commit/galaxy-central: 16 new changesets
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 - - - -[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=galaxyLogoTrimmed.png + :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=galaxyLogoTrimmed.png - :alt: Galaxy Logo - - Galaxy Logo -`galaxyproject.org <http://galaxyproject.org/>`__ +`.. figure:: https://wiki.galaxyproject.org/Images/Logos?action=AttachFile&do=get&target=galaxyLogoTrimmed.png + :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=galaxyLogoTrimmed.png - :alt: Galaxy Logo <http://galaxyproject.org/>`__ +.. figure:: https://wiki.galaxyproject.org/Images/Logos?action=AttachFile&do=get&target=galaxyLogoTrimmed.png + :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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