{"push_id":1381150326,"size":44,"distinct_size":13,"ref":"refs/heads/download_hf","head":"5e40f284a3f5ca07db658a349aae08ef4a0ffe0c","before":"d68eb31c5dd948c2faeba2298d900e1bdcc1689a","commits":[{"sha":"39f959029a8db34b78fa0433d44e00675ef993b9","author":{"name":"Sander Tan","email":"3ccbb954d2012c975fed0b77bde54651cc315760@thehyve.nl"},"message":"If swissprot column contains any invalid UniProt *name*, give warning instead of error\n\nChanged 2 errors to warnings in test","distinct":true,"url":"https://api.github.com/repos/JiaoJiao123/cbioportal/commits/39f959029a8db34b78fa0433d44e00675ef993b9"},{"sha":"925374f187a6b81b27888a869a594e2eb06fda77","author":{"name":"Fedde Schaeffer","email":"df03c27336c23170f2694c611fd5b649095fe21c@thehyve.nl"},"message":"Validate that cancer type colors are web colors","distinct":false,"url":"https://api.github.com/repos/JiaoJiao123/cbioportal/commits/925374f187a6b81b27888a869a594e2eb06fda77"},{"sha":"91da6cf5380ab9d6da93a88f020c23f9333ffe68","author":{"name":"Fedde Schaeffer","email":"df03c27336c23170f2694c611fd5b649095fe21c@thehyve.nl"},"message":"Resolve symlinks locating validator Jinja template\n\nTo account for scenarios where a symbolic link to the dataset validation\nscript is added to the shell's executable search path.","distinct":false,"url":"https://api.github.com/repos/JiaoJiao123/cbioportal/commits/91da6cf5380ab9d6da93a88f020c23f9333ffe68"},{"sha":"c416329e2614274c7994a7bbb2e6ccf2a1772f3f","author":{"name":"Fedde Schaeffer","email":"df03c27336c23170f2694c611fd5b649095fe21c@thehyve.nl"},"message":"Add validation for hard-coded clinical attributes\n\nSo that the database will not get configured in ways inconsistent with\nthe frontend code, with patient-level attributes loaded as sample-level\nor vice versa.\n\nSome of the attributes were not previously documented or have changed in\na recent rewrite of the frontend.","distinct":false,"url":"https://api.github.com/repos/JiaoJiao123/cbioportal/commits/c416329e2614274c7994a7bbb2e6ccf2a1772f3f"},{"sha":"273f58270af78b8e432897876cf3a195739c746e","author":{"name":"Fedde Schaeffer","email":"df03c27336c23170f2694c611fd5b649095fe21c@thehyve.nl"},"message":"Adjust names of hard-coded clinical attrs\n\nSpecifically, replace punctuation with underscores in\nETS/RAF/SPINK1_STATUS, TMPRSS2-ERG_FUSION_STATUS and ERG-FUSION_ACGH to\nmatch what is actually used in data.","distinct":false,"url":"https://api.github.com/repos/JiaoJiao123/cbioportal/commits/273f58270af78b8e432897876cf3a195739c746e"},{"sha":"aa9a48cb1d5601a840267aabc86f5bc6482edd5a","author":{"name":"Fedde Schaeffer","email":"df03c27336c23170f2694c611fd5b649095fe21c@thehyve.nl"},"message":"Validate values of the OS_* and DFS_* attributes","distinct":false,"url":"https://api.github.com/repos/JiaoJiao123/cbioportal/commits/aa9a48cb1d5601a840267aabc86f5bc6482edd5a"},{"sha":"d3b36ba19299f8d7871b836f9fed7ef9336b5624","author":{"name":"schultzn","email":"ca0e172f1fc8867c514f3fb97f2e5cfece21190b@cbio.mskcc.org"},"message":"Update News.md","distinct":false,"url":"https://api.github.com/repos/JiaoJiao123/cbioportal/commits/d3b36ba19299f8d7871b836f9fed7ef9336b5624"},{"sha":"b1c1b467b146566639bd34c5004d5f696843d426","author":{"name":"Robert Sheridan","email":"330f20dd7a05df2f39e3b4018cd9de64eb8d46b0@cbio.mskcc.org"},"message":"Bugfix (1799) : migration.sql\n- move ALTER TABLE line beneath a needed CREATE TABLE line","distinct":false,"url":"https://api.github.com/repos/JiaoJiao123/cbioportal/commits/b1c1b467b146566639bd34c5004d5f696843d426"},{"sha":"c883d04f4b27f5a4611fe5a0318bdefbe249031e","author":{"name":"Robert Sheridan","email":"330f20dd7a05df2f39e3b4018cd9de64eb8d46b0@cbio.mskcc.org"},"message":"Merge pull request #1803 from sheridancbio/hotfix\n\nBugfix (1799) : migration.sql","distinct":false,"url":"https://api.github.com/repos/JiaoJiao123/cbioportal/commits/c883d04f4b27f5a4611fe5a0318bdefbe249031e"},{"sha":"90b80751d2eed1eb22f1c12fa03a89017a9d288e","author":{"name":"Robert Sheridan","email":"330f20dd7a05df2f39e3b4018cd9de64eb8d46b0@cbio.mskcc.org"},"message":"correct comment syntax in mysql scripts","distinct":false,"url":"https://api.github.com/repos/JiaoJiao123/cbioportal/commits/90b80751d2eed1eb22f1c12fa03a89017a9d288e"},{"sha":"f699003dbf5b04a2424aad07c535c374191234d8","author":{"name":"JianJiong Gao","email":"a36f8b2c2e96470c39979df26ffa731a02b5510a@gmail.com"},"message":"Merge pull request #1809 from thehyve/add_validation_scenarios-hotfix\n\nAdd validation for clinical attributes with set meanings","distinct":false,"url":"https://api.github.com/repos/JiaoJiao123/cbioportal/commits/f699003dbf5b04a2424aad07c535c374191234d8"},{"sha":"0cfd0034e378563deb360142ca9ee83d8504ab9e","author":{"name":"Abeshouse, Adam A./Sloan Kettering Institute","email":"643804f1b4dd9090f95dea9060ef6a71817b95bc@mskcc.org"},"message":"Mutation annotation optimizations\n\n(1) Only try to query annotation information for missense mutations,\ninstead of all mutations, since for now we're only filtering out\nmissense mutations anyway.\n\n(2) If no missense mutations, then don't query for any annotation information\n\nSigned-off-by: Abeshouse, Adam A./Sloan Kettering Institute <abeshoua@mskcc.org>","distinct":false,"url":"https://api.github.com/repos/JiaoJiao123/cbioportal/commits/0cfd0034e378563deb360142ca9ee83d8504ab9e"},{"sha":"cc6277b016c514f90c5cbfc894170860e0c60da9","author":{"name":"JianJiong Gao","email":"a36f8b2c2e96470c39979df26ffa731a02b5510a@gmail.com"},"message":"Merge pull request #1827 from adamabeshouse/dont-try-to-annotate-with-no-mutation-data\n\nMutation annotation optimizations","distinct":false,"url":"https://api.github.com/repos/JiaoJiao123/cbioportal/commits/cc6277b016c514f90c5cbfc894170860e0c60da9"},{"sha":"23150c43c0bba9bc01c247b6feb208e88dc43656","author":{"name":"Fedde Schaeffer","email":"df03c27336c23170f2694c611fd5b649095fe21c@thehyve.nl"},"message":"Remove db validation for clinical attributes\n\nClinical attributes used to share a single namespace across all\nstudies, meaning that once the meaning of an attribute name was\ndefined (with a display name, mouseover description, data type,\nsample or patient level and priority), all subsequent studies would\nhave to adhere to that. Commit b6dcfc082116293178b0cd762b0be7aba3152d51\nmade clinical attributes study-specific. Because of that, validating\nwhether the definitions of attributes in a study are consistent\nwith those configured in the portal is now no longer applicable.","distinct":false,"url":"https://api.github.com/repos/JiaoJiao123/cbioportal/commits/23150c43c0bba9bc01c247b6feb208e88dc43656"},{"sha":"c7a3b16be238b0a9df81b8809f3fba9fb16720b4","author":{"name":"Fedde Schaeffer","email":"df03c27336c23170f2694c611fd5b649095fe21c@thehyve.nl"},"message":"Clarify clinical attribute data type error message\n\nThe error message emitted by the validator when metadata for a\nclinical attribute conflicted with requirements built into the\nportal, such as age being a numeric patient-level attribute,\npreviously only named the metadatum that was incorrect. Adding the\nline and column number clarifies the meaning of the message to\npeople not already intimately familiar with the data file format.","distinct":false,"url":"https://api.github.com/repos/JiaoJiao123/cbioportal/commits/c7a3b16be238b0a9df81b8809f3fba9fb16720b4"},{"sha":"65be7cde36667579fecb49fed5b8c74b9d8d3c92","author":{"name":"Fedde Schaeffer","email":"df03c27336c23170f2694c611fd5b649095fe21c@thehyve.nl"},"message":"Remove clinical attribute API calls from validator\n\nSince this API is no longer used by any validations, the validation\nscript no longer depends on it. Removing the calls fixes the problems\nresulting from duplicate entries introduced to this API's output.","distinct":false,"url":"https://api.github.com/repos/JiaoJiao123/cbioportal/commits/65be7cde36667579fecb49fed5b8c74b9d8d3c92"},{"sha":"b76ee962ddcd7854a233cfc1497131a2955afd22","author":{"name":"Fedde Schaeffer","email":"df03c27336c23170f2694c611fd5b649095fe21c@thehyve.nl"},"message":"Clarify phrasing of code based on review comments","distinct":false,"url":"https://api.github.com/repos/JiaoJiao123/cbioportal/commits/b76ee962ddcd7854a233cfc1497131a2955afd22"},{"sha":"5e738a6dd5ad889445363aafef3b8f7dd8c8d865","author":{"name":"Robert Sheridan","email":"330f20dd7a05df2f39e3b4018cd9de64eb8d46b0@cbio.mskcc.org"},"message":"Merge pull request #1822 from sheridancbio/hotfix\n\ncorrect comment syntax in mysql scripts","distinct":false,"url":"https://api.github.com/repos/JiaoJiao123/cbioportal/commits/5e738a6dd5ad889445363aafef3b8f7dd8c8d865"},{"sha":"dc42bb052a777ac71fd72b7b4fec4a41adb1d2a6","author":{"name":"Fedde Schaeffer","email":"df03c27336c23170f2694c611fd5b649095fe21c@thehyve.nl"},"message":"Combine PyUnit test cases to reflect their purpose\n\nThe several system test cases for the validation script that used\nthe study in `test_data/study_maf_test/` no longer serve primarily\nto test what their documentation states they do. Combining these into a\nsingle test case avoids redundancy and clears up their purpose.","distinct":false,"url":"https://api.github.com/repos/JiaoJiao123/cbioportal/commits/dc42bb052a777ac71fd72b7b4fec4a41adb1d2a6"},{"sha":"d806d67392248374056e15b5e0aeba69d2b751af","author":{"name":"Fedde Schaeffer","email":"df03c27336c23170f2694c611fd5b649095fe21c@thehyve.nl"},"message":"Simplify file diff assertions in validator tests\n\nUsing features built in to PyUnit instead of using a separate diff\nmodule from the standard library.","distinct":false,"url":"https://api.github.com/repos/JiaoJiao123/cbioportal/commits/d806d67392248374056e15b5e0aeba69d2b751af"}]}
{"actor":{"display_login":"JiaoJiao123"}}