From a544fa0567f9a48ac554565dea07fdc0f56bb98b Mon Sep 17 00:00:00 2001
From: henrietteharmse <henrietteharmse@gmail.com>
Date: Thu, 11 Jan 2024 15:48:06 +0000
Subject: [PATCH] Fix for #607. Removed override for PCL.

---
 dataload/configs/pcl.json |  2 +-
 dataload/pre_download.sh  |  4 +++-
 ebi_ontologies.json       | 23 -----------------------
 3 files changed, 4 insertions(+), 25 deletions(-)
 mode change 100644 => 100755 dataload/pre_download.sh

diff --git a/dataload/configs/pcl.json b/dataload/configs/pcl.json
index c77ba1f6b..41cbaece5 100644
--- a/dataload/configs/pcl.json
+++ b/dataload/configs/pcl.json
@@ -123,6 +123,6 @@
       "title": "Provisional Cell Ontology",
       "tracker": "https://github.com/obophenotype/provisional_cell_ontology/issues"
     }
-  ]
+]
 }
   
diff --git a/dataload/pre_download.sh b/dataload/pre_download.sh
old mode 100644
new mode 100755
index 152cf4357..e580b79fd
--- a/dataload/pre_download.sh
+++ b/dataload/pre_download.sh
@@ -7,6 +7,8 @@ fi
 # exit if anything fails
 set -e
 
+SCRIPT_PATH=$(dirname $(readlink -f $0))
+
 config_url=$1
 download_dir=$2
 
@@ -14,4 +16,4 @@ mkdir -p $download_dir
 
 
 java -DentityExpansionLimit=0 -DtotalEntitySizeLimit=0 -Djdk.xml.totalEntitySizeLimit=0 -Djdk.xml.entityExpansionLimit=0 \
-        -jar ./predownloader/target/predownloader-1.0-SNAPSHOT.jar --config $config_url --downloadPath $download_dir
+        -jar $SCRIPT_PATH/predownloader/target/predownloader-1.0-SNAPSHOT.jar --config $config_url --downloadPath $download_dir
diff --git a/ebi_ontologies.json b/ebi_ontologies.json
index 157f62933..c3a8c705d 100644
--- a/ebi_ontologies.json
+++ b/ebi_ontologies.json
@@ -997,29 +997,6 @@
       "ontology_purl": "file:///nfs/production/parkinso/spot/ols4/prod/local_ontologies/snomed.owl",
       "allowDownload": false
     },
-    {
-      "id": "pcl",
-      "preferredPrefix": "PCL",
-      "title": "Provisional Cell Ontology",
-      "description": "Cell types that are provisionally defined by experimental techniques such as single cell or single nucleus transcriptomics rather than a straightforward \u0026 coherent set of properties.",
-      "uri": "https://raw.githubusercontent.com/obophenotype/provisional_cell_ontology/master/pcl-full.owl",
-      "base_uri": [
-        "http://purl.obolibrary.org/obo/PCL_"
-      ],
-      "synonym_property": [
-        "http://www.geneontology.org/formats/oboInOwl#hasExactSynonym"
-      ],
-      "definition_property": [
-        "http://purl.obolibrary.org/obo/IAO_0000115"
-      ],
-      "preferred_root_term": [
-        "http://purl.obolibrary.org/obo/CL_0000000"
-      ],
-      "reasoner": "EL",
-      "oboSlims": false,
-      "ontology_purl": "https://raw.githubusercontent.com/obophenotype/provisional_cell_ontology/master/pcl-full.owl",
-      "allowDownload": false
-    },
     {
       "id": "shareloc",
       "preferredPrefix": "SHARELOC",