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Merge pull request #2961 from jmchilton/xsd_fixes_1

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Improve ``version_command`` tag.
This commit is contained in:
Martin Cech
2016-10-17 13:31:52 -04:00
committed by GitHub
parent 22839eeee0 e8f35310ba
commit 7eb413f4e8
9 changed files with 120 additions and 22 deletions
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doc/schema_template.md
+1 -1
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@@ -17,7 +17,7 @@ $toc
$tag:tool://element[@name='tool']
$tag:tool|description://element[@name='tool']//element[@name='description']
$tag:tool|version_command://element[@name='tool']//element[@name='version_command']
$tag:tool|version_command://complexType[@name='VersionCommand']
$tag:tool|command://element[@name='tool']//element[@name='command'] hide_attributes
$tag:tool|inputs://complexType[@name='Inputs']
$tag:tool|inputs|section://complexType[@name='Section']
lib/galaxy/jobs/__init__.py
+5 -2
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@@ -8,6 +8,7 @@ import os
import pwd
import random
import shutil
import string
import subprocess
import sys
import time
@@ -919,8 +920,10 @@ class JobWrapper( object ):
self.sa_session.flush()
# Return list of all extra files
self.param_dict = tool_evaluator.param_dict
version_string_cmd = self.tool.version_string_cmd
if version_string_cmd:
version_string_cmd_raw = self.tool.version_string_cmd
if version_string_cmd_raw:
version_command_template = string.Template(version_string_cmd_raw)
version_string_cmd = version_command_template.safe_substitute({"__tool_directory__": compute_environment.tool_directory() })
self.write_version_cmd = "%s > %s 2>&1" % ( version_string_cmd, compute_environment.version_path() )
else:
self.write_version_cmd = None
lib/galaxy/tools/xsd/galaxy.xsd
+48 -19
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@@ -61,23 +61,7 @@ the tool menu immediately following the hyperlink for the tool (based on the
</xs:annotation>
</xs:element>
<xs:element name="parallelism" type="Parallelism" minOccurs="0"/>
<xs:element name="version_command" type="xs:string" minOccurs="0">
<xs:annotation>
<xs:documentation xml:lang="en"><![CDATA[Specifies the command to be run in
order to get the tool's version string. The resulting value will be found in the
"Info" field of the history dataset.
Unlike the [``command``](#tool|command) tag, this value is taken as a literal and so there is no
need to escape values like ``$`` and command inputs are not available for variable
substitution.
### Example
```xml
<version_command>tophat -version</version_command>
```
]]></xs:documentation>
</xs:annotation>
<xs:element name="version_command" type="VersionCommand" minOccurs="0">
</xs:element>
<xs:element name="action" type="ToolAction" minOccurs="0" maxOccurs="1" />
<xs:element name="environment_variables" type="EnvironmentVariables" minOccurs="0" maxOccurs="1"/>
@@ -1428,7 +1412,7 @@ many of the default assertion tags that come with Galaxy and examples of each
can be found below.
The implementation of these tags are simply Python functions defined in the
[``galaxy.tools.verify.asserts``](https://github.com/galaxyproject/galaxy/tree/dev/lib/galaxy/tools/verify/asserts]
[``galaxy.tools.verify.asserts``](https://github.com/galaxyproject/galaxy/tree/dev/lib/galaxy/tools/verify/asserts)
module.
]]>
</xs:documentation>
@@ -4215,7 +4199,6 @@ define.</xs:documentation>
</xs:simpleContent>
</xs:complexType>
<xs:complexType name="ConfigFiles">
<xs:annotation>
<xs:documentation xml:lang="en"><![CDATA[See
@@ -4351,6 +4334,52 @@ response to this directive.
</xs:simpleContent>
</xs:complexType>
<xs:complexType name="VersionCommand">
<xs:annotation>
<xs:documentation xml:lang="en"><![CDATA[Specifies the command to be run in
order to get the tool's version string. The resulting value will be found in the
"Info" field of the history dataset.
Unlike the [``command``](#tool|command) tag, with the exception of the string
``$__tool_directory__`` this value is taken as a literal and so there is no
need to escape values like ``$`` and command inputs are not available for variable
substitution.
### Examples
A simple example for a [TopHat](https://ccb.jhu.edu/software/tophat/index.shtml)
tool definition might just be:
```xml
<version_command>tophat -version</version_command>
```
An example that leverages a Python script (e.g. ``count_reads.py``) shipped with
the tool might be:
```xml
<version_command>python $__tool_directory__/count_reads.py</version_command>
```
Examples are included in the test tools directory including:
- [version_command_plain.xml](https://github.com/galaxyproject/galaxy/blob/dev/test/functional/tools/version_command_plain.xml)
- [version_command_tool_dir.xml](https://github.com/galaxyproject/galaxy/blob/dev/test/functional/tools/version_tool_dir.xml)
- [version_command_interpreter.xml](https://github.com/galaxyproject/galaxy/blob/dev/test/functional/tools/version_command_interpreter.xml) (*deprecated*)
]]></xs:documentation>
</xs:annotation>
<xs:simpleContent>
<xs:extension base="xs:string">
<xs:attribute name="interpreter" type="xs:string">
<xs:annotation>
<xs:documentation xml:lang="en"><![CDATA[*Deprecated*: Prefix the version command with an interpreter and the tool directory in order to execute a script shipped with the tool. It is better to just use ``<interpreter> $__tool_directory__/<script_name>``.]]></xs:documentation>
</xs:annotation>
</xs:attribute>
</xs:extension>
</xs:simpleContent>
</xs:complexType>
<xs:complexType name="RequestParameterTranslation">
<xs:annotation>
<xs:documentation xml:lang="en"><![CDATA[
test/functional/tools/samples_tool_conf.xml
+3
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@@ -40,6 +40,9 @@
<tool file="maxseconds.xml" />
-->
<tool file="job_properties.xml" />
<tool file="version_command_plain.xml" />
<tool file="version_command_interpreter.xml" />
<tool file="version_command_tool_dir.xml" />
<tool file="exit_code_from_file.xml" />
<tool file="gzipped_inputs.xml" />
<tool file="output_order.xml" />
test/functional/tools/version_command.py
+2
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@@ -0,0 +1,2 @@
from __future__ import print_function
print("4.0.0")
test/functional/tools/version_command_interpreter.xml
+20
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@@ -0,0 +1,20 @@
<tool id="version_command_interpreter" name="version_command_interpreter" version="1.0.0">
<version_command interpreter="python">
version_command.py
</version_command>
<command>
cp $input $output
</command>
<inputs>
<param name="input" type="data" format="txt" />
</inputs>
<outputs>
<data name="output" format="txt" />
</outputs>
<tests>
<test>
<param name="input" value="simple_line.txt" />
<output name="out_file1" checksum="sha1$8156d7ca0f46ed7abac98f82e36cfaddb2aca041" />
</test>
</tests>
</tool>
test/functional/tools/version_command_plain.xml
+20
View File
@@ -0,0 +1,20 @@
<tool id="version_command_plain" name="version_command_plain" version="1.0.0">
<version_command>
echo "4.0.0"
</version_command>
<command>
cp $input $output
</command>
<inputs>
<param name="input" type="data" format="txt" />
</inputs>
<outputs>
<data name="output" format="txt" />
</outputs>
<tests>
<test>
<param name="input" value="simple_line.txt" />
<output name="out_file1" checksum="sha1$8156d7ca0f46ed7abac98f82e36cfaddb2aca041" />
</test>
</tests>
</tool>
test/functional/tools/version_command_tool_dir.xml
+20
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@@ -0,0 +1,20 @@
<tool id="version_command_tool_dir" name="version_command_tool_dir" version="1.0.0">
<version_command>
python $__tool_directory__/version_command.py
</version_command>
<command>
cp $input $output
</command>
<inputs>
<param name="input" type="data" format="txt" />
</inputs>
<outputs>
<data name="output" format="txt" />
</outputs>
<tests>
<test>
<param name="input" value="simple_line.txt" />
<output name="out_file1" checksum="sha1$8156d7ca0f46ed7abac98f82e36cfaddb2aca041" />
</test>
</tests>
</tool>
test/unit/jobs/test_job_wrapper.py
+1
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@@ -157,6 +157,7 @@ class MockTool(object):
def __init__(self, app):
self.version_string_cmd = TEST_VERSION_COMMAND
self.tool_dir = "/path/to/tools"
self.dependencies = []
def build_dependency_shell_commands(self, job_directory):