Fix test ontologies in ODK

INCATools · May 26, 2023 · 6be4241 · 6be4241
1 parent b6336f8
commit 6be4241
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Showing 27 changed files with 57 additions and 16 deletions.
diff --git a/tests/test-base.yaml b/tests/test-base.yaml
@@ -11,8 +11,10 @@ import_group:
   mirror_max_time_download: 400
   products:
     - id: ro
+      mirror_from: https://raw.githubusercontent.com/INCATools/ontology-development-kit/master/tests/ontologies/ro.owl
     - id: pato
       use_base: TRUE
+      # This test cannot be easily replaced, because use_base and custom URL dont mix
     - id: pr
       make_base: TRUE
-      mirror_from: https://raw.githubusercontent.com/obophenotype/pro_obo_slim/master/pr_slim.owl
+      mirror_from: https://raw.githubusercontent.com/INCATools/ontology-development-kit/master/tests/ontologies/pr_slim.owl
diff --git a/tests/test-components-make-base.yaml b/tests/test-components-make-base.yaml
@@ -12,11 +12,13 @@ export_formats:
 import_group:
   products: 
     - id: ro
+      mirror_from: https://raw.githubusercontent.com/INCATools/ontology-development-kit/master/tests/ontologies/ro.owl
     - id: bfo
+      mirror_from: https://raw.githubusercontent.com/INCATools/ontology-development-kit/master/tests/ontologies/bfo.owl
 components:
   products:
     - filename: pato.owl
-      source: http://purl.obolibrary.org/obo/pato.owl
+      source: https://raw.githubusercontent.com/INCATools/ontology-development-kit/master/tests/ontologies/pato.owl
       base_iris:
         - http://purl.obolibrary.org/obo/PATO_
         - http://purl.obolibrary.org/obo/pato#

diff --git a/tests/test-components.yaml b/tests/test-components.yaml
@@ -17,8 +17,11 @@ export_formats:
 import_group:
   products: 
     - id: pato
+      mirror_from: https://raw.githubusercontent.com/INCATools/ontology-development-kit/master/tests/ontologies/pato.owl
     - id: ro
+      mirror_from: https://raw.githubusercontent.com/INCATools/ontology-development-kit/master/tests/ontologies/ro.owl
     - id: bfo
+      mirror_from: https://raw.githubusercontent.com/INCATools/ontology-development-kit/master/tests/ontologies/bfo.owl
 components:
   products:
     - filename: wbphenotype-equivalent-axioms-subq.owl

diff --git a/tests/test-dosdp-matches.yaml b/tests/test-dosdp-matches.yaml
@@ -11,7 +11,9 @@ export_formats:
 import_group:
   products:
     - id: ro
+      mirror_from: https://raw.githubusercontent.com/INCATools/ontology-development-kit/master/tests/ontologies/ro.owl
     - id: pato
+      mirror_from: https://raw.githubusercontent.com/INCATools/ontology-development-kit/master/tests/ontologies/pato.owl
 pattern_pipelines_group:
   products:
     - id: manual

diff --git a/tests/test-edit-obo.yaml b/tests/test-edit-obo.yaml
@@ -6,4 +6,5 @@ report_fail_on: ERROR
 edit_format: obo
 import_group:
   products:
-    - id: ro
+    - id: ro
+      mirror_from: https://raw.githubusercontent.com/INCATools/ontology-development-kit/master/tests/ontologies/ro.owl
diff --git a/tests/test-github-release.yaml b/tests/test-github-release.yaml
@@ -13,8 +13,11 @@ primary_release: simple
 import_group:
   products:
     - id: ro
+      mirror_from: https://raw.githubusercontent.com/INCATools/ontology-development-kit/master/tests/ontologies/ro.owl
     - id: pato
+      mirror_from: https://raw.githubusercontent.com/INCATools/ontology-development-kit/master/tests/ontologies/pato.owl
     - id: mpath
+      mirror_from: https://raw.githubusercontent.com/INCATools/ontology-development-kit/master/tests/ontologies/mpath.owl
 public_release: github_curl
 public_release_assets:
   - rtgh.owl

diff --git a/tests/test-import-minimal.yaml b/tests/test-import-minimal.yaml
@@ -15,8 +15,9 @@ primary_release: full
 import_group:
   products:
     - id: ro
-    - id: iao
-    - id: pco
+      mirror_from: https://raw.githubusercontent.com/INCATools/ontology-development-kit/master/tests/ontologies/ro.owl
+    - id: omo
+      mirror_from: https://raw.githubusercontent.com/INCATools/ontology-development-kit/master/tests/ontologies/omo.owl
 components:
   products:
     - filename: pato_ext.owl

diff --git a/tests/test-module-custom.yaml b/tests/test-module-custom.yaml
@@ -11,6 +11,7 @@ import_group:
   products:
     - id: ro
       mirror_type: base
+      mirror_from: https://raw.githubusercontent.com/INCATools/ontology-development-kit/master/tests/ontologies/ro.owl
     - id: wikidata
       mirror_type: no_mirror
   module_type: custom

diff --git a/tests/test-module-minimal-large.yaml b/tests/test-module-minimal-large.yaml
@@ -10,7 +10,7 @@ export_formats:
 import_group:
   products:
     - id: ro
-      use_base: TRUE
+      mirror_from: https://raw.githubusercontent.com/INCATools/ontology-development-kit/master/tests/ontologies/ro.owl
     - id: pato
       is_large: TRUE
   module_type: minimal

diff --git a/tests/test-module-minimal.yaml b/tests/test-module-minimal.yaml
@@ -10,6 +10,8 @@ export_formats:
 import_group:
   products:
     - id: ro
+      mirror_from: https://raw.githubusercontent.com/INCATools/ontology-development-kit/master/tests/ontologies/ro.owl
     - id: pato
+      mirror_from: https://raw.githubusercontent.com/INCATools/ontology-development-kit/master/tests/ontologies/pato.owl
   module_type: minimal
 
diff --git a/tests/test-module-mireot.yaml b/tests/test-module-mireot.yaml
@@ -10,6 +10,8 @@ export_formats:
 import_group:
   products:
     - id: ro
+      mirror_from: https://raw.githubusercontent.com/INCATools/ontology-development-kit/master/tests/ontologies/ro.owl
     - id: pato
+      mirror_from: https://raw.githubusercontent.com/INCATools/ontology-development-kit/master/tests/ontologies/pato.owl
   module_type: mireot
 
diff --git a/tests/test-module-mirror.yaml b/tests/test-module-mirror.yaml
@@ -1,5 +1,5 @@
 id: modmir
-title: "Test ROBOT extract minimal with base and large option"
+title: "Test ROBOT extract with module type mirror"
 github_org: INCATools
 repo: ontology-development-kit
 edit_format: obo
@@ -8,7 +8,8 @@ export_formats:
   - obo
 import_group:
   products:
-    - id: envo
+    - id: pato
+      mirror_from: https://raw.githubusercontent.com/INCATools/ontology-development-kit/master/tests/ontologies/pato.owl
       module_type: mirror
 allow_equivalents: all
 
diff --git a/tests/test-module-star.yaml b/tests/test-module-star.yaml
@@ -10,7 +10,9 @@ export_formats:
 import_group:
   products:
     - id: ro
+      mirror_from: https://raw.githubusercontent.com/INCATools/ontology-development-kit/master/tests/ontologies/ro.owl
     - id: pato
+      mirror_from: https://raw.githubusercontent.com/INCATools/ontology-development-kit/master/tests/ontologies/pato.owl
   module_type: slme
   module_type_slme: STAR
   slme_individuals: exclude

diff --git a/tests/test-non-import-release.yaml b/tests/test-non-import-release.yaml
@@ -14,4 +14,6 @@ import_group:
   release_imports: TRUE
   products:
     - id: ro
-    - id: pato
+      mirror_from: https://raw.githubusercontent.com/INCATools/ontology-development-kit/master/tests/ontologies/ro.owl
+    - id: pato
+      mirror_from: https://raw.githubusercontent.com/INCATools/ontology-development-kit/master/tests/ontologies/pato.owl
diff --git a/tests/test-patterns.yaml b/tests/test-patterns.yaml
@@ -11,7 +11,9 @@ export_formats:
 import_group:
   products:
     - id: ro
+      mirror_from: https://raw.githubusercontent.com/INCATools/ontology-development-kit/master/tests/ontologies/ro.owl
     - id: pato
+      mirror_from: https://raw.githubusercontent.com/INCATools/ontology-development-kit/master/tests/ontologies/pato.owl
 pattern_pipelines_group:
   products:
     - id: manual

diff --git a/tests/test-release-format-patterns.yaml b/tests/test-release-format-patterns.yaml
@@ -22,7 +22,9 @@ export_formats:
 import_group:
   products:
     - id: ro
+      mirror_from: https://raw.githubusercontent.com/INCATools/ontology-development-kit/master/tests/ontologies/ro.owl
     - id: pato
+      mirror_from: https://raw.githubusercontent.com/INCATools/ontology-development-kit/master/tests/ontologies/pato.owl
 pattern_pipelines_group:
   products:
     - id: manual

diff --git a/tests/test-release-format.yaml b/tests/test-release-format.yaml
@@ -22,5 +22,8 @@ export_formats:
 import_group:
   products:
     - id: ro
+      mirror_from: https://raw.githubusercontent.com/INCATools/ontology-development-kit/master/tests/ontologies/ro.owl
     - id: pato
-    - id: mpath
+      mirror_from: https://raw.githubusercontent.com/INCATools/ontology-development-kit/master/tests/ontologies/pato.owl
+    - id: mpath
+      mirror_from: https://raw.githubusercontent.com/INCATools/ontology-development-kit/master/tests/ontologies/mpath.owl
diff --git a/tests/test-release-imports-not-edit.yaml b/tests/test-release-imports-not-edit.yaml
@@ -19,3 +19,4 @@ import_group:
   release_imports: TRUE
   products:
     - id: ro
+      mirror_from: https://raw.githubusercontent.com/INCATools/ontology-development-kit/master/tests/ontologies/ro.owl
diff --git a/tests/test-release.yaml b/tests/test-release.yaml
@@ -21,5 +21,8 @@ import_group:
   release_imports: TRUE
   products:
     - id: ro
+      mirror_from: https://raw.githubusercontent.com/INCATools/ontology-development-kit/master/tests/ontologies/ro.owl
     - id: pato
-    - id: mpath
+      mirror_from: https://raw.githubusercontent.com/INCATools/ontology-development-kit/master/tests/ontologies/pato.owl
+    - id: mpath
+      mirror_from: https://raw.githubusercontent.com/INCATools/ontology-development-kit/master/tests/ontologies/mpath.owl
diff --git a/tests/test-robot-report-baseiri.yaml b/tests/test-robot-report-baseiri.yaml
@@ -8,7 +8,9 @@ namespaces:
 import_group:
   products:
     - id: ro
+      mirror_from: https://raw.githubusercontent.com/INCATools/ontology-development-kit/master/tests/ontologies/ro.owl
     - id: omo
+      mirror_from: https://raw.githubusercontent.com/INCATools/ontology-development-kit/master/tests/ontologies/omo.owl
 robot_report:
   use_base_iris: True
   release_reports: True

diff --git a/tests/test-robot-report.yaml b/tests/test-robot-report.yaml
@@ -14,7 +14,9 @@ release_artefacts:
 import_group:
   products:
     - id: ro
-    - id: iao
+      mirror_from: https://raw.githubusercontent.com/INCATools/ontology-development-kit/master/tests/ontologies/ro.owl
+    - id: omo
+      mirror_from: https://raw.githubusercontent.com/INCATools/ontology-development-kit/master/tests/ontologies/omo.owl
 robot_report:
   release_reports: True
   fail_on : ERROR

diff --git a/tests/test-robot-validate-profile.yaml b/tests/test-robot-validate-profile.yaml
@@ -8,6 +8,7 @@ export_formats:
 import_group:
   products:
     - id: ro
+      mirror_from: https://raw.githubusercontent.com/INCATools/ontology-development-kit/master/tests/ontologies/ro.owl
 robot_report:
   release_reports: True
   fail_on : ERROR

diff --git a/tests/test-sparql-report.yaml b/tests/test-sparql-report.yaml
@@ -11,6 +11,7 @@ release_artefacts:
 import_group:
   products:
     - id: ro
+      mirror_from: https://raw.githubusercontent.com/INCATools/ontology-development-kit/master/tests/ontologies/ro.owl
 robot_report:
   release_reports: True
   fail_on : ERROR

diff --git a/tests/test-sssom.yaml b/tests/test-sssom.yaml
@@ -8,6 +8,7 @@ export_formats:
 import_group:
   products:
     - id: ro
+      mirror_from: https://raw.githubusercontent.com/INCATools/ontology-development-kit/master/tests/ontologies/ro.owl
 sssom_mappingset_group:
   products:
     - id: modmini-onta

diff --git a/tests/test-templates.yaml b/tests/test-templates.yaml
@@ -8,6 +8,7 @@ export_formats:
 import_group:
   products:
     - id: ro
+      mirror_from: https://raw.githubusercontent.com/INCATools/ontology-development-kit/master/tests/ontologies/ro.owl
 components:
   products:
     - filename: test-with-context.owl

diff --git a/tests/test-uribase-suffix.yaml b/tests/test-uribase-suffix.yaml
@@ -7,5 +7,4 @@ uribase_suffix: ontology
 import_group:
   products:
     - id: ro
-    - id: pato
-      use_base: TRUE
+      mirror_from: https://raw.githubusercontent.com/INCATools/ontology-development-kit/master/tests/ontologies/ro.owl
diff --git a/tests/test-uribase.yaml b/tests/test-uribase.yaml
@@ -6,5 +6,4 @@ uribase: https://w3id.org/odk
 import_group:
   products:
     - id: ro
-    - id: pato
-      use_base: TRUE
+      mirror_from: https://raw.githubusercontent.com/INCATools/ontology-development-kit/master/tests/ontologies/ro.owl