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Initial argument parser and defining classes at runtime
This allows us to define python decider classes at runtime Former-commit-id: 35f4cea
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‎.pydevproject

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<?xml version="1.0" encoding="UTF-8" standalone="no"?>
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<?eclipse-pydev version="1.0"?><pydev_project>
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<pydev_property name="org.python.pydev.PYTHON_PROJECT_INTERPRETER">Default</pydev_property>
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<pydev_property name="org.python.pydev.PYTHON_PROJECT_VERSION">python 3.0</pydev_property>
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</pydev_project>

‎pom.xml

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<artifactId>maven-source-plugin</artifactId>
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<version>2.2.1</version>
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</plugin>
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<!--This plugin's configuration is used to store Eclipse m2e settings only. It has no influence on the Maven build itself.-->
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<plugin>
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<groupId>org.eclipse.m2e</groupId>
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<artifactId>lifecycle-mapping</artifactId>
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<version>1.0.0</version>
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<configuration>
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<lifecycleMappingMetadata>
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<pluginExecutions>
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<pluginExecution>
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<pluginExecutionFilter>
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<groupId>org.jacoco</groupId>
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<artifactId>
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jacoco-maven-plugin
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</artifactId>
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<versionRange>
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[0.6.3.201306030806,)
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</versionRange>
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<goals>
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<goal>prepare-agent</goal>
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</goals>
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</pluginExecutionFilter>
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<action>
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<ignore></ignore>
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</action>
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</pluginExecution>
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<pluginExecution>
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<pluginExecutionFilter>
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<groupId>
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org.apache.maven.plugins
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</groupId>
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<artifactId>
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maven-checkstyle-plugin
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</artifactId>
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<versionRange>
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[2.12.1,)
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</versionRange>
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<goals>
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<goal>check</goal>
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</goals>
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</pluginExecutionFilter>
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<action>
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<ignore></ignore>
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</action>
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</pluginExecution>
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</pluginExecutions>
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</lifecycleMappingMetadata>
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</configuration>
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</plugin>
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</plugins>
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</pluginManagement>
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‎scripts/deciders/abstractDeciderImpl.py

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#! /usr/bin/env python3
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import argparse
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from abc import ABCMeta, abstractmethod
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from argparse import PARSER
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####################################################
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## This defines what methods are customizable
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## by decider developers.
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####################################################
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class AbstractDecider( metaclass=ABCMeta ):
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@abstractmethod
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def init (self, PARSER):
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pass
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@abstractmethod
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def provideTargetQuery (self):
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pass
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@abstractmethod
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def checkFileDetails (self):
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pass
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@abstractmethod
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def doFinalCheck(self):
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pass
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‎scripts/deciders/basicDeciderImpl.py

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#! /usr/bin/env python3
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from abstractDeciderImpl import AbstractDecider
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####################################################
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## This is an implementation of a barebones decider
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## usable for running simple workflows
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####################################################
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class Decider (AbstractDecider):
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def init (self, PARSER):
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print("oogly")
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def provideTargetQuery (self):
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pass
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def checkFileDetails (self):
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pass
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def doFinalCheck(self):
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pass

‎scripts/deciders/deciderFramework.py

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#! /usr/bin/env python3
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import subprocess, sys, argparse, importlib
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from builtins import int
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###################################################################
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## This is an implementation of a
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## decider framework. This class is not designed for inheritance.
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###################################################################
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def __main():
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parser = argparse.ArgumentParser(description='Run a SeqWare decider in order to schedule workflow runs')
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targetGroup = parser.add_mutually_exclusive_group(required=True)
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bigTargetGroup = targetGroup.add_mutually_exclusive_group()
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bigTargetGroup.add_argument('--all', help='Target the decider at all data in your SeqWare provenance report', action='store_true')
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smallTargetGroup = targetGroup.add_mutually_exclusive_group()
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supportedConstraints = ['study-name', 'lane-SWID', 'ius-SWID', 'sample-name', 'root-sample-name', 'sequencer-run-name', 'organism', 'processing-SWID']
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for constraint in supportedConstraints:
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smallTargetGroup.add_argument('--'+ constraint, help='Target the decider at a ' + constraint + ', can be specified multiple times', action='append')
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parser.add_argument('--test', help='Output commands for scheduling potential workflow runs instead of actually scheduling them', action='store_true')
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parser.add_argument('--host', help='Schedule onto a particular host')
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parser.add_argument('--launch-max', help='The maximum number of jobs to launch at once', default=sys.maxsize, type=int)
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parser.add_argument('--meta-types', help='The meta-type(s) of files to run a workflow with', action='append')
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parser.add_argument('--deciderImpl', help='The name of a Python class that contains the implementation of the decider', default='basicDeciderImpl')
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args = parser.parse_args()
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## for debugging print the arguments
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print(args)
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decider = importlib.import_module(args.deciderImpl)
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Decider = getattr(decider, 'Decider')
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deciderImpl = Decider()
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deciderImpl.init(parser)
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__main()

‎seqware-admin-webservice/pom.xml

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</configuration>
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</plugin>
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</plugins>
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<pluginManagement>
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<plugins>
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<!--This plugin's configuration is used to store Eclipse m2e settings only. It has no influence on the Maven build itself.-->
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<plugin>
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<groupId>org.eclipse.m2e</groupId>
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<artifactId>lifecycle-mapping</artifactId>
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<version>1.0.0</version>
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<configuration>
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<lifecycleMappingMetadata>
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<pluginExecutions>
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<pluginExecution>
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<pluginExecutionFilter>
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<groupId>
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org.apache.maven.plugins
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</groupId>
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<artifactId>
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maven-dependency-plugin
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</artifactId>
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<versionRange>
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[2.8,)
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</versionRange>
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<goals>
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<goal>copy</goal>
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</goals>
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</pluginExecutionFilter>
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<action>
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<ignore></ignore>
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</action>
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</pluginExecution>
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</pluginExecutions>
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</lifecycleMappingMetadata>
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</configuration>
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</plugin>
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</plugins>
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</pluginManagement>
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</build>
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<repositories>
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<repository>

‎seqware-distribution/pom.xml

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</plugin>
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</plugins>
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<pluginManagement>
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<plugins>
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<!--This plugin's configuration is used to store Eclipse m2e settings only. It has no influence on the Maven build itself.-->
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<plugin>
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<groupId>org.eclipse.m2e</groupId>
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<artifactId>lifecycle-mapping</artifactId>
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<version>1.0.0</version>
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<configuration>
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<lifecycleMappingMetadata>
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<pluginExecutions>
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<pluginExecution>
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<pluginExecutionFilter>
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<groupId>org.jacoco</groupId>
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<artifactId>
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jacoco-maven-plugin
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</artifactId>
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<versionRange>
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[0.6.3.201306030806,)
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</versionRange>
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<goals>
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<goal>prepare-agent</goal>
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</goals>
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</pluginExecutionFilter>
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<action>
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<ignore></ignore>
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</action>
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</pluginExecution>
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</pluginExecutions>
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</lifecycleMappingMetadata>
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</configuration>
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</plugin>
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</plugins>
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</pluginManagement>
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</build>
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</project>

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