{"payload":{"feedbackUrl":"https://github.com/orgs/community/discussions/53140","repo":{"id":67535054,"defaultBranch":"master","name":"ecoli_serotyping","ownerLogin":"phac-nml","currentUserCanPush":false,"isFork":false,"isEmpty":false,"createdAt":"2016-09-06T18:20:40.000Z","ownerAvatar":"https://avatars.githubusercontent.com/u/15620262?v=4","public":true,"private":false,"isOrgOwned":true},"refInfo":{"name":"","listCacheKey":"v0:1701177604.0","currentOid":""},"activityList":{"items":[{"before":"5d2da4d41d4ca1bb3b55e2a2761c8d7ac64f7f35","after":"d70a025460018684d5161293ba130bf2d51e609d","ref":"refs/heads/v2.0.0","pushedAt":"2024-08-01T15:48:00.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"kbessonov1984","name":"Kirill Bessonov","path":"/kbessonov1984","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/16680511?s=80&v=4"},"commit":{"message":"Fixed bugs related to batch mode output files displaying only last sample results instead of results from All samples. Also added automatic clceaner for the main output files to prevent excesive file output growth especially of Blastn results","shortMessageHtmlLink":"Fixed bugs related to batch mode output files displaying only last sa…"}},{"before":"8002091fdcf783be8f3d18de2e4ceb87c08b3f6d","after":"5d2da4d41d4ca1bb3b55e2a2761c8d7ac64f7f35","ref":"refs/heads/v2.0.0","pushedAt":"2024-08-01T15:36:44.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"kbessonov1984","name":"Kirill Bessonov","path":"/kbessonov1984","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/16680511?s=80&v=4"},"commit":{"message":"Fixed bugs related to batch mode output files displaying only last sample results instead of results from All samples. Also added automatic clceaner for the main output files to prevent excesive file output growth especially of Blastn results","shortMessageHtmlLink":"Fixed bugs related to batch mode output files displaying only last sa…"}},{"before":"41a509398fc4a9580e084dd0f61d406891c13f05","after":"8002091fdcf783be8f3d18de2e4ceb87c08b3f6d","ref":"refs/heads/v2.0.0","pushedAt":"2024-07-31T02:57:11.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"kbessonov1984","name":"Kirill Bessonov","path":"/kbessonov1984","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/16680511?s=80&v=4"},"commit":{"message":"fixed pytest issues","shortMessageHtmlLink":"fixed pytest issues"}},{"before":"6cca0357595222652fa64058c9f1c3c39257bd95","after":"41a509398fc4a9580e084dd0f61d406891c13f05","ref":"refs/heads/v2.0.0","pushedAt":"2024-07-31T02:25:41.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"kbessonov1984","name":"Kirill Bessonov","path":"/kbessonov1984","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/16680511?s=80&v=4"},"commit":{"message":"fixed batch mode error when one of the files fails FASTA test causing other files in a pool not being analyzed.","shortMessageHtmlLink":"fixed batch mode error when one of the files fails FASTA test causing…"}},{"before":"4ef852623b9174bcc22d14d8bfecab4fdaa707f3","after":"6cca0357595222652fa64058c9f1c3c39257bd95","ref":"refs/heads/v2.0.0","pushedAt":"2024-07-30T19:06:23.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"kbessonov1984","name":"Kirill Bessonov","path":"/kbessonov1984","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/16680511?s=80&v=4"},"commit":{"message":"Fixing small pytest errors","shortMessageHtmlLink":"Fixing small pytest errors"}},{"before":"22b6a98b9b1608ffe8e8d861628de478aaffa969","after":"4ef852623b9174bcc22d14d8bfecab4fdaa707f3","ref":"refs/heads/v2.0.0","pushedAt":"2024-07-30T18:50:08.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"kbessonov1984","name":"Kirill Bessonov","path":"/kbessonov1984","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/16680511?s=80&v=4"},"commit":{"message":"Fixed pytest small error with test_emtpy_BLAST_antigen_hits","shortMessageHtmlLink":"Fixed pytest small error with test_emtpy_BLAST_antigen_hits"}},{"before":"74edb8155a4641276751605b1d43ad69f08baf72","after":"22b6a98b9b1608ffe8e8d861628de478aaffa969","ref":"refs/heads/v2.0.0","pushedAt":"2024-07-30T18:26:02.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"kbessonov1984","name":"Kirill Bessonov","path":"/kbessonov1984","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/16680511?s=80&v=4"},"commit":{"message":"Making tool and its module more robust to errors","shortMessageHtmlLink":"Making tool and its module more robust to errors"}},{"before":"f8cd8595a80dee6d922549c66ca9e1c23ef06f57","after":"74edb8155a4641276751605b1d43ad69f08baf72","ref":"refs/heads/v2.0.0","pushedAt":"2024-07-29T20:49:27.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"kbessonov1984","name":"Kirill Bessonov","path":"/kbessonov1984","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/16680511?s=80&v=4"},"commit":{"message":"added wildcard characters in path specification and also multiple directories are allowed now to be specified","shortMessageHtmlLink":"added wildcard characters in path specification and also multiple dir…"}},{"before":"58b956e3a81e0ed05285375635f7831051210768","after":"f8cd8595a80dee6d922549c66ca9e1c23ef06f57","ref":"refs/heads/v2.0.0","pushedAt":"2024-07-29T17:21:00.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"kbessonov1984","name":"Kirill Bessonov","path":"/kbessonov1984","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/16680511?s=80&v=4"},"commit":{"message":"fixed multiprocess Pool freeze on subprocess error and added better messages when file list is provided listing missing files","shortMessageHtmlLink":"fixed multiprocess Pool freeze on subprocess error and added better m…"}},{"before":"33eac5d8368cf9f0069a42c13954574c97c38de8","after":"58b956e3a81e0ed05285375635f7831051210768","ref":"refs/heads/v2.0.0","pushedAt":"2024-07-22T20:54:40.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"kbessonov1984","name":"Kirill Bessonov","path":"/kbessonov1984","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/16680511?s=80&v=4"},"commit":{"message":"Added STEC O157:H7 GCA_000181775.1 gzip compressed for testing","shortMessageHtmlLink":"Added STEC O157:H7 GCA_000181775.1 gzip compressed for testing"}},{"before":"86e1542ffcb43b2437cebef640a2c7d1e8c08dff","after":"33eac5d8368cf9f0069a42c13954574c97c38de8","ref":"refs/heads/v2.0.0","pushedAt":"2024-07-22T17:35:17.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"kbessonov1984","name":"Kirill Bessonov","path":"/kbessonov1984","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/16680511?s=80&v=4"},"commit":{"message":"github actions pytest CI feature added","shortMessageHtmlLink":"github actions pytest CI feature added"}},{"before":"eacee169629ca9f5ac1430af487717e5ecad0f46","after":"86e1542ffcb43b2437cebef640a2c7d1e8c08dff","ref":"refs/heads/v2.0.0","pushedAt":"2024-07-22T16:44:27.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"kbessonov1984","name":"Kirill Bessonov","path":"/kbessonov1984","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/16680511?s=80&v=4"},"commit":{"message":"github actions pytest CI feature added","shortMessageHtmlLink":"github actions pytest CI feature added"}},{"before":"0e65432c593496d84deced06dc4ab7d9440ee0b1","after":"eacee169629ca9f5ac1430af487717e5ecad0f46","ref":"refs/heads/v2.0.0","pushedAt":"2024-07-22T16:43:29.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"kbessonov1984","name":"Kirill Bessonov","path":"/kbessonov1984","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/16680511?s=80&v=4"},"commit":{"message":"github actions pytest CI feature added","shortMessageHtmlLink":"github actions pytest CI feature added"}},{"before":"f92a8dd2fb0124766ece61a446799682d163d93d","after":"0e65432c593496d84deced06dc4ab7d9440ee0b1","ref":"refs/heads/v2.0.0","pushedAt":"2024-07-22T16:35:27.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"kbessonov1984","name":"Kirill Bessonov","path":"/kbessonov1984","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/16680511?s=80&v=4"},"commit":{"message":"github actions pytest CI feature added","shortMessageHtmlLink":"github actions pytest CI feature added"}},{"before":"367051421193a97515fdf7db6ed362360fc883b7","after":"f92a8dd2fb0124766ece61a446799682d163d93d","ref":"refs/heads/v2.0.0","pushedAt":"2024-07-22T16:26:17.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"kbessonov1984","name":"Kirill Bessonov","path":"/kbessonov1984","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/16680511?s=80&v=4"},"commit":{"message":"github actions pytest CI feature added","shortMessageHtmlLink":"github actions pytest CI feature added"}},{"before":"434316a7f4581c20647d7a88b68362c9e0849810","after":"367051421193a97515fdf7db6ed362360fc883b7","ref":"refs/heads/v2.0.0","pushedAt":"2024-07-19T18:39:07.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"kbessonov1984","name":"Kirill Bessonov","path":"/kbessonov1984","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/16680511?s=80&v=4"},"commit":{"message":"added PMID to pathotype rules in the database","shortMessageHtmlLink":"added PMID to pathotype rules in the database"}},{"before":"003c11491b4d9e79dbb73c05b2a47125cbda53c1","after":"434316a7f4581c20647d7a88b68362c9e0849810","ref":"refs/heads/v2.0.0","pushedAt":"2024-07-17T20:24:50.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"kbessonov1984","name":"Kirill Bessonov","path":"/kbessonov1984","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/16680511?s=80&v=4"},"commit":{"message":"renamed ectyper_pathotyping_database_v2.json pathotype database to ectyper_patho_stx_toxin_typing_database.json","shortMessageHtmlLink":"renamed ectyper_pathotyping_database_v2.json pathotype database to ec…"}},{"before":"9f5344b3c3359e9e7686f4d2acc42f36ab76b1cc","after":"003c11491b4d9e79dbb73c05b2a47125cbda53c1","ref":"refs/heads/v2.0.0","pushedAt":"2024-07-17T20:20:03.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"kbessonov1984","name":"Kirill Bessonov","path":"/kbessonov1984","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/16680511?s=80&v=4"},"commit":{"message":"Report EHEC as EHEC-STEC, add number of genes linked to pathotype(s)","shortMessageHtmlLink":"Report EHEC as EHEC-STEC, add number of genes linked to pathotype(s)"}},{"before":"adbec57efd2c44bdef9535b0960c0eae9344a362","after":"9f5344b3c3359e9e7686f4d2acc42f36ab76b1cc","ref":"refs/heads/v2.0.0","pushedAt":"2024-07-17T01:04:04.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"kbessonov1984","name":"Kirill Bessonov","path":"/kbessonov1984","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/16680511?s=80&v=4"},"commit":{"message":"added gunzip compression support, added pathotype gene count, sorting of O and H antigens ascending order by #, add dashes when no stx genes found","shortMessageHtmlLink":"added gunzip compression support, added pathotype gene count, sorting…"}},{"before":"476cb3c6d7e8768e1be791678a69df6208bea147","after":"adbec57efd2c44bdef9535b0960c0eae9344a362","ref":"refs/heads/v2.0.0","pushedAt":"2024-06-19T20:37:52.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"kbessonov1984","name":"Kirill Bessonov","path":"/kbessonov1984","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/16680511?s=80&v=4"},"commit":{"message":"fixed --verify bug when pathotyping is run on non-E.coli species but should not","shortMessageHtmlLink":"fixed --verify bug when pathotyping is run on non-E.coli species but …"}},{"before":"890f78b96f518332e65d41891d2184d8603de1c4","after":"476cb3c6d7e8768e1be791678a69df6208bea147","ref":"refs/heads/v2.0.0","pushedAt":"2024-06-06T19:26:26.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"kbessonov1984","name":"Kirill Bessonov","path":"/kbessonov1984","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/16680511?s=80&v=4"},"commit":{"message":"stx2l sequence for AM904726.1 corrected based on https://doi.org/10.3390/microorganisms10061245","shortMessageHtmlLink":"stx2l sequence for AM904726.1 corrected based on https://doi.org/10.3…"}},{"before":"b7ba36704d2f618d880054fa877738145559c569","after":"890f78b96f518332e65d41891d2184d8603de1c4","ref":"refs/heads/v2.0.0","pushedAt":"2024-05-29T18:32:26.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"kbessonov1984","name":"Kirill Bessonov","path":"/kbessonov1984","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/16680511?s=80&v=4"},"commit":{"message":"Fixed contig naming reporting for FASTA headers with | symbol replaced by _ as it conflicts with contig name extraction","shortMessageHtmlLink":"Fixed contig naming reporting for FASTA headers with | symbol replace…"}},{"before":"d5ca377e8ed8f0113f6dd859ba1fd08a2d19cb88","after":"b7ba36704d2f618d880054fa877738145559c569","ref":"refs/heads/v2.0.0","pushedAt":"2024-05-28T19:32:04.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"kbessonov1984","name":"Kirill Bessonov","path":"/kbessonov1984","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/16680511?s=80&v=4"},"commit":{"message":"shiga toxin module several improvements and application of a threshold","shortMessageHtmlLink":"shiga toxin module several improvements and application of a threshold"}},{"before":"8b0281b62ae381eb4c253855f61f817cf36fc884","after":"d5ca377e8ed8f0113f6dd859ba1fd08a2d19cb88","ref":"refs/heads/v2.0.0","pushedAt":"2024-05-11T08:49:26.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"kbessonov1984","name":"Kirill Bessonov","path":"/kbessonov1984","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/16680511?s=80&v=4"},"commit":{"message":"big update for Shiga toxin module typing supporting reporting of multiple stx subtypes including mixed truncated cases with smart hit parsing. Improved shiga toxin database complete sequences coverage (units A and B) of subtypes","shortMessageHtmlLink":"big update for Shiga toxin module typing supporting reporting of mult…"}},{"before":"3d8c291ae054dc3c8b41f7bdd6a6fa2c608444be","after":"8b0281b62ae381eb4c253855f61f817cf36fc884","ref":"refs/heads/v2.0.0","pushedAt":"2024-04-20T04:21:53.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"kbessonov1984","name":"Kirill Bessonov","path":"/kbessonov1984","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/16680511?s=80&v=4"},"commit":{"message":"Fixed empty or invalid FASTA file error generated from FASTQ and improved multicore performance on single sample","shortMessageHtmlLink":"Fixed empty or invalid FASTA file error generated from FASTQ and impr…"}},{"before":"4c2362d07be8f5a6a4a9b2476be330a96c8d3032","after":"3d8c291ae054dc3c8b41f7bdd6a6fa2c608444be","ref":"refs/heads/v2.0.0","pushedAt":"2024-04-18T03:31:33.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"kbessonov1984","name":"Kirill Bessonov","path":"/kbessonov1984","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/16680511?s=80&v=4"},"commit":{"message":"Fixed empty O- and H- antigen BLAST output file found in metagenomic samples and added full length STX1 and STX2 sequences to database, homogenized gene names","shortMessageHtmlLink":"Fixed empty O- and H- antigen BLAST output file found in metagenomic …"}},{"before":"decee6141fcc51ee5aad4b875ce5a6626b7186b7","after":"4c2362d07be8f5a6a4a9b2476be330a96c8d3032","ref":"refs/heads/v2.0.0","pushedAt":"2024-03-23T01:44:55.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"kbessonov1984","name":"Kirill Bessonov","path":"/kbessonov1984","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/16680511?s=80&v=4"},"commit":{"message":"Added Singularity.def file","shortMessageHtmlLink":"Added Singularity.def file"}},{"before":"2f55ae8f75d782b89e924f51fe567fe688f7a3f9","after":"decee6141fcc51ee5aad4b875ce5a6626b7186b7","ref":"refs/heads/v2.0.0","pushedAt":"2024-03-22T19:18:30.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"kbessonov1984","name":"Kirill Bessonov","path":"/kbessonov1984","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/16680511?s=80&v=4"},"commit":{"message":"fixed speciesID dbpath reduntant variable","shortMessageHtmlLink":"fixed speciesID dbpath reduntant variable"}},{"before":"2a19b842beb8fd6e4089bc2f2a2aec290a5e5ad4","after":"2f55ae8f75d782b89e924f51fe567fe688f7a3f9","ref":"refs/heads/v2.0.0","pushedAt":"2024-03-22T18:31:37.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"kbessonov1984","name":"Kirill Bessonov","path":"/kbessonov1984","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/16680511?s=80&v=4"},"commit":{"message":"updated speciesID download link","shortMessageHtmlLink":"updated speciesID download link"}},{"before":"2c6bf1258927d0782aa99867fad95f98aec646b0","after":"2a19b842beb8fd6e4089bc2f2a2aec290a5e5ad4","ref":"refs/heads/v2.0.0","pushedAt":"2024-03-22T18:06:07.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"kbessonov1984","name":"Kirill Bessonov","path":"/kbessonov1984","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/16680511?s=80&v=4"},"commit":{"message":"init.py added","shortMessageHtmlLink":"init.py added"}}],"hasNextPage":true,"hasPreviousPage":false,"activityType":"all","actor":null,"timePeriod":"all","sort":"DESC","perPage":30,"cursor":"djE6ks8AAAAEj1I-vwA","startCursor":null,"endCursor":null}},"title":"Activity · phac-nml/ecoli_serotyping"}