeter Amstutz
Extract subset of the all-sequences fasta by running a sparql query. Also includes some tweaks to the permalinks.
2020-11-09Extract PDH from result and construct URIs from thatfasta-subset-from-queryPeter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-11-09Make resource link work for both portable data hashes and sample idPeter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-11-09Make it so "pangenome analysis" only runs collect-seqs.Peter Amstutz
Will ensure that metadata is kept up to date. GFA isn't being generated. Will introduce new workflow that uses from_sparql to analyze a subset. Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-11-09Rename schema param to metadataSchemaPeter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
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