Nicola Soranzo
de46a0edba
Merge pull request #3935 from jmchilton/more_maf_fixes
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[17.01] More careful inspection of fixes for MAF tools requiring Galaxy.
2017-05-02 14:53:08 +01:00
Martin Cech
a6415b25fd
Merge pull request #3909 from mvdbeek/speedup_toolbox
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Speedup startup and toolbox operations
2017-05-02 09:29:37 -04:00
John Chilton
86ebe28667
Enhance filenames with collection context when downloading datasets from GUI.
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- Reduce duplication related to calculating filename.
- Formalized pattern for normal dataset download using string.Tempalte - "Galaxy${hid}-[${name}].${ext}".
- In the context of collections, hid and name of the datasets are pretty worthless so I used a second pattern for collections based on where it is in the current GUI frame. The new pattern is "Galaxy${hdca_hid}-[${hdca_name}__${element_identifier}].${ext}".
- The patterns make this a little more tweakable - for people who want something different it should be pretty straight forward to make these patterns configurable.
Fixes #2140 I think.
2017-05-01 21:19:13 -04:00
anuprulez
490b11bfc5
Converting run mako to plain javascript and modifying menu for url
2017-05-01 20:39:55 +02:00
Eric Rasche
09404117b9
Merge pull request #3980 from jmchilton/ie_for_mac_os_x_fixes
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Rework Jupyter IE for additional_ids handling.
2017-05-01 18:08:43 +00:00
John Chilton
8afcfa4ec9
Merge remote-tracking branch 'jmchilton/dev' into feature/pr_fs_access_job_version
2017-05-01 10:28:40 -04:00
mvdbeek
af156a8f74
Build search index at startup, rebuild repository cache during toolbox or datamanager reload
2017-05-01 16:06:48 +02:00
mvdbeek
2587ab55b8
Remove operations from custom_datatype_manager
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Updating the upload file formats is handled when loading the datatype
into the registry, and reloading the upload tool seems unnecessary and
insufficient, since this would only affect the current web handler. In
any case removed and added datatypes are immediately propagated to the
upload tool.
2017-05-01 16:06:48 +02:00
mvdbeek
cdad5bee9b
Attempt to speedup proprietary datatype loading
2017-05-01 16:06:48 +02:00
mvdbeek
86684df5ef
Skip time-based reloading, rely on detecting DetachedInstanceErrors to trigger cache rebuild
2017-05-01 16:06:47 +02:00
mvdbeek
b666649c81
Work around InstanceDetached errors
2017-05-01 16:06:47 +02:00
mvdbeek
84351de20b
Send control task as postfork function
2017-05-01 16:06:47 +02:00
mvdbeek
ff1b66afb3
Fix thread local cache use
2017-05-01 16:06:47 +02:00
mvdbeek
b4e4f3ce7a
Use current session
2017-05-01 16:06:47 +02:00
mvdbeek
f199d5b434
Keep cache thread-local
2017-05-01 16:06:47 +02:00
mvdbeek
5a26896745
Write out datatype registry when loading set_metadata tool
2017-05-01 16:06:46 +02:00
mvdbeek
5e7da2c910
Don't fail tests without internet connectivity
2017-05-01 16:06:46 +02:00
mvdbeek
f88304b65b
Build toolbox search in a local control task
2017-05-01 16:06:46 +02:00
mvdbeek
3079d0c239
Write out the datatype registry only once
2017-05-01 16:06:46 +02:00
mvdbeek
869d7bf481
Replace getchildren(), which has been deprecated ( https://docs.python.org/2/library/xml.etree.elementtree.html#xml.etree.ElementTree.Element.getchildren )
2017-05-01 16:06:46 +02:00
mvdbeek
73c7c364a2
Use tool_shed_repository_cache in populate_tool_shed_info
2017-05-01 16:06:46 +02:00
mvdbeek
141f15256e
Use ExecutionTimer
2017-05-01 16:06:45 +02:00
mvdbeek
7e61f8c047
Revert "Use cElementTree for light xml parsing speedup"
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This reverts commit 556469f5171ef9897a5c40de9d661d2d4f4deb86.
2017-05-01 16:06:45 +02:00
mvdbeek
15e2c9b61a
Revert "Fix cElementTree imports"
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This reverts commit 6d365f03e888ef12527105119f0a7adebae23b95.
2017-05-01 16:06:45 +02:00
mvdbeek
8411b0253a
Restore deactivate/activate functionality
2017-05-01 16:06:45 +02:00
mvdbeek
456d1b47b6
Refresh TSR cache when needed
2017-05-01 16:06:45 +02:00
mvdbeek
89f57f2aa7
Allow looking up repositories by repository_id via ToolShedRepositoryCache
2017-05-01 16:06:45 +02:00
mvdbeek
f940c797ff
Fix import order in lib/galaxy/config.py
2017-05-01 16:06:44 +02:00
mvdbeek
677d98622d
Always refresh tool_shed_repository_cache before fetching repositories by ids (since that is only called from admin_toolshed.py and installed_repository_metadata_manager.py)
2017-05-01 16:06:44 +02:00
mvdbeek
07da123e9d
Reference old_toolbox earlier, since reloading can happen in a different thread, which will lead to a hang when waiting for another toolbox reload
2017-05-01 16:06:44 +02:00
mvdbeek
3d6bc1d563
Refresh tool_data_path_files if we know that a new table has been written
2017-05-01 16:06:44 +02:00
mvdbeek
586f49486c
Don't crash if a tool has not been added to the cache properly
2017-05-01 16:06:44 +02:00
mvdbeek
d15813cb2a
Avoid having tools in tool_cache marked as new when they have rapidly shifted from new to expired.
2017-05-01 16:06:44 +02:00
mvdbeek
5069815c0e
Rebuild repo cache when deciding if repository should be created.
2017-05-01 16:06:43 +02:00
mvdbeek
4c44338144
Be more defesive when accessing app.tool_cache
2017-05-01 16:06:43 +02:00
mvdbeek
dc1617596e
Remove unused time import
2017-05-01 16:06:43 +02:00
mvdbeek
4dd49c938d
Use ExecutionTimer abstraction to report startup time
2017-05-01 16:06:43 +02:00
mvdbeek
cbed78fbfb
Don't return toolbox (thx @nsoranzo)
2017-05-01 16:06:43 +02:00
mvdbeek
0504dcd299
Use generator instead of list comprehenesion followed converting it to a set. (Thanks @nsoranzo)
2017-05-01 16:06:43 +02:00
mvdbeek
84c1559d47
Fix path checking for files that are not in the tool_data_path directory
2017-05-01 16:06:42 +02:00
mvdbeek
b72994fe02
Add possibility explicitly rebuild ToolShedRepositoryCache
2017-05-01 16:06:42 +02:00
mvdbeek
c905c4217b
Fix import order in lib/galaxy/tools/data/__init__.py
2017-05-01 16:06:42 +02:00
mvdbeek
3ff2a7832a
Fix cElementTree imports
2017-05-01 16:06:42 +02:00
mvdbeek
a83ef0b86c
Log startup time
2017-05-01 16:06:42 +02:00
John Chilton
beae93bf76
Re-use ExecutionTimer abstractions for consistent log patterns.
2017-05-01 16:06:41 +02:00
mvdbeek
475b8866ba
Fix unittests that access app.tool_cache
2017-05-01 16:06:41 +02:00
mvdbeek
9aa5556ded
Reduce logging during toolbox reloads
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We don't log loading of tools that have not changed when reloading the
toolbox.
2017-05-01 16:06:41 +02:00
mvdbeek
db910f4f81
Reset the tool cache once all tools are loaded after starting up galaxy
2017-05-01 16:06:41 +02:00
mvdbeek
ea9ecdf571
Remove replace_existing option for data managers
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If a data manager is defined twice for the same data manager id in the
shed_tool_conf.xml the first data manager will be loaded. This is not a
problem when updating a data manager through the toolshed, because the
outdated data manager will be removed from the tool cache and a new
toolbox is being built.
2017-05-01 16:06:41 +02:00
mvdbeek
431a4824ab
Make sure re-indexing the toolbox occurs on the new toolbox
2017-05-01 15:59:26 +02:00
Nicola Soranzo