Updated validation results

wikipathways · Feb 29, 2024 · 34723d5 · 34723d5
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diff --git a/index2.md b/index2.md
diff --git a/reports/WP100.json b/reports/WP100.json
@@ -1,6 +1,6 @@
 {
   "schemaVersion": 1,
   "label": "curation",
-  "message": "1 issue",
-  "color": "red"
+  "message": "success",
+  "color": "brightgreen"
 }
diff --git a/reports/WP100.md b/reports/WP100.md
@@ -21,14 +21,7 @@
 * PathwayTests: all 7 tests OK!
 * ProteinsTests: all 2 tests OK!
 * PubChemMetabolitesTests: all 3 tests OK!
-* ReferencesTests
-    * nonNumericPubMedIDs: .. all OK!
-    * unexpectedPubMedIdentifier: .. all OK!
-    * zeroPubMedIDs: .. all OK!
-    * atLeastOneReference: .x we found 1 problem(s):
-        * [Found 1 pathways with zero (PubMed) references](#d0a459f0)
-    * citesRetractedArticle: .. all OK!
-    * outdatedPubMedIdentifiers: .. all OK!
+* ReferencesTests: all 6 tests OK!
 * UniProtTests: all 5 tests OK!
 * WikidataTests: all 4 tests OK!
 
@@ -38,18 +31,7 @@
 * Number of test classes: 20
 * Number of tests: 97
 * Number of assertions: 196
-* Number of fails: 1
+* Number of fails: 0
 
 ## Fails
 
-<a name="d0a459f0" />
-
-## ReferencesTests.atLeastOneReference
-
-Found 1 pathways with zero (PubMed) references
-```
-http://classic.wikipathways.org/instance/WP100_rr107114 'Glutathione metabolism' in Homo sapiens has zero references; 
-```
-
-More details at [https://wikipathways.github.io/WikiPathwaysCurator/ReferencesTests/atLeastOneReference](https://wikipathways.github.io/WikiPathwaysCurator/ReferencesTests/atLeastOneReference)
-
diff --git a/reports/WP1349.md b/reports/WP1349.md
@@ -46,13 +46,13 @@
 
 The following DataNodes have no identifier: 8
 ```
-http://classic.wikipathways.org/instance/WP1349_rr82353 http://rdf.wikipathways.org/Pathway/WP1349_rr82353/DataNode/d07 (CCND3)
-http://classic.wikipathways.org/instance/WP1349_rr82353 http://rdf.wikipathways.org/Pathway/WP1349_rr82353/DataNode/a58 (FRAT1)
-http://classic.wikipathways.org/instance/WP1349_rr82353 http://rdf.wikipathways.org/Pathway/WP1349_rr82353/DataNode/c3d (FZD7)
-http://classic.wikipathways.org/instance/WP1349_rr82353 http://rdf.wikipathways.org/Pathway/WP1349_rr82353/DataNode/b4d (FZD8)
-http://classic.wikipathways.org/instance/WP1349_rr82353 http://rdf.wikipathways.org/Pathway/WP1349_rr82353/DataNode/f11 (MYC)
-http://classic.wikipathways.org/instance/WP1349_rr82353 http://rdf.wikipathways.org/Pathway/WP1349_rr82353/DataNode/a19 (PLAU)
-http://classic.wikipathways.org/instance/WP1349_rr82353 http://rdf.wikipathways.org/Pathway/WP1349_rr82353/DataNode/cdf (SFRP4)
-http://classic.wikipathways.org/instance/WP1349_rr82353 http://rdf.wikipathways.org/Pathway/WP1349_rr82353/DataNode/d7f (WNT4)
+http://classic.wikipathways.org/instance/WP1349_rr128984 http://rdf.wikipathways.org/Pathway/WP1349_rr128984/DataNode/d07 (CCND3)
+http://classic.wikipathways.org/instance/WP1349_rr128984 http://rdf.wikipathways.org/Pathway/WP1349_rr128984/DataNode/a58 (FRAT1)
+http://classic.wikipathways.org/instance/WP1349_rr128984 http://rdf.wikipathways.org/Pathway/WP1349_rr128984/DataNode/c3d (FZD7)
+http://classic.wikipathways.org/instance/WP1349_rr128984 http://rdf.wikipathways.org/Pathway/WP1349_rr128984/DataNode/b4d (FZD8)
+http://classic.wikipathways.org/instance/WP1349_rr128984 http://rdf.wikipathways.org/Pathway/WP1349_rr128984/DataNode/f11 (MYC)
+http://classic.wikipathways.org/instance/WP1349_rr128984 http://rdf.wikipathways.org/Pathway/WP1349_rr128984/DataNode/a19 (PLAU)
+http://classic.wikipathways.org/instance/WP1349_rr128984 http://rdf.wikipathways.org/Pathway/WP1349_rr128984/DataNode/cdf (SFRP4)
+http://classic.wikipathways.org/instance/WP1349_rr128984 http://rdf.wikipathways.org/Pathway/WP1349_rr128984/DataNode/d7f (WNT4)
 ```
 
diff --git a/reports/WP2817.json b/reports/WP2817.json
@@ -1,6 +1,6 @@
 {
   "schemaVersion": 1,
   "label": "curation",
-  "message": "4 issues",
+  "message": "3 issues",
   "color": "red"
 }
diff --git a/reports/WP2817.md b/reports/WP2817.md
@@ -15,21 +15,7 @@
     * unknownTypes_Reactome: .. all OK!
 * EnsemblTests: all 4 tests OK!
 * GeneTests: all 4 tests OK!
-* GeneralTests
-    * curationAndHypothetical: .. all OK!
-    * curationAndNeedsWork: .. all OK!
-    * curationAndReactome: .. all OK!
-    * dataNodeWithoutGraphId: .. all OK!
-    * duplicateTitles: .. all OK!
-    * emptyLabelOfNodeWithIdentifier: .x we found 1 problem(s):
-        * [Data nodes with an identifier but empty label: 1](#a07a01aa)
-    * groupsHaveDetail: .. all OK!
-    * noTags: .. all OK!
-    * nullDataSources: .. all OK!
-    * titlesShortEnough: .. all OK!
-    * undefinedDataSources: .. all OK!
-    * undefinedIdentifier: .. all OK!
-    * weirdCharacterTitles: .. all OK!
+* GeneralTests: all 13 tests OK!
 * HMDBSecMetabolitesTests: all 3 tests OK!
 * InteractionTests
     * noMetaboliteToNonMetaboliteConversions: .. all OK!
@@ -60,7 +46,7 @@
 * Number of test classes: 20
 * Number of tests: 97
 * Number of assertions: 196
-* Number of fails: 4
+* Number of fails: 3
 
 ## Fails
 
@@ -70,21 +56,12 @@
 
 The following DataNodes have no identifier: 6
 ```
-http://classic.wikipathways.org/instance/WP2817_rr128683 http://rdf.wikipathways.org/Pathway/WP2817_rr128683/DataNode/a0fe6 (CEBP)
-http://classic.wikipathways.org/instance/WP2817_rr128683 http://rdf.wikipathways.org/Pathway/WP2817_rr128683/DataNode/aac1c (NFI)
-http://classic.wikipathways.org/instance/WP2817_rr128683 http://rdf.wikipathways.org/Pathway/WP2817_rr128683/DataNode/ab653 (NFKB)
-http://classic.wikipathways.org/instance/WP2817_rr128683 http://rdf.wikipathways.org/Pathway/WP2817_rr128683/DataNode/e6d5c (NRG)
-http://classic.wikipathways.org/instance/WP2817_rr128683 http://rdf.wikipathways.org/Pathway/WP2817_rr128683/DataNode/e2a53 (USF)
-http://classic.wikipathways.org/instance/WP2817_rr128683 http://rdf.wikipathways.org/Pathway/WP2817_rr128683/DataNode/f487b (WFDC)
-```
-
-<a name="a07a01aa" />
-
-## GeneralTests.emptyLabelOfNodeWithIdentifier
-
-Data nodes with an identifier but empty label: 1
-```
-https://identifiers.org/wikipathways/WP382 (), http://classic.wikipathways.org/instance/WP2817_rr128683
+http://classic.wikipathways.org/instance/WP2817_rr128957 http://rdf.wikipathways.org/Pathway/WP2817_rr128957/DataNode/a0fe6 (CEBP)
+http://classic.wikipathways.org/instance/WP2817_rr128957 http://rdf.wikipathways.org/Pathway/WP2817_rr128957/DataNode/aac1c (NFI)
+http://classic.wikipathways.org/instance/WP2817_rr128957 http://rdf.wikipathways.org/Pathway/WP2817_rr128957/DataNode/ab653 (NFKB)
+http://classic.wikipathways.org/instance/WP2817_rr128957 http://rdf.wikipathways.org/Pathway/WP2817_rr128957/DataNode/e6d5c (NRG)
+http://classic.wikipathways.org/instance/WP2817_rr128957 http://rdf.wikipathways.org/Pathway/WP2817_rr128957/DataNode/e2a53 (USF)
+http://classic.wikipathways.org/instance/WP2817_rr128957 http://rdf.wikipathways.org/Pathway/WP2817_rr128957/DataNode/f487b (WFDC)
 ```
 
 <a name="630d2679" />
@@ -93,8 +70,8 @@ https://identifiers.org/wikipathways/WP382 (), http://classic.wikipathways.org/i
 
 Interactions found that involve Labels: 2
 ```
-http://classic.wikipathways.org/instance/WP2817_rr128683 "Differentiation" with graphId fe7d5
-http://classic.wikipathways.org/instance/WP2817_rr128683 "Proliferation" with graphId e2476
+http://classic.wikipathways.org/instance/WP2817_rr128957 "Differentiation" with graphId fe7d5
+http://classic.wikipathways.org/instance/WP2817_rr128957 "Proliferation" with graphId e2476
 ```
 
 <a name="1c118206" />
@@ -103,7 +80,7 @@ http://classic.wikipathways.org/instance/WP2817_rr128683 "Proliferation" with gr
 
 Interactions between identical nodes: 1
 ```
-http://classic.wikipathways.org/instance/WP2817_rr128683 http://rdf.wikipathways.org/Pathway/WP2817_rr128683/WP/Interaction/id4e033ea6 "BCL2L1" (https://identifiers.org/ensembl/ENSG00000171552) and 
+http://classic.wikipathways.org/instance/WP2817_rr128957 http://rdf.wikipathways.org/Pathway/WP2817_rr128957/WP/Interaction/id4e033ea6 "BCL2L1" (https://identifiers.org/ensembl/ENSG00000171552) and 
 BCL2L1" (https://identifiers.org/ensembl/ENSG00000171552)
 ```
 

diff --git a/reports/WP3668.json b/reports/WP3668.json
@@ -1,6 +1,6 @@
 {
   "schemaVersion": 1,
   "label": "curation",
-  "message": "2 issues",
+  "message": "3 issues",
   "color": "red"
 }
diff --git a/reports/WP3668.md b/reports/WP3668.md
@@ -9,9 +9,10 @@
 * ChemSpiderTests: all 2 tests OK!
 * DataNodesTests
     * dataNodesWithoutIdentifier: .x we found 1 problem(s):
-        * [The following DataNodes have no identifier: 1](#d2d32fa0)
+        * [The following DataNodes have no identifier: 3](#d2d32fa2)
     * unknownTypes_knownDatasource: .. all OK!
-    * unknownTypes: .. all OK!
+    * unknownTypes: .x we found 1 problem(s):
+        * [The following DataNodes have Unknown @Type: 11](#ef950832)
     * unknownTypes_Reactome: .. all OK!
 * EnsemblTests: all 4 tests OK!
 * GeneTests: all 4 tests OK!
@@ -23,7 +24,7 @@
     * noGeneProteinConversions: .. all OK!
     * nonNumericIDs: .. all OK!
     * interactionsWithLabels: .x we found 1 problem(s):
-        * [Interactions found that involve Labels: 3](#630d267a)
+        * [Interactions found that involve Labels: 1](#630d2678)
     * possibleTranslocations: .. all OK!
     * noProteinProteinConversions: .. all OK!
     * incorrectKEGGIdentifiers: .. all OK!
@@ -45,34 +46,51 @@
 * Number of test classes: 20
 * Number of tests: 97
 * Number of assertions: 196
-* Number of fails: 2
+* Number of fails: 3
 
 ## Fails
 
-<a name="d2d32fa0" />
+<a name="d2d32fa2" />
 
 ## DataNodesTests.dataNodesWithoutIdentifier
 
-The following DataNodes have no identifier: 1
+The following DataNodes have no identifier: 3
 ```
-http://classic.wikipathways.org/instance/WP3668_rr123393 http://rdf.wikipathways.org/Pathway/WP3668_rr123393/DataNode/b681d (Calcium Calneurin Pathway)
+http://classic.wikipathways.org/instance/WP3668_rr128974 http://rdf.wikipathways.org/Pathway/WP3668_rr128974/DataNode/c0eeb (Calcium calneurin pathway)
+http://classic.wikipathways.org/instance/WP3668_rr128974 http://rdf.wikipathways.org/Pathway/WP3668_rr128974/DataNode/dd571 (Development and maintenance 
+of cardiovascular structure 
+and function)
+http://classic.wikipathways.org/instance/WP3668_rr128974 http://rdf.wikipathways.org/Pathway/WP3668_rr128974/DataNode/e159b (ECM remodeling)
 ```
 
-<a name="630d267a" />
+<a name="ef950832" />
+
+## DataNodesTests.unknownTypes
+
+The following DataNodes have Unknown @Type: 11
+```
+http://classic.wikipathways.org/instance/WP3668_rr128974 http://rdf.wikipathways.org/Pathway/WP3668_rr128974/DataNode/a4415 (Aortic aneurysm)
+http://classic.wikipathways.org/instance/WP3668_rr128974 http://rdf.wikipathways.org/Pathway/WP3668_rr128974/DataNode/bafd8 (Atherosclerosis)
+http://classic.wikipathways.org/instance/WP3668_rr128974 http://rdf.wikipathways.org/Pathway/WP3668_rr128974/DataNode/e388d (Cardiomyopathy)
+http://classic.wikipathways.org/instance/WP3668_rr128974 http://rdf.wikipathways.org/Pathway/WP3668_rr128974/DataNode/cf2ee (Cell differentiation)
+http://classic.wikipathways.org/instance/WP3668_rr128974 http://rdf.wikipathways.org/Pathway/WP3668_rr128974/DataNode/dd571 (Development and maintenance 
+of cardiovascular structure 
+and function)
+http://classic.wikipathways.org/instance/WP3668_rr128974 http://rdf.wikipathways.org/Pathway/WP3668_rr128974/DataNode/e159b (ECM remodeling)
+http://classic.wikipathways.org/instance/WP3668_rr128974 http://rdf.wikipathways.org/Pathway/WP3668_rr128974/DataNode/efaff (Endocardial and epicardial EMT)
+http://classic.wikipathways.org/instance/WP3668_rr128974 http://rdf.wikipathways.org/Pathway/WP3668_rr128974/DataNode/b0123 (Heart valve disease)
+http://classic.wikipathways.org/instance/WP3668_rr128974 http://rdf.wikipathways.org/Pathway/WP3668_rr128974/DataNode/fde54 (Hypertension)
+http://classic.wikipathways.org/instance/WP3668_rr128974 http://rdf.wikipathways.org/Pathway/WP3668_rr128974/DataNode/c5c4d (Kawasaki disease)
+http://classic.wikipathways.org/instance/WP3668_rr128974 http://rdf.wikipathways.org/Pathway/WP3668_rr128974/DataNode/b0487 (Neural crest migration)
+```
+
+<a name="630d2678" />
 
 ## InteractionTests.interactionsWithLabels
 
-Interactions found that involve Labels: 3
+Interactions found that involve Labels: 1
 ```
-http://classic.wikipathways.org/instance/WP3668_rr123393 "Valvular Heart Disease
-Cardiomyopathy
-Aortic Aneurysm
-Hypertension
-Atherosclerosis
-Kawasaki Disease" with graphId e8d1a
-http://classic.wikipathways.org/instance/WP3668_rr123393 "Endocardial and Epicardial EMT, neural crest migration, ECM remodeling, cell differentiation,
-development and maintenance of cardiovascular structure and function" with graphId e443b
-http://classic.wikipathways.org/instance/WP3668_rr123393 "TGFB Ligands, 
+http://classic.wikipathways.org/instance/WP3668_rr128974 "TGFB ligands, 
 Receptors, 
 Activators, 
 Effectors" with graphId c9d97

diff --git a/reports/WP3878.json b/reports/WP3878.json
@@ -1,6 +1,6 @@
 {
   "schemaVersion": 1,
   "label": "curation",
-  "message": "3 issues",
+  "message": "2 issues",
   "color": "red"
 }
diff --git a/reports/WP3878.md b/reports/WP3878.md
@@ -14,12 +14,7 @@
     * unknownTypes: .. all OK!
     * unknownTypes_Reactome: .. all OK!
 * EnsemblTests: all 4 tests OK!
-* GeneTests
-    * entrezGeneIdentifiersNotNumber: .. all OK!
-    * affyProbeIdentifiersNotCorrect: .. all OK!
-    * outdatedIdentifiers: ...x we found 1 problem(s):
-        * [Found integer HGNC symbols (did you mean 'HGNC Accession number'?): 1](#7c6b1fb0)
-    * nonNumericHGNCAccessionNumbers: .. all OK!
+* GeneTests: all 4 tests OK!
 * GeneralTests: all 13 tests OK!
 * HMDBSecMetabolitesTests: all 3 tests OK!
 * InteractionTests
@@ -50,7 +45,7 @@
 * Number of test classes: 20
 * Number of tests: 97
 * Number of assertions: 196
-* Number of fails: 3
+* Number of fails: 2
 
 ## Fails
 
@@ -60,17 +55,8 @@
 
 The following DataNodes have no identifier: 2
 ```
-http://classic.wikipathways.org/instance/WP3878_rr128600 http://rdf.wikipathways.org/Pathway/WP3878_rr128600/DataNode/b8df3 (DNA repair)
-http://classic.wikipathways.org/instance/WP3878_rr128600 http://rdf.wikipathways.org/Pathway/WP3878_rr128600/DataNode/c98f2 (PPP activation)
-```
-
-<a name="7c6b1fb0" />
-
-## GeneTests.outdatedIdentifiers
-
-Found integer HGNC symbols (did you mean 'HGNC Accession number'?): 1
-```
-http://classic.wikipathways.org/instance/WP3878_rr128600 H2AX has 4739
+http://classic.wikipathways.org/instance/WP3878_rr128977 http://rdf.wikipathways.org/Pathway/WP3878_rr128977/DataNode/b8df3 (DNA repair)
+http://classic.wikipathways.org/instance/WP3878_rr128977 http://rdf.wikipathways.org/Pathway/WP3878_rr128977/DataNode/c98f2 (PPP activation)
 ```
 
 <a name="630d267b" />
@@ -79,9 +65,9 @@ http://classic.wikipathways.org/instance/WP3878_rr128600 H2AX has 4739
 
 Interactions found that involve Labels: 4
 ```
-http://classic.wikipathways.org/instance/WP3878_rr128600 "V(D)J" with graphId c43f9
-http://classic.wikipathways.org/instance/WP3878_rr128600 "CSR" with graphId f1315
-http://classic.wikipathways.org/instance/WP3878_rr128600 "DNA damage" with graphId dfa16
-http://classic.wikipathways.org/instance/WP3878_rr128600 "Hypotonic stress " with graphId ac954
+http://classic.wikipathways.org/instance/WP3878_rr128977 "V(D)J" with graphId c43f9
+http://classic.wikipathways.org/instance/WP3878_rr128977 "DNA damage" with graphId dfa16
+http://classic.wikipathways.org/instance/WP3878_rr128977 "Hypotonic stress " with graphId ac954
+http://classic.wikipathways.org/instance/WP3878_rr128977 "CSR" with graphId f1315
 ```
 
diff --git a/reports/WP4485.md b/reports/WP4485.md
@@ -46,9 +46,9 @@
 
 The following DataNodes have no identifier: 2
 ```
-http://classic.wikipathways.org/instance/WP4485_rr119318 http://rdf.wikipathways.org/Pathway/WP4485_rr119318/DataNode/fb41b (2-pyridone-
+http://classic.wikipathways.org/instance/WP4485_rr128983 http://rdf.wikipathways.org/Pathway/WP4485_rr128983/DataNode/fb41b (2-pyridone-
 5-carboxamide-
 N1-ribofuranoside)
-http://classic.wikipathways.org/instance/WP4485_rr119318 http://rdf.wikipathways.org/Pathway/WP4485_rr119318/DataNode/b27d3 (N6-threonylcarbomoyladenosine)
+http://classic.wikipathways.org/instance/WP4485_rr128983 http://rdf.wikipathways.org/Pathway/WP4485_rr128983/DataNode/b27d3 (N6-threonylcarbomoyladenosine)
 ```