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20352 Commits
Author SHA1 Message Date
Marius van den Beek 4bd8644b24 Merge pull request #7800 from nsoranzo/fix_deprecations 
Fix various Python deprecations
 2019-04-24 10:52:34 +02:00
John Chilton 2589d4d394 Merge pull request #7796 from mvdbeek/param_parser_tool 
Add general purpose expression tool
 2019-04-23 16:20:39 -04:00
Martin Cech da127e1c12 Merge pull request #7773 from bgruening/geojson 
Add GeoJSON datatype
 2019-04-23 15:57:43 -04:00
Martin Cech 9c8f0e70e9 add newline 2019-04-23 13:21:28 -04:00
Nicola Soranzo d53112aa43 Use `yaml.safe_load() instead of load()` 
See https://msg.pyyaml.org/load
 2019-04-23 16:50:55 +01:00
Dannon 2c6e99a4a0 Merge pull request #7785 from martenson/bump-deps 
bump python dependencies
 2019-04-23 10:35:41 -04:00
Nicola Soranzo fe2c14d329 Fix typo 2019-04-23 15:21:49 +01:00
Nicola Soranzo a00ce60002 Use `log.warning() instead of deprecated log.warn()` 
See https://docs.python.org/3/library/logging.html#logging.Logger.warning
 2019-04-23 15:07:39 +01:00
Nicola Soranzo 0faa479f94 Fix deprecated `getchildren()` 
See https://docs.python.org/2/library/xml.etree.elementtree.html#xml.etree.ElementTree.Element.getchildren
 2019-04-23 12:51:13 +01:00
mvdbeek bd8187538d Allow filtering expression tool outputs 2019-04-23 12:00:45 +02:00
mvdbeek 780b07f505 Add load_contents attribute to data inputs 
If set to a non-zero value will make Galaxy deposit the first n bytes of
content within in the job.<param_name>.<content> dict.
This is similar to the `loadContents` flag in the CWL input binding
which will load the first 64KB.
See https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding
 2019-04-23 11:56:04 +02:00
mvdbeek 6b3aecdcc4 Restrict search to items in owned histories 
This was an oversight in https://github.com/galaxyproject/galaxy/pull/7745.
This is the quick fix, but I think it's feasible to implement the
accessible logic as a query, which means we could push this down to
a Mixin, and treat it as a regular fiter (so admins could for instance
search/sort for the largest datasets, which is already possible in the
reports app).
 2019-04-20 16:27:34 +02:00
John Chilton ef62c3662c Merge pull request #7782 from mvdbeek/fix_ts_install_py3 
Make url_get return unicode
 2019-04-19 16:19:57 -04:00
Martin Cech 1c3d8d6cd4 this seems also needed 2019-04-19 14:15:03 -04:00
Martin Cech 198a4481e4 do not update sqlalchemy 2019-04-19 14:06:33 -04:00
Martin Cech 4cfed5bbd0 bump dependencies 2019-04-19 14:01:08 -04:00
Marius van den Beek a21b73d675 Merge pull request #7770 from davebx/repo_path_bug 
Create repository clone path if it doesn't exist.
 2019-04-19 16:54:06 +02:00
mvdbeek 5cd9192d37 Convert get_url to unicode 
We almost always consume this using `json.loads()`,
so this would fail on python 3.
Where we don't do this it should still be fine.
Fixes https://github.com/galaxyproject/galaxy/issues/7769
 2019-04-19 16:46:10 +02:00
Dannon 53734336e0 Merge pull request #7772 from mvdbeek/syntax_fix 
Fix raise syntax error
 2019-04-19 10:02:32 -04:00
John Chilton 32604d9b03 Merge pull request #7745 from mvdbeek/dataset_search_api 
Extend dataset search and add search API endpoint
 2019-04-19 09:00:28 -04:00
Björn Grüning 3955644ab1 fix linting 2019-04-19 14:32:34 +02:00
Bjoern Gruening 375d3fa795 add GeoJSON test data 2019-04-19 14:11:34 +02:00
Bjoern Gruening a48e61e994 add GeoJSON datatype 2019-04-19 14:11:19 +02:00
mvdbeek 6c39563388 Fix raise syntax error 
I'm not sure if this is really an error, but my IDE tells me this
is invalid.
 2019-04-19 10:38:13 +02:00
Dave B da26d96bfc Create repository clone path if it doesn't exist. 2019-04-18 16:32:20 -04:00
mvdbeek e7b0867602 Make sure orm filters operate on correct model 
In practice we use ParsedFiler.filter_type to discriminate
the different filter types. Filters that require the correct
model class for a specific query are now functions that take
a model_class and generate the correct filter.
 2019-04-18 18:55:14 +02:00
mvdbeek 2b95d6911d Need to use unique function name 2019-04-17 17:11:18 +02:00
mvdbeek 885d9d1766 Fix err_msg assertion 2019-04-17 16:30:24 +02:00
mvdbeek ae5e781edf Make TaggableFilterMixin use orm_filters 
This is way more peformant and also doesn't give
weird results when a limit is used.
 2019-04-17 16:03:27 +02:00
John Chilton 1e731b7c03 Add HDCA support to model persistence script. 2019-04-17 08:51:18 -04:00
John Chilton ca1b1fd854 Fix nested composite files during history import/export. 
Fixes #3628
 2019-04-17 08:49:09 -04:00
John Chilton f06211a2d7 Model store - fix for composite files stored by UUID. 2019-04-17 08:49:08 -04:00
John Chilton e333f3ba06 Refactor output_collect.py for reuse in sessionless context. 
Collected refactorings that should have probably been included in #7541.
 2019-04-17 08:49:08 -04:00
John Chilton 656cb93e0c Merge pull request #7760 from mvdbeek/add_singularity_to_valid_types 
Add singularity to valid types, allow customization of test history name
 2019-04-17 08:47:51 -04:00
mvdbeek 4dee02ff3b Allow defining orm filters as function and move tool_id filter to separate mixin 2019-04-17 14:13:51 +02:00
mvdbeek 9b12268add Very primitive in-database tool id filter 2019-04-17 12:43:52 +02:00
mvdbeek f112a10d98 Allow singularity as container type in xsd 2019-04-17 10:45:11 +02:00
Martin Cech 93da1fc0bd Merge pull request #7684 from jmchilton/build_objects_script 
Script to populate datasets/libraries directly into an objectstore and model store.
 2019-04-16 22:16:31 -04:00
John Chilton 79027f1856 Merge pull request #7404 from natefoo/auto-cookie-path 
Automatically set cookie_path using url_for()
 2019-04-16 17:49:22 -04:00
Nate Coraor fed86eb598 Remove cookie_path configuration documentation since it's now set 
automatically.
 2019-04-16 17:48:36 -04:00
Nate Coraor 58d311f2e0 Make the cookie_path an attribute on trans so that consumers don't need 
to duplicate logic. Unfortunately it isn't usable for the proxy setup
since trans isn't available when the command line is generated.
 2019-04-16 17:48:36 -04:00
Nate Coraor 449932b229 Automatically set cookie_path using url_for() 2019-04-16 17:48:34 -04:00
John Chilton 14cb68fc60 Merge pull request #7718 from pvanheus/dev 
spaln database type
 2019-04-16 17:47:04 -04:00
John Chilton 89090545a8 Merge pull request #7246 from davebx/csv_tsv_converters 
Add converters between tabular and CSV.
 2019-04-16 17:41:18 -04:00
mvdbeek 82d21b4743 Copy-paste and adjust documentation from HistoryContentsController.__index_v2 2019-04-16 19:31:36 +02:00
mvdbeek 234193889e Allow filtering history contents by annotation 2019-04-16 19:31:03 +02:00
mvdbeek a642147ada Add contains alias to filter operators 2019-04-16 19:31:03 +02:00
mvdbeek d98dcf6340 Apply function filters after query 2019-04-16 19:31:03 +02:00
mvdbeek f0a77cbf0c Allow quering for extension in the database 2019-04-16 19:31:03 +02:00
mvdbeek c7a69f9ad0 Add API andpoint to search for dataset 
This re-uses the existing ModelFilterParser for database querying
and modifies the HistoryContentsManager to not require a container
(= history).
 2019-04-16 19:31:03 +02:00