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Watch tool data table *.loc files, and reload if modified. #3533

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merged 3 commits into from Feb 6, 2017

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@mvdbeek
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commented Feb 1, 2017

The approach here is quite similar to monitoring a directory of tools. This is optional and requires the watchdog library to be installed. Initial testing on our server that accesses the tool-data folder over sshfs indicate that things are going smooth.

This could be extended to become the default, but I think this is a good first step.

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I'll give some early feedback, hope that's OK.

@@ -309,6 +309,17 @@ paste.app_factory = galaxy.web.buildapp:app_factory
# when installed from a ToolShed. Defaults to tool_data_path.
#shed_tool_data_path = tool-data

# Set to True to enable monitoring of the tool_data and shed_tool_data_path
# directories. If changes in tool data table files are found, the tool data
# tables for that data manager are automatically reloaded

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nsoranzo Feb 1, 2017

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Missing period at the end of this line.

"""
Reload tool data tables.
Reload tool data tables. If neither table_names not path is given, reloads all tool data tables.

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nsoranzo Feb 1, 2017

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s/not/nor/

@@ -11,7 +11,10 @@
send_control_task
)
from galaxy.tools.data import TabularToolDataTable
from galaxy.tools.toolbox.watcher import get_tool_conf_watcher
from galaxy.tools.toolbox.watcher import (
get_loc_dir_watcher,

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nsoranzo Feb 1, 2017

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I feel that using tool_data_dir instead of loc_dir everywhere would be better for consistency, if I'm not missing something.

@mvdbeek mvdbeek force-pushed the mvdbeek:tdt_reload branch 5 times, most recently from c89f1ca to 596432c Feb 2, 2017

mvdbeek added some commits Feb 1, 2017

Implement automatic tool_data_table reload
if *.loc files have been modified.

@mvdbeek mvdbeek force-pushed the mvdbeek:tdt_reload branch from 43053f8 to 732e296 Feb 2, 2017

@mvdbeek mvdbeek changed the title WIP: work on automatic tool_data_table reload Watch tool data table *.loc files, and reload if modified. Feb 3, 2017

@mvdbeek mvdbeek added status/review and removed status/WIP labels Feb 3, 2017

@jmchilton jmchilton merged commit 900c8d2 into galaxyproject:dev Feb 6, 2017

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api test Build finished. 260 tests run, 0 skipped, 0 failed.
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framework test Build finished. 137 tests run, 0 skipped, 0 failed.
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integration test Build finished. 24 tests run, 0 skipped, 0 failed.
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toolshed test Build finished. 580 tests run, 0 skipped, 0 failed.
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@mvdbeek mvdbeek referenced this pull request Apr 5, 2017

Merged

Run data managers #30

@mvdbeek mvdbeek deleted the mvdbeek:tdt_reload branch Jun 12, 2018

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