Merge pull request #608 from EBISPOT/dev

PCL fix
EBISPOT · Jan 11, 2024 · 4a0c400 · 4a0c400
2 parents 706280a + a544fa0
commit 4a0c400
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Showing 6 changed files with 19 additions and 26 deletions.
diff --git a/.github/ISSUE_TEMPLATE/add-a-new-ontology-to-the-ebi-ols-instance-.md b/.github/ISSUE_TEMPLATE/add-a-new-ontology-to-the-ebi-ols-instance-.md
@@ -0,0 +1,14 @@
+---
+name: 'Add a new ontology to the EBI OLS instance '
+about: Describes a new ontology to be added to the EBI instance of OLS
+title: ''
+labels: new ontology
+assignees: ''
+
+---
+
+**Steps to add your ontology**
+   1. Download and fill out this [spreadsheet](https://github.com/EBISPOT/ols4/blob/dev/New%20OLS%20ontology%20request.xlsx).
+   1. In filling out the spreadsheet the 2 most important fields are:
+      - preferredPrefix: This should be a string of lowercase character at least 5 characters long. This string must be unique on OLS.
+      - ontology_purl: This is the permanent publicly accessible URL from where OLS will load your. This is also the URL that OLS checks on a frequent basis to check for new releases of your ontology.
diff --git a/.github/ISSUE_TEMPLATE/bug_report.md b/.github/ISSUE_TEMPLATE/bug_report.md
@@ -2,7 +2,7 @@
 name: Bug report
 about: Create a report to help us improve
 title: ''
-labels: bug
+labels: bug, outdated ontology
 assignees: ''
 
 ---

diff --git a/New OLS ontology request.xlsx b/New OLS ontology request.xlsx
diff --git 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
@@ -7,11 +7,13 @@ fi
 # exit if anything fails
 set -e
 
+SCRIPT_PATH=$(dirname $(readlink -f $0))
+
 config_url=$1
 download_dir=$2
 
 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
@@ -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",
-Original file line number
+Diff line change
@@ Expand Up / @@ -123,6 +123,6 @@ @@
           "title": "Provisional Cell Ontology",
           "tracker": "https://github.com/obophenotype/provisional_cell_ontology/issues"
         }
-      ]
+    ]
     }