- galaxy-commits - lists.galaxyproject.org

[galaxyproject/usegalaxy-playbook] 1293cb: update mutable config
by GitHub 20 Feb '15

20 Feb '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 1293cbbc6d117988b24c6241c396e2057f0de4d0 https://github.com/galaxyproject/usegalaxy-playbook/commit/1293cbbc6d117988… Author: Martin Cech <emulatorer(a)gmail.com> Date: 2015-02-20 (Fri, 20 Feb 2015) Changed paths: M files/galaxy/test.galaxyproject.org/var/integrated_tool_panel.xml Log Message: ----------- update mutable config

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[galaxyproject/usegalaxy-playbook] b43644: set user_library_import_dir to the ftp dir
by GitHub 20 Feb '15

20 Feb '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: b436445b888037330f15a39b1b4a529958286008 https://github.com/galaxyproject/usegalaxy-playbook/commit/b436445b88803733… Author: Martin Cech <emulatorer(a)gmail.com> Date: 2015-02-20 (Fri, 20 Feb 2015) Changed paths: M stage/group_vars/galaxyservers.yml Log Message: ----------- set user_library_import_dir to the ftp dir

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[galaxyproject/usegalaxy-playbook] b5e4cb: Dropped slide for February 2015 Meetup.
by GitHub 19 Feb '15

19 Feb '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: b5e4cbda98106790880cbac2ad25816f38af6917 https://github.com/galaxyproject/usegalaxy-playbook/commit/b5e4cbda98106790… Author: Dave Clements <clements(a)Clements-Galaxy.local> Date: 2015-02-19 (Thu, 19 Feb 2015) Changed paths: M templates/galaxy/common/static/welcome.html.j2 Log Message: ----------- Dropped slide for February 2015 Meetup.

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[galaxyproject/usegalaxy-playbook] 859c4c: Update test.
by GitHub 19 Feb '15

19 Feb '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 859c4c0e1078e00f5b089467142196aae51b6d01 https://github.com/galaxyproject/usegalaxy-playbook/commit/859c4c0e1078e00f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-02-19 (Thu, 19 Feb 2015) Changed paths: M stage/group_vars/all.yml Log Message: ----------- Update test.

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commit/galaxy-central: 16 new changesets
by commits-noreply＠bitbucket.org 19 Feb '15

19 Feb '15

16 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f3e04f22b499/ Changeset: f3e04f22b499 User: natefoo Date: 2015-02-19 15:34:53+00:00 Summary: Commit convert-mangled .hgtags so the .hgtags removal from git will patch cleanly. Affected #: 1 file diff -r 43b850d3b54a9f0df417f80ce3d8a03fc28d4452 -r f3e04f22b499b1d602419f86a7757e8bdb304d4f .hgtags --- a/.hgtags +++ b/.hgtags @@ -1,25 +1,25 @@ -a4113cc1cb5eaa68091c9a73375f00555b66dd11 release_2013.01.13 -1c717491139269651bb59687563da9410b84c65d release_2013.02.08 -75f09617abaadbc8cc732bb8ee519decaeb56ea7 release_2013.04.01 -2cc8d10988e03257dc7b97f8bb332c7df745d1dd security_2013.04.08 -524f246ca85395082719ae7a6ff72260d7ad5612 release_2013.06.03 -1ae95b3aa98d1ccf15b243ac3ce6a895eb7efc53 release_2013.08.12 -26f58e05aa1068761660681583821e21e6cbf7ab release_2013.11.04 -5e605ed6069fe4c5ca9875e95e91b2713499e8ca release_2014.02.10 -9e53251b0b7e93b9563008a2b112f2e815a04bbc release_2014.04.14 -7e257c7b10badb65772b1528cb61d58175a42e47 release_2014.06.02 -c52dc4c72b77e4b0849a596b6d05e4341236642a latest_2014.06.02 -b2c0570f52e18d8661ca1d80c42867e4b036f22b latest_2014.04.14 -9c323aad4ffdd65a3deb06a4a36f6b2c5115a60f latest_2013.01.13 -b986c184be88947b5d1d90be7f36cfd2627dd938 latest_2013.02.08 -dec9431d66b837a208e2f060d90afd913c721227 latest_2013.04.01 -aae74ee09e4667e270750711327c8167e1dfae05 latest_2013.06.03 -db967a25c5db969ee4b3e138fe2be4d979665bdf latest_2013.08.12 -52a18b44474f017fce92850fb3892a4f76a7374a latest_2013.11.04 -746db2bf4da081a7491b5a4602aeadd2611b3b1d latest_2014.02.10 -ca45b78adb4152fc6e7395514d46eba6b7d0b838 release_2014.08.11 -6d6d7f8b321725a21a96ce21e7d18a3a66f7b72e latest_2014.08.11 -2092948937ac30ef82f71463a235c66d34987088 release_2014.10.06 -782fa60fc65488aea0c618d723e9a63d42caf865 latest_2014.10.06 -2e8dd2949dd3eee0f56f9a3a5ebf1b2baca24aee release_2015.01.13 -d677cb314dccedd8743eba26f1d446cdf97ebf16 latest_2015.01.13 +341377bb04676680712f364300e96d70d721df7e release_2013.01.13 +ce310deaf25ee229d05e76f26b5ab263cbd1a226 release_2013.02.08 +3f759aada36a285e85aed002b4912562bce6fb3f release_2013.04.01 +390890ae16e01130b6ad88b0ea33460f7bbda54f security_2013.04.08 +cabc7d8d856fd9d121fc27c7b7db7c8d21274bfe release_2013.06.03 +842e723fdfdb32bfd89dd49606d5d354fc12f544 release_2013.08.12 +6ef33f49b880c8ea5cc2eab9ef3fd76ee0e028d3 release_2013.11.04 +ec716dc9acf551946c24ed41e9f3b98602952c62 release_2014.02.10 +c0271c9b6143c06608fc0d0c50fa38a7e02a9675 release_2014.04.14 +8e38b9ed63b4fd57212f1cfa7003e249fbd07c17 release_2014.06.02 +98c193028cb5f892bcf7dcdd28e4fe5a695c4da4 latest_2014.06.02 +875f1563818f2cf66f867b65836d86d17b76a67f latest_2014.04.14 +a762ca2d670d3412c62a9e56f968a3dca02e37e5 latest_2013.01.13 +1d2795215e72840c76e0888abd80504f960b7129 latest_2013.02.08 +7215b52e6a1ecedf3a960f9b75be8b6ba3771b00 latest_2013.04.01 +59abd0392a52e12e70011863a627b2fe6d64ef20 latest_2013.06.03 +f650fb0cf5b130244b0c35f25ab153dbdd6f1505 latest_2013.08.12 +75e030bbf1b493734dbe98f3df17a31d51f32231 latest_2013.11.04 +9535c43388e4d8e0c9ec3c471a5040d7c22d1c2d latest_2014.02.10 +aac76e72f525efbee1c5ad661e0a036fab97d624 release_2014.08.11 +f26ffe6c2b7a4d157474ff3cdd715900977e91a0 latest_2014.08.11 +3c804ef126e7ab979b76c2ac02bbc0a1fd0ee321 release_2014.10.06 +51005a4e48b624eb79703dd20a32729e474f7a7a latest_2014.10.06 +41027440fcfcb7fc7bc183d9eddbbce6362668d0 release_2015.01.13 +fcdd22776cc21b6f0f64d9dd944174e8503627a6 latest_2015.01.13 https://bitbucket.org/galaxy/galaxy-central/commits/67432ab8f64d/ Changeset: 67432ab8f64d User: erasche2 Date: 2015-02-18 18:15:40+00:00 Summary: Pandoc conversion to rST due to pypi, see #1 Affected #: 2 files diff -r f3e04f22b499b1d602419f86a7757e8bdb304d4f -r 67432ab8f64d7cf54a528082e36dd2a61ec60f40 README.md --- a/README.md +++ /dev/null @@ -1,45 +0,0 @@ -# Galaxy - -![Galaxy Logo](https://wiki.galaxyproject.org/Images/Logos?action=AttachFile&do=get&… - -[galaxyproject.org](http://galaxyproject.org/) - -The latest information about Galaxy is always available via the Galaxy -website above. - -## Starting Galaxy - -Galaxy requires Python 2.6 or 2.7. To check your python version, run: - -```console -$ python -V -Python 2.7.3 -``` - -Start Galaxy: - -```console -$ sh run.sh -``` - -Once Galaxy completes startup, you should be able to view Galaxy in your -browser at: - -http://localhost:8080 - -You may wish to make changes from the default configuration. This can be done -in the `config/galaxy.ini` file. Tools can be either installed from the Tool Shed -or added manually. For details please see the Galaxy wiki: - -https://wiki.galaxyproject.org/Admin/Tools/AddToolFromToolShedTutorial - -Not all dependencies are included for the tools provided in the sample -`tool_conf.xml`. A full list of external dependencies is available at: - -https://wiki.galaxyproject.org/Admin/Tools/ToolDependencies - -## Issues - -Issues can be submitted to trello via the [galaxyproject -website](http://galaxyproject.org/trello/) and viewed on the [Galaxy Trello -Board](https://trello.com/b/75c1kASa/galaxy-development) diff -r f3e04f22b499b1d602419f86a7757e8bdb304d4f -r 67432ab8f64d7cf54a528082e36dd2a61ec60f40 README.rst --- /dev/null +++ b/README.rst @@ -0,0 +1,51 @@ +Galaxy +====== + +.. figure:: https://wiki.galaxyproject.org/Images/Logos?action=AttachFile&do=get&target… + :alt: Galaxy Logo + + Galaxy Logo +`galaxyproject.org <http://galaxyproject.org/>`__ + +The latest information about Galaxy is always available via the Galaxy +website above. + +Starting Galaxy +--------------- + +Galaxy requires Python 2.6 or 2.7. To check your python version, run: + +.. code:: console + + $ python -V + Python 2.7.3 + +Start Galaxy: + +.. code:: console + + $ sh run.sh + +Once Galaxy completes startup, you should be able to view Galaxy in your +browser at: + +http://localhost:8080 + +You may wish to make changes from the default configuration. This can be +done in the ``config/galaxy.ini`` file. Tools can be either installed +from the Tool Shed or added manually. For details please see the Galaxy +wiki: + +https://wiki.galaxyproject.org/Admin/Tools/AddToolFromToolShedTutorial + +Not all dependencies are included for the tools provided in the sample +``tool_conf.xml``. A full list of external dependencies is available at: + +https://wiki.galaxyproject.org/Admin/Tools/ToolDependencies + +Issues +------ + +Issues can be submitted to trello via the `galaxyproject +website <http://galaxyproject.org/trello/>`__ and viewed on the `Galaxy +Trello Board <https://trello.com/b/75c1kASa/galaxy-development>`__ https://bitbucket.org/galaxy/galaxy-central/commits/c0e79f384381/ Changeset: c0e79f384381 User: erasche2 Date: 2015-02-18 18:17:07+00:00 Summary: Nicer header Affected #: 1 file diff -r 67432ab8f64d7cf54a528082e36dd2a61ec60f40 -r c0e79f38438112d7130f63b2cc4aa6ed180fb3e5 README.rst --- a/README.rst +++ b/README.rst @@ -1,14 +1,8 @@ -Galaxy -====== - -.. figure:: https://wiki.galaxyproject.org/Images/Logos?action=AttachFile&do=get&target… - :alt: Galaxy Logo - - Galaxy Logo -`galaxyproject.org <http://galaxyproject.org/>`__ +`.. figure:: https://wiki.galaxyproject.org/Images/Logos?action=AttachFile&do=get&target… + :alt: Galaxy Logo <http://galaxyproject.org/>`__ The latest information about Galaxy is always available via the Galaxy -website above. +website: `galaxyproject.org http://galaxyproject.org/>`__ Starting Galaxy --------------- https://bitbucket.org/galaxy/galaxy-central/commits/3704fb0e27bc/ Changeset: 3704fb0e27bc User: erasche2 Date: 2015-02-18 18:20:17+00:00 Summary: Add dev/run instructions to readme Affected #: 1 file diff -r c0e79f38438112d7130f63b2cc4aa6ed180fb3e5 -r 3704fb0e27bcf43c6daa5a5fbaeae27b2330e0fd README.rst --- a/README.rst +++ b/README.rst @@ -4,8 +4,8 @@ The latest information about Galaxy is always available via the Galaxy website: `galaxyproject.org http://galaxyproject.org/>`__ -Starting Galaxy ---------------- +Galaxy Quickstart +================= Galaxy requires Python 2.6 or 2.7. To check your python version, run: @@ -43,3 +43,22 @@ Issues can be submitted to trello via the `galaxyproject website <http://galaxyproject.org/trello/>`__ and viewed on the `Galaxy Trello Board <https://trello.com/b/75c1kASa/galaxy-development>`__ + + +Galaxy Development +================== + +Syncing a Fork +-------------- + +If you fork Galaxy to work on it, you may be interested in keeping your copy +up to date with respect to the main repository. Github has `good documentation +<https://help.github.com/articles/syncing-a-fork/>__` on this. + +.. code:: console + + $ git remote add upstream https://github.com/galaxyproject/galaxy + $ git fetch upstream + $ git checkout dev + $ git merge upstream/dev + https://bitbucket.org/galaxy/galaxy-central/commits/1b98e289d2a7/ Changeset: 1b98e289d2a7 User: erasche2 Date: 2015-02-18 18:22:36+00:00 Summary: Can't write rST to save my life Affected #: 1 file diff -r 3704fb0e27bcf43c6daa5a5fbaeae27b2330e0fd -r 1b98e289d2a73e65fa9af62a0d899b92e4e0f47f README.rst --- a/README.rst +++ b/README.rst @@ -1,8 +1,8 @@ -`.. figure:: https://wiki.galaxyproject.org/Images/Logos?action=AttachFile&do=get&target… - :alt: Galaxy Logo <http://galaxyproject.org/>`__ +.. figure:: https://wiki.galaxyproject.org/Images/Logos?action=AttachFile&do=get&target… + :alt: Galaxy Logo The latest information about Galaxy is always available via the Galaxy -website: `galaxyproject.org http://galaxyproject.org/>`__ +website: `http://galaxyproject.org/ <http://galaxyproject.org/>`__ Galaxy Quickstart ================= @@ -53,7 +53,7 @@ If you fork Galaxy to work on it, you may be interested in keeping your copy up to date with respect to the main repository. Github has `good documentation -<https://help.github.com/articles/syncing-a-fork/>__` on this. +<https://help.github.com/articles/syncing-a-fork/>`__ on this. .. code:: console https://bitbucket.org/galaxy/galaxy-central/commits/e386371ff84b/ Changeset: e386371ff84b User: erasche2 Date: 2015-02-18 18:24:11+00:00 Summary: Link to wiki Affected #: 1 file diff -r 1b98e289d2a73e65fa9af62a0d899b92e4e0f47f -r e386371ff84ba4e3d81437b699176b26b58da670 README.rst --- a/README.rst +++ b/README.rst @@ -48,6 +48,9 @@ Galaxy Development ================== +Galaxy welcomes new development! There is extensive documentation on developing +with `Galaxy <https://wiki.galaxyproject.org/Develop>`__ on the wiki. + Syncing a Fork -------------- https://bitbucket.org/galaxy/galaxy-central/commits/5222e50ca45d/ Changeset: 5222e50ca45d User: erasche2 Date: 2015-02-18 18:25:04+00:00 Summary: Fix link location Affected #: 1 file diff -r e386371ff84ba4e3d81437b699176b26b58da670 -r 5222e50ca45d5c450173a10b504ead1fd5cb96a7 README.rst --- a/README.rst +++ b/README.rst @@ -49,7 +49,7 @@ ================== Galaxy welcomes new development! There is extensive documentation on developing -with `Galaxy <https://wiki.galaxyproject.org/Develop>`__ on the wiki. +with Galaxy on the `wiki <https://wiki.galaxyproject.org/Develop>`__. Syncing a Fork -------------- https://bitbucket.org/galaxy/galaxy-central/commits/1600bf5d7532/ Changeset: 1600bf5d7532 User: dannon Date: 2015-02-18 21:37:55+00:00 Summary: Remove old .svn entry and regex def Affected #: 1 file diff -r 5222e50ca45d5c450173a10b504ead1fd5cb96a7 -r 1600bf5d75323ef7d45a4aa79f87cd916f88e1c0 .gitignore --- a/.gitignore +++ b/.gitignore @@ -1,9 +1,3 @@ -syntax: regexp - -\.svn$ - -syntax: glob - .hg* # Downloaded and locally built eggs eggs https://bitbucket.org/galaxy/galaxy-central/commits/0ee5becd6bcf/ Changeset: 0ee5becd6bcf User: dannon Date: 2015-02-18 23:03:31+00:00 Summary: Set datatype extension to default datatype extension when preview=False and to_ext is unsupplied in GET args. Affected #: 1 file diff -r 1600bf5d75323ef7d45a4aa79f87cd916f88e1c0 -r 0ee5becd6bcf251c0167c1140d923bae4e1e2b9a lib/galaxy/datatypes/tabular.py --- a/lib/galaxy/datatypes/tabular.py +++ b/lib/galaxy/datatypes/tabular.py @@ -279,6 +279,7 @@ if chunk: return self.get_chunk(trans, dataset, chunk) elif to_ext or not preview: + to_ext = to_ext or dataset.extension return self._serve_raw(trans, dataset, to_ext) elif dataset.metadata.columns > 50: #Fancy tabular display is only suitable for datasets without an incredibly large number of columns. https://bitbucket.org/galaxy/galaxy-central/commits/19aadae7af81/ Changeset: 19aadae7af81 User: dannon Date: 2015-02-18 23:35:23+00:00 Summary: Style adjustments to tabular dataset headers; use consistent padding. Affected #: 2 files diff -r 0ee5becd6bcf251c0167c1140d923bae4e1e2b9a -r 19aadae7af81a39edeeda4d10f110008e63a5553 static/style/blue/base.css --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -2286,6 +2286,7 @@ #tool-search{padding-top:5px;padding-bottom:10px;position:relative} #loading_indicator{position:fixed;right:10px;top:10px;height:32px;width:32px;display:none;background:url(largespinner.gif)} #content_table td{text-align:right;white-space:nowrap;padding:2px 10px} +#content_table th{white-space:nowrap;padding:2px 10px} #content_table td.stringalign{text-align:left} #content_table .dark_row{background-color:#DDD} #content_table th{background-color:#AAA} diff -r 0ee5becd6bcf251c0167c1140d923bae4e1e2b9a -r 19aadae7af81a39edeeda4d10f110008e63a5553 static/style/src/less/base.less --- a/static/style/src/less/base.less +++ b/static/style/src/less/base.less @@ -1548,6 +1548,11 @@ padding:2px 10px; } +#content_table th{ + white-space:nowrap; + padding:2px 10px; +} + #content_table td.stringalign{ text-align:left; } https://bitbucket.org/galaxy/galaxy-central/commits/2480519470a9/ Changeset: 2480519470a9 User: dannon Date: 2015-02-19 12:52:27+00:00 Summary: Custom types cleanup/pep8. Affected #: 1 file diff -r 19aadae7af81a39edeeda4d10f110008e63a5553 -r 2480519470a93059626251a5ec7c8e6cba3eed5d lib/galaxy/model/custom_types.py --- a/lib/galaxy/model/custom_types.py +++ b/lib/galaxy/model/custom_types.py @@ -1,25 +1,23 @@ -from sqlalchemy.types import * +import binascii +import copy +import json +import logging +import uuid -import json -import pickle -import copy -import uuid -import binascii -from galaxy.util.bunch import Bunch +from galaxy import eggs +eggs.require("SQLAlchemy") +import sqlalchemy + from galaxy.util.aliaspickler import AliasPickleModule +from sqlalchemy.types import CHAR, LargeBinary, String, TypeDecorator -# For monkeypatching BIGINT -import sqlalchemy.dialects.sqlite -import sqlalchemy.dialects.postgresql -import sqlalchemy.dialects.mysql - -import logging log = logging.getLogger( __name__ ) # Default JSON encoder and decoder json_encoder = json.JSONEncoder( sort_keys=True ) json_decoder = json.JSONDecoder( ) + def _sniffnfix_pg9_hex(value): """ Sniff for and fix postgres 9 hex decoding issue @@ -31,9 +29,10 @@ return binascii.unhexlify( value[2:] ) else: return value - except Exception, ex: + except Exception: return value + class JSONType( TypeDecorator ): """ Defines a JSONType for SQLAlchemy. Takes a primitive as input and @@ -73,9 +72,10 @@ metadata_pickler = AliasPickleModule( { - ( "cookbook.patterns", "Bunch" ) : ( "galaxy.util.bunch" , "Bunch" ) + ( "cookbook.patterns", "Bunch" ): ( "galaxy.util.bunch", "Bunch" ) } ) + class MetadataType( JSONType ): """ Backward compatible metadata type. Can read pickles or JSON, but always @@ -96,6 +96,7 @@ ret = None return ret + class UUIDType(TypeDecorator): """ Platform-independent UUID type. @@ -129,31 +130,9 @@ class TrimmedString( TypeDecorator ): impl = String + def process_bind_param( self, value, dialect ): """Automatically truncate string values""" if self.impl.length and value is not None: value = value[0:self.impl.length] return value - - -#class BigInteger( Integer ): - #""" - #A type for bigger ``int`` integers. - - #Typically generates a ``BIGINT`` in DDL, and otherwise acts like - #a normal :class:`Integer` on the Python side. - - #""" - -#class BIGINT( BigInteger ): - #"""The SQL BIGINT type.""" - -#class SLBigInteger( BigInteger ): - #def get_col_spec( self ): - #return "BIGINT" - -#sqlalchemy.dialects.sqlite.SLBigInteger = SLBigInteger -#sqlalchemy.dialects.sqlite.colspecs[BigInteger] = SLBigInteger -#sqlalchemy.dialects.sqlite.ischema_names['BIGINT'] = SLBigInteger -#sqlalchemy.dialects.postgres.colspecs[BigInteger] = sqlalchemy.dialects.postgres.PGBigInteger -#sqlalchemy.dialects.mysql.colspecs[BigInteger] = sqlalchemy.dialects.mysql.MSBigInteger https://bitbucket.org/galaxy/galaxy-central/commits/bf564c0703c5/ Changeset: bf564c0703c5 User: nsoranzo Date: 2015-02-19 18:46:29+00:00 Summary: Remove .hgtags file. The hashes got mangled in the transition to Git. Affected #: 1 file diff -r 2480519470a93059626251a5ec7c8e6cba3eed5d -r bf564c0703c57dae79535a4a7ff0c7acd7e87e32 .hgtags --- a/.hgtags +++ /dev/null @@ -1,25 +0,0 @@ -341377bb04676680712f364300e96d70d721df7e release_2013.01.13 -ce310deaf25ee229d05e76f26b5ab263cbd1a226 release_2013.02.08 -3f759aada36a285e85aed002b4912562bce6fb3f release_2013.04.01 -390890ae16e01130b6ad88b0ea33460f7bbda54f security_2013.04.08 -cabc7d8d856fd9d121fc27c7b7db7c8d21274bfe release_2013.06.03 -842e723fdfdb32bfd89dd49606d5d354fc12f544 release_2013.08.12 -6ef33f49b880c8ea5cc2eab9ef3fd76ee0e028d3 release_2013.11.04 -ec716dc9acf551946c24ed41e9f3b98602952c62 release_2014.02.10 -c0271c9b6143c06608fc0d0c50fa38a7e02a9675 release_2014.04.14 -8e38b9ed63b4fd57212f1cfa7003e249fbd07c17 release_2014.06.02 -98c193028cb5f892bcf7dcdd28e4fe5a695c4da4 latest_2014.06.02 -875f1563818f2cf66f867b65836d86d17b76a67f latest_2014.04.14 -a762ca2d670d3412c62a9e56f968a3dca02e37e5 latest_2013.01.13 -1d2795215e72840c76e0888abd80504f960b7129 latest_2013.02.08 -7215b52e6a1ecedf3a960f9b75be8b6ba3771b00 latest_2013.04.01 -59abd0392a52e12e70011863a627b2fe6d64ef20 latest_2013.06.03 -f650fb0cf5b130244b0c35f25ab153dbdd6f1505 latest_2013.08.12 -75e030bbf1b493734dbe98f3df17a31d51f32231 latest_2013.11.04 -9535c43388e4d8e0c9ec3c471a5040d7c22d1c2d latest_2014.02.10 -aac76e72f525efbee1c5ad661e0a036fab97d624 release_2014.08.11 -f26ffe6c2b7a4d157474ff3cdd715900977e91a0 latest_2014.08.11 -3c804ef126e7ab979b76c2ac02bbc0a1fd0ee321 release_2014.10.06 -51005a4e48b624eb79703dd20a32729e474f7a7a latest_2014.10.06 -41027440fcfcb7fc7bc183d9eddbbce6362668d0 release_2015.01.13 -fcdd22776cc21b6f0f64d9dd944174e8503627a6 latest_2015.01.13 https://bitbucket.org/galaxy/galaxy-central/commits/86b814c0bdd2/ Changeset: 86b814c0bdd2 User: dannon Date: 2015-02-19 14:02:31+00:00 Summary: Custom types mutable+pickle fix. Previously failing unit and framework.multi_output functional tests pass now. Affected #: 1 file diff -r bf564c0703c57dae79535a4a7ff0c7acd7e87e32 -r 86b814c0bdd212e0162e358c56feb6ca6350a16d lib/galaxy/model/custom_types.py --- a/lib/galaxy/model/custom_types.py +++ b/lib/galaxy/model/custom_types.py @@ -10,6 +10,7 @@ from galaxy.util.aliaspickler import AliasPickleModule from sqlalchemy.types import CHAR, LargeBinary, String, TypeDecorator +from sqlalchemy.ext.mutable import Mutable log = logging.getLogger( __name__ ) @@ -33,6 +34,40 @@ return value +class MutableDict(Mutable, dict): + # MutableDict following http://docs.sqlalchemy.org/en/latest/orm/extensions/mutable.html + @classmethod + def coerce(cls, key, value): + "Convert plain dictionaries to MutableDict." + + if not isinstance(value, MutableDict): + if isinstance(value, dict): + return MutableDict(value) + + # this call will raise ValueError + return Mutable.coerce(key, value) + else: + return value + + def __setitem__(self, key, value): + "Detect dictionary set events and emit change events." + + dict.__setitem__(self, key, value) + self.changed() + + def __delitem__(self, key): + "Detect dictionary del events and emit change events." + + dict.__delitem__(self, key) + self.changed() + + def __getstate__(self): + return dict(self) + + def __setstate__(self, state): + self.update(state) + + class JSONType( TypeDecorator ): """ Defines a JSONType for SQLAlchemy. Takes a primitive as input and @@ -61,9 +96,6 @@ # return json_encoder.encode( x ) == json_encoder.encode( y ) return ( x == y ) - def is_mutable( self ): - return True - def load_dialect_impl(self, dialect): if dialect.name == "mysql": return dialect.type_descriptor(sqlalchemy.dialects.mysql.MEDIUMBLOB) @@ -71,6 +103,9 @@ return self.impl +MutableDict.associate_with(JSONType) + + metadata_pickler = AliasPickleModule( { ( "cookbook.patterns", "Bunch" ): ( "galaxy.util.bunch", "Bunch" ) } ) https://bitbucket.org/galaxy/galaxy-central/commits/f862e3546f76/ Changeset: f862e3546f76 User: dannon Date: 2015-02-19 15:14:27+00:00 Summary: Remove .hgignore since it has no relevance to the .git repository; will be maintained downstream in hg as necessary. Affected #: 1 file diff -r 86b814c0bdd212e0162e358c56feb6ca6350a16d -r f862e3546f76d4f7990608cac34f2d0db5491a02 .hgignore --- a/.hgignore +++ /dev/null @@ -1,124 +0,0 @@ -syntax: regexp - -\.svn$ - -syntax: glob - -.hg* -# Downloaded and locally built eggs -eggs -scripts/scramble/build -scripts/scramble/lib -scripts/scramble/archives - -# Python virtualenv -.venv - -# Database stuff -database/beaker_sessions -database/citations -database/community_files -database/compiled_templates -database/files -database/job_working_directory -database/pbs -database/tmp -database/*.sqlite -database/openid_consumer_cache - -# Python bytecode -*.pyc - -# Galaxy Runtime Files -*.lock -*.log -*.pid - -# Tool Shed Runtime Files -tool_shed_webapp.lock -tool_shed_webapp.log -tool_shed_webapp.pid -hgweb.config* -lib/tool_shed/scripts/bootstrap_tool_shed/user_info.xml - -# Reports Runtime Files -reports_webapp.lock -reports_webapp.log -reports_webapp.pid - -# Config files -universe_wsgi.ini -reports_wsgi.ini -tool_shed_wsgi.ini - -# Config files. -datatypes_conf.xml -tool_conf.xml -external_service_types_conf.xml -migrated_tools_conf.xml -shed_tool_conf.xml -tool_data_table_conf.xml -tool_sheds_conf.xml -integrated_tool_panel.xml -openid_conf.xml -shed_tool_data_table_conf.xml -job_conf.xml -data_manager_conf.xml -shed_data_manager_conf.xml -object_store_conf.xml -job_metrics_conf.xml -workflow_schedulers_conf.xml -config/* -static/welcome.html.* -static/welcome.html - -# Tool data. -tool-data/annotation_profiler_options.xml -tool-data/annotation_profiler_valid_builds.txt -tool-data/gatk_annotations.txt -tool-data/gd.restriction_enzymes.txt -tool-data/gd.species.txt -tool-data/shared/igv/igv_build_sites.txt -tool-data/shared/rviewer/rviewer_build_sites.txt -tool-data/shared/ncbi/builds.txt -tool-data/shared/ucsc/builds.txt -tool-data/shared/ensembl/builds.txt -tool-data/shared/ucsc/publicbuilds.txt -tool-data/shared/ucsc/ucsc_build_sites.txt -tool-data/*.loc -tool-data/genome/* - -# Test output -test-data-cache -run_functional_tests.html -test/tool_shed/tmp/* -.coverage -htmlcov -run_unit_tests.html -test/unit/**.log - -# Project files -*.kpf - -# Chrom len files -*.len - -# Jars -tool-data/shared/jars/ - -# CSS build artifacts. -sprite-*.less - -# Local node_modules and bower_components directories -node_modules -bower_components - -# Documentation build files. -doc/build - -# Misc -*.orig -.DS_Store -*.rej -*~ - https://bitbucket.org/galaxy/galaxy-central/commits/d11852b77046/ Changeset: d11852b77046 User: natefoo Date: 2015-02-19 15:36:44+00:00 Summary: Recommit correct .hgtags Affected #: 1 file diff -r f862e3546f76d4f7990608cac34f2d0db5491a02 -r d11852b77046481a3cc3ada94ebcc0f2929b524c .hgtags --- /dev/null +++ b/.hgtags @@ -0,0 +1,25 @@ +a4113cc1cb5eaa68091c9a73375f00555b66dd11 release_2013.01.13 +1c717491139269651bb59687563da9410b84c65d release_2013.02.08 +75f09617abaadbc8cc732bb8ee519decaeb56ea7 release_2013.04.01 +2cc8d10988e03257dc7b97f8bb332c7df745d1dd security_2013.04.08 +524f246ca85395082719ae7a6ff72260d7ad5612 release_2013.06.03 +1ae95b3aa98d1ccf15b243ac3ce6a895eb7efc53 release_2013.08.12 +26f58e05aa1068761660681583821e21e6cbf7ab release_2013.11.04 +5e605ed6069fe4c5ca9875e95e91b2713499e8ca release_2014.02.10 +9e53251b0b7e93b9563008a2b112f2e815a04bbc release_2014.04.14 +7e257c7b10badb65772b1528cb61d58175a42e47 release_2014.06.02 +c52dc4c72b77e4b0849a596b6d05e4341236642a latest_2014.06.02 +b2c0570f52e18d8661ca1d80c42867e4b036f22b latest_2014.04.14 +9c323aad4ffdd65a3deb06a4a36f6b2c5115a60f latest_2013.01.13 +b986c184be88947b5d1d90be7f36cfd2627dd938 latest_2013.02.08 +dec9431d66b837a208e2f060d90afd913c721227 latest_2013.04.01 +aae74ee09e4667e270750711327c8167e1dfae05 latest_2013.06.03 +db967a25c5db969ee4b3e138fe2be4d979665bdf latest_2013.08.12 +52a18b44474f017fce92850fb3892a4f76a7374a latest_2013.11.04 +746db2bf4da081a7491b5a4602aeadd2611b3b1d latest_2014.02.10 +ca45b78adb4152fc6e7395514d46eba6b7d0b838 release_2014.08.11 +6d6d7f8b321725a21a96ce21e7d18a3a66f7b72e latest_2014.08.11 +2092948937ac30ef82f71463a235c66d34987088 release_2014.10.06 +782fa60fc65488aea0c618d723e9a63d42caf865 latest_2014.10.06 +2e8dd2949dd3eee0f56f9a3a5ebf1b2baca24aee release_2015.01.13 +d677cb314dccedd8743eba26f1d446cdf97ebf16 latest_2015.01.13 https://bitbucket.org/galaxy/galaxy-central/commits/503b95e63d0a/ Changeset: 503b95e63d0a User: natefoo Date: 2015-02-19 15:38:16+00:00 Summary: Recommit .hgignore removed from git. Affected #: 1 file diff -r d11852b77046481a3cc3ada94ebcc0f2929b524c -r 503b95e63d0a5268c16a0a87016449bfe969e382 .hgignore --- /dev/null +++ b/.hgignore @@ -0,0 +1,124 @@ +syntax: regexp + +\.svn$ + +syntax: glob + +.hg* +# Downloaded and locally built eggs +eggs +scripts/scramble/build +scripts/scramble/lib +scripts/scramble/archives + +# Python virtualenv +.venv + +# Database stuff +database/beaker_sessions +database/citations +database/community_files +database/compiled_templates +database/files +database/job_working_directory +database/pbs +database/tmp +database/*.sqlite +database/openid_consumer_cache + +# Python bytecode +*.pyc + +# Galaxy Runtime Files +*.lock +*.log +*.pid + +# Tool Shed Runtime Files +tool_shed_webapp.lock +tool_shed_webapp.log +tool_shed_webapp.pid +hgweb.config* +lib/tool_shed/scripts/bootstrap_tool_shed/user_info.xml + +# Reports Runtime Files +reports_webapp.lock +reports_webapp.log +reports_webapp.pid + +# Config files +universe_wsgi.ini +reports_wsgi.ini +tool_shed_wsgi.ini + +# Config files. +datatypes_conf.xml +tool_conf.xml +external_service_types_conf.xml +migrated_tools_conf.xml +shed_tool_conf.xml +tool_data_table_conf.xml +tool_sheds_conf.xml +integrated_tool_panel.xml +openid_conf.xml +shed_tool_data_table_conf.xml +job_conf.xml +data_manager_conf.xml +shed_data_manager_conf.xml +object_store_conf.xml +job_metrics_conf.xml +workflow_schedulers_conf.xml +config/* +static/welcome.html.* +static/welcome.html + +# Tool data. +tool-data/annotation_profiler_options.xml +tool-data/annotation_profiler_valid_builds.txt +tool-data/gatk_annotations.txt +tool-data/gd.restriction_enzymes.txt +tool-data/gd.species.txt +tool-data/shared/igv/igv_build_sites.txt +tool-data/shared/rviewer/rviewer_build_sites.txt +tool-data/shared/ncbi/builds.txt +tool-data/shared/ucsc/builds.txt +tool-data/shared/ensembl/builds.txt +tool-data/shared/ucsc/publicbuilds.txt +tool-data/shared/ucsc/ucsc_build_sites.txt +tool-data/*.loc +tool-data/genome/* + +# Test output +test-data-cache +run_functional_tests.html +test/tool_shed/tmp/* +.coverage +htmlcov +run_unit_tests.html +test/unit/**.log + +# Project files +*.kpf + +# Chrom len files +*.len + +# Jars +tool-data/shared/jars/ + +# CSS build artifacts. +sprite-*.less + +# Local node_modules and bower_components directories +node_modules +bower_components + +# Documentation build files. +doc/build + +# Misc +*.orig +.DS_Store +*.rej +*~ + Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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1 0

commit/galaxy-central: 7 new changesets
by commits-noreply＠bitbucket.org 18 Feb '15

18 Feb '15

7 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/7ad6939e186d/ Changeset: 7ad6939e186d User: dannon Date: 2015-02-18 16:16:26+00:00 Summary: Add .gitignore Affected #: 1 file diff -r b3a0812f9129f8e1e8bdad3a273c3410edba4e7a -r 7ad6939e186d05233166b6a5fc55f16e14de1309 .gitignore --- /dev/null +++ b/.gitignore @@ -0,0 +1,124 @@ +syntax: regexp + +\.svn$ + +syntax: glob + +.hg* +# Downloaded and locally built eggs +eggs +scripts/scramble/build +scripts/scramble/lib +scripts/scramble/archives + +# Python virtualenv +.venv + +# Database stuff +database/beaker_sessions +database/citations +database/community_files +database/compiled_templates +database/files +database/job_working_directory +database/pbs +database/tmp +database/*.sqlite +database/openid_consumer_cache + +# Python bytecode +*.pyc + +# Galaxy Runtime Files +*.lock +*.log +*.pid + +# Tool Shed Runtime Files +tool_shed_webapp.lock +tool_shed_webapp.log +tool_shed_webapp.pid +hgweb.config* +lib/tool_shed/scripts/bootstrap_tool_shed/user_info.xml + +# Reports Runtime Files +reports_webapp.lock +reports_webapp.log +reports_webapp.pid + +# Config files +universe_wsgi.ini +reports_wsgi.ini +tool_shed_wsgi.ini + +# Config files. +datatypes_conf.xml +tool_conf.xml +external_service_types_conf.xml +migrated_tools_conf.xml +shed_tool_conf.xml +tool_data_table_conf.xml +tool_sheds_conf.xml +integrated_tool_panel.xml +openid_conf.xml +shed_tool_data_table_conf.xml +job_conf.xml +data_manager_conf.xml +shed_data_manager_conf.xml +object_store_conf.xml +job_metrics_conf.xml +workflow_schedulers_conf.xml +config/* +static/welcome.html.* +static/welcome.html + +# Tool data. +tool-data/annotation_profiler_options.xml +tool-data/annotation_profiler_valid_builds.txt +tool-data/gatk_annotations.txt +tool-data/gd.restriction_enzymes.txt +tool-data/gd.species.txt +tool-data/shared/igv/igv_build_sites.txt +tool-data/shared/rviewer/rviewer_build_sites.txt +tool-data/shared/ncbi/builds.txt +tool-data/shared/ucsc/builds.txt +tool-data/shared/ensembl/builds.txt +tool-data/shared/ucsc/publicbuilds.txt +tool-data/shared/ucsc/ucsc_build_sites.txt +tool-data/*.loc +tool-data/genome/* + +# Test output +test-data-cache +run_functional_tests.html +test/tool_shed/tmp/* +.coverage +htmlcov +run_unit_tests.html +test/unit/**.log + +# Project files +*.kpf + +# Chrom len files +*.len + +# Jars +tool-data/shared/jars/ + +# CSS build artifacts. +sprite-*.less + +# Local node_modules and bower_components directories +node_modules +bower_components + +# Documentation build files. +doc/build + +# Misc +*.orig +.DS_Store +*.rej +*~ + https://bitbucket.org/galaxy/galaxy-central/commits/a76dbb051400/ Changeset: a76dbb051400 User: erasche2 Date: 2015-02-18 15:21:38+00:00 Summary: Touch up readme for github Affected #: 2 files diff -r 7ad6939e186d05233166b6a5fc55f16e14de1309 -r a76dbb051400b26f50ee9709e0ad8d9950eb8ff5 README.md --- /dev/null +++ b/README.md @@ -0,0 +1,37 @@ +# Galaxy + +[galaxyproject.org](http://galaxyproject.org/) + +The latest information about Galaxy is always available via the Galaxy +website above. + +# Starting Galaxy + +Galaxy requires Python 2.6 or 2.7. To check your python version, run: + +```console +$ python -V +Python 2.7.3 +``` + +Start Galaxy: + +```console +$ sh run.sh +``` + +Once Galaxy completes startup, you should be able to view Galaxy in your +browser at: + +http://localhost:8080 + +You may wish to make changes from the default configuration. This can be done +in the `config/galaxy.ini` file. Tools can be either installed from the Tool Shed +or added manually. For details please see the Galaxy wiki: + +https://wiki.galaxyproject.org/Admin/Tools/AddToolFromToolShedTutorial + +Not all dependencies are included for the tools provided in the sample +`tool_conf.xml`. A full list of external dependencies is available at: + +https://wiki.galaxyproject.org/Admin/Tools/ToolDependencies diff -r 7ad6939e186d05233166b6a5fc55f16e14de1309 -r a76dbb051400b26f50ee9709e0ad8d9950eb8ff5 README.txt --- a/README.txt +++ /dev/null @@ -1,34 +0,0 @@ -GALAXY -====== -http://galaxyproject.org/ - -The latest information about Galaxy is always available via the Galaxy -website above. - -HOW TO START -============ -Galaxy requires Python 2.6 or 2.7. To check your python version, run: - -% python -V -Python 2.7.3 - -Start Galaxy: - -% sh run.sh - -Once Galaxy completes startup, you should be able to view Galaxy in your -browser at: - -http://localhost:8080 - -You may wish to make changes from the default configuration. This can be done -in the config/galaxy.ini file. Tools can be either installed from the Tool Shed -or added manually. For details please see the Galaxy wiki: - -https://wiki.galaxyproject.org/Admin/Tools/AddToolFromToolShedTutorial - - -Not all dependencies are included for the tools provided in the sample -tool_conf.xml. A full list of external dependencies is available at: - -https://wiki.galaxyproject.org/Admin/Tools/ToolDependencies https://bitbucket.org/galaxy/galaxy-central/commits/74a3d684e584/ Changeset: 74a3d684e584 User: erasche2 Date: 2015-02-18 15:22:01+00:00 Summary: Fix section heading Affected #: 1 file diff -r a76dbb051400b26f50ee9709e0ad8d9950eb8ff5 -r 74a3d684e58419b6d78c75db9b16ac094caf597b README.md --- a/README.md +++ b/README.md @@ -5,7 +5,7 @@ The latest information about Galaxy is always available via the Galaxy website above. -# Starting Galaxy +## Starting Galaxy Galaxy requires Python 2.6 or 2.7. To check your python version, run: https://bitbucket.org/galaxy/galaxy-central/commits/0aa8ee4a94d8/ Changeset: 0aa8ee4a94d8 User: erasche2 Date: 2015-02-18 15:29:13+00:00 Summary: Add link to issues Affected #: 1 file diff -r 74a3d684e58419b6d78c75db9b16ac094caf597b -r 0aa8ee4a94d8adda2d71d3f765cebc4eabb865a5 README.md --- a/README.md +++ b/README.md @@ -35,3 +35,9 @@ `tool_conf.xml`. A full list of external dependencies is available at: https://wiki.galaxyproject.org/Admin/Tools/ToolDependencies + +## Issues + +Issues can be submitted to trello via the [galaxyproject +website](http://galaxyproject.org/trello/) and viewed on the [Galaxy Trello +Board](https://trello.com/b/75c1kASa/galaxy-development) https://bitbucket.org/galaxy/galaxy-central/commits/02986af924ce/ Changeset: 02986af924ce User: dannon Date: 2015-02-18 16:37:01+00:00 Summary: Update CONTRIBUTING Affected #: 1 file diff -r 0aa8ee4a94d8adda2d71d3f765cebc4eabb865a5 -r 02986af924ce0f6afbbed78a2829fdc38a8c890c CONTRIBUTING.md --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -25,27 +25,24 @@ ## How to Contribute -* If you are new to Mercurial - please check out this [official - tutorial](http://mercurial.selenic.com/wiki/Tutorial) +* If you are new to Git - please check out the very useful tutorials on the [GitHub training hub](https://training.github.com/kit/) -* Make sure you have a free [Bitbucket - account](https://bitbucket.org/account/signup/) +* Make sure you have a free [GitHub account](https://github.com/) -* Fork the galaxy-central repository on - [Bitbucket](https://bitbucket.org/galaxy/galaxy-central/fork) to - make your changes. (Many Galaxy instances target - [galaxy-dist](https://bitbucket.org/galaxy/galaxy-dist) - but active - development happens on galaxy-central and this is where pull - requests should be made). +* Fork the galaxy repository on + [GitHub](https://github.com/galaxyproject/galaxy) to make your changes. + (While many Galaxy instances track + [galaxy-dist](https://bitbucket.org/galaxy/galaxy-dist), active development + happens in the galaxy GitHub repository and this is where pull requests + should be made). -* Choose the correct Mercurial branch to develop your changes against. +* Choose the correct branch to develop your changes against. - * Additions to the code base should be pushed to the `default` - branch (`hg checkout default`). + * Additions to the code base should be pushed to the `dev` branch (`git + checkout dev`). - * Most bug fixes to previously release components (things in - galaxy-dist) should be pushed to the `stable` branch (`hg checkout - stable`). + * Most bug fixes to previously release components (things in galaxy-dist) + should be made against the `master` branch (`git checkout master`). * Serious security problems should not be fixed via pull request - please responsibly disclose these by e-mailing them (with or @@ -76,9 +73,9 @@ with these changes. You pull request message should include: * A description of why the change should be made. - + * A description of implementation of the change. - + * A description of how to test the change. ## Ideas https://bitbucket.org/galaxy/galaxy-central/commits/93b67ff10b23/ Changeset: 93b67ff10b23 User: erasche2 Date: 2015-02-18 16:15:46+00:00 Summary: Add logo Affected #: 1 file diff -r 02986af924ce0f6afbbed78a2829fdc38a8c890c -r 93b67ff10b239978fbb38e78eba9c54b4fa5dd39 README.md --- a/README.md +++ b/README.md @@ -1,5 +1,7 @@ # Galaxy +![Galaxy Logo](https://wiki.galaxyproject.org/Images/Logos?action=AttachFile&do=get&… + [galaxyproject.org](http://galaxyproject.org/) The latest information about Galaxy is always available via the Galaxy https://bitbucket.org/galaxy/galaxy-central/commits/43b850d3b54a/ Changeset: 43b850d3b54a User: jmchilton Date: 2015-02-18 05:38:06+00:00 Summary: Add --dockerize and --db [postgres|mysql|sqlite] options to run_tests.sh. Runs tests in a Dockerfile with pre-migrated databases and all testing dependencies (postgres, mysql, npm, casper, phantomjs, etc...). Hopefully this makes it easier to run more interesting tests - down the road I would like to add more options for things like condor, slurm, run as real user, etc.... Affected #: 7 files diff -r 93b67ff10b239978fbb38e78eba9c54b4fa5dd39 -r 43b850d3b54a9f0df417f80ce3d8a03fc28d4452 run_tests.sh --- a/run_tests.sh +++ b/run_tests.sh @@ -29,6 +29,9 @@ --no_cleanup Do not delete temp files for Python functional tests (-toolshed, -framework, etc...) --report_file Path of HTML report to produce (for Python Galaxy functional tests). --xunit_report_file Path of XUnit report to produce (for Python Galaxy functional tests). + --dockerize Run tests in a pre-configured Docker container (must be first argument if present). + --db <type> For use with --dockerize, run tests using partially migrated 'postgres', 'mysql', + or 'sqlite' databases. EOF } @@ -60,6 +63,22 @@ driver="python" +if [ "$1" = "--dockerize" ]; +then + shift + if [ "$1" = "--db" ]; then + db_type=$2 + shift 2 + else + db_type="sqlite" + fi + DOCKER_EXTRA_ARGS=${DOCKER_ARGS:-""} + DOCKER_RUN_EXTRA_ARGS=${DOCKER_ARGS:-""} + DOCKER_IMAGE=${DOCKER_IMAGE:-"galaxyprojectdotorg/testing-base"} + docker $DOCKER_EXTRA_ARGS run $DOCKER_RUN_EXTRA_ARGS -e "GALAXY_TEST_DATABASE_TYPE=$db_type" --rm -v `pwd`:/galaxy $DOCKER_IMAGE "$@" + exit $? +fi + while : do case "$1" in diff -r 93b67ff10b239978fbb38e78eba9c54b4fa5dd39 -r 43b850d3b54a9f0df417f80ce3d8a03fc28d4452 test/docker/README.md --- /dev/null +++ b/test/docker/README.md @@ -0,0 +1,9 @@ +Setup Docker environment for use with testing using the following +commands (until this is on Docker hub). + + % cd test/base + % docker build -t galaxyprojectdotorg/testing-base . + +This will create a docker container ready to run most of Galaxy tests +(functional tests for specific bioinformatics tools may still fail for +now until they are migrated out of Galaxy and to the tool shed). diff -r 93b67ff10b239978fbb38e78eba9c54b4fa5dd39 -r 43b850d3b54a9f0df417f80ce3d8a03fc28d4452 test/docker/base/Dockerfile --- /dev/null +++ b/test/docker/base/Dockerfile @@ -0,0 +1,63 @@ +FROM toolshed/requirements +MAINTAINER John Chilton <jmchilton(a)gmail.com> + +ENV MYSQL_MAJOR=5.7 \ + MYSQL_VERSION=5.7.5-m15 + +# Pre-install a bunch of packages to speed up ansible steps. +RUN apt-get update -y && apt-get install -y software-properties-common curl && \ + apt-add-repository -y ppa:ansible/ansible && \ + curl -s https://deb.nodesource.com/gpgkey/nodesource.gpg.key | apt-key add - && \ + echo 'deb https://deb.nodesource.com/node trusty main' > /etc/apt/sources.list.d/nodesource.list && \ + apt-key adv --keyserver pool.sks-keyservers.net --recv-keys A4A9406876FCBD3C456770C88C718D3B5072E1F5 && \ + echo "deb http://repo.mysql.com/apt/ubuntu/ trusty mysql-${MYSQL_MAJOR}-dmr" > /etc/apt/sources.list.d/mysql.list && \ + { \ + echo mysql-community-server mysql-community-server/data-dir select ''; \ + echo mysql-community-server mysql-community-server/root-pass password ''; \ + echo mysql-community-server mysql-community-server/re-root-pass password ''; \ + echo mysql-community-server mysql-community-server/remove-test-db select false; \ + } | debconf-set-selections && \ + apt-get update -y && \ + apt-get install -y libpq-dev postgresql postgresql-client postgresql-plpython-9.3 \ + ansible postgresql-server-dev-9.3 wget mysql-server="${MYSQL_VERSION}"* \ + nodejs && \ + npm install -g grunt-contrib-qunit grunt grunt-cli casperjs phantomjs && \ + apt-get autoremove -y && apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* + +RUN mkdir -p /tmp/ansible && \ + mkdir -p /opt/galaxy/db && \ + chown -R postgres:postgres /opt/galaxy/db && \ + sed -Ei 's/^(bind-address|log)/#&/' /etc/mysql/my.cnf + +ADD start_mysql.sh /opt/galaxy/start_mysql.sh +ADD ansible_vars.yml /tmp/ansible/ansible_vars.yml +ADD provision.yml /tmp/ansible/provision.yml + +ENV PYTHON_EGG_CACHE=/root/.python-eggs \ + GALAXY_ROOT=/opt/galaxy/galaxy-app + +RUN cd /tmp/ansible && \ + mkdir roles && \ + mkdir roles/galaxyprojectdotorg.galaxy-os && \ + wget -qO- https://github.com/galaxyproject/ansible-galaxy-os/archive/master.tar.gz | tar -xzvf- --strip-components=1 -C roles/galaxyprojectdotorg.galaxy-os && \ + mkdir roles/galaxyprojectdotorg.cloudman-database && \ + wget -qO- https://github.com/galaxyproject/ansible-cloudman-database/archive/master.t… | tar -xzvf- --strip-components=1 -C roles/galaxyprojectdotorg.cloudman-database && \ + mkdir roles/galaxyprojectdotorg.galaxy && \ + wget -qO- https://github.com/galaxyproject/ansible-galaxy/archive/master.tar.gz | tar -xzvf- --strip-components=1 -C roles/galaxyprojectdotorg.galaxy && \ + ANSIBLE_FORCE_COLOR=1 PYTHONUNBUFFERED=1 ansible-playbook /tmp/ansible/provision.yml --tags=image -c local -e "@ansible_vars.yml" && \ + ANSIBLE_FORCE_COLOR=1 PYTHONUNBUFFERED=1 ansible-playbook /tmp/ansible/provision.yml --tags=database -c local -e "@ansible_vars.yml" && \ + ANSIBLE_FORCE_COLOR=1 PYTHONUNBUFFERED=1 ansible-playbook /tmp/ansible/provision.yml --tags=galaxy -c local -e "@ansible_vars.yml" && \ + apt-get autoremove -y && apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* + +RUN cd $GALAXY_ROOT && \ + echo "Prepopuating postgres database" && \ + su -c '/usr/lib/postgresql/9.3/bin/pg_ctl -o "-F" start -D /opt/galaxy/db' postgres && \ + GALAXY_CONFIG_DATABASE_CONNECTION="postgresql://galaxy@localhost:5930/galaxy" sh create_db.sh && \ + echo "Prepopuating sqlite database" && \ + GALAXY_CONFIG_DATABASE_CONNECTION="sqlite:////opt/galaxy/galaxy.sqlite" sh create_db.sh && \ + sh /opt/galaxy/start_mysql.sh && \ + GALAXY_CONFIG_DATABASE_CONNECTION="mysql://galaxy:galaxy@localhost/galaxy?unix_socket=/var/run/mysqld/mysqld.sock" sh create_db.sh + +ADD run_test_wrapper.sh /usr/local/bin/run_test_wrapper.sh + +ENTRYPOINT ["/bin/bash", "/usr/local/bin/run_test_wrapper.sh"] diff -r 93b67ff10b239978fbb38e78eba9c54b4fa5dd39 -r 43b850d3b54a9f0df417f80ce3d8a03fc28d4452 test/docker/base/ansible_vars.yml --- /dev/null +++ b/test/docker/base/ansible_vars.yml @@ -0,0 +1,21 @@ +--- +add_system_users: no +galaxyFS_base_dir: /opt/galaxy +# TODO: use GALAXY_ROOT via cmd line instead +galaxy_server_dir: "{{ galaxyFS_base_dir }}/galaxy-app" +galaxy_venv_dir: "{{ galaxy_server_dir }}/.venv" +galxy_egg_cache: "/home/{{ galaxy_user_name }}/.python-eggs" +galaxy_repo: https://bitbucket.org/galaxy/galaxy-central +galaxy_changeset_id: stable +galaxy_manage_clone: no +galaxy_manage_download: yes +galaxy_root: "{{ galaxy_server_dir}}" +galaxy_db_dir: "{{ galaxyFS_base_dir }}/db" +galaxy_db_port: 5930 +galaxy_db_log: /tmp/pSQL.log +psql_galaxyftp_password: ignoredthis +galaxy_config_file: "{{ galaxy_server_dir }}/config/galaxy.ini" +configure_docker: no +postgresql_bin_dir: /usr/lib/postgresql/9.3/bin +galaxy_manage_database: no + diff -r 93b67ff10b239978fbb38e78eba9c54b4fa5dd39 -r 43b850d3b54a9f0df417f80ce3d8a03fc28d4452 test/docker/base/provision.yml --- /dev/null +++ b/test/docker/base/provision.yml @@ -0,0 +1,15 @@ +- hosts: localhost + connection: local + roles: + - role: galaxyprojectdotorg.galaxy-os + tags: image + sudo: yes + - role: galaxyprojectdotorg.cloudman-database + sudo: yes + sudo_user: postgres + tags: database + - role: galaxyprojectdotorg.galaxy + sudo: yes + tags: galaxy + + diff -r 93b67ff10b239978fbb38e78eba9c54b4fa5dd39 -r 43b850d3b54a9f0df417f80ce3d8a03fc28d4452 test/docker/base/run_test_wrapper.sh --- /dev/null +++ b/test/docker/base/run_test_wrapper.sh @@ -0,0 +1,23 @@ +#!/bin/bash +set -e + +# TODO: switch on environment to boot mysql here... +if [ "$GALAXY_TEST_DATABASE_TYPE" = "postgres" ]; +then + su -c '/usr/lib/postgresql/9.3/bin/pg_ctl -o "-F" start -D /opt/galaxy/db' postgres + sleep 3 + export GALAXY_TEST_DBURI="postgres://galaxy@localhost:5930/galaxy" +elif [ "$GALAXY_TEST_DATABASE_TYPE" = "mysql" ]; +then + sh /opt/galaxy/start_mysql.sh + export GALAXY_TEST_DBURI="mysql://galaxy:galaxy@localhost/galaxy?unix_socket=/var/run/mysqld/mysqld.sock" +elif [ "$GALAXY_TEST_DATABASE_TYPE" = "sqlite" ]; +then + export GALAXY_TEST_DBURI="sqlite:////opt/galaxy/galaxy.sqlite" +else + echo "Unknown database type" + exit 1 +fi +cd /galaxy +GALAXY_CONFIG_OVERRIDE_DATABASE_CONNECTION="$GALAXY_TEST_DBURI" sh manage_db.sh upgrade +sh run_tests.sh $@ diff -r 93b67ff10b239978fbb38e78eba9c54b4fa5dd39 -r 43b850d3b54a9f0df417f80ce3d8a03fc28d4452 test/docker/base/start_mysql.sh --- /dev/null +++ b/test/docker/base/start_mysql.sh @@ -0,0 +1,39 @@ +#!/bin/bash +set -e + +MYSQL_USER=galaxy +MYSQL_PASSWORD=galaxy +MYSQL_DATABASE=galaxy + +mkdir -p /var/lib/mysql +chown -R mysql:mysql /var/lib/mysql + +# Derived from +# https://github.com/docker-library/mysql/blob/master/5.7/docker-entrypoint.sh + +DATADIR="$(mysqld --verbose --help 2>/dev/null | awk '$1 == "datadir" { print $2; exit }')" + +tempSqlFile='/tmp/mysql-first-time.sql' +cat > "$tempSqlFile" <<-EOSQL + DELETE FROM mysql.user ; + CREATE USER 'root'@'%' IDENTIFIED BY '${MYSQL_ROOT_PASSWORD}' ; + GRANT ALL ON *.* TO 'root'@'%' WITH GRANT OPTION ; + DROP DATABASE IF EXISTS test ; +EOSQL + +if [ "$MYSQL_DATABASE" ]; then + echo "CREATE DATABASE IF NOT EXISTS \`$MYSQL_DATABASE\` ;" >> "$tempSqlFile" +fi + +if [ "$MYSQL_USER" -a "$MYSQL_PASSWORD" ]; then + echo "CREATE USER '$MYSQL_USER'@'%' IDENTIFIED BY '$MYSQL_PASSWORD' ;" >> "$tempSqlFile" + + if [ "$MYSQL_DATABASE" ]; then + echo "GRANT ALL ON \`$MYSQL_DATABASE\`.* TO '$MYSQL_USER'@'%' ;" >> "$tempSqlFile" + fi +fi + +echo 'FLUSH PRIVILEGES ;' >> "$tempSqlFile" + +mysqld_safe --init-file="$tempSqlFile" & +sleep 5 \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: dannon: Merge back from next-stable.
by commits-noreply＠bitbucket.org 17 Feb '15

17 Feb '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b3a0812f9129/ Changeset: b3a0812f9129 User: dannon Date: 2015-02-17 20:20:40+00:00 Summary: Merge back from next-stable. Affected #: 0 files Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 4 new changesets
by commits-noreply＠bitbucket.org 17 Feb '15

17 Feb '15

4 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b63caa7dfa98/ Changeset: b63caa7dfa98 Branch: next-stable User: dannon Date: 2015-02-17 20:18:08+00:00 Summary: Fix xml.etree relative import error happening in test/asserts/xml.py Affected #: 1 file diff -r b6d15f14d0b392c4e9d9db56129bc67d6d4ba26b -r b63caa7dfa9865430d87d6023efd45ccf02228ca test/base/asserts/xml.py --- a/test/base/asserts/xml.py +++ b/test/base/asserts/xml.py @@ -1,3 +1,4 @@ +from __future__ import absolute_import import xml.etree import re https://bitbucket.org/galaxy/galaxy-central/commits/9f2731b49115/ Changeset: 9f2731b49115 User: dannon Date: 2015-02-17 20:18:45+00:00 Summary: Merge bugfix from next-stable. Affected #: 1 file diff -r 798e912004b2b26b219d5ed2214f1e65e8c099fa -r 9f2731b49115c44da4dc9bc4d91e9514b4c0b8ba test/base/asserts/xml.py --- a/test/base/asserts/xml.py +++ b/test/base/asserts/xml.py @@ -1,3 +1,4 @@ +from __future__ import absolute_import import xml.etree import re https://bitbucket.org/galaxy/galaxy-central/commits/6310fc863764/ Changeset: 6310fc863764 Branch: next-stable User: dannon Date: 2015-02-17 20:19:00+00:00 Summary: Merge. Affected #: 1 file diff -r b63caa7dfa9865430d87d6023efd45ccf02228ca -r 6310fc863764ef515861a64638bacebad8079514 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -886,14 +886,15 @@ legal_values = self.get_legal_values( trans, context ) if not legal_values and self.optional: return None - assert legal_values, "Parameter %s requires a value, but has no legal values defined" % self.name + if not legal_values: + raise ValueError( "Parameter %s requires a value, but has no legal values defined." % self.name ) if isinstance( value, list ): - if not(self.repeat): - assert self.multiple, "Multiple values provided but parameter %s is not expecting multiple values" % self.name + if not self.repeat and not self.multiple: + raise ValueError( "Multiple values provided but parameter %s is not expecting multiple values." % self.name ) rval = [] for v in value: if v not in legal_values: - raise ValueError( "An invalid option was selected for %s, %r, please verify" % (self.name, v)) + raise ValueError( "An invalid option was selected for %s, %r, please verify." % ( self.name, v ) ) rval.append( v ) return rval else: @@ -903,9 +904,9 @@ if self.optional: return [] else: - raise ValueError( "No option was selected for %s but input is not optional." % self.name) + raise ValueError( "No option was selected for %s but input is not optional." % self.name ) if value not in legal_values: - raise ValueError( "An invalid option was selected for %s, %r, please verify" % (self.name, value)) + raise ValueError( "An invalid option was selected for %s, %r, please verify." % ( self.name, value ) ) return value def to_html_value( self, value, app ): @@ -918,8 +919,8 @@ if value is None: return "None" if isinstance( value, list ): - if not( self.repeat ): - assert self.multiple, "Multiple values provided but parameter %s is not expecting multiple values" % self.name + if not self.repeat and not self.multiple: + raise ValueError( "Multiple values provided but parameter %s is not expecting multiple values." % self.name ) value = map( str, value ) else: value = str( value ) https://bitbucket.org/galaxy/galaxy-central/commits/cc01fa14d826/ Changeset: cc01fa14d826 User: dannon Date: 2015-02-17 20:19:40+00:00 Summary: Merge. Affected #: 1 file diff -r a49498479b2e71f8d2abf955ce4c7c041de730b9 -r cc01fa14d8269a5dc40b09fa3658ff3b58c2bc67 test/base/asserts/xml.py --- a/test/base/asserts/xml.py +++ b/test/base/asserts/xml.py @@ -1,3 +1,4 @@ +from __future__ import absolute_import import xml.etree import re Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: For select tool parameter, when testing input values, raise ValueErrors instead of assert/AssertionErrors, as ValueError are cased to be caught. Fixes errors on rerun, when options have been removed.
by commits-noreply＠bitbucket.org 17 Feb '15

17 Feb '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/83fb18cb8c3d/ Changeset: 83fb18cb8c3d Branch: next-stable User: dan Date: 2015-02-17 20:17:17+00:00 Summary: For select tool parameter, when testing input values, raise ValueErrors instead of assert/AssertionErrors, as ValueError are cased to be caught. Fixes errors on rerun, when options have been removed. Affected #: 1 file diff -r b6d15f14d0b392c4e9d9db56129bc67d6d4ba26b -r 83fb18cb8c3d21351f6267e574ed75c72eeb770a lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -886,14 +886,15 @@ legal_values = self.get_legal_values( trans, context ) if not legal_values and self.optional: return None - assert legal_values, "Parameter %s requires a value, but has no legal values defined" % self.name + if not legal_values: + raise ValueError( "Parameter %s requires a value, but has no legal values defined." % self.name ) if isinstance( value, list ): - if not(self.repeat): - assert self.multiple, "Multiple values provided but parameter %s is not expecting multiple values" % self.name + if not self.repeat and not self.multiple: + raise ValueError( "Multiple values provided but parameter %s is not expecting multiple values." % self.name ) rval = [] for v in value: if v not in legal_values: - raise ValueError( "An invalid option was selected for %s, %r, please verify" % (self.name, v)) + raise ValueError( "An invalid option was selected for %s, %r, please verify." % ( self.name, v ) ) rval.append( v ) return rval else: @@ -903,9 +904,9 @@ if self.optional: return [] else: - raise ValueError( "No option was selected for %s but input is not optional." % self.name) + raise ValueError( "No option was selected for %s but input is not optional." % self.name ) if value not in legal_values: - raise ValueError( "An invalid option was selected for %s, %r, please verify" % (self.name, value)) + raise ValueError( "An invalid option was selected for %s, %r, please verify." % ( self.name, value ) ) return value def to_html_value( self, value, app ): @@ -918,8 +919,8 @@ if value is None: return "None" if isinstance( value, list ): - if not( self.repeat ): - assert self.multiple, "Multiple values provided but parameter %s is not expecting multiple values" % self.name + if not self.repeat and not self.multiple: + raise ValueError( "Multiple values provided but parameter %s is not expecting multiple values." % self.name ) value = map( str, value ) else: value = str( value ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: For select tool parameter, when testing input values, raise ValueErrors instead of assert/AssertionErrors, as ValueError are cased to be caught. Fixes errors on rerun, when options have been removed.
by commits-noreply＠bitbucket.org 17 Feb '15

17 Feb '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a49498479b2e/ Changeset: a49498479b2e User: dan Date: 2015-02-17 20:17:17+00:00 Summary: For select tool parameter, when testing input values, raise ValueErrors instead of assert/AssertionErrors, as ValueError are cased to be caught. Fixes errors on rerun, when options have been removed. Affected #: 1 file diff -r 798e912004b2b26b219d5ed2214f1e65e8c099fa -r a49498479b2e71f8d2abf955ce4c7c041de730b9 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -886,14 +886,15 @@ legal_values = self.get_legal_values( trans, context ) if not legal_values and self.optional: return None - assert legal_values, "Parameter %s requires a value, but has no legal values defined" % self.name + if not legal_values: + raise ValueError( "Parameter %s requires a value, but has no legal values defined." % self.name ) if isinstance( value, list ): - if not(self.repeat): - assert self.multiple, "Multiple values provided but parameter %s is not expecting multiple values" % self.name + if not self.repeat and not self.multiple: + raise ValueError( "Multiple values provided but parameter %s is not expecting multiple values." % self.name ) rval = [] for v in value: if v not in legal_values: - raise ValueError( "An invalid option was selected for %s, %r, please verify" % (self.name, v)) + raise ValueError( "An invalid option was selected for %s, %r, please verify." % ( self.name, v ) ) rval.append( v ) return rval else: @@ -903,9 +904,9 @@ if self.optional: return [] else: - raise ValueError( "No option was selected for %s but input is not optional." % self.name) + raise ValueError( "No option was selected for %s but input is not optional." % self.name ) if value not in legal_values: - raise ValueError( "An invalid option was selected for %s, %r, please verify" % (self.name, value)) + raise ValueError( "An invalid option was selected for %s, %r, please verify." % ( self.name, value ) ) return value def to_html_value( self, value, app ): @@ -918,8 +919,8 @@ if value is None: return "None" if isinstance( value, list ): - if not( self.repeat ): - assert self.multiple, "Multiple values provided but parameter %s is not expecting multiple values" % self.name + if not self.repeat and not self.multiple: + raise ValueError( "Multiple values provided but parameter %s is not expecting multiple values." % self.name ) value = map( str, value ) else: value = str( value ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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