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Create galaxy-tool-util package.

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This is (so far a subset of) the tool utilities from galaxy-lib. galaxy-lib mocked out a fake galaxy.tools to allow these to all exist below the galaxy.tools - but this was a terrible hack - in order for the new packages to be true subsets of Galaxy they need to be refactored into a new package that doesn't depend on models, SA, galaxy.jobs, etc...

[x] galaxy.tools.deps -> galaxy.tool_util.deps
[x] galaxy.tools.loader -> galaxy.tool_util.loader
[x] galaxy.tools.cwl -> galaxy.tool_util.cwl
[x] galaxy.tools.loader -> galaxy.tool_util.loader
[x] galaxy.tools.fetcher -> galaxy.tool_util.fetcher
[x] galaxy.tools.locations -> galaxy.tool_util.locations
[x] galaxy.tools.parser -> galaxy.tool_util.parser
This commit is contained in:
John Chilton
2019-05-16 16:45:25 -04:00
parent 151f967676
commit 939e7774a8
118 changed files with 261 additions and 99 deletions
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scripts/manage_tool_dependencies.py
+2 -2
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@@ -9,7 +9,7 @@ from galaxy.config import (
find_root,
parse_dependency_options,
)
from galaxy.tools.deps import CachedDependencyManager, DependencyManager, NullDependencyManager
from galaxy.tool_util.deps import CachedDependencyManager, DependencyManager, NullDependencyManager
from galaxy.util.script import main_factory
DESCRIPTION = "Script to manage tool dependencies (with focus on a Conda environments)."
@@ -21,7 +21,7 @@ def _init_if_needed(args, kwargs):
def _build_dependency_manager_no_config(kwargs):
"""Simplified variant of build_dependency_manager from galaxy.tools.deps.
"""Simplified variant of build_dependency_manager from galaxy.tool_util.deps.
The canonical factory method requires a full Galaxy configuration object
which we do not have available in this script (an optimization).
scripts/validate_tools.sh
+1 -1
View File
@@ -21,7 +21,7 @@ for p in "$@"; do
echo $path
PYTHONPATH=lib:$PYTHONPATH
export PYTHONPATH
result=`python -c "import galaxy.tools.loader; import xml.etree; xml.etree.ElementTree.dump(galaxy.tools.loader.load_tool('$path').getroot())" | xmllint --nowarning --noout --schema "$xsd_path" - 2> "$err_tmp"`
result=`python -c "import galaxy.tool_util.loader; import xml.etree; xml.etree.ElementTree.dump(galaxy.tool_util.loader.load_tool('$path').getroot())" | xmllint --nowarning --noout --schema "$xsd_path" - 2> "$err_tmp"`
if [ $? -eq 0 ]
then
echo "ok $count";