{"payload":{"feedbackUrl":"https://github.com/orgs/community/discussions/53140","repo":{"id":536435731,"defaultBranch":"main","name":"genenetwork-machines","ownerLogin":"genenetwork","currentUserCanPush":false,"isFork":false,"isEmpty":false,"createdAt":"2022-09-14T06:03:43.000Z","ownerAvatar":"https://avatars.githubusercontent.com/u/1666481?v=4","public":true,"private":false,"isOrgOwned":true},"refInfo":{"name":"","listCacheKey":"v0:1688984068.0","currentOid":""},"activityList":{"items":[{"before":"2f5329cea2a3c0b62373279114e207568e2820b6","after":"a881630ed133c740127b9f74682119e60d09badd","ref":"refs/heads/main","pushedAt":"2023-08-10T18:11:49.000Z","pushType":"push","commitsCount":3,"pusher":{"login":"arunisaac","name":"Arun Isaac","path":"/arunisaac","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/6452653?s=80&v=4"},"commit":{"message":"Set up cgit service.\n\n* genenetwork-development.scm: Import (forge cgit).\n(operating-system)[services]: Add cgit service.\n* genenetwork-development-deploy.sh: Expose cgit repository directory.","shortMessageHtmlLink":"Set up cgit service."}},{"before":"c300665c887350ff346e3d49fcd087240435e996","after":"2f5329cea2a3c0b62373279114e207568e2820b6","ref":"refs/heads/main","pushedAt":"2023-07-27T14:47:09.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"arunisaac","name":"Arun Isaac","path":"/arunisaac","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/6452653?s=80&v=4"},"commit":{"message":"README: Remove references to penguin2.\n\npenguin2 is no more. We now use tux02 for development.\n\n* README.org: Change references to penguin2 to tux02.","shortMessageHtmlLink":"README: Remove references to penguin2."}},{"before":"fc65c2a2c056ee9f313631da6e5f93adec277dd5","after":"c300665c887350ff346e3d49fcd087240435e996","ref":"refs/heads/main","pushedAt":"2023-07-27T13:15:39.000Z","pushType":"push","commitsCount":4,"pusher":{"login":"arunisaac","name":"Arun Isaac","path":"/arunisaac","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/6452653?s=80&v=4"},"commit":{"message":"Use tissue from guix-forge.\n\nThe libgit2 patch is now in guix-forge. So, we don't have to repeat it\nhere.\n\n* genenetwork-development.scm (libgit2-1.3, guile-git-for-tissue,\ntissue): Delete variables.\n(operating-system)[services]: Do not specify package for tissue\nservice.","shortMessageHtmlLink":"Use tissue from guix-forge."}},{"before":"8514264af133ee221dd487adbeaed72673d48172","after":"fc65c2a2c056ee9f313631da6e5f93adec277dd5","ref":"refs/heads/main","pushedAt":"2023-07-11T07:29:28.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"pjotrp","name":"Pjotr Prins","path":"/pjotrp","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/13551?s=80&v=4"},"commit":{"message":"README: host names","shortMessageHtmlLink":"README: host names"}},{"before":"076ff77ee2ec8e6cac299ed3dee3720260f0a813","after":"8514264af133ee221dd487adbeaed72673d48172","ref":"refs/heads/main","pushedAt":"2023-07-11T07:17:52.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"BonfaceKilz","name":"BonfaceKilz","path":"/BonfaceKilz","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/11820306?s=80&v=4"},"commit":{"message":"Revert \"Disable tests\"\n\nThis reverts commit 37fa3c11908d7aada419be296ebef67415de3bc9.","shortMessageHtmlLink":"Revert \"Disable tests\""}},{"before":"f09a5c00f76b897c96de8e59370811dd39476d0c","after":"076ff77ee2ec8e6cac299ed3dee3720260f0a813","ref":"refs/heads/main","pushedAt":"2023-07-10T19:18:01.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"BonfaceKilz","name":"BonfaceKilz","path":"/BonfaceKilz","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/11820306?s=80&v=4"},"commit":{"message":"Add a troubleshooting subsection to README","shortMessageHtmlLink":"Add a troubleshooting subsection to README"}},{"before":"ecd97bc513323459898b34db45fda6c9edd7ca22","after":"f09a5c00f76b897c96de8e59370811dd39476d0c","ref":"refs/heads/main","pushedAt":"2023-07-10T15:29:19.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"BonfaceKilz","name":"BonfaceKilz","path":"/BonfaceKilz","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/11820306?s=80&v=4"},"commit":{"message":"Revert \"Fix genotype file path\"\n\nThis reverts commit ecd97bc513323459898b34db45fda6c9edd7ca22.","shortMessageHtmlLink":"Revert \"Fix genotype file path\""}},{"before":"37fa3c11908d7aada419be296ebef67415de3bc9","after":"ecd97bc513323459898b34db45fda6c9edd7ca22","ref":"refs/heads/main","pushedAt":"2023-07-10T15:13:00.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"BonfaceKilz","name":"BonfaceKilz","path":"/BonfaceKilz","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/11820306?s=80&v=4"},"commit":{"message":"Fix genotype file path","shortMessageHtmlLink":"Fix genotype file path"}},{"before":"252d3fd72c61bde40872ef12138346571ed88b57","after":"37fa3c11908d7aada419be296ebef67415de3bc9","ref":"refs/heads/main","pushedAt":"2023-07-10T10:24:41.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"BonfaceKilz","name":"BonfaceKilz","path":"/BonfaceKilz","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/11820306?s=80&v=4"},"commit":{"message":"Disable tests\n\nRob is giving a demo, so disable tests and fix them later.\n\nSigned-off-by: Munyoki Kilyungi ","shortMessageHtmlLink":"Disable tests"}},{"before":null,"after":"fc54705449337afb75b0c4bc1659e06a6532b04f","ref":"refs/heads/disable-tests","pushedAt":"2023-07-10T10:14:28.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"BonfaceKilz","name":"BonfaceKilz","path":"/BonfaceKilz","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/11820306?s=80&v=4"},"commit":{"message":"Disable tests\n\nRob is giving a demo, so disable tests and fix them later.\n\nSigned-off-by: Munyoki Kilyungi ","shortMessageHtmlLink":"Disable tests"}},{"before":"2ef9cebfa7daaf79ccd1d3a336d19da78af83256","after":"252d3fd72c61bde40872ef12138346571ed88b57","ref":"refs/heads/main","pushedAt":"2023-07-10T05:51:08.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"pjotrp","name":"Pjotr Prins","path":"/pjotrp","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/13551?s=80&v=4"},"commit":{"message":"Basic mail/opensmtpd service added","shortMessageHtmlLink":"Basic mail/opensmtpd service added"}},{"before":"396ec5d042c9883a847007b25300f7da90c2580b","after":"2ef9cebfa7daaf79ccd1d3a336d19da78af83256","ref":"refs/heads/main","pushedAt":"2023-06-26T13:34:27.606Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"BonfaceKilz","name":"BonfaceKilz","path":"/BonfaceKilz","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/11820306?s=80&v=4"},"commit":{"message":"Add virtuoso allowed dirs","shortMessageHtmlLink":"Add virtuoso allowed dirs"}},{"before":"ff4e69b4b2da29ab35627864b0e5d839fa758a96","after":"396ec5d042c9883a847007b25300f7da90c2580b","ref":"refs/heads/main","pushedAt":"2023-06-15T10:14:52.851Z","pushType":"push","commitsCount":2,"pusher":{"login":"arunisaac","name":"Arun Isaac","path":"/arunisaac","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/6452653?s=80&v=4"},"commit":{"message":"Increase threshold for number-of-buffers and maximum-dirty-buffers.\n\n* genenetwork-development.scm,\npublic-sparql.scm (operating-system)[services]: Set\nnumber-of-buffers and maximum-dirty-buffers.\n\nSigned-off-by: Arun Isaac ","shortMessageHtmlLink":"Increase threshold for number-of-buffers and maximum-dirty-buffers."}},{"before":"6f13dfd5c5aacef518b7f97e0d903e6927fb7e3f","after":"ff4e69b4b2da29ab35627864b0e5d839fa758a96","ref":"refs/heads/main","pushedAt":"2023-06-08T11:30:44.434Z","pushType":"push","commitsCount":1,"pusher":{"login":"arunisaac","name":"Arun Isaac","path":"/arunisaac","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/6452653?s=80&v=4"},"commit":{"message":"Share auth-db-path with genenetwork3-pola-wrapper.\n\n* genenetwork-development.scm (genenetwork-shepherd-services): Share\nauth-db-path with genenetwork3-pola-wrapper.\n\nSigned-off-by: Arun Isaac ","shortMessageHtmlLink":"Share auth-db-path with genenetwork3-pola-wrapper."}},{"before":"67d3f5dc46422c6b1812547109680c147fdde341","after":"6f13dfd5c5aacef518b7f97e0d903e6927fb7e3f","ref":"refs/heads/main","pushedAt":"2023-06-06T13:26:52.469Z","pushType":"push","commitsCount":2,"pusher":{"login":"arunisaac","name":"Arun Isaac","path":"/arunisaac","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/6452653?s=80&v=4"},"commit":{"message":"Set AUTH_DB, not AUTH_DB_PATH.\n\ngenenetwork3 expects AUTH_DB, not AUTH_DB_PATH.\n\n* genenetwork-development.scm (genenetwork3-cd-gexp): Set AUTH_DB, not\nAUTH_DB_PATH.\n\nSigned-off-by: Arun Isaac ","shortMessageHtmlLink":"Set AUTH_DB, not AUTH_DB_PATH."}},{"before":"b663a689c8e584127f894652debc2a5b5339db50","after":"67d3f5dc46422c6b1812547109680c147fdde341","ref":"refs/heads/main","pushedAt":"2023-05-31T15:47:48.493Z","pushType":"push","commitsCount":1,"pusher":{"login":"arunisaac","name":"Arun Isaac","path":"/arunisaac","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/6452653?s=80&v=4"},"commit":{"message":"Use an absolute GN_SERVER_URL.\n\nA relative GN_SERVER_URL sometimes leads to issues when code (in\nlibraries e.g. requests and the like) cannot expand the URI since it\ndoes not have context about the running server.\n\n* genenetwork-development.scm (genenetwork2-cd-gexp): Use an absolute\nGN_SERVER_URL.\n\nSigned-off-by: Arun Isaac ","shortMessageHtmlLink":"Use an absolute GN_SERVER_URL."}},{"before":"f0c32ce4353338c3cfaa3c768fe2efc271059543","after":"b663a689c8e584127f894652debc2a5b5339db50","ref":"refs/heads/main","pushedAt":"2023-05-31T12:19:20.486Z","pushType":"push","commitsCount":1,"pusher":{"login":"arunisaac","name":"Arun Isaac","path":"/arunisaac","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/6452653?s=80&v=4"},"commit":{"message":"Add trailing slash to GN_SERVER_URL.\n\nWithout the trailing slash, the urllib.parse.urljoin function produces\nthe wrong endpoint.\n\n* genenetwork-development.scm (genenetwork2-cd-gexp): Add trailing\nslash to GN_SERVER_URL.\n\nSigned-off-by: Arun Isaac ","shortMessageHtmlLink":"Add trailing slash to GN_SERVER_URL."}},{"before":"2d648a1934d3c9f3861fba5f15482911af535aad","after":"f0c32ce4353338c3cfaa3c768fe2efc271059543","ref":"refs/heads/main","pushedAt":"2023-05-22T10:14:41.048Z","pushType":"push","commitsCount":1,"pusher":{"login":"fredmanglis","name":"Muriithi Frederick Muriuki","path":"/fredmanglis","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1607145?s=80&v=4"},"commit":{"message":"Document getting a shell into container\n\nFor some tasks (e.g. debugging the xapian index build), we need to\nmanually queue the job, which means we need a shell into the\ncontainer.\n\nGetting a shell using the default command displayed actually fails\nwith:\n\n nsenter: failed to execute /bin/bash: No such file or directory\n\nso we need to provide the correct path to bash, and optionally,\ninitialise the shell to setup the correct paths.","shortMessageHtmlLink":"Document getting a shell into container"}},{"before":"bc52bc93696e2d2f1e82d1b8ca5bc997493d87cb","after":"2d648a1934d3c9f3861fba5f15482911af535aad","ref":"refs/heads/main","pushedAt":"2023-05-05T19:40:00.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"arunisaac","name":"Arun Isaac","path":"/arunisaac","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/6452653?s=80&v=4"},"commit":{"message":"Run migrations after tests and before restarting genenetwork3.\n\nAdd a CI job that applies the auth database migrations. This job is\nrun after the genenetwork3 tests have passed but before genenetwork3\nis restarted.\n\n* genenetwork-development-deploy.sh: Share\n/export/data/genenetwork-sqlite.\n* genenetwork-development.scm: Import yoyo-migrations from (gnu\npackages databases).\n()[auth-db-path]: New field.\n(genenetwork3-auth-migrations-genenetwork,\ngenenetwork3-auth-migrations-laminar, genenetwork-activation): New\nfunctions.\n(genenetwork-projects): Add genenetwork3-auth-migrations CI\njob. Trigger this job after genenetwork3 tests.\n(genenetwork3-cd-gexp): Configure AUTH_DB_PATH in gn3.conf.\n(genenetwork-service-type): Extend activation-service-type with\ngenenetwork-activation.\n(operating-system)[sudoers-file]: Permit the laminar user to run auth\ndatabase migrations as the genenetwork user.\n\nSigned-off-by: Arun Isaac ","shortMessageHtmlLink":"Run migrations after tests and before restarting genenetwork3."}},{"before":"00de34960f973424990f1bcbdf4b1436f746f319","after":"fadc8bc0c900835e1b727e7615342c9495b478c5","ref":"refs/heads/ci-for-auth","pushedAt":"2023-05-05T04:46:38.000Z","pushType":"force_push","commitsCount":0,"pusher":{"login":"fredmanglis","name":"Muriithi Frederick Muriuki","path":"/fredmanglis","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1607145?s=80&v=4"},"commit":{"message":"Run migrations after tests and before restarting GN3\n\nAdd a job that applies the auth migrations and is not triggered by\ndefault to be run after the GN3 tests have passed but before GN3 is\nrestarted.","shortMessageHtmlLink":"Run migrations after tests and before restarting GN3"}},{"before":"20ce6da71ebfa539ad59060f5482c8ff00698444","after":"00de34960f973424990f1bcbdf4b1436f746f319","ref":"refs/heads/ci-for-auth","pushedAt":"2023-05-04T10:23:16.000Z","pushType":"force_push","commitsCount":0,"pusher":{"login":"fredmanglis","name":"Muriithi Frederick Muriuki","path":"/fredmanglis","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1607145?s=80&v=4"},"commit":{"message":"Run migrations after tests and before restarting GN3\n\nAdd a job that applies the auth migrations and is not triggered by\ndefault to be run after the GN3 tests have passed but before GN3 is\nrestarted.","shortMessageHtmlLink":"Run migrations after tests and before restarting GN3"}},{"before":"dae923f64e0742ac35e392033cc43d43e7ccd583","after":"20ce6da71ebfa539ad59060f5482c8ff00698444","ref":"refs/heads/ci-for-auth","pushedAt":"2023-05-02T01:20:22.000Z","pushType":"force_push","commitsCount":0,"pusher":{"login":"fredmanglis","name":"Muriithi Frederick Muriuki","path":"/fredmanglis","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1607145?s=80&v=4"},"commit":{"message":"Run migrations after tests and before restarting GN3\n\nAdd a job that applies the auth migrations and is not triggered by\ndefault to be run after the GN3 tests have passed but before GN3 is\nrestarted.","shortMessageHtmlLink":"Run migrations after tests and before restarting GN3"}},{"before":"312e2618b02bdec1597b6bb39425119f2dcc761b","after":"dae923f64e0742ac35e392033cc43d43e7ccd583","ref":"refs/heads/ci-for-auth","pushedAt":"2023-04-28T11:32:15.000Z","pushType":"force_push","commitsCount":0,"pusher":{"login":"fredmanglis","name":"Muriithi Frederick Muriuki","path":"/fredmanglis","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1607145?s=80&v=4"},"commit":{"message":"Run migrations after tests and before restarting GN3\n\nAdd a job that applies the auth migrations and is not triggered by\ndefault to be run after the GN3 tests have passed but before GN3 is\nrestarted.","shortMessageHtmlLink":"Run migrations after tests and before restarting GN3"}},{"before":null,"after":"312e2618b02bdec1597b6bb39425119f2dcc761b","ref":"refs/heads/ci-for-auth","pushedAt":"2023-04-27T16:03:42.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"fredmanglis","name":"Muriithi Frederick Muriuki","path":"/fredmanglis","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1607145?s=80&v=4"},"commit":{"message":"Run migrations after tests and before restarting GN3\n\nAdd a job that applies the auth migrations and is not triggered by\ndefault to be run after the GN3 tests have passed but before GN3 is\nrestarted.","shortMessageHtmlLink":"Run migrations after tests and before restarting GN3"}},{"before":"aa7bdb78104812f811929d5a1770d5cfb227bc35","after":"bc52bc93696e2d2f1e82d1b8ca5bc997493d87cb","ref":"refs/heads/main","pushedAt":"2023-04-12T15:17:24.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"arunisaac","name":"Arun Isaac","path":"/arunisaac","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/6452653?s=80&v=4"},"commit":{"message":"Run tissue on an IP socket.\n\ntissue fails to clean up its Unix socket when deployed with\nshepherd. So, when tissue crashes, it fails to restart. Until this\nissue is resolved, run tissue on an IP socket.\n\n* genenetwork-development.scm (%tissue-port): New variable.\n(tissue-reverse-proxy-server-block): Forward tissue requests to IP\nsocket.\n(operating-system)[services]: Run tissue on an IP socket.","shortMessageHtmlLink":"Run tissue on an IP socket."}},{"before":"d968a5bbb969a3032f4460afcb294e4672dc5aa6","after":"aa7bdb78104812f811929d5a1770d5cfb227bc35","ref":"refs/heads/main","pushedAt":"2023-04-11T15:04:48.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"arunisaac","name":"Arun Isaac","path":"/arunisaac","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/6452653?s=80&v=4"},"commit":{"message":"Use tissue package from Guix upstream.\n\nThe tissue package is now in Guix upstream and longer in the\nguix-forge channel.\n\n* genenetwork-development.scm: Import tissue from (gnu packages web).","shortMessageHtmlLink":"Use tissue package from Guix upstream."}},{"before":null,"after":"1fc0198aaf595719e9e5f1a182731073458c449e","ref":"refs/heads/current_app_db_utils_configs_update","pushedAt":"2023-04-04T07:13:31.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"fredmanglis","name":"Muriithi Frederick Muriuki","path":"/fredmanglis","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/1607145?s=80&v=4"},"commit":{"message":"Provide URI to database server to the indexing script.","shortMessageHtmlLink":"Provide URI to database server to the indexing script."}}],"hasNextPage":false,"hasPreviousPage":false,"activityType":"all","actor":null,"timePeriod":"all","sort":"DESC","perPage":30,"cursor":"djE6ks8AAAADaEqsaAA","startCursor":null,"endCursor":null}},"title":"Activity ยท genenetwork/genenetwork-machines"}