Add script for aggregating impact indicators at the project level
This commit is contained in:
Serafeim Chatzopoulos
parent
102aa5ab81
commit
7256c8d3c7
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@ -90,3 +90,6 @@ oozie.wf.application.path=${wfAppPath}
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# Path where the final output should be?
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actionSetOutputPath=${workflowDataDir}/bip_actionsets/
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# The directory to store project impact indicators
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projectImpactIndicatorsOutput=${workflowDataDir}/project_indicators
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@ -0,0 +1,109 @@
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import sys
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from pyspark.sql import SparkSession
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from pyspark import SparkConf, SparkContext
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import pyspark.sql.functions as F
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from pyspark.sql.types import StringType, IntegerType, StructType, StructField
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if len(sys.argv) < 8:
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print("Usage: projects_impact.py <relations_folder> <influence_file> <popularity_file> <cc_file> <impulse_file> <num_partitions> <output_dir>")
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sys.exit(-1)
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appName = 'Project Impact Indicators'
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conf = SparkConf().setAppName(appName)
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sc = SparkContext(conf = conf)
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spark = SparkSession.builder.appName(appName).getOrCreate()
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sc.setLogLevel('OFF')
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# input parameters
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relations_fd = sys.argv[1]
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influence_fd = sys.argv[2]
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popularity_fd = sys.argv[3]
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cc_fd = sys.argv[4]
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impulse_fd = sys.argv[5]
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num_partitions = int(sys.argv[6])
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output_dir = sys.argv[7]
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# schema for impact indicator files
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impact_files_schema = StructType([
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StructField('resultId', StringType(), False),
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StructField('score', IntegerType(), False),
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StructField('class', StringType(), False),
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])
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# list of impact indicators
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impact_indicators = [
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('influence', influence_fd, 'class'),
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('popularity', popularity_fd, 'class'),
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('impulse', impulse_fd, 'score'),
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('citation_count', cc_fd, 'score')
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]
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'''
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* Read impact indicator file and return a dataframe with the following schema:
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* resultId: String
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* indicator_name: Integer
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'''
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def read_df(fd, indicator_name, column_name):
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return spark.read.schema(impact_files_schema)\
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.option('delimiter', '\t')\
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.option('header', False)\
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.csv(fd)\
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.select('resultId', F.col(column_name).alias(indicator_name))\
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.repartition(num_partitions, 'resultId')
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# Print dataframe schema, first 5 rows, and count
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def print_df(df):
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df.show(50)
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df.printSchema()
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print(df.count())
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# Sets a null value to the column if the value is equal to the given value
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def set_class_value_to_null(column, value):
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return F.when(column != value, column).otherwise(F.lit(None))
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# load and filter Project-to-Result relations
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print("Reading relations")
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relations = spark.read.json(relations_fd)\
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.select(F.col('source').alias('projectId'), F.col('target').alias('resultId'), 'relClass', 'dataInfo.deletedbyinference', 'dataInfo.invisible')\
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.where( (F.col('relClass') == 'produces') \
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& (F.col('deletedbyinference') == "false")\
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& (F.col('invisible') == "false"))\
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.drop('deletedbyinference')\
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.drop('invisible')\
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.drop('relClass')\
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.repartition(num_partitions, 'resultId')
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for indicator_name, fd, column_name in impact_indicators:
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print("Reading {} '{}' field from file".format(indicator_name, column_name))
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df = read_df(fd, indicator_name, column_name)
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# sets a zero value to the indicator column if the value is C5
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if (column_name == 'class'):
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df = df.withColumn(indicator_name, F.when(F.col(indicator_name).isin("C5"), 0).otherwise(1))
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# print_df(df)
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print("Joining {} to relations".format(indicator_name))
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# NOTE: we use inner join because we want to keep only the results that have an impact score
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# also note that all impact scores have the same set of results
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relations = relations.join(df, 'resultId', 'inner')\
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.repartition(num_partitions, 'resultId')
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# uncomment to print non-null values count for each indicator
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# for indicator_name, fd, column_name in impact_indicators:
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# print("Counting non null values for {}".format(indicator_name))
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# print(relations.filter(F.col(indicator_name).isNotNull()).count())
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sum the impact indicator values for each project
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relations.groupBy('projectId')\
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.agg(\
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F.sum('influence').alias('influence'),\
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F.sum('popularity').alias('popularity'),\
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F.sum('impulse').alias('impulse'),\
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F.sum('citation_count').alias('citation_count')\
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)\
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.write.mode("overwrite")\
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.option("delimiter", "\t")\
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.csv(output_dir, compression="gzip")
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@ -15,6 +15,8 @@
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<case to="map-openaire-to-doi">${resume eq "map-ids"}</case>
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<case to="map-scores-to-dois">${resume eq "map-scores"}</case>
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<case to="create-openaire-ranking-graph">${resume eq "start"}</case>
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<case to="project-impact-indicators">${resume eq "projects-impact"}</case>
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<!-- TODO: add action set creation here -->
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<default to="create-openaire-ranking-graph" />
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</switch>
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@ -334,7 +336,7 @@
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<!-- This should give the machine/root of the hdfs -->
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<name-node>${nameNode}</name-node>
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<!-- Exec is needed foor shell comands - points to type of shell command -->
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<!-- Exec is needed for shell commands - points to type of shell command -->
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<exec>/usr/bin/bash</exec>
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<!-- name of script to run -->
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<argument>get_ranking_files.sh</argument>
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@ -558,7 +560,7 @@
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</action>
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<action name="deleteOutputPathForActionSet">
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<action name="deleteOutputPathForActionSet">
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<fs>
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<delete path="${actionSetOutputPath}"/>
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<mkdir path="${actionSetOutputPath}"/>
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@ -592,11 +594,63 @@
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<arg>--inputPath</arg><arg>${bipScorePath}</arg>
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<arg>--outputPath</arg><arg>${actionSetOutputPath}</arg>
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</spark>
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<ok to="end"/>
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<ok to="project-impact-indicators"/>
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<error to="actionset-creation-fail"/>
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</action>
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<!-- PAGERANK here -->
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<action name="project-impact-indicators">
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<!-- This is required as a tag for spark jobs, regardless of programming language -->
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<spark xmlns="uri:oozie:spark-action:0.2">
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<!-- Is this yarn? Probably the answers are at the link serafeim sent me -->
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<job-tracker>${jobTracker}</job-tracker>
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<!-- This should give the machine/root of the hdfs, serafeim has provided a link with the required job properties -->
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<name-node>${nameNode}</name-node>
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<!-- using configs from an example on openaire -->
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<master>yarn-cluster</master>
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<mode>cluster</mode>
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<!-- This is the name of our job -->
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<name>Spark Pagerank</name>
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<!-- Script name goes here -->
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<jar>PageRank.py</jar>
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<!-- spark configuration options: I've taken most of them from an example from dhp workflows / Master value stolen from sandro -->
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<spark-opts>--executor-memory 18G --executor-cores 4 --driver-memory 10G
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--master yarn
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--deploy-mode cluster
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--conf spark.sql.shuffle.partitions=7680
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--conf spark.extraListeners=${spark2ExtraListeners}
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--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
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--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
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--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}</spark-opts>
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<!-- Script arguments here -->
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<!-- graph data folder from which to read relations -->
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<arg>${openaireDataInput}/relations</arg>
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<!-- input files with impact indicators for results -->
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<arg>${nameNode}/${workflowDataDir}/${wf:actionData('get-file-names')['pr_file']}</arg>
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<arg>${nameNode}/${workflowDataDir}/${wf:actionData('get-file-names')['attrank_file']}</arg>
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<arg>${nameNode}/${workflowDataDir}/${wf:actionData('get-file-names')['cc_file']}</arg>
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<arg>${nameNode}/${workflowDataDir}/${wf:actionData('get-file-names')['impulse_file']}</arg>
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<!-- number of partitions to be used on joins -->
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<arg>7680</arg>
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<arg>${projectImpactIndicatorsOutput}</arg>
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<!-- This needs to point to the file on the hdfs i think -->
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<file>${wfAppPath}/projects_impact.py#projects_impact.py</file>
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</spark>
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<!-- Do this after finishing okay -->
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<ok to="end" />
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<!-- Go there if we have an error -->
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<error to="project-impact-indicators-fail" />
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</action>
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<!-- TODO: end the workflow-->
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@ -644,4 +698,8 @@
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<message>ActionSet creation failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
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</kill>
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<kill name="project-impact-indicators-fail">
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<message>Calculating project impact indicators failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
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</kill>
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</workflow-app>
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