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Nate Coraor natefoo @galaxyproject State College, PA System Administrator, Programmer, Whatever else

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Nate Coraor

commit sha 1213651a45888490197ddba3db0a743990f220d3

Convert "liteenv" to Kerberos/LDAP auth/NSS, support it on EL, and make the TTS part of liteenv. General overhaul of the kerberos and ldap roles plus a new minimal sssd role.

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Nate Coraor

commit sha b071748f220d7167236f6f3e21477cfac13ba9f6

Enable user access to TS database

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GollumEvent

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Björn Grüning

commit sha 2547ebc694a2cfc17489e29c334b0543295f309b

Make mol2 visible

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Marius van den Beek

commit sha 707e64e1046c2b6648f318bb8a59dbd40a0bcc0e

Merge pull request #8995 from galaxyproject/mol2_vis Make mol2 visible

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John Chilton

commit sha 766c2bdaf7e2a6b533cb5bbe9bbe9d1c1129994c

Simplify implicit snippy dependencies. biocontainer tar doesn't support tar -z

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Björn Grüning

commit sha 401528f2dba371d4ca2491aaa83e0b2bfe36f81a

Merge pull request #2676 from jmchilton/snippy_deps Simplify implicit snippy dependencies.

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Nate Coraor

commit sha 78aa3b8a53341442bfe8f53083e19fffe8171690

Main mutable configs

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Nate Coraor

commit sha 2697d2a76f06b731c820a3dc0f93c09a04805c49

Limit naive variant caller jobs

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Dave B

commit sha fac514723414f6e97c40cbfb9349fc6c649a12f2

Install dada2 tool suite on test.

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Martin Cech

commit sha d45c0e43d673e1437773de8432208ab39ac7ca25

drop travis badge

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Martin Cech

commit sha 19743ce413ce694099209d4cbb3a77c833d5f187

Merge pull request #85 from davebx/dada2 Install dada2 tool suite on test.

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John Chilton

commit sha 4a3b58f96b5eb7cb9955009eb23e364344619b92

Assorted fixes for extended metadata handling.

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Martin Cech

commit sha 9662164ad68b39adf5a5606a7aa8e388f6a79f1e

Merge pull request #8990 from jmchilton/extended_metadata_fixes_1 Assorted fixes for extended metadata handling.

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mvdbeek

commit sha 0d2cba0166a4e3364e63a6ebbd3c02445f946fa3

Use path as source of truth for installed_changeset_revision It appears that the xml tag in shed_tool_conf.xml is frequently wrong. Fixes https://github.com/galaxyproject/galaxy/issues/8892

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mvdbeek

commit sha 1e218e05d7a3719f3b665e3268f29dd779d0e606

Provide old logic as fallback Mostly for unit tests.

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mvdbeek

commit sha 2f67794c78b66bd1c49c8464dc86da0804fb7adc

Fix Tool._repository dir when tool in base of repository

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John Chilton

commit sha 4414aef74eaed87410f2f65ad4181c48891ca57b

Merge pull request #8985 from mvdbeek/use_path_installed_changeset_revision [19.09] Use path as source of truth for installed_changeset_revision

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John Chilton

commit sha 843967003c77f09936f87316fbcc6f977bb9126d

Remove unused code from twilltestcase.

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Björn Grüning

commit sha c0ef6ffb93c60b95090362e351cbd22a7a23d7c4

Merge pull request #8989 from jmchilton/ts_cleanup_2 Remove unused helper code from twilltestcase.

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Jennifer Hillman-Jackson

commit sha d321fa9f1031ba681f99dfa69cb1d79879076037

Update index.md Added in more context and updated stale links

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Ivan Kuzmin

commit sha fd67c3d66fa8999dd9d5966e6ddb8b26891e4c67

add gprofiler

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Ivan Kuzmin

commit sha 176b4bc006c00334d804e6088cd13042be230529

update README

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Ivan Kuzmin

commit sha 2ebdc5d3b0d0bd8c745dbf4e5f272efd40c4bdcd

add random tool, update gprofiler2 version, major refactoring, add tests

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Ivan Kuzmin

commit sha 31e36c5845d84733dc9bdd03d5f5cc8f2f2a38ba

improve formatting

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Ivan Kuzmin

commit sha 5b4f9a3b0006ce96b38d63c8e7ae083bfd759f7d

fix order of output for tests on travis

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Ivan Kuzmin

commit sha 1b60d96f04fb1eb211c221bc0768709a9f2574b6

add notification, fix tests

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Ivan Kuzmin

commit sha 21800f1e96da33d34bf11e8ec8558cbfab0fb79e

update readme

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Ivan Kuzmin

commit sha 0121ca72cc3c6dc76ea2e7da178c5e80c80ed835

add useful messages

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Ivan Kuzmin

commit sha 0c35961379a021976719aba3c5a3b72f3c123f0d

fix random tool dependencies

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Ivan Kuzmin

commit sha 50ed91d74bb1319bfa12667ccc3e12ed707aa767

bump version

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Ivan Kuzmin

commit sha b70af56401124c8f2a721c058a58a117e009fc80

fix tests

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Ivan Kuzmin

commit sha a048c993a6f9992128e1bd9e6add3013bc5ae133

improve wording

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M Bernt

commit sha ed9b518a6aaf6a5aada47e39c039f6936e41b290

Merge pull request #2667 from inkuzmin/master add gprofiler tools

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pull request commentgalaxyproject/galaxy

[19.09] Fix non-version (minor) tool shed repository updates when installing revisions through the API

Yes, I used it to (I think) update tools on Main. Was this addressed in #8959?

natefoo

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Nate Coraor

commit sha 10c2e922154509ee59ee8e6db87c5b04b256928a

Install vim and tmpwatch on TS servers

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Nate Coraor

commit sha ea0e690af12b4ab1a493a11fb21d2a57f7481089

Relocate Tool Sheds to Jetstream

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mvdbeek

commit sha 35336683363d3260cf17ccc1215bda7446af7e44

Try harder to get shed_config_dict The path based approach might be less desirable, but works if the repository metadata isn't correct and lists a wrong shed_config_filename. And default to returning a dict instead of `None` if that doesn't succeed.

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mvdbeek

commit sha fc7fd7a918c9ca6ec8761accccc60da6be941d2a

Clone repository if repository not on disk

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mvdbeek

commit sha dd01b610cbe136fe1cdf6c55696c5785876c7c06

Don't error repository installation if tool appears invalid

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mvdbeek

commit sha 9c5d111b44b1e16d32d43a7964598a675d2b9731

Skip installation if requesting uninstallable revision and next revision is already installed

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mvdbeek

commit sha 7e57146b04a54162bfe40c5d43d46b243e6eff67

Drop `default` argument to get_shed_config_dict/get_shed_config Their only use is to set them to `{}`. Thanks for the suggestion @nsoranzo.

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mvdbeek

commit sha fa4cb22f8071a994cc3ac4dfe5ea5f47d7bdd711

Try path based approach if no luck getting shed_tool_conf dict via toolbox

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mvdbeek

commit sha 1afe6a1c5532b765036d6c89bbb2e839d3bcd76b

Only skip installation if repository status is installed And update repository states throughout process.

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mvdbeek

commit sha 62706acee443b1aa47ed4520a13077400b84aef9

Attempt to update instead of clone if destinatino exists

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mvdbeek

commit sha f3044424d135b785032fde49eaa5bc2fcdde2a4e

Fix unit test

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mvdbeek

commit sha 1dbd284988774d78b1a6afef679bc94be1502e92

Prefer shed_tool_conf.xml file if no shed_tool_conf file specified when intalling repositories through API

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mvdbeek

commit sha e71257a15ef2d6fcc588f4ea34ca48016c2a4b8b

Test repository install/uninstall and upgrade

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John Chilton

commit sha 25f108f97e918f1a3a1d0f9997d59dae015d22f3

Merge pull request #8959 from mvdbeek/dont_fail_if_repository_metadata_is_wrong [19.09] Make repository updates more robust

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Dannon Baker

commit sha 8a9f29cbf9298e182955d5cfdcb11134aa3e006a

Pass explicit props to login index component -- this fixes the bug where previously stuff nested under config wasn't unpacked.

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Dannon Baker

commit sha f32148168d5f910f0bb945fef043a88995a135e1

When it's defined, add terms_url to registration interface in an iframe.

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Dannon Baker

commit sha 09eedace59f515784aca30dca5bfaec834052d8b

Fix registration warning message display (never worked?)

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Marius van den Beek

commit sha 7aa73016fe0da9ca35b0efad23f0c0b0df110c30

Merge pull request #8951 from dannon/login-terms [19.09] Several registration fixes.

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mvdbeek

commit sha 056b3ded2b16eabe6cc16ecfe17023a3b8f97102

Only index latest version of tools

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Björn Grüning

commit sha e7b64e969743a42071cc9b77f7bd0fde2f5a6a34

Merge pull request #8971 from mvdbeek/only_index_latest_version [19.09] Only index latest version of tools

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Slugger70

commit sha d2e1ee6304af1062175ca87aab59c4042ace3116

Fixed roary to include inverted quotes around input filenames (#2546) * Fixed roary to include inverted quotes around input filenames * Changed to single quotes. * address review comments

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mvdbeek

commit sha 0ee509deb51a1dcf6a31654c6a194bb92a7f1e31

Use more concise list/dict comprehensions to serialize Tool object

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mvdbeek

commit sha 0d25661c2a05cac647c8c42c9a0b700c963b3256

Don't try to move files in handler when using extended_metadata This would fail with ``` Job 169's output dataset(s) could not be read ```

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mvdbeek

commit sha 4c6e1d836feab529b9d74e2ce25bd176beb8e61a

First import job, then set output dataset state Otherwise doscovered datasets remain in new state

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mvdbeek

commit sha c945cb8b424d9e8720cb8036f86144a8c74fa725

Use new galaxy_test package to get integration_util

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Marius van den Beek

commit sha 7c25ad7bb5622b57e3d15818b61e5bb788763621

Merge pull request #8984 from mvdbeek/extended_metadata Implement extended job metadata collection + fixes

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M Bernt

commit sha d0dcab46285cdf64895e37a9fc17c75c21307b54

grouping: strip newlines fixes https://github.com/galaxyproject/galaxy/issues/8383 more generally: if grouping is done on the last column then the newline was retained and contained in the output.

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M Bernt

commit sha dbe440df3e2f7c519bfc6b636ac95a45d054f3bd

grouping: redecided for the less intrusive rstrip

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John Chilton

commit sha 34e217b32832dd65de7542a9c359d1936f849f9d

[19.05] Fix test repository self reference URL broken in dev.

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Marius van den Beek

commit sha abe6abef401b1ddef919a2c6d6b3e6f022fbd98b

Merge pull request #8970 from bernt-matthias/topic/19.05-grouping-strip-newline [19.05] Backport #8953 grouping strip newline

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Marius van den Beek

commit sha f58850a4b92d64cd90797431ec4e2f65e95e0081

Merge pull request #8980 from jmchilton/selenium_fixes_54 [19.05] Fix test repository self reference URL broken in dev.

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mvdbeek

commit sha e792b551c7a18a0f0bee080c94d0b24a2148f5c7

Merge branch 'release_19.05' into release_19.09

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M Bernt

commit sha d0dcab46285cdf64895e37a9fc17c75c21307b54

grouping: strip newlines fixes https://github.com/galaxyproject/galaxy/issues/8383 more generally: if grouping is done on the last column then the newline was retained and contained in the output.

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M Bernt

commit sha dbe440df3e2f7c519bfc6b636ac95a45d054f3bd

grouping: redecided for the less intrusive rstrip

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John Chilton

commit sha 34e217b32832dd65de7542a9c359d1936f849f9d

[19.05] Fix test repository self reference URL broken in dev.

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Marius van den Beek

commit sha abe6abef401b1ddef919a2c6d6b3e6f022fbd98b

Merge pull request #8970 from bernt-matthias/topic/19.05-grouping-strip-newline [19.05] Backport #8953 grouping strip newline

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Marius van den Beek

commit sha f58850a4b92d64cd90797431ec4e2f65e95e0081

Merge pull request #8980 from jmchilton/selenium_fixes_54 [19.05] Fix test repository self reference URL broken in dev.

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John Chilton

commit sha 7483ce269ec26a0b8acc34a4df2fdec4d396d027

Various refactorings ahead of extended metadata impl.

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John Chilton

commit sha 904ac4d070d8980d49b4e468a5fbf377832c7254

Implement extended metadata collection.

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John Chilton

commit sha dded01438ed06081f0ad5e5caafc3f5fc2433218

Eliminate shed_functional imports so we can refactor.

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John Chilton

commit sha aed933e7e78d5f806373eb937ced1ffebd82d413

Rework API tests to depend on test_base.driver at just one place. Mirrors what we do with Selenium to some degree and makes it easier to chance all tests at once. We can then rework ApiTestCase and produce a different implementation if driver_util isn't available at some point.

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John Chilton

commit sha 180d96c5408192479cb5c197385040695081b7ca

Refactor tool shed tests into tool shed namespace.

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John Chilton

commit sha d04c020747a9946de8339a80e4f7e7777ef3f6ce

Migrate api tests into lib/galaxy_test for packaging.

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John Chilton

commit sha 72bae339230cac4233a36bbd6494f024b2a7d37d

Migrate selenium tests into lib/galaxy_test for packaging.

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John Chilton

commit sha fd5679ad559cc8770f87bfd6c600a03c924dc758

New packages for Galaxy tests.

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John Chilton

commit sha 2266ffd87d43461a2e8f838ed9e34d3d356b6aac

Exclude galaxy_test when running unit tests.

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John Chilton

commit sha 97c05748983e9b27187dc64b9dae933f761cc3fe

Update lib/galaxy_test/api/_framework.py Co-Authored-By: Marius van den Beek <m.vandenbeek@gmail.com>

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John Chilton

commit sha 792ffd84095b32d4f97e75011ebee6eb84261e6f

Merge pull request #8962 from jmchilton/package_tests_2 Create packages for Galaxy tests and infrastructure.

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John Chilton

commit sha f308c05f61153500eeaac7e6cbecc156c3efc992

[19.05] Fix test repository self reference URL broken in dev.

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John Chilton

commit sha b404dc0b6347534193e356809841c4237de01fc1

Remove workflows from tool shed.

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Marius van den Beek

commit sha 18db389113915af16128f4250be29583663f9d31

Merge pull request #8930 from jmchilton/extended_metadata Implement extended job metadata collection

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Marius van den Beek

commit sha b04f7328800535d5696fd5e2ac036a872e91597d

Merge pull request #8978 from jmchilton/remove_workflows_ts Remove workflow support from tool shed.

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Peter Briggs

commit sha f3d9db3063d2cba26e6fbe82a3eee4e1a6fe0bd5

trinity: update README to clarify specification of memory limit (#2521) * trinity: update the README to clarify how memory limit should be specified for the tool. * Clarify README

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tnabtaf

commit sha 0d5b5f813e03fbbaab2023e68fd48094479f35e3

Added link to Migale newsletter to Migale announcement in November newsletter.

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Nate Coraor

commit sha b11becb5ebbeb981939acdf2e76fa2cfb0a6cd32

WIP MTS in JS

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Nate Coraor

commit sha affeb767ea0aca36b9f90539b7e29d4de3ea1ac6

Really Don't default owner/group/mode of mountpoints

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Nate Coraor

commit sha 8cd2d24f2180a6809d9ad8ec5217a61ab33ba4c1

Use correct password store entry in .pass

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Nate Coraor

commit sha 8599d0a0bd670b12a6a14870357b3a21f3315614

Install TS role from Ansible Galaxy

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Nate Coraor

commit sha 57e27f036958bf32dcf8520ddcc3680d7a1a48f0

Use galaxyproject.postgresql from Ansible Galaxy

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created taggalaxyproject/ansible-postgresql

tag1.0.2

An Ansible role for managing a PostgreSQL server

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Nate Coraor

commit sha d3c29ac96813fc17d92e473cf991db3e3abd509e

Additional fixes for yum repo changes upstream

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Nate Coraor

commit sha 1507fbe5eda946fc9f4c9aabef4e73a9b11a8315

Merge pull request #22 from galaxyproject/el-repo-changes Additional fixes for yum repo changes upstream

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PR opened galaxyproject/ansible-postgresql

Additional fixes for yum repo changes upstream

Continuation of the work in #21.

+34 -40

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create barnchgalaxyproject/ansible-postgresql

branch : el-repo-changes

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created taggalaxyproject/ansible-nginx

tag0.6.4

An Ansible role for managing an nginx server.

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Nate Coraor

commit sha 2a01e4d555f312e3ae6a6975a6eab05a63fbae80

Ensure certbot_well_known_root exists before attempting to set SELinux fcontext

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Nate Coraor

commit sha c0a833adaa9c70d43ef0edf9b87c46421525f147

Merge pull request #7 from galaxyproject/mkdir-well-known Ensure certbot_well_known_root exists before attempting to set SELinux fcontext

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issue closedgalaxyproject/ansible-nginx

Not check safe

00:00:55 TASK [galaxyproject.nginx : Make nginx -V output a single line] ****************
00:00:55 fatal: [stats.galaxyproject.eu]: FAILED! => {"msg": "The task includes an option with an undefined variable. The error was: 'dict object' has no attribute 'stderr'\n\nThe error appears to have been in '/home/centos/workspace/usegalaxy-eu/playbooks/stats/roles/galaxyproject.nginx/tasks/main.yml': line 18, column 3, but may\nbe elsewhere in the file depending on the exact syntax problem.\n\nThe offending line appears to be:\n\n\n- name: Make nginx -V output a single line\n  ^ here\n"}

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erasche

issue commentgalaxyproject/ansible-nginx

Not check safe

Fixed by #6.

erasche

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pull request commentgalaxyproject/ansible-nginx

Check mode - supply fake nginx version

Fixes #4.

erasche

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Helena Rasche

commit sha c04e3107aea1be6d8a5cc09fa55806c007fa18a6

real extra true facts™

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Helena Rasche

commit sha 41e37ddabf5809a1c09dff177e0ac6efadf48054

also this

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Helena Rasche

commit sha e158da36d16b62fde5fa165080701185b51b97a2

also this

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Nate Coraor

commit sha e30ac5d1bca288fd8e75394d19cce8c3ed0dd582

Line wrap

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Nate Coraor

commit sha 77abd3fe029c698de8f26a00eab1684b47b5220c

Merge pull request #6 from galaxyproject/real-facts Check mode - supply fake nginx version

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PR merged galaxyproject/ansible-nginx

Check mode - supply fake nginx version

This should permit check mode to work properly-ish. When running under check mode we'll use some plausible values for nginx / nginx version (totally not fake news) and just remind the user "hey this might not be right, the diff could be unexpected, here's how to fix it"

+20 -0

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erasche

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Nate Coraor

commit sha e30ac5d1bca288fd8e75394d19cce8c3ed0dd582

Line wrap

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create barnchgalaxyproject/ansible-nginx

branch : mkdir-well-known

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created taggalaxyproject/ansible-galaxy-toolshed

tag0.2.0

An Ansible role for managing a Galaxy (http://galaxyproject.org) Tool Shed server. For a role to install Galaxy itself, see https://github.com/galaxyproject/ansible-galaxy

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Nate Coraor

commit sha a48688831bd6f9518df2047296e18705fefb3d65

Bring some stuff over from the galaxy role (mostly YAML config). At this point we should maybe just document how to run the galaxy role to install a TS since this is all duplication.

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Nate Coraor

commit sha 594e2bfdf80c5a8e5569be6684aa0722cb7d6917

Rename jsts -> testtoolshed

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tnabtaf

commit sha 27d66e550d7a2e5a7dafd7c748645314abcf0d58

Updated Galaxy-Updates page to link to recent newsletters.

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John Chilton

commit sha 45019c3fbd6f1efbd3aab61f9be802d7940e1f72

Move galaxy testing utilities into more sane package structure. Split test/base into lib/galaxy_test/base and lib/galaxy_test/driver. Dividing things on whether they import galaxy-app code or not - with the goal of a galaxy-test-base package that doesn't depend on galaxy-app and a galaxy-test-driver package that does. I've been refactoring around this division for a long time. Certain tests (namely the integration tests) always need to bootstrap Galaxy - but the API tests and the Selenium tests should be installable and runnable without Galaxy in the Python environment. So future galaxy-test-api and galaxy-test-selenium packages should have only an optional dependency on galaxy-test-driver. Properly sturcturing these namespaces is a precursor for real packages on PyPI, clean separation of the tool shed testing code, and cleans up all the flake8 noqa hacks in test/.

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Martin Cech

commit sha b5afa3c1a90d269f1d438ffde481ff2e4178a72b

Merge pull request #8960 from jmchilton/package_tests_1 Move galaxy testing utilities into cleaner package structure.

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John Chilton

commit sha 301d026bfbf2ed5516965cc10d0d2e424f33c97a

Small fixes for k8s.

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Martin Cech

commit sha 711e32f3c24248a6cd178ed11540be34d6f1efa1

Merge pull request #8969 from jmchilton/8759_backport [19.09] Backport 8759 (k8s fixes)

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Simon Bray

commit sha 2599eb1ebf04f1c5ce144d4c2aa4b4546df549db

add new gmx datatypes: ndx, xvg, edr

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Simon Bray

commit sha 8f45f7c59a285e540e957bda7c67203af19f23b4

fix

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Simon Bray

commit sha a115122deaa7a2eb23077a79cdd57dc056e4bda0

point gromacs magic number refs to a specific commit

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Marius van den Beek

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Merge pull request #8964 from simonbray/gmx Add new GROMACS datatypes: ndx, xvg, edr

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Martin Cech

commit sha 984195af7a12f77857d216a781e17d10e6bcb9d9

trim the loaded value, since Galaxy tends to start with a newline

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Martin Cech

commit sha bcf219ee702a81388973365db344fb06c93eeb1f

strip the named tag prefix do not store tags like "name:name:value"

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Martin Cech

commit sha e5b5e04ef6632eb260ab5396ac65a79eca88470b

bring some clarity to library tag handling fix tag list handling when updating ldda add test for ldda tag update add doc tests for tag parsing methods refactor

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Martin Cech

commit sha ffce700fe1e1d32acdcb2b896f025928e7bc441e

prevent bootstrap to inject "!important" overflow css rule it makes library dataset page unscrollable xref https://github.com/galaxyproject/galaxy/pull/8787

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Martin Cech

commit sha 86e6dc983e8ed9ecefc8e8362c0dcce8b2705dac

avoid different unicode str behavior on py2/3

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M Bernt

commit sha 3a0d9325a6df4c2fa6e8ce8cc39e6c067890a7fe

grouping: strip newlines fixes https://github.com/galaxyproject/galaxy/issues/8383 more generally: if grouping is done on the last column then the newline was retained and contained in the output.

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M Bernt

commit sha 2ea05e81f8549eb63bfd4db9f6b2971e1d0848e3

grouping: redecided for the less intrusive rstrip

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John Chilton

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Refactor tool_shed webapp out of Galaxy.

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John Chilton

commit sha 81ea8a9af0750b02c6543bbf70bd9930c112be57

Separate Shed and Galaxy makos, package shed makos. Another step toward toward proper packaging of tool_shed and separation of Galaxy and ToolShed. Builds on #8949.

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John Chilton

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Remove unused tool_shed.tool_shed_registry.

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Frederic Sapet

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add gff3.gz and gff3.bz2 datatypes

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Björn Grüning

commit sha 61683ad3ac20c02be59839de74b0e60e2438c64e

Merge pull request #8967 from FredericBGA/gff_gz add gff3.gz and gff3.bz2 datatypes

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Marius van den Beek

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Merge pull request #8949 from jmchilton/refactor_ts_2 Refactor Toolshed webapp into tool_shed package.

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Marius van den Beek

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Merge pull request #8958 from jmchilton/refactor_ts_3 Separate Shed and Galaxy makos, package shed makos.

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Marius van den Beek

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Merge pull request #8953 from bernt-matthias/topic/grouping-strip-newline grouping: strip newlines

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Marius van den Beek

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Merge pull request #8947 from martenson/libtags Library tags tweaks and tests

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Lance Parsons

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Update gffread to version 0.11.6

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Björn Grüning

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Update gffread.xml

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Björn Grüning

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remove comment

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Björn Grüning

commit sha 35e5b87300fb4e64d6d4eab376012ca9c524a432

Merge pull request #2674 from lparsons/gffread_0.11.6 Update gffread to version 0.11.6

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issue closedgalaxyproject/ansible-postgresql

Ansible deprecation warning: Using tests as filters is deprecated.

This line occurs twice in tasks/main.yml:

when: "{{ postgresql_version | version_compare('9.3', '>=') }}"

Replacing it with:

when: postgresql_version  >= '9.3'

avoids this deprecation warning from Ansible 2.5:

Using tests as filters is deprecated.
Instead of using`result|version_compare` instead use `result is version_compare`. 
This feature will be removed in version 2.9.

closed time in 5 days

dpneumo

issue commentgalaxyproject/ansible-postgresql

Ansible deprecation warning: Using tests as filters is deprecated.

Thanks @dpneumo, this was fixed in #18.

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Yaroslav Shabalin

commit sha dc162fb20c8a5172aae7e39dc966d7e37eb2c83e

Properly handle WAL directory in backup scripts for PostgreSQL version >=10

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Nate Coraor

commit sha 9da5cccd39711a56725bf61f631c4c3ec324a841

Use `version` instead of `version_compare` and other minor changes

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Nate Coraor

commit sha ea4135d8d69c26da1546af45e9d897d5ac3a08fc

Merge pull request #20 from yaroslav-shabalin/wal_dir_rename Properly handle WAL directory in backup scripts for version >=10

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PR merged galaxyproject/ansible-postgresql

Properly handle WAL directory in backup scripts for version >=10

According to official documentation in version 10 'pg_xlog' directory was renamed to 'pg_wal'. This pull request introduces conditional template evaluation depending on PostgreSQL version being installed.

Links to documentation: https://www.postgresql.org/docs/10/release-10.html#id-1.11.6.13.4 https://wiki.postgresql.org/wiki/New_in_postgres_10#Renaming_of_.22xlog.22_to_.22wal.22_Globally_.28and_location.2Flsn.29

+5 -4

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yaroslav-shabalin

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pull request commentgalaxyproject/ansible-postgresql

Properly handle WAL directory in backup scripts for version >=10

@yaroslav-shabalin thanks! I added a couple very minor changes.

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Nate Coraor

commit sha 9da5cccd39711a56725bf61f631c4c3ec324a841

Use `version` instead of `version_compare` and other minor changes

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Davor Racic

commit sha 91f424c7c73ba8349e612af37a08cb900ebb7005

Check pgdg repository package task for RHEL repos checks pgdg-redhat-repo package As of 15 April 2019, there is only one repository RPM per distro, and it includes repository information for all available PostgreSQL releases.

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Nate Coraor

commit sha c20db044e9dd147dee7d29eec2fa5d9ab732ef56

Merge pull request #21 from dracic/master Check pgdg repository package task for RHEL based distros should check pgdg-redhat-repo package

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PR merged galaxyproject/ansible-postgresql

Check pgdg repository package task for RHEL based distros should check pgdg-redhat-repo package

As of 15 April 2019, there is only one repository RPM per distro, and it includes repository information for all available PostgreSQL releases.

+1 -1

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dracic

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pull request commentgalaxyproject/ansible-postgresql

Check pgdg repository package task for RHEL based distros should check pgdg-redhat-repo package

Thanks @dracic! I think there's a way to do the second part with yum_repository that'd be a bit cleaner, so I'm looking in to that.

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tnabtaf

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Added training to newsletter

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Martin Cech

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add note to RN about GS

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Martin Cech

commit sha 3f7a0a84413a8c771924f573f7609b60437ad0fd

Update doc/source/releases/19.09_announce.rst Co-Authored-By: Nicola Soranzo <nicola.soranzo@gmail.com>

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Nicola Soranzo

commit sha 0e4fb6a22af62a76fc8f98e15f3d633c0dedb0c3

Merge pull request #8961 from martenson/gs-deprec [19.09] add note to RN about GS

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tnabtaf

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Publishing November newsletter

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John Chilton

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Fix ts tests on Mac OS X.

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John Chilton

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Replace toolshed util symlink with package safe re-export.

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John Chilton

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Fixup links in common_util for migration tool Galaxy.

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John Chilton

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Refactor tool_shed basic_util into Galaxy.

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John Chilton

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Refactor hg_util into Galaxy.

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John Chilton

commit sha 6fd2fac89cc1c4dd28602fa4fdf66d7c4002afd7

Rework various tool shed imports head of big refactor.

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John Chilton

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CLeanup metadata_util imports ahead of refactor.

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John Chilton

commit sha 6b651ae2579717c8b775be94989a153d5fd4642d

Migrate data_table_manager to Galaxy.

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John Chilton

commit sha 052bd83ced3419abac556e426adb093f9585a81e

Migrate tool_shed_registry to Galaxy.

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John Chilton

commit sha 135190fde66ff3b7c54b1c5f078851e12b570422

Cleanup tool_shed_registry imports.

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John Chilton

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Break up tool validator into Galaxy/TS variants.

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John Chilton

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Separate repository_util into Galaxy and Toolshed variants.

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John Chilton

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Separate shed_util_common into Galaxy and TS variants.

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John Chilton

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Refactor TS metadata_util into parts in Galaxy/TS.

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John Chilton

commit sha 7055e39170426c588300d98f74a037fc732325e4

Refactor tool_shed.util.tool_dependency_util into galaxy.

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John Chilton

commit sha 542399b17b6979f37d090f1d980c1634e30f6952

Cleanup imports for tool_dependency_util.

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John Chilton

commit sha 3e3c9e8bc070939d2e73602b544eeb4aabfcad71

Refactor tool_shed.util.tool_util into galaxy.

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John Chilton

commit sha aa8f32a6712508a39816a4ab6bb1fbe1faafb1ef

Refactor tool_shed.galaxy_install.tool_dependencies into galaxy. TODO:

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John Chilton

commit sha 23395f41d6dd1ca47d7011276afcc545c1a8bb1f

Fix imports in env_manager for refactor into galaxy.

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John Chilton

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Fix up imports in install_environment for transition into galaxy.

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John Chilton

commit sha d4196b61a492249e59cfea1aedd975d960824b77

Remove tool shed API examples. These aren't tested, bioblend likely has better documentation (https://bioblend.readthedocs.io/en/latest/api_docs/toolshed/all.html), and we should be encouraging TS interactions to be done through Planemo and not raw API calls. Excluding scripts used by bootstrap.

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Martin Cech

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Merge pull request #8956 from jmchilton/remove_ts_api Remove tool shed API examples.

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Dannon Baker

commit sha fd9e61a0d615328f32d69cb50f8910ce005278d9

Fix the running wobblies

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Marius van den Beek

commit sha c3c8a1728a3714da97fa9a91aa7285ed7231c320

Merge pull request #8950 from dannon/no-more-wobbles [19.09] Fix the running icon wobblies

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Nicola Soranzo

commit sha 8e4371e3bc8b660cc10ac36ae7a546b21f86ab20

Remove unused code These grid operations were dropped in commit f3b08e6e019f45117d4100fc90d7f45a8e285ae4 .

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Nicola Soranzo

commit sha ec774ab64474c86b4aed103ca3818928e8c144fe

Set `deleted` attribute of history datasets when purging histories from grid Use `history_manager.purge()` which implements that correctly. Also remove unused `delete()` method of `HistoryController`, last use removed in PR https://github.com/galaxyproject/galaxy/pull/4574 .

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Nicola Soranzo

commit sha f30cad5be79f1aff7a04efb0e77c82df4a92914a

Move migration 134 to 160

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John Chilton

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Remove tool dependency scripts.

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John Chilton

commit sha a27beb0fd8c86d50403cec46aa09a1dddcea0892

Remove script for migrating tools to the tool shed... from an older tool shed? I completely forgot there even was an older tool shed.

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Nicola Soranzo

commit sha ab232d9f92028b4d4d79a52d3f9690d0b254771a

Merge pull request #8955 from jmchilton/deprecate_tool_dependencies Remove deprecated tool dependency scripts.

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Nicola Soranzo

commit sha 6b1bacc2b810da5a978729b23055611d1987c85a

Merge pull request #8957 from jmchilton/remove_legacy_shed Remove script for migrating tools to the tool shed...

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Marius van den Beek

commit sha 9055c51befb3ccee3062d569125237b4e0ddeab1

Merge pull request #8940 from nsoranzo/delete_when_purging_histories Set `deleted` attribute of history datasets when purging histories from grid

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tnabtaf

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first draft of November newsletter.

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tnabtaf

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Updating newsletter draft.

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tnabtaf

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Draft newsletter update.

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M Bernt

commit sha 0042ba1f297463b87a75b5ce04ac73673b7cd154

dada2: initial commit moved over from here https://github.com/bernt-matthias/mb-galaxy-tools/pulls

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M Bernt

commit sha 15a10d3a8b623ba0daf6369fe7cb5716dcf1907e

travis: test for mixed tool data_manager PR if there is more than 1 changed repo (eg 1 tool and 1 data manager) then planemo is called per repo, which fails for data manager because the path to the xml is needed. hence if the repo is in the data_managers directory the path to the xml file is determined with an additional call to `planemo ci_find_tools` and then used in the planemo test call.

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Björn Grüning

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Merge pull request #2483 from bernt-matthias/topic/dada2 dada2

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tnabtaf

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Added Table Compute news item.

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Nate Coraor

commit sha 8341825d95119f4c829923e6341244578958e742

Upgrade CVMFS module for HTTPS snapshots

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Nate Coraor

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WIP Toolshed server on Jetstream

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Nate Coraor

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Don't default owner/group/mode of mountpoints

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Updated support for PepSimili platform.

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publishing open life science news item.

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tnabtaf

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Cleanup of ABRF and admin training pages; moved news item to blog post, where it should have gone in the first place.

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John Chilton

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Structured access to Galaxy internals for ITs.

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John Chilton

commit sha 2912094de012e74f9af017d0c4f5e34bb0087801

Allow per-destination overrride of galaxy_url for tools. The proper interaction between tools and jobs for determining Galaxy's URL from the destination of the tool.

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John Chilton

commit sha 4ccef702bea18bc88998be5dd225daa6ab216017

Cleanup structured IT internals access commit. - Unit test fixes and added tests. - Change __history_id to __history_id__ per comment from @bgruening

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John Chilton

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Update galaxy.xsd for injecting API keys.

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John Chilton

commit sha 1240ab276babfde88cc7a6ee98312e9f560d1a88

Fix id convention for test interactive tools.

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John Chilton

commit sha 8807a8f39f857f48f7ce953bf1022e9d01bdb4d6

Separate new inject tests into new tool.

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John Chilton

commit sha 58f2382ad0cf070ee2c04119e4fc4c13cdb99192

Allow anonymous users to use tools with injected API keys. https://github.com/galaxyproject/galaxy/pull/8897/files#r342997635

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Bjoern Gruening

commit sha 61b9aee3ff687184be7e66b63d41f32e31ec188d

check_for_entry_points() more agressively in the condor job runner

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Marius van den Beek

commit sha 75402b4bab204a2e313c6f2c0ec252c3b71aaea5

Merge pull request #8897 from jmchilton/it_tool_interface [19.09] Structured access to Galaxy internals for (Interactive) Tools

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mvdbeek

commit sha ac1768c8d8ffd05f9f3c0116a51669b69a22e4ef

Fix reading loc file samples This must've been broken for some time. Fixes https://github.com/galaxyproject/galaxy/issues/8534

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Bjoern Gruening

commit sha 695d94bf8c47fbcce05fb224a36a9f3aff1568b4

adopt to Marius suggestion

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mvdbeek

commit sha 81532d9c647e3cda4c7410c3071640cac82998e6

Validate tag strings as well as list of tags I think it'd be better if we consistently used lists for tags, but it seems too late in 19.09 to make possibly bigger changes here. Fixes https://github.com/galaxyproject/galaxy/issues/8851 broken in https://github.com/galaxyproject/galaxy/pull/8530.

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Marius van den Beek

commit sha 97d6af0b6ea82bb7d7295686be1b751578cd1ef8

Merge pull request #8939 from bgruening/its_condor_fix [19.09] check_for_entry_points() more agressively in the condor job runner

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mvdbeek

commit sha 2423a5b2dcba77582c25a554d6a75d79c726a42d

Fix send_local_control_task argument passing `kwargs` used to be the second argument, but it is now being interpreted as `get_response`. Since there's no response coming it'll hang until a timeout occurs. Fixes ``` galaxy.queue_worker: ERROR: Error waiting for task: '{'kwargs': {}, 'task': 'recalculate_user_disk_usage'}' sent with routing key 'control.main@613c834ba62c' Traceback (most recent call last): File "/galaxy_venv3/lib/python3.5/site-packages/kombu/transport/virtual/base.py", line 979, in drain_events get(self._deliver, timeout=timeout) File "/galaxy_venv3/lib/python3.5/site-packages/kombu/utils/scheduling.py", line 56, in get return self.fun(resource, callback, **kwargs) File "/galaxy_venv3/lib/python3.5/site-packages/kombu/transport/virtual/base.py", line 1017, in _drain_channel return channel.drain_events(callback=callback, timeout=timeout) File "/galaxy_venv3/lib/python3.5/site-packages/kombu/transport/virtual/base.py", line 761, in drain_events return self._poll(self.cycle, callback, timeout=timeout) File "/galaxy_venv3/lib/python3.5/site-packages/kombu/transport/virtual/base.py", line 402, in _poll return cycle.get(callback) File "/galaxy_venv3/lib/python3.5/site-packages/kombu/utils/scheduling.py", line 56, in get return self.fun(resource, callback, **kwargs) File "/galaxy_venv3/lib/python3.5/site-packages/kombu/transport/virtual/base.py", line 405, in _get_and_deliver message = self._get(queue) File "/galaxy_venv3/lib/python3.5/site-packages/kombu/transport/sqlalchemy/__init__.py", line 109, in _get raise Empty() queue.Empty During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/galaxy/lib/galaxy/queue_worker.py", line 130, in send_task self.connection.drain_events(timeout=timeout) File "/galaxy_venv3/lib/python3.5/site-packages/kombu/connection.py", line 321, in drain_events return self.transport.drain_events(self.connection, **kwargs) File "/galaxy_venv3/lib/python3.5/site-packages/kombu/transport/virtual/base.py", line 982, in drain_events raise socket.timeout() socket.timeout ``` That occasionally occurs in the selenium tests.

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Dannon

commit sha 3194eda08b05bb143a59e97e490a39c2ecc8e9cd

Merge pull request #8945 from mvdbeek/fix_send_local_control_task_usage [19.09] Fix send local control task usage

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mvdbeek

commit sha 3013895f785bcff07686a22061b32a1da4c7da7c

Use listify to convert tag string to list tag should be a list in `_set_from_dict`. Thanks @nsoranzo.

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Björn Grüning

commit sha 4e3a3350b5030c57c9d39b23589d90d3ef3212cf

Merge pull request #8942 from mvdbeek/fix_sample_reading [19.09] Fix reading loc file samples

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Martin Cech

commit sha e3b9eb62f6a453e6c41f5fe9041c42dbd7546b2d

Merge pull request #8944 from mvdbeek/fix_library_tag_validation [19.09] Validate tag strings as well as list of tags

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Martin Cech

commit sha 67a3950c271e3b27d29beaf1ec827c73f2eaba68

Merge branch 'release_19.09' into dev

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Bérénice Batut

commit sha b3fac5875747a3b905193d5c98d9e5fc92b80760

Update the date for webinar

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Bérénice Batut

commit sha 74032cca7b3a9bbce0c4c1268f14241937af160a

Update src/news/2019-11-open-life-science/index.md Co-Authored-By: Dannon <dannon.baker@gmail.com>

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Dannon

commit sha 3620e17355627cb5a00107fcae5ceab2b4e45eec

Merge pull request #563 from galaxyproject/bebatut-patch-1 Update the date for webinar (Open Life Science)

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created taggalaxyproject/ansible-cvmfs

tag0.2.7

An Ansible role for installing and configuring CernVM-FS (CVMFS)

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Nate Coraor

commit sha b7d3665652ff7af247b8be3ee3146cea10a07e99

Add support for performing Stratum 1 snapshots over HTTPS

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Nate Coraor

commit sha ac9180ac78ecb7c5512983fd393e0d8af794caf9

Merge pull request #18 from galaxyproject/https-snapshot Add support for performing Stratum 1 snapshots over HTTPS

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Nate Coraor

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Add Makefile as an alternative to ansible-env

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Nate Coraor

commit sha ee38a57acc8b636617497ac0c411a6be7036a2c9

Rename playbook Makefile target to all

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Nate Coraor

commit sha aa054ab09fdd6156080e872e7a284b0599a45f7c

Drop cluster back to 1 node

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Nate Coraor

commit sha f6ef17d2afe563bf0c4cd308c51be3b5544c3591

Add smart2 and smart3

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mvdbeek

commit sha 81532d9c647e3cda4c7410c3071640cac82998e6

Validate tag strings as well as list of tags I think it'd be better if we consistently used lists for tags, but it seems too late in 19.09 to make possibly bigger changes here. Fixes https://github.com/galaxyproject/galaxy/issues/8851 broken in https://github.com/galaxyproject/galaxy/pull/8530.

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mvdbeek

commit sha 3013895f785bcff07686a22061b32a1da4c7da7c

Use listify to convert tag string to list tag should be a list in `_set_from_dict`. Thanks @nsoranzo.

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Martin Cech

commit sha e3b9eb62f6a453e6c41f5fe9041c42dbd7546b2d

Merge pull request #8944 from mvdbeek/fix_library_tag_validation [19.09] Validate tag strings as well as list of tags

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Gianmauro Cuccuru

commit sha 0e8bab90bd8603ee8c01a26e297d114b19d16b9f

add exomedepth

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Gianmauro Cuccuru

commit sha f3330642f651b3883ac3e4b59db4fc5286f0dc48

update url

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Gianmauro Cuccuru

commit sha 431a67c29ff26e28848863edd4f7106abfe29e1a

4 space

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Gianmauro Cuccuru

commit sha d4b2e86ec69eb4c8e4444a637492a30250140701

smaller datasets

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Björn Grüning

commit sha 5c4c7fe10135fa322379228177f214ae25a79ff0

Update .shed.yml

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Björn Grüning

commit sha 91a0182476a7fc26be7bef1677790518c4e88348

Merge pull request #2672 from sigu-training/master add exomedepth

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mvdbeek

commit sha ac1768c8d8ffd05f9f3c0116a51669b69a22e4ef

Fix reading loc file samples This must've been broken for some time. Fixes https://github.com/galaxyproject/galaxy/issues/8534

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Björn Grüning

commit sha 4e3a3350b5030c57c9d39b23589d90d3ef3212cf

Merge pull request #8942 from mvdbeek/fix_sample_reading [19.09] Fix reading loc file samples

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mvdbeek

commit sha 2423a5b2dcba77582c25a554d6a75d79c726a42d

Fix send_local_control_task argument passing `kwargs` used to be the second argument, but it is now being interpreted as `get_response`. Since there's no response coming it'll hang until a timeout occurs. Fixes ``` galaxy.queue_worker: ERROR: Error waiting for task: '{'kwargs': {}, 'task': 'recalculate_user_disk_usage'}' sent with routing key 'control.main@613c834ba62c' Traceback (most recent call last): File "/galaxy_venv3/lib/python3.5/site-packages/kombu/transport/virtual/base.py", line 979, in drain_events get(self._deliver, timeout=timeout) File "/galaxy_venv3/lib/python3.5/site-packages/kombu/utils/scheduling.py", line 56, in get return self.fun(resource, callback, **kwargs) File "/galaxy_venv3/lib/python3.5/site-packages/kombu/transport/virtual/base.py", line 1017, in _drain_channel return channel.drain_events(callback=callback, timeout=timeout) File "/galaxy_venv3/lib/python3.5/site-packages/kombu/transport/virtual/base.py", line 761, in drain_events return self._poll(self.cycle, callback, timeout=timeout) File "/galaxy_venv3/lib/python3.5/site-packages/kombu/transport/virtual/base.py", line 402, in _poll return cycle.get(callback) File "/galaxy_venv3/lib/python3.5/site-packages/kombu/utils/scheduling.py", line 56, in get return self.fun(resource, callback, **kwargs) File "/galaxy_venv3/lib/python3.5/site-packages/kombu/transport/virtual/base.py", line 405, in _get_and_deliver message = self._get(queue) File "/galaxy_venv3/lib/python3.5/site-packages/kombu/transport/sqlalchemy/__init__.py", line 109, in _get raise Empty() queue.Empty During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/galaxy/lib/galaxy/queue_worker.py", line 130, in send_task self.connection.drain_events(timeout=timeout) File "/galaxy_venv3/lib/python3.5/site-packages/kombu/connection.py", line 321, in drain_events return self.transport.drain_events(self.connection, **kwargs) File "/galaxy_venv3/lib/python3.5/site-packages/kombu/transport/virtual/base.py", line 982, in drain_events raise socket.timeout() socket.timeout ``` That occasionally occurs in the selenium tests.

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Dannon

commit sha 3194eda08b05bb143a59e97e490a39c2ecc8e9cd

Merge pull request #8945 from mvdbeek/fix_send_local_control_task_usage [19.09] Fix send local control task usage

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Bjoern Gruening

commit sha 61b9aee3ff687184be7e66b63d41f32e31ec188d

check_for_entry_points() more agressively in the condor job runner

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Bjoern Gruening

commit sha 695d94bf8c47fbcce05fb224a36a9f3aff1568b4

adopt to Marius suggestion

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Marius van den Beek

commit sha 97d6af0b6ea82bb7d7295686be1b751578cd1ef8

Merge pull request #8939 from bgruening/its_condor_fix [19.09] check_for_entry_points() more agressively in the condor job runner

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guerler

commit sha 9d277f0e0689449f3ec08cc5dbe81688bef1d28f

Fix default logo path in configuration manager

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Björn Grüning

commit sha 0df7ac6bfd2b1f89a7051e6787831cd0b7d3eeb2

Merge pull request #8941 from guerler/fix_logo_default Fix default logo path in configuration manager

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tnabtaf

commit sha c78fbbcb4232214e8889b72dbc6b6e00406599c6

Added draft news item on Open Life Science

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Anup Kumar

commit sha 4565a313abbda140a6f24b534feda315e44e5b59

Add link for interactive tools

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Anup Kumar

commit sha d008baed163474aa37fbffcb917477219101dfd8

Format vue

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Anup Kumar

commit sha 1132e858b04ff0e4f0ef273ba6997c169b516681

Set url in computed property

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Anup Kumar

commit sha 3ffc8b400443dc1f0062ea459a35e73cd011e559

Merge branch 'dev' of github.com:anuprulez/galaxy into link_live

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Anup Kumar

commit sha ac5e259aa053be66466c0156a10c0c2c0510035f

Remove usused method

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Dannon

commit sha cb62e4445f206e0acc77c8d2da5b261e5499c807

Merge pull request #8936 from anuprulez/link_live Add link for interactive tools

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John Chilton

commit sha 2e7a0720e7083a319ff97d898a1cd8f27c448d82

Structured access to Galaxy internals for ITs.

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John Chilton

commit sha 2912094de012e74f9af017d0c4f5e34bb0087801

Allow per-destination overrride of galaxy_url for tools. The proper interaction between tools and jobs for determining Galaxy's URL from the destination of the tool.

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John Chilton

commit sha 4ccef702bea18bc88998be5dd225daa6ab216017

Cleanup structured IT internals access commit. - Unit test fixes and added tests. - Change __history_id to __history_id__ per comment from @bgruening

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John Chilton

commit sha c9ca348c620e2bf33571c83934f091b40fbfcae2

Update galaxy.xsd for injecting API keys.

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John Chilton

commit sha 1240ab276babfde88cc7a6ee98312e9f560d1a88

Fix id convention for test interactive tools.

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John Chilton

commit sha 8807a8f39f857f48f7ce953bf1022e9d01bdb4d6

Separate new inject tests into new tool.

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John Chilton

commit sha 58f2382ad0cf070ee2c04119e4fc4c13cdb99192

Allow anonymous users to use tools with injected API keys. https://github.com/galaxyproject/galaxy/pull/8897/files#r342997635

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Marius van den Beek

commit sha 75402b4bab204a2e313c6f2c0ec252c3b71aaea5

Merge pull request #8897 from jmchilton/it_tool_interface [19.09] Structured access to Galaxy internals for (Interactive) Tools

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John Chilton

commit sha 352e751927cd6e8e521db383cbd21f50a51c1b74

Revert hacking IPs in container monitor script. It breaks the Mac setup and seems just wrong, docker might not be on localhost. This needs to be made more specific in some way and should handle those socker commands not working on OS X.

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John Chilton

commit sha ff08885c2ea0215430c86b7377c1d1bf291e51f3

Only re-map container monitor host if can find IP and have 0.0.0.0.

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John Chilton

commit sha 391381d3c40b16c7b9fdbadd9fa8f1f215cb7a59

small doctest for docker port parsing

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Nicola Soranzo

commit sha 1663c9e331ee2445ce86a2bca1a6cbd19dae64e1

Check `host_ip` only once

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John Chilton

commit sha af1b704bad2f32c571490ae6ef0460511ebac9a2

Merge pull request #8901 from jmchilton/revert_ip_adjustments [19.09] Revert hacking IPs in container monitor script.

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John Chilton

commit sha 352e751927cd6e8e521db383cbd21f50a51c1b74

Revert hacking IPs in container monitor script. It breaks the Mac setup and seems just wrong, docker might not be on localhost. This needs to be made more specific in some way and should handle those socker commands not working on OS X.

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John Chilton

commit sha ff08885c2ea0215430c86b7377c1d1bf291e51f3

Only re-map container monitor host if can find IP and have 0.0.0.0.

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John Chilton

commit sha 391381d3c40b16c7b9fdbadd9fa8f1f215cb7a59

small doctest for docker port parsing

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Nicola Soranzo

commit sha 1663c9e331ee2445ce86a2bca1a6cbd19dae64e1

Check `host_ip` only once

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mvdbeek

commit sha 22b1a3c7238406d63e38e6e775cec45a7e024afe

Also eagerload tool_dependency to tool shed repository relation

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mvdbeek

commit sha d6b69cf6d591459949110bed3aa4ee3cb74abb77

Use final_job_state in data manager exec_after_process This was all working correctly in my test, but removes some custom logic. It was theoretically possible for the old logic to fail if there was no output dataset for the job.

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mvdbeek

commit sha bb38795e75e7fbcb43794a7c23deab5c196a8e44

Give test data managers distinct ids and names

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Martin Cech

commit sha 68eb3b000fbb31f3d24ad8db7a7ee5cbe7fe32ab

if ldda message is not present but ldda info is, return it instead this is a bit of a hack but given the lack of clarity of what field does what on what object (info/message/description on ldda/ld/folder) it should help with the data presentation

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John Chilton

commit sha 657764cfb460af48bf877096611f7f176c5ccc47

Merge pull request #8934 from mvdbeek/dont_run_exec_after_process_if_job_failed [19.09] Don't re-determine if job failed in exec_after_process hook

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John Chilton

commit sha 9aec1803414e0e6b5c0ca6ebcacb773eda46a43a

Merge pull request #8933 from mvdbeek/one_more_detached_instance [19.09] Fix DetachedInstanceError when tool shed packages are in play

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Marius van den Beek

commit sha 21cdf9bcbc90a281db0625150794da4941202ed0

Merge pull request #8938 from martenson/fix-infomessage [19.09] Broaden library description/info/message

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John Chilton

commit sha af1b704bad2f32c571490ae6ef0460511ebac9a2

Merge pull request #8901 from jmchilton/revert_ip_adjustments [19.09] Revert hacking IPs in container monitor script.

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Nicola Soranzo

commit sha f779f1af313e15d98cddfe2915dff408aa4e3b37

Merge branch 'release_19.09' into dev

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Martin Cech

commit sha 68eb3b000fbb31f3d24ad8db7a7ee5cbe7fe32ab

if ldda message is not present but ldda info is, return it instead this is a bit of a hack but given the lack of clarity of what field does what on what object (info/message/description on ldda/ld/folder) it should help with the data presentation

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Marius van den Beek

commit sha 21cdf9bcbc90a281db0625150794da4941202ed0

Merge pull request #8938 from martenson/fix-infomessage [19.09] Broaden library description/info/message

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mvdbeek

commit sha 22b1a3c7238406d63e38e6e775cec45a7e024afe

Also eagerload tool_dependency to tool shed repository relation

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John Chilton

commit sha 9aec1803414e0e6b5c0ca6ebcacb773eda46a43a

Merge pull request #8933 from mvdbeek/one_more_detached_instance [19.09] Fix DetachedInstanceError when tool shed packages are in play

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