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[galaxyproject/galaxy] 49d940: Bam index is only available for coordinate sorted ...
by GitHub 30 Oct '18

30 Oct '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: 49d9409f007dfe6288de4d6a2c0e15a4b45af022 https://github.com/galaxyproject/galaxy/commit/49d9409f007dfe6288de4d6a2c0e… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-30 (Tue, 30 Oct 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Bam index is only available for coordinate sorted bam files Commit: 4c7ba6f0fe4a99c1324f70785d27b655ac8b5538 https://github.com/galaxyproject/galaxy/commit/4c7ba6f0fe4a99c1324f70785d27… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-30 (Tue, 30 Oct 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Merge pull request #6946 from mvdbeek/bam_index_for_coordinate_sorted_only [18.09] Make Bam index only available for coordinate sorted bam files Compare: https://github.com/galaxyproject/galaxy/compare/1482cacee51a...4c7ba6f0fe4a **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] a1b710: add option to strip url prefix from pair names
by GitHub 30 Oct '18

30 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a1b7105b389e8a7b8f9ed9aab630c8b543825da4 https://github.com/galaxyproject/galaxy/commit/a1b7105b389e8a7b8f9ed9aab630… Author: Saskia Hiltemann <zazkia(a)gmail.com> Date: 2018-10-30 (Tue, 30 Oct 2018) Changed paths: M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js Log Message: ----------- add option to strip url prefix from pair names Commit: 41d60f576122a74a87ca060a6813d0e6ca903c05 https://github.com/galaxyproject/galaxy/commit/41d60f576122a74a87ca060a6813… Author: Saskia Hiltemann <zazkia(a)gmail.com> Date: 2018-10-30 (Tue, 30 Oct 2018) Changed paths: M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js Log Message: ----------- always strip url prefix Commit: 17efac853ad1b5a7f319e010b00a79d4694a09ac https://github.com/galaxyproject/galaxy/commit/17efac853ad1b5a7f319e010b00a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-30 (Tue, 30 Oct 2018) Changed paths: M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js Log Message: ----------- Merge pull request #6943 from shiltemann/collection-strip-urlprefix Collection builder: add option to strip url prefix from pair names Compare: https://github.com/galaxyproject/galaxy/compare/9713556b16ac...17efac853ad1 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 9a2433: Name datatype test files according to datatype ext...
by GitHub 30 Oct '18

30 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9a24338d12001cdcea336703ce41ac4032c275b8 https://github.com/galaxyproject/galaxy/commit/9a24338d12001cdcea336703ce41… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-30 (Tue, 30 Oct 2018) Changed paths: M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/sniff.py R lib/galaxy/datatypes/test/1.vcf.gz A lib/galaxy/datatypes/test/1.vcf_bgzip R lib/galaxy/datatypes/test/Acanium.hmm A lib/galaxy/datatypes/test/Acanium.snaphmm R lib/galaxy/datatypes/test/biom2_sparse_otu_table_hdf5.biom A lib/galaxy/datatypes/test/biom2_sparse_otu_table_hdf5.biom2 R lib/galaxy/datatypes/test/test.CEL A lib/galaxy/datatypes/test/test.cel R lib/galaxy/datatypes/test/test.idpDB A lib/galaxy/datatypes/test/test.idpdb R lib/galaxy/datatypes/test/test_ensembl.tab A lib/galaxy/datatypes/test/test_ensembl.tabular A test/integration/test_datatype_upload.py M test/unit/datatypes/test_vcf.py Log Message: ----------- Name datatype test files according to datatype extension Commit: b2276319d409c7d88bf3af7ff0cfa8cd4df2ab98 https://github.com/galaxyproject/galaxy/commit/b2276319d409c7d88bf3af7ff0cf… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-30 (Tue, 30 Oct 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Change more biom2 instances Commit: 7ce69df57c7a2bb6e7c34108a8e2e0b67487cd5d https://github.com/galaxyproject/galaxy/commit/7ce69df57c7a2bb6e7c34108a8e2… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-30 (Tue, 30 Oct 2018) Changed paths: M test/integration/test_datatype_upload.py Log Message: ----------- Add integration test for uploading datasets of known datatype We upload everything in lib/galaxy/datatypes/test and make sure that we get the correct datatype. For datatypes that have a sniffer we use `auto`, otherwise we set the correct datatype. This is fairly basic for now, but it would be trivial to extend this to also verify file integrity and metadata elements as well as testing options that affect uploads, like `auto_decompress` settings. Commit: f2d8218a5366f25601dac8342601c02a74ca6f22 https://github.com/galaxyproject/galaxy/commit/f2d8218a5366f25601dac8342601… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-30 (Tue, 30 Oct 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Fix uncompressed bcf This actually also fails, but at least doesn't crash the interpreter. Commit: 63eb6a145c9683651532fc7afaded7a5d930743a https://github.com/galaxyproject/galaxy/commit/63eb6a145c9683651532fc7afade… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-30 (Tue, 30 Oct 2018) Changed paths: M lib/galaxy/datatypes/sequence.py Log Message: ----------- Tighten up memepsp sniffer Values need to be floats, but float("1") also doesn't raise an exception. This prevents 454qual files to be sniffed as memepsp. Commit: f7773c39b1fb7d9ac31115b69c60f5f487e40a13 https://github.com/galaxyproject/galaxy/commit/f7773c39b1fb7d9ac31115b69c60… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-30 (Tue, 30 Oct 2018) Changed paths: M lib/galaxy/datatypes/blast.py A lib/galaxy/datatypes/test/tblastn_four_human_vs_rhodopsin.blastxml R lib/galaxy/datatypes/test/tblastn_four_human_vs_rhodopsin.xml Log Message: ----------- Move tblastn_four_human_vs_rhodopsin.xml to tblastn_four_human_vs_rhodopsin.blastxml Commit: 38e18c9daff58a02f1da0be23329ec9ec5d4cbe7 https://github.com/galaxyproject/galaxy/commit/38e18c9daff58a02f1da0be23329… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-30 (Tue, 30 Oct 2018) Changed paths: M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/sniff.py A lib/galaxy/datatypes/test/gff.gff3 R lib/galaxy/datatypes/test/gff_version_3.gff Log Message: ----------- Rename gff3 test file Commit: 3529295d5512bee68e7981d036147b18a518fc6c https://github.com/galaxyproject/galaxy/commit/3529295d5512bee68e7981d03614… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-30 (Tue, 30 Oct 2018) Changed paths: R lib/galaxy/datatypes/test/sequence.qual Log Message: ----------- Delete unused test file Commit: bc0a3c5244181a5b6af2a4d394a0d4375ceff453 https://github.com/galaxyproject/galaxy/commit/bc0a3c5244181a5b6af2a4d394a0… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-30 (Tue, 30 Oct 2018) Changed paths: M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/sniff.py A lib/galaxy/datatypes/test/interv1.bed R lib/galaxy/datatypes/test/interval1.bed Log Message: ----------- Rename interval1.bed to interv1.bed Otherwise guess_datatype would expect interval as the datatype. Commit: 81155c635a38eb0ad1201f92bb70fbdf9faf170b https://github.com/galaxyproject/galaxy/commit/81155c635a38eb0ad1201f92bb70… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-30 (Tue, 30 Oct 2018) Changed paths: R lib/galaxy/datatypes/test/2.shuffled.bam A lib/galaxy/datatypes/test/2.shuffled.unsorted.bam M test/unit/datatypes/test_bam.py Log Message: ----------- Rename 2.shuffled.bam to 2.shuffled.unsorted.bam Commit: a151b63a622424c1f5f21f97169121b4c7bcc5d5 https://github.com/galaxyproject/galaxy/commit/a151b63a622424c1f5f21f971691… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-30 (Tue, 30 Oct 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sequence.py R lib/galaxy/datatypes/test/2.fastqsanger A lib/galaxy/datatypes/test/3.fastq Log Message: ----------- Tighten up fastq sniffers significantly This requires the sequence regex to match over the entire sequence, which precludes fastqcssanger files to be sniffed as fastqsanger (fixes https://github.com/galaxyproject/galaxy/issues/6734) Further adds a sniffer for FastqCSSanger, which contains numbers in the sequence and so shouldn't interfere with the other fastq datatypes. Commit: b74f225f189688ea885ea6b52bf0f36367cd8d03 https://github.com/galaxyproject/galaxy/commit/b74f225f189688ea885ea6b52bf0… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-30 (Tue, 30 Oct 2018) Changed paths: M test/integration/test_datatype_upload.py Log Message: ----------- Map fastqsolex to fastq datatype in integration test Commit: 720386999828150ed3b639c3600f491e75c7217b https://github.com/galaxyproject/galaxy/commit/720386999828150ed3b639c3600f… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-30 (Tue, 30 Oct 2018) Changed paths: M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/test/1.bcf_uncompressed Log Message: ----------- Drop index file for bcf_uncompressed Even `bcftools index` complains that the file is not compressed. I think this is just not supported. Commit: 85a47ccc47b6f3504360e9f4a0486cefe3f6faa8 https://github.com/galaxyproject/galaxy/commit/85a47ccc47b6f3504360e9f4a048… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-30 (Tue, 30 Oct 2018) Changed paths: M lib/galaxy/datatypes/sequence.py Log Message: ----------- Fix totally broken memepsp sniffer The sniffer could never reach 100 sniffed lines, and the test file contains an empty line, so the comment and code that says that empty lines are not valid is wrong, but was never called. Commit: 48bdc97fce177c5f867cd31e3600ad5670a6c958 https://github.com/galaxyproject/galaxy/commit/48bdc97fce177c5f867cd31e3600… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-30 (Tue, 30 Oct 2018) Changed paths: M test/base/populators.py M test/integration/test_datatype_upload.py Log Message: ----------- Verify state of uploaded datasets and download datasets to verify that the file is intact after upload Commit: be939310fbd4736eaaf8e3ecb00081e7fc080463 https://github.com/galaxyproject/galaxy/commit/be939310fbd4736eaaf8e3ecb000… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-30 (Tue, 30 Oct 2018) Changed paths: A lib/galaxy/datatypes/test/1.fastqcssanger Log Message: ----------- Add a fastqcssanger test file Commit: 7b955277566a8cb647b1a689cf1c0d18fba274f2 https://github.com/galaxyproject/galaxy/commit/7b955277566a8cb647b1a689cf1c… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-30 (Tue, 30 Oct 2018) Changed paths: M lib/galaxy/datatypes/sniff.py Log Message: ----------- Missed one idpDB instance Commit: dd6a4bb2f33e39889577e9a0b60a6314355eab6b https://github.com/galaxyproject/galaxy/commit/dd6a4bb2f33e39889577e9a0b60a… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-30 (Tue, 30 Oct 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py A lib/galaxy/datatypes/test/1.excel.xls R lib/galaxy/datatypes/test/1.xls Log Message: ----------- Move xls file to excel.xls and change xls to be excel.xls Commit: d80e4bd0a13dc5996c35cd5ecbca9c4439e5e2a1 https://github.com/galaxyproject/galaxy/commit/d80e4bd0a13dc5996c35cd5ecbca… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-30 (Tue, 30 Oct 2018) Changed paths: M test/base/populators.py M test/integration/test_datatype_upload.py Log Message: ----------- Fix test logic Commit: e01e6ba2bdcf557668995f402812ff8b93474134 https://github.com/galaxyproject/galaxy/commit/e01e6ba2bdcf557668995f402812… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-30 (Tue, 30 Oct 2018) Changed paths: M lib/galaxy/datatypes/test/1.afg M lib/galaxy/datatypes/test/1.fastq M lib/galaxy/datatypes/test/1.fastqsanger M lib/galaxy/datatypes/test/1.fastqsolexa M lib/galaxy/datatypes/test/1.owl M lib/galaxy/datatypes/test/1.stockholm M lib/galaxy/datatypes/test/2.fastq M lib/galaxy/datatypes/test/2.fastqsolexa M lib/galaxy/datatypes/test/2.txt M lib/galaxy/datatypes/test/3.fastq M lib/galaxy/datatypes/test/3.txt M lib/galaxy/datatypes/test/454Score.pdf M lib/galaxy/datatypes/test/alignment.lav M lib/galaxy/datatypes/test/interv1.bed M lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.filter M lib/galaxy/datatypes/test/sequence.qual454 M lib/galaxy/datatypes/test/sequence.qualsolid M lib/galaxy/datatypes/test/test_tab.bed M lib/galaxy/datatypes/test/ucsc.customtrack M lib/galaxy/datatypes/test/wiggle.wig Log Message: ----------- Fix up various test datasets Commit: ec193d929fd81b8f0438c097ebbb3aa3fb55e224 https://github.com/galaxyproject/galaxy/commit/ec193d929fd81b8f0438c097ebbb… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-30 (Tue, 30 Oct 2018) Changed paths: M lib/galaxy/datatypes/sequence.py Log Message: ----------- Fix minor typo Commit: d3cd57e29975b66ca3883b6e8dfb63839a49aaee https://github.com/galaxyproject/galaxy/commit/d3cd57e29975b66ca3883b6e8dfb… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-30 (Tue, 30 Oct 2018) Changed paths: M lib/galaxy/model/custom_types.py Log Message: ----------- Safe JSON encoding of MetadataParameters, JSONType This fixes a couple of upload tests on python 3 (loom, Biom2). Commit: 09601ad4efdd877375dfda3e62e2657899101ae2 https://github.com/galaxyproject/galaxy/commit/09601ad4efdd877375dfda3e62e2… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-30 (Tue, 30 Oct 2018) Changed paths: M lib/galaxy/datatypes/sniff.py Log Message: ----------- Skip newlines/space2tab conversion for binary datatypes that fail is_binary check Commit: d168042b366dcdbacabfabe692f120e9118a2de9 https://github.com/galaxyproject/galaxy/commit/d168042b366dcdbacabfabe692f1… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-30 (Tue, 30 Oct 2018) Changed paths: M lib/galaxy/datatypes/sniff.py Log Message: ----------- Fix newline conversion on python 3 if no encoding is set Commit: 738bde01278c50a62f4d97c7afc6e4f8b919254f https://github.com/galaxyproject/galaxy/commit/738bde01278c50a62f4d97c7afc6… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-30 (Tue, 30 Oct 2018) Changed paths: M lib/galaxy/util/checkers.py Log Message: ----------- Fix check_html on python 3 We can open the file in binary mode and then use unicodify on the lines, as we have to do that anyway if `chunks` is provided. Also adds the unicode flag to re.compile. Commit: 1a407429ba7ffe1476317c5ac0f5b1ad19f1e0d7 https://github.com/galaxyproject/galaxy/commit/1a407429ba7ffe1476317c5ac0f5… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-30 (Tue, 30 Oct 2018) Changed paths: M lib/galaxy/datatypes/mothur.py M lib/galaxy/datatypes/phylip.py Log Message: ----------- Tighten up mothur and phylip sniffers Commit: c50a0fccace2d94565ba85f0703e516139132b4b https://github.com/galaxyproject/galaxy/commit/c50a0fccace2d94565ba85f0703e… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-30 (Tue, 30 Oct 2018) Changed paths: M lib/galaxy/datatypes/text.py Log Message: ----------- Don't sniff simple json types These should instead be text. Commit: 0fae117e672e626cc7093d0169dae241c4f54128 https://github.com/galaxyproject/galaxy/commit/0fae117e672e626cc7093d0169da… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-30 (Tue, 30 Oct 2018) Changed paths: M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py Log Message: ----------- Use raw strings in regex and allow lowercase fastq sequences Commit: ecc02bb659ce89e78b1a5aeb49dd020280864617 https://github.com/galaxyproject/galaxy/commit/ecc02bb659ce89e78b1a5aeb49dd… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-30 (Tue, 30 Oct 2018) Changed paths: M lib/galaxy/datatypes/upload_util.py Log Message: ----------- Fix UploadProblemException Commit: ba5d76eb934598227102ae1cb0ff4e89e0ab0b9c https://github.com/galaxyproject/galaxy/commit/ba5d76eb934598227102ae1cb0ff… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-30 (Tue, 30 Oct 2018) Changed paths: M lib/galaxy/datatypes/sequence.py Log Message: ----------- Avoid exception if no match This fixes the sniffing unit test, the datatype framework would just continue anyway. Commit: 16962ad6a16c5b5dcc5b3d06921d2c4c89c6d9d0 https://github.com/galaxyproject/galaxy/commit/16962ad6a16c5b5dcc5b3d06921d… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-30 (Tue, 30 Oct 2018) Changed paths: M lib/galaxy/datatypes/test/5e5z.pqr Log Message: ----------- Add newline to lib/galaxy/datatypes/test/5e5z.pqr Commit: 9713556b16acb3e4218fc9e28463cdaba654a0c5 https://github.com/galaxyproject/galaxy/commit/9713556b16acb3e4218fc9e28463… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-30 (Tue, 30 Oct 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/blast.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/mothur.py M lib/galaxy/datatypes/phylip.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/test/1.afg M lib/galaxy/datatypes/test/1.bcf_uncompressed A lib/galaxy/datatypes/test/1.excel.xls M lib/galaxy/datatypes/test/1.fastq A lib/galaxy/datatypes/test/1.fastqcssanger M lib/galaxy/datatypes/test/1.fastqsanger M lib/galaxy/datatypes/test/1.fastqsolexa M lib/galaxy/datatypes/test/1.owl M lib/galaxy/datatypes/test/1.stockholm R lib/galaxy/datatypes/test/1.vcf.gz A lib/galaxy/datatypes/test/1.vcf_bgzip R lib/galaxy/datatypes/test/1.xls M lib/galaxy/datatypes/test/2.fastq R lib/galaxy/datatypes/test/2.fastqsanger M lib/galaxy/datatypes/test/2.fastqsolexa R lib/galaxy/datatypes/test/2.shuffled.bam A lib/galaxy/datatypes/test/2.shuffled.unsorted.bam M lib/galaxy/datatypes/test/2.txt A lib/galaxy/datatypes/test/3.fastq M lib/galaxy/datatypes/test/3.txt M lib/galaxy/datatypes/test/454Score.pdf M lib/galaxy/datatypes/test/5e5z.pqr R lib/galaxy/datatypes/test/Acanium.hmm A lib/galaxy/datatypes/test/Acanium.snaphmm M lib/galaxy/datatypes/test/alignment.lav R lib/galaxy/datatypes/test/biom2_sparse_otu_table_hdf5.biom A lib/galaxy/datatypes/test/biom2_sparse_otu_table_hdf5.biom2 A lib/galaxy/datatypes/test/gff.gff3 R lib/galaxy/datatypes/test/gff_version_3.gff A lib/galaxy/datatypes/test/interv1.bed R lib/galaxy/datatypes/test/interval1.bed M lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.filter R lib/galaxy/datatypes/test/sequence.qual M lib/galaxy/datatypes/test/sequence.qual454 M lib/galaxy/datatypes/test/sequence.qualsolid A lib/galaxy/datatypes/test/tblastn_four_human_vs_rhodopsin.blastxml R lib/galaxy/datatypes/test/tblastn_four_human_vs_rhodopsin.xml R lib/galaxy/datatypes/test/test.CEL A lib/galaxy/datatypes/test/test.cel R lib/galaxy/datatypes/test/test.idpDB A lib/galaxy/datatypes/test/test.idpdb R lib/galaxy/datatypes/test/test_ensembl.tab A lib/galaxy/datatypes/test/test_ensembl.tabular M lib/galaxy/datatypes/test/test_tab.bed M lib/galaxy/datatypes/test/ucsc.customtrack M lib/galaxy/datatypes/test/wiggle.wig M lib/galaxy/datatypes/text.py M lib/galaxy/datatypes/upload_util.py M lib/galaxy/model/custom_types.py M lib/galaxy/util/checkers.py M test/base/populators.py A test/integration/test_datatype_upload.py M test/unit/datatypes/test_bam.py M test/unit/datatypes/test_vcf.py Log Message: ----------- Merge pull request #6869 from mvdbeek/datatype_upload_integration_test Datatype upload integration test and fixes Compare: https://github.com/galaxyproject/galaxy/compare/0de9c738cf8c...9713556b16ac **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 9c8108: Catch IOErrors when the k8s runner tries to collec...
by GitHub 30 Oct '18

30 Oct '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: 9c81089ed1c9d5c434ecb991be8fd542bbe3c75e https://github.com/galaxyproject/galaxy/commit/9c81089ed1c9d5c434ecb991be8f… Author: Luca Pireddu <pireddu(a)crs4.it> Date: 2018-10-17 (Wed, 17 Oct 2018) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Catch IOErrors when the k8s runner tries to collect job logs This commit should fix cases where successful job can't be marked as done by Galaxy because the logs have gone missing. Commit: ac7c2d0473d09e8a3b4b39734527a383835478ab https://github.com/galaxyproject/galaxy/commit/ac7c2d0473d09e8a3b4b39734527… Author: Luca Pireddu <pireddu(a)crs4.it> Date: 2018-10-17 (Wed, 17 Oct 2018) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Print full job object to the DEBUG log if k8s runner finds it in an unrecognized state Commit: cd6c4d4db8bcb72ae931797c216b9829313850cf https://github.com/galaxyproject/galaxy/commit/cd6c4d4db8bcb72ae931797c216b… Author: Luca Pireddu <pireddu(a)crs4.it> Date: 2018-10-22 (Mon, 22 Oct 2018) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Add job id to missing k8s log text Commit: c434c271598d95130439ac86c8b9060f42455e9a https://github.com/galaxyproject/galaxy/commit/c434c271598d95130439ac86c8b9… Author: Luca Pireddu <pireddu(a)gmail.com> Date: 2018-10-26 (Fri, 26 Oct 2018) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Improve k8s runner debug log message Commit: e235343f7674a5b74a707a693e94b80633d1ca2b https://github.com/galaxyproject/galaxy/commit/e235343f7674a5b74a707a693e94… Author: Luca Pireddu <pireddu(a)crs4.it> Date: 2018-10-26 (Fri, 26 Oct 2018) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Push k8s log IOError handling into `__produce_log_file` Handling the IOError within the function should result in other call sites within the kubernets.py module properly setting the job state even if the job directory has been removed. Commit: cf02c9812759505d61f284d6d33ee9ce2dc994e8 https://github.com/galaxyproject/galaxy/commit/cf02c9812759505d61f284d6d33e… Author: Luca Pireddu <pireddu(a)crs4.it> Date: 2018-10-26 (Fri, 26 Oct 2018) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Prefer `with open` syntax within kubernetes.py Commit: c13da94fd75d4b0010e4e3284649366c213a205d https://github.com/galaxyproject/galaxy/commit/c13da94fd75d4b0010e4e3284649… Author: Luca Pireddu <pireddu(a)crs4.it> Date: 2018-10-26 (Fri, 26 Oct 2018) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Fix inverted log message arguments Thanks @pcm32! Commit: 1482cacee51a9fd91f65d54704c7bc36120f3a34 https://github.com/galaxyproject/galaxy/commit/1482cacee51a9fd91f65d54704c7… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-10-30 (Tue, 30 Oct 2018) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Merge pull request #6886 from ilveroluca/fix/k8s_error_handling Improve k8s job error handling Compare: https://github.com/galaxyproject/galaxy/compare/cea9521b1a01...1482cacee51a **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] d9ce92: adjust the panel resize cursor, update docs link
by GitHub 30 Oct '18

30 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d9ce92a8a2bd4323a18d69936995fc62e24458e6 https://github.com/galaxyproject/galaxy/commit/d9ce92a8a2bd4323a18d69936995… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-10-08 (Mon, 08 Oct 2018) Changed paths: M client/galaxy/style/scss/base.scss M static/style/blue/base.css M static/welcome.html.sample Log Message: ----------- adjust the panel resize cursor, update docs link Commit: 0de9c738cf8cb11b814d1d758268f0bcf9b71652 https://github.com/galaxyproject/galaxy/commit/0de9c738cf8cb11b814d1d758268… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-10-30 (Tue, 30 Oct 2018) Changed paths: M client/galaxy/style/scss/base.scss M static/style/blue/base.css M static/welcome.html.sample Log Message: ----------- Merge pull request #6833 from martenson/tinies adjust the panel resize cursor, update docs link Compare: https://github.com/galaxyproject/galaxy/compare/8e8ff78b459c...0de9c738cf8c **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 4dce06: Adjust code block to try to fix release doc format...
by GitHub 29 Oct '18

29 Oct '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/galaxy Commit: 4dce069209c4da228629e7dddfbeda836098aedc https://github.com/galaxyproject/galaxy/commit/4dce069209c4da228629e7dddfbe… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-29 (Mon, 29 Oct 2018) Changed paths: M doc/source/releases/18.09_announce.rst Log Message: ----------- Adjust code block to try to fix release doc formatting -- I hate RST Commit: cea9521b1a0194c93c5e2bf7b7f02fa88bd2c0b9 https://github.com/galaxyproject/galaxy/commit/cea9521b1a0194c93c5e2bf7b7f0… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-29 (Mon, 29 Oct 2018) Changed paths: M doc/source/releases/18.09_announce.rst Log Message: ----------- Merge pull request #6938 from dannon/codeblock_formatting [18.09] Release announce codeblock formatting fix Compare: https://github.com/galaxyproject/galaxy/compare/d0a93ff62808...cea9521b1a01 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] c59169: Fix typos in ``scripts/bootstrap_history.py``
by GitHub 29 Oct '18

29 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c5916912093ffaca57281db486c263108f263e88 https://github.com/galaxyproject/galaxy/commit/c5916912093ffaca57281db486c2… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-10-29 (Mon, 29 Oct 2018) Changed paths: M scripts/bootstrap_history.py Log Message: ----------- Fix typos in ``scripts/bootstrap_history.py`` Commit: a4abbb1d8a244e260412df8551f9f3d0f25f78c7 https://github.com/galaxyproject/galaxy/commit/a4abbb1d8a244e260412df8551f9… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-10-29 (Mon, 29 Oct 2018) Changed paths: M lib/galaxy/datatypes/molecules.py Log Message: ----------- Fix flake8 errors introduced in #6816 Commit: 8e8ff78b459c68c4b54c0c722ed5619f9d117c62 https://github.com/galaxyproject/galaxy/commit/8e8ff78b459c68c4b54c0c722ed5… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-10-29 (Mon, 29 Oct 2018) Changed paths: M lib/galaxy/datatypes/molecules.py M scripts/bootstrap_history.py Log Message: ----------- Merge pull request #6941 from nsoranzo/bootstrap_history_typos Fix typos in ``scripts/bootstrap_history.py`` Compare: https://github.com/galaxyproject/galaxy/compare/d41837cd9ccd...8e8ff78b459c **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 09e6b1: Eliminate some mutable defaults in populators.py.
by GitHub 29 Oct '18

29 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 09e6b1dcde5eb30a76e7487eba9ee75475b29753 https://github.com/galaxyproject/galaxy/commit/09e6b1dcde5eb30a76e7487eba9e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-29 (Mon, 29 Oct 2018) Changed paths: M test/base/populators.py Log Message: ----------- Eliminate some mutable defaults in populators.py. Commit: d41837cd9ccde259941c8b643ebf1c38ebed871b https://github.com/galaxyproject/galaxy/commit/d41837cd9ccde259941c8b643ebf… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-10-29 (Mon, 29 Oct 2018) Changed paths: M test/base/populators.py Log Message: ----------- Merge pull request #6933 from jmchilton/mutable_default Eliminate some mutable defaults in populators.py. Compare: https://github.com/galaxyproject/galaxy/compare/e89773a20d5c...d41837cd9ccd **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 4dce06: Adjust code block to try to fix release doc format...
by GitHub 29 Oct '18

29 Oct '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: 4dce069209c4da228629e7dddfbeda836098aedc https://github.com/galaxyproject/galaxy/commit/4dce069209c4da228629e7dddfbe… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-29 (Mon, 29 Oct 2018) Changed paths: M doc/source/releases/18.09_announce.rst Log Message: ----------- Adjust code block to try to fix release doc formatting -- I hate RST Commit: cea9521b1a0194c93c5e2bf7b7f02fa88bd2c0b9 https://github.com/galaxyproject/galaxy/commit/cea9521b1a0194c93c5e2bf7b7f0… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-29 (Mon, 29 Oct 2018) Changed paths: M doc/source/releases/18.09_announce.rst Log Message: ----------- Merge pull request #6938 from dannon/codeblock_formatting [18.09] Release announce codeblock formatting fix Compare: https://github.com/galaxyproject/galaxy/compare/d0a93ff62808...cea9521b1a01 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] f1a3a4: galaxy test needs to count data sets and collectio...
by GitHub 29 Oct '18

29 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f1a3a44b444d9914a97d26a0b0f5667efc211ac5 https://github.com/galaxyproject/galaxy/commit/f1a3a44b444d9914a97d26a0b0f5… Author: M Bernt <m.bernt(a)ufz.de> Date: 2018-10-29 (Mon, 29 Oct 2018) Changed paths: M lib/galaxy/tools/verify/interactor.py Log Message: ----------- galaxy test needs to count data sets and collection outputs Commit: 1ec18484df22ec0d226415a6aa9379bb176fe329 https://github.com/galaxyproject/galaxy/commit/1ec18484df22ec0d226415a6aa93… Author: M Bernt <m.bernt(a)ufz.de> Date: 2018-10-29 (Mon, 29 Oct 2018) Changed paths: M test/functional/tools/output_filter.xml Log Message: ----------- added test Commit: e89773a20d5c3f18fd9b4766c1c7deb6485e88da https://github.com/galaxyproject/galaxy/commit/e89773a20d5c3f18fd9b4766c1c7… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-10-29 (Mon, 29 Oct 2018) Changed paths: M lib/galaxy/tools/verify/interactor.py M test/functional/tools/output_filter.xml Log Message: ----------- Merge pull request #6931 from bernt-matthias/topic/test-colouts tests need to count data sets and collections Compare: https://github.com/galaxyproject/galaxy/compare/adc62f6ba7d8...e89773a20d5c **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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