- Update testcases

dev-testing/teststack-mac.sh

@@ -0,0 +1,69 @@
+#!/usr/bin/env bash
+
+if [ $# == 0 ]; then
+    echo "Usage: $0 <rel_json_config_url> <rel_output_dir>"
+    echo "If <rel_json_config_url> is a file it will read and load this single configuration."
+    echo "If <rel_json_config_url> as a directory, it will read and load all json configuration in the directory and
+    subdirectories."
+    exit 1
+fi
+
+config_url=$1
+out_dir=$2
+
+# Create or clean output directory
+if [ -d "$out_dir" ]; then
+    echo "$out_dir already exists and will now be cleaned."
+    rm -Rf $out_dir/*
+else
+    echo "$out_dir does not exist and will now be created."
+    mkdir "$out_dir"
+fi
+
+function process_config {
+  echo "process_config param1="$1
+  echo "process_config param2="$2
+
+  local config_url=$1
+  local out_dir=$2
+
+
+  if [ -d "$config_url" ]; then
+      echo "$config_url is a directory. Processing config files in $config_url"
+      local basename=$(basename $config_url)
+      echo "basename for config_url="$basename
+      local out_dir_basename=$out_dir/$basename
+      mkdir $out_dir_basename
+      for filename in $config_url/*.json; do
+          echo "filename="$filename
+          process_config $filename $out_dir_basename
+      done
+      for dir in $config_url/*/; do
+          process_config $dir $out_dir_basename
+      done
+  elif [ -f "$config_url"  ]; then
+    echo "$config_url is a file. Processing single config file."
+    local basename=$(basename $config_url .json)
+
+    local relative_out_dir=$out_dir/$basename
+    mkdir $relative_out_dir
+
+    local absolute_out_dir=$(realpath -q $relative_out_dir)
+    echo "absolute_out_dir="$absolute_out_dir
+
+    $OLS4_HOME/dataload/create_datafiles.sh $config_url $absolute_out_dir --noDates
+
+    $OLS4_HOME/dev-testing/load_test_into_solr.sh $absolute_out_dir
+  else
+    echo "$config_url does not exist."
+  fi
+}
+
+$OLS4_HOME/dev-testing/clean-neo4j.sh
+$OLS4_HOME/dev-testing/clean-solr.sh
+$OLS4_HOME/dev-testing/start-solr.sh
+
+process_config $config_url $out_dir
+
+$OLS4_HOME/dev-testing/load_test_into_neo4j.sh $out_dir
+$OLS4_HOME/dev-testing/start-neo4j.sh

testcases_expected_output/annotation-properties/gitIssue502/oio_edges.csv

@@ -0,0 +1,9 @@
+":START_ID",":TYPE",":END_ID","_json"
+"oio+property+http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym","http://www.w3.org/2000/01/rdf-schema#subPropertyOf","oio+property+http://www.geneontology.org/formats/oboInOwl#hasSynonym","{}"
+"oio+property+http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym","directParent","oio+property+http://www.geneontology.org/formats/oboInOwl#hasSynonym","{}"
+"oio+property+http://www.geneontology.org/formats/oboInOwl#hasExactSynonym","http://www.w3.org/2000/01/rdf-schema#subPropertyOf","oio+property+http://www.geneontology.org/formats/oboInOwl#hasSynonym","{}"
+"oio+property+http://www.geneontology.org/formats/oboInOwl#hasExactSynonym","directParent","oio+property+http://www.geneontology.org/formats/oboInOwl#hasSynonym","{}"
+"oio+property+http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym","http://www.w3.org/2000/01/rdf-schema#subPropertyOf","oio+property+http://www.geneontology.org/formats/oboInOwl#hasSynonym","{}"
+"oio+property+http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym","directParent","oio+property+http://www.geneontology.org/formats/oboInOwl#hasSynonym","{}"
+"oio+property+http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym","http://www.w3.org/2000/01/rdf-schema#subPropertyOf","oio+property+http://www.geneontology.org/formats/oboInOwl#hasSynonym","{}"
+"oio+property+http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym","directParent","oio+property+http://www.geneontology.org/formats/oboInOwl#hasSynonym","{}"

testcases_expected_output/annotation-properties/gitIssue502/oio_individuals.csv

@@ -0,0 +1 @@
+"id:ID",":LABEL","_json"

testcases_expected_output/annotation-properties/gitIssue502/oio_ontologies.csv

@@ -0,0 +1,6 @@
+"id:ID",":LABEL","_json","iri","numberOfIndividuals:string[]","linkedEntities:string[]","ontology_purl:string[]","numDescendants:string[]","numberOfProperties:string[]","numberOfClasses:string[]","language:string[]","numHierarchicalDescendants:string[]","isObsolete:string[]","label:string[]","importsFrom:string[]","type:string[]","directAncestor:string[]","exportsTo:string[]","base_uri:string[]","http__//www.w3.org/2000/01/rdf-schema#comment:string[]","imported:string[]","numberOfEntities:string[]","ontologyId:string[]","http__//www.w3.org/2000/01/rdf-schema#label:string[]","definition:string[]","http__//www.w3.org/1999/02/22-rdf-syntax-ns#type:string[]"
+"oio+ontology+http://www.geneontology.org/formats/oboInOwl","Ontology","{""ontologyId"":""oio"",""importsFrom"":[],""exportsTo"":[""gitissue502""],""iri"":""http://www.geneontology.org/formats/oboInOwl"",""ontology_purl"":""https://gist.githubusercontent.com/haideriqbal/4a2b1a9aa81d9fa26cae81e0b0b7730b/raw/527665128b9be9d7d6133f9a796379600151c737/oboInOwl.owl"",""base_uri"":[""http://www.geneontology.org/formats/oboInOwl#""],""type"":[""ontology""],""definition"":[{""type"":[""literal""],""value"":""OBO Format metamodel. This meta-ontology is self-describing. OBO metamodel properties are described using OBO metamodel properties""},{""type"":[""literal""],""value"":""\n          This is an OWL translation of an ontology whose native representational form is .obo. The translation was performed using the oboInOwl xslt library. For details, see http://www.berkeleybop.org/obo-conv.cgi\n        ""}],""directAncestor"":[],""http://www.w3.org/1999/02/22-rdf-syntax-ns#type"":""http://www.w3.org/2002/07/owl#Ontology"",""http://www.w3.org/2000/01/rdf-schema#comment"":[{""type"":[""literal""],""value"":""OBO Format metamodel. This meta-ontology is self-describing. OBO metamodel properties are described using OBO metamodel properties""},{""type"":[""literal""],""value"":""\n          This is an OWL translation of an ontology whose native representational form is .obo. The translation was performed using the oboInOwl xslt library. For details, see http://www.berkeleybop.org/obo-conv.cgi\n        ""}],""http://www.w3.org/2000/01/rdf-schema#label"":{""type"":[""literal""],""value"":""""},""imported"":false,""isObsolete"":false,""label"":{""type"":[""literal""],""value"":""""},""language"":{""type"":[""literal""],""value"":""en""},""numDescendants"":0.0,""numHierarchicalDescendants"":0.0,""numberOfClasses"":{""type"":[""literal""],""value"":""12""},""numberOfEntities"":{""type"":[""literal""],""value"":""56""},""numberOfIndividuals"":{""type"":[""literal""],""value"":""0""},""numberOfProperties"":{""type"":[""literal""],""value"":""44""},""searchableAnnotationValues"":[false,{""type"":[""literal""],""value"":""en""},{""type"":[""literal""],""value"":""12""},{""type"":[""literal""],""value"":""56""},{""type"":[""literal""],""value"":""0""},{""type"":[""literal""],""value"":""44""}],""linkedEntities"":{""http://www.w3.org/2000/01/rdf-schema#comment"":{""definedBy"":[""rdfs""],""numAppearsIn"":2.0,""hasLocalDefinition"":false,""label"":{""type"":[""literal""],""value"":""comment""},""curie"":{""type"":[""literal""],""value"":""RDFS:comment""},""type"":[""property"",""entity""]},""http://www.w3.org/2000/01/rdf-schema#label"":{""definedBy"":[""rdfs""],""numAppearsIn"":3.0,""hasLocalDefinition"":false,""label"":{""type"":[""literal""],""value"":""label""},""curie"":{""type"":[""literal""],""value"":""RDFS:label""},""type"":[""property"",""entity""]}}}","http://www.geneontology.org/formats/oboInOwl","0","","https://gist.githubusercontent.com/haideriqbal/4a2b1a9aa81d9fa26cae81e0b0b7730b/raw/527665128b9be9d7d6133f9a796379600151c737/oboInOwl.owl","0.0","44","12","en","0.0","false","","","ontology","","gitissue502","http://www.geneontology.org/formats/oboInOwl#","OBO Format metamodel. This meta-ontology is self-describing. OBO metamodel properties are described using OBO metamodel properties|
+          This is an OWL translation of an ontology whose native representational form is .obo. The translation was performed using the oboInOwl xslt library. For details, see http://www.berkeleybop.org/obo-conv.cgi
+        ","false","56","oio","","OBO Format metamodel. This meta-ontology is self-describing. OBO metamodel properties are described using OBO metamodel properties|
+          This is an OWL translation of an ontology whose native representational form is .obo. The translation was performed using the oboInOwl xslt library. For details, see http://www.berkeleybop.org/obo-conv.cgi
+        ","http://www.w3.org/2002/07/owl#Ontology"