Tapestry - Arvados

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9027 9027 Incorporate coverage info from get-evidence dataset_reports in publication statistics New New 1 9027 31 131 2
8707 8707 Tom Clegg Tom Clegg 3 Third party integration 48 Third party integration Arvados job: download data from remote site into Keep In Progress In Progress 2 1.0 1.0 1.0 8707 31 3 131 2 1.0		8795 8795 download script Tom Clegg 3 0 8707 3 31 -c-a 5 8897 8897 Review 8707-download Tom Clegg 3 0 8707 3 31 -c-a 5 8708 8708 open firewall rules on su92l to allow download from veritas Ward Vandewege 1 0 8707 3 31 -c-a 5
8689 8689 Tom Clegg Tom Clegg 3 Third party integration 48 Third party integration Trigger an arvados job to retrieve the data and import it into Keep In Progress In Progress 2 1.0 1.0 1.0 8689 31 3 131 2 1.0	8794 8794 Notify user that transfer has been initiated Tom Clegg 3 0 8689 1 31 -c-a 5	8948 8948 Make arvados SDK work in ruby 1.8.7 Tom Clegg 3 0 8689 3 31 -c-a 5 8927 8927 Run job in huXXXXXX project, create & share one if necessary Tom Clegg 3 0 8689 3 31 -c-a 5 8793 8793 Generate user log entry Tom Clegg 3 0 8689 3 31 -c-a 5 8960 8960 Review 8689-use-downloaded-filename Ward Vandewege 1 0 8689 3 31 -c-a 5 8949 8949 Review 8697-ruby187-compat commit:arvados\|fd696fa Ward Vandewege 1 0 8689 3 31 -c-a 5 8950 8950 Review 8689-participant-project at commit:492d441 Ward Vandewege 1 0 8689 3 31 -c-a 5 8902 8902 Use actual filename in "add user_file" callback instead of FIXME Tom Clegg 3 0 8689 3 31 -c-a 5
8697 8697 Tom Clegg Tom Clegg 3 Publishing 44 Publishing Check for finished download/processing jobs In Progress In Progress 2 1.0 1.0 1.0 8697 31 3 131 2 1.0	9026 9026 Retrieve coverage metadata from get-evidence jobs Tom Clegg 3 0 8697 1 31 -c-a 5 8796 8796 Poll arvados for finished pipelines, resolve/reject relevant ArvadosJob Tom Clegg 3 0 8697 1 31 -c-a 5
8698 8698 When UserFile data is updated, if it has a suitable data type, submit report-generator jobs New New 1 2.0 2.0 2.0 8698 31 131 2 2.0
8701 8701 Abram Connelly Abram Connelly 99 Arvados job/pipeline generates ClinVar HTML report from VCF Closed Closed 5 2.0 2.0 2.0 8701 31 99 131 2 2.0		8768 8768 Review #8701 Review code and pipeline: * https://github.com/abeconnelly/ClinVarReport * https://github.com/abeconnelly/ClinVarReportHTML * https://workbench.su92l.arvadosapi.com/pipeline_templates/su92l-p5p6p-oopbp7ikcycckcw Sample run: * https://workbench.su92l.arvadosapi.com/pipeline_instances/su92l-d1hrv-0fq6djbem3pcrvo Ward Vandewege 1 0 8701 3 31 -c-a 5
8700 8700 Abram Connelly Abram Connelly 99 Arvados job/pipeline generates GET-Evidence HTML report from VCF Closed Closed 5 2.0 2.0 2.0 8700 31 99 131 2 2.0		8859 8859 Review #8700 The GET-Evidence pipeline is producing HTML reports for VCF and non-VCF (e.g. CGI-Var) data files. An example run with a data file that was converted to VCF from 23andMe: * https://workbench.su92l.arvadosapi.com/pipeline_instances/su92l-d1hrv-z9qiho889d52uid * https://workbench.su92l.arvadosapi.com/collections/e1fa7630e0762d1b22090fda681b827a+1882/get-evidence-report.html An example run with a date file that was originally a CGI-Var file: * https://workbench.su92l.arvadosapi.com/pipeline_instances/su92l-d1hrv-nhin4h27bqzjyvf * https://workbench.su92l.arvadosapi.com/collections/2b4703eb27aeb44eaaa320ae1ec67669+1925/get-evidence-report.html The pipeline template is "su92l-p5p6p-2hdis7roemcaokr":https://workbench.su92l.arvadosapi.com/pipeline_templates/su92l-p5p6p-2hdis7roemcaokr The three repositories for each leg of the pipeline can be found at: * https://github.com/abeconnelly/GETEvidenceReport * https://github.com/abeconnelly/GETEvidenceReportRefresh * https://github.com/abeconnelly/GETEvidenceReportHTML This closely resembles how the pipeline was setup. The initial report is generated with @GETEvidenceReport@, then refreshed with the latest GET-Evidence database by running @GETEvidenceReportRefresh@. Finally, the HTML is created with @GETEvidenceReportHTML@. The major differences from the previous incarnation of the GET-Evidence pipeline from this one are that this one is able to injects VCF and create a report and the final report resides completely in Arvados, rather than the GET-Evidence server. Ward Vandewege 1 0 8700 3 31 -c-a 5	8705 8705 Make sure VCF input files are processed properly 0 8700 5 31 -c-a 5 8706 8706 Generate HTML from GET-Evidence JSON report 0 8700 5 31 -c-a 5
8699 8699 Tom Clegg Tom Clegg 3 Publishing 44 Publishing Add report status/links to "show user_files" page Resolved Resolved 3 1.0 1.0 1.0 8699 31 3 131 2 1.0		8924 8924 "View report" link on user_files index Tom Clegg 3 0 8699 3 31 -c-a 5 8925 8925 "View report" link on public profile page Tom Clegg 3 0 8699 3 31 -c-a 5 8926 8926 "Download" link on user_files index Tom Clegg 3 0 8699 3 31 -c-a 5
8688 8688 Tom Clegg Tom Clegg 3 Third party integration 48 Third party integration Accept authenticated API calls from data providers to add datasets to a public profile Resolved Resolved 3 2.0 2.0 2.0 8688 31 3 131 2 2.0		8792 8792 Review 8688-pull-data-api Ward Vandewege 1 0 8688 3 31 -c-a 5
8710 8710 Check UserFiles too when checking for Datasets that are ready to publish Closed Closed 5 0.5 0.5 0.5 8710 31 131 1 0.5