From 78301359a76425274498687073a7b4cb516b2f17 Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Thu, 30 Jan 2025 06:27:40 +0100 Subject: [PATCH] New validation results --- index2.md | 6 ++++- reports/WP3302.md | 2 +- reports/WP4204.md | 59 ++++++++++++++++++++++++----------------------- reports/WP5189.md | 20 ++++++++-------- 4 files changed, 46 insertions(+), 41 deletions(-) diff --git a/index2.md b/index2.md index b7ae8ef2..561712e5 100644 --- a/index2.md +++ b/index2.md @@ -34,7 +34,7 @@ Read more about why these fails happen and how to fix them in these [instruction Read more about why these fails happen and how to fix them in these [instructions](https://www.wikipathways.org/WikiPathwaysCurator/InteractionTests/interactionsWithLabels). -[WP1403](reports/WP1403#interactions-with-labels) [WP1425](reports/WP1425#interactions-with-labels) [WP1433](reports/WP1433#interactions-with-labels) [WP1434](reports/WP1434#interactions-with-labels) 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[WP4746](reports/WP4746#interactions-with-labels) [WP4747](reports/WP4747#interactions-with-labels) [WP4751](reports/WP4751#interactions-with-labels) [WP4754](reports/WP4754#interactions-with-labels) [WP4760](reports/WP4760#interactions-with-labels) [WP4767](reports/WP4767#interactions-with-labels) [WP4784](reports/WP4784#interactions-with-labels) [WP4786](reports/WP4786#interactions-with-labels) [WP4787](reports/WP4787#interactions-with-labels) [WP4788](reports/WP4788#interactions-with-labels) [WP4789](reports/WP4789#interactions-with-labels) [WP4790](reports/WP4790#interactions-with-labels) [WP4806](reports/WP4806#interactions-with-labels) [WP4808](reports/WP4808#interactions-with-labels) [WP4815](reports/WP4815#interactions-with-labels) [WP4829](reports/WP4829#interactions-with-labels) [WP4835](reports/WP4835#interactions-with-labels) [WP4838](reports/WP4838#interactions-with-labels) [WP4842](reports/WP4842#interactions-with-labels) [WP4844](reports/WP4844#interactions-with-labels) [WP4868](reports/WP4868#interactions-with-labels) [WP4871](reports/WP4871#interactions-with-labels) [WP4872](reports/WP4872#interactions-with-labels) [WP4877](reports/WP4877#interactions-with-labels) [WP4879](reports/WP4879#interactions-with-labels) [WP4883](reports/WP4883#interactions-with-labels) [WP4900](reports/WP4900#interactions-with-labels) [WP4905](reports/WP4905#interactions-with-labels) [WP4906](reports/WP4906#interactions-with-labels) [WP4914](reports/WP4914#interactions-with-labels) [WP4918](reports/WP4918#interactions-with-labels) [WP4919](reports/WP4919#interactions-with-labels) [WP4921](reports/WP4921#interactions-with-labels) [WP4923](reports/WP4923#interactions-with-labels) [WP4925](reports/WP4925#interactions-with-labels) [WP4932](reports/WP4932#interactions-with-labels) [WP4936](reports/WP4936#interactions-with-labels) [WP4942](reports/WP4942#interactions-with-labels) [WP4947](reports/WP4947#interactions-with-labels) [WP4949](reports/WP4949#interactions-with-labels) [WP4950](reports/WP4950#interactions-with-labels) [WP4961](reports/WP4961#interactions-with-labels) [WP4962](reports/WP4962#interactions-with-labels) [WP5027](reports/WP5027#interactions-with-labels) [WP5029](reports/WP5029#interactions-with-labels) [WP5035](reports/WP5035#interactions-with-labels) [WP5036](reports/WP5036#interactions-with-labels) [WP5043](reports/WP5043#interactions-with-labels) [WP5044](reports/WP5044#interactions-with-labels) [WP5046](reports/WP5046#interactions-with-labels) [WP5049](reports/WP5049#interactions-with-labels) [WP5050](reports/WP5050#interactions-with-labels) [WP5051](reports/WP5051#interactions-with-labels) [WP5053](reports/WP5053#interactions-with-labels) [WP5083](reports/WP5083#interactions-with-labels) [WP5085](reports/WP5085#interactions-with-labels) [WP5087](reports/WP5087#interactions-with-labels) [WP5088](reports/WP5088#interactions-with-labels) [WP5090](reports/WP5090#interactions-with-labels) [WP5092](reports/WP5092#interactions-with-labels) [WP5094](reports/WP5094#interactions-with-labels) [WP5097](reports/WP5097#interactions-with-labels) [WP5101](reports/WP5101#interactions-with-labels) [WP5103](reports/WP5103#interactions-with-labels) [WP5104](reports/WP5104#interactions-with-labels) [WP5113](reports/WP5113#interactions-with-labels) [WP5115](reports/WP5115#interactions-with-labels) [WP5116](reports/WP5116#interactions-with-labels) [WP5120](reports/WP5120#interactions-with-labels) [WP5122](reports/WP5122#interactions-with-labels) [WP5124](reports/WP5124#interactions-with-labels) [WP5128](reports/WP5128#interactions-with-labels) [WP5130](reports/WP5130#interactions-with-labels) [WP5133](reports/WP5133#interactions-with-labels) [WP5143](reports/WP5143#interactions-with-labels) [WP5144](reports/WP5144#interactions-with-labels) [WP5146](reports/WP5146#interactions-with-labels) [WP5148](reports/WP5148#interactions-with-labels) [WP5150](reports/WP5150#interactions-with-labels) [WP5151](reports/WP5151#interactions-with-labels) [WP5152](reports/WP5152#interactions-with-labels) [WP5158](reports/WP5158#interactions-with-labels) [WP5166](reports/WP5166#interactions-with-labels) [WP5169](reports/WP5169#interactions-with-labels) [WP5171](reports/WP5171#interactions-with-labels) [WP5172](reports/WP5172#interactions-with-labels) [WP5173](reports/WP5173#interactions-with-labels) [WP5174](reports/WP5174#interactions-with-labels) [WP5175](reports/WP5175#interactions-with-labels) [WP5176](reports/WP5176#interactions-with-labels) [WP5178](reports/WP5178#interactions-with-labels) [WP5180](reports/WP5180#interactions-with-labels) [WP5181](reports/WP5181#interactions-with-labels) [WP5182](reports/WP5182#interactions-with-labels) [WP5187](reports/WP5187#interactions-with-labels) [WP5189](reports/WP5189#interactions-with-labels) [WP5190](reports/WP5190#interactions-with-labels) [WP5192](reports/WP5192#interactions-with-labels) [WP5193](reports/WP5193#interactions-with-labels) [WP5195](reports/WP5195#interactions-with-labels) [WP5198](reports/WP5198#interactions-with-labels) [WP5202](reports/WP5202#interactions-with-labels) [WP5205](reports/WP5205#interactions-with-labels) [WP5221](reports/WP5221#interactions-with-labels) [WP5222](reports/WP5222#interactions-with-labels) [WP5223](reports/WP5223#interactions-with-labels) [WP5224](reports/WP5224#interactions-with-labels) [WP5231](reports/WP5231#interactions-with-labels) [WP5234](reports/WP5234#interactions-with-labels) [WP5236](reports/WP5236#interactions-with-labels) [WP5242](reports/WP5242#interactions-with-labels) [WP5256](reports/WP5256#interactions-with-labels) [WP5258](reports/WP5258#interactions-with-labels) [WP5269](reports/WP5269#interactions-with-labels) [WP5272](reports/WP5272#interactions-with-labels) [WP5273](reports/WP5273#interactions-with-labels) [WP5275](reports/WP5275#interactions-with-labels) [WP5289](reports/WP5289#interactions-with-labels) [WP5293](reports/WP5293#interactions-with-labels) [WP5294](reports/WP5294#interactions-with-labels) [WP5300](reports/WP5300#interactions-with-labels) [WP5304](reports/WP5304#interactions-with-labels) [WP5312](reports/WP5312#interactions-with-labels) [WP5321](reports/WP5321#interactions-with-labels) [WP5331](reports/WP5331#interactions-with-labels) [WP5333](reports/WP5333#interactions-with-labels) [WP5342](reports/WP5342#interactions-with-labels) [WP5343](reports/WP5343#interactions-with-labels) [WP5345](reports/WP5345#interactions-with-labels) [WP5346](reports/WP5346#interactions-with-labels) [WP5347](reports/WP5347#interactions-with-labels) [WP5348](reports/WP5348#interactions-with-labels) [WP5352](reports/WP5352#interactions-with-labels) [WP5353](reports/WP5353#interactions-with-labels) [WP5355](reports/WP5355#interactions-with-labels) [WP5356](reports/WP5356#interactions-with-labels) [WP5360](reports/WP5360#interactions-with-labels) [WP5362](reports/WP5362#interactions-with-labels) [WP5365](reports/WP5365#interactions-with-labels) [WP5366](reports/WP5366#interactions-with-labels) [WP5367](reports/WP5367#interactions-with-labels) [WP5376](reports/WP5376#interactions-with-labels) [WP5380](reports/WP5380#interactions-with-labels) [WP5381](reports/WP5381#interactions-with-labels) [WP5382](reports/WP5382#interactions-with-labels) [WP5399](reports/WP5399#interactions-with-labels) [WP5401](reports/WP5401#interactions-with-labels) [WP5402](reports/WP5402#interactions-with-labels) [WP5406](reports/WP5406#interactions-with-labels) [WP5407](reports/WP5407#interactions-with-labels) [WP5408](reports/WP5408#interactions-with-labels) [WP5414](reports/WP5414#interactions-with-labels) [WP5420](reports/WP5420#interactions-with-labels) [WP5422](reports/WP5422#interactions-with-labels) [WP5434](reports/WP5434#interactions-with-labels) [WP5440](reports/WP5440#interactions-with-labels) [WP5443](reports/WP5443#interactions-with-labels) [WP5475](reports/WP5475#interactions-with-labels) [WP5485](reports/WP5485#interactions-with-labels) [WP5489](reports/WP5489#interactions-with-labels) [WP5490](reports/WP5490#interactions-with-labels) [WP5493](reports/WP5493#interactions-with-labels) [WP5502](reports/WP5502#interactions-with-labels) [WP5504](reports/WP5504#interactions-with-labels) [WP5506](reports/WP5506#interactions-with-labels) ## No metabolite to non-metabolite conversions @@ -50,6 +50,10 @@ Read more about why these fails happen and how to fix them in these [instruction [WP3193](reports/WP3193#no-non-metabolite-to-metabolite-conversions) [WP3538](reports/WP3538#no-non-metabolite-to-metabolite-conversions) [WP369](reports/WP369#no-non-metabolite-to-metabolite-conversions) [WP4673](reports/WP4673#no-non-metabolite-to-metabolite-conversions) [WP5258](reports/WP5258#no-non-metabolite-to-metabolite-conversions) [WP5318](reports/WP5318#no-non-metabolite-to-metabolite-conversions) +## PathwayTests.testRoundedRectangle + +[WP4204](reports/WP4204#pathwayteststestroundedrectangle) + ## Possible MIM translocation diff --git a/reports/WP3302.md b/reports/WP3302.md index dd0c6792..8bda3304 100644 --- a/reports/WP3302.md +++ b/reports/WP3302.md @@ -51,7 +51,7 @@ Interactions found that involve Labels: 1 -* [http://classic.wikipathways.org/instance/WP3302_r123388](http://classic.wikipathways.org/instance/WP3302_r123388) "SINE" with graphId b7b8f +* [http://classic.wikipathways.org/instance/WP3302_r136355](http://classic.wikipathways.org/instance/WP3302_r136355) "Cell survival" with graphId d05b8 More details at [https://www.wikipathways.org/WikiPathwaysCurator/InteractionTests/interactionsWithLabels](https://www.wikipathways.org/WikiPathwaysCurator/InteractionTests/interactionsWithLabels) diff --git a/reports/WP4204.md b/reports/WP4204.md index 07b877b7..0a789c57 100644 --- a/reports/WP4204.md +++ b/reports/WP4204.md @@ -10,7 +10,7 @@ * 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: 9](#d2d32fa8) * unknownTypes_knownDatasource: .. all OK! * unknownTypes: .. all OK! * unknownTypes_Reactome: .. all OK! @@ -19,22 +19,21 @@ * GeneTests: all 5 tests OK! * GeneralTests: all 15 tests OK! * HMDBSecMetabolitesTests: all 3 tests OK! -* InteractionTests - * noMetaboliteToNonMetaboliteConversions: .. all OK! - * noNonMetaboliteToMetaboliteConversions: .. all OK! - * noGeneProteinConversions: .. all OK! - * nonNumericIDs: .. all OK! - * interactionsWithLabels: .x we found 1 problem(s): - * [Interactions found that involve Labels: 6](#630d267d) - * possibleTranslocations: .. all OK! - * noProteinProteinConversions: .. all OK! - * incorrectKEGGIdentifiers: .. all OK! +* InteractionTests: all 8 tests OK! * KEGGMetaboliteTests: all 2 tests OK! * LIPIDMAPSTests: all 1 tests OK! * MetaboliteStructureTests: all 1 tests OK! * MetabolitesTests: all 14 tests OK! * OudatedDataSourcesTests: all 24 tests OK! -* PathwayTests: all 7 tests OK! +* PathwayTests + * deletedPathways: .. all OK! + * linksToDeletedPathways: .. all OK! + * linksToDeletedPathways_All: .. all OK! + * speciesMismatch: .. all OK! + * testRoundedRectangle: .x we found 1 problem(s): + * [Pathways DataNodes with WikiPathways ID that can be converted to have a RoundedRectangle ShapeType so that they become clickable: 3](#16e17dd) + * youMustCite: .. all OK! + * oldLicenses: .. all OK! * ProteinsTests: all 2 tests OK! * PubChemMetabolitesTests: all 3 tests OK! * ReferencesTests: all 6 tests OK! @@ -51,31 +50,33 @@ ## Fails - + ## Data nodes without an identifier -The following DataNodes have no identifier: 1 +The following DataNodes have no identifier: 9 -* [http://classic.wikipathways.org/instance/WP4204_r123410](http://classic.wikipathways.org/instance/WP4204_r123410) http://rdf.wikipathways.org/Pathway/WP4204_r123410/DataNode/e0a18 (Polycomb pathway) +* [http://classic.wikipathways.org/instance/WP4204_r136357](http://classic.wikipathways.org/instance/WP4204_r136357) http://rdf.wikipathways.org/Pathway/WP4204_r136357/DataNode/e1de9 (Apoptosis suppression) +* [http://classic.wikipathways.org/instance/WP4204_r136357](http://classic.wikipathways.org/instance/WP4204_r136357) http://rdf.wikipathways.org/Pathway/WP4204_r136357/DataNode/f658d (Chromatin remodeling) +* [http://classic.wikipathways.org/instance/WP4204_r136357](http://classic.wikipathways.org/instance/WP4204_r136357) http://rdf.wikipathways.org/Pathway/WP4204_r136357/DataNode/d6486 (G0/G1 transition) +* [http://classic.wikipathways.org/instance/WP4204_r136357](http://classic.wikipathways.org/instance/WP4204_r136357) http://rdf.wikipathways.org/Pathway/WP4204_r136357/DataNode/e0a18 (Polycomb pathway) +* [http://classic.wikipathways.org/instance/WP4204_r136357](http://classic.wikipathways.org/instance/WP4204_r136357) http://rdf.wikipathways.org/Pathway/WP4204_r136357/DataNode/fc178 (Proliferation) +* [http://classic.wikipathways.org/instance/WP4204_r136357](http://classic.wikipathways.org/instance/WP4204_r136357) http://rdf.wikipathways.org/Pathway/WP4204_r136357/DataNode/ad476 (Transcription) +* [http://classic.wikipathways.org/instance/WP4204_r136357](http://classic.wikipathways.org/instance/WP4204_r136357) http://rdf.wikipathways.org/Pathway/WP4204_r136357/DataNode/d6e06 (Transcription) +* [http://classic.wikipathways.org/instance/WP4204_r136357](http://classic.wikipathways.org/instance/WP4204_r136357) http://rdf.wikipathways.org/Pathway/WP4204_r136357/DataNode/e73a3 (Transcription) +* [http://classic.wikipathways.org/instance/WP4204_r136357](http://classic.wikipathways.org/instance/WP4204_r136357) http://rdf.wikipathways.org/Pathway/WP4204_r136357/DataNode/e4940 (Transctiptional regulation) More details at [https://www.wikipathways.org/WikiPathwaysCurator/DataNodesTests/dataNodesWithoutIdentifier](https://www.wikipathways.org/WikiPathwaysCurator/DataNodesTests/dataNodesWithoutIdentifier) - + -## Interactions with Labels +## PathwayTests.testRoundedRectangle -Interactions found that involve Labels: 6 - -* [http://classic.wikipathways.org/instance/WP4204_r123410](http://classic.wikipathways.org/instance/WP4204_r123410) "Chromatin remodeling / transctiptional regulation" with graphId a4ebe -* [http://classic.wikipathways.org/instance/WP4204_r123410](http://classic.wikipathways.org/instance/WP4204_r123410) "Transcription" with graphId a7f3c -* [http://classic.wikipathways.org/instance/WP4204_r123410](http://classic.wikipathways.org/instance/WP4204_r123410) "Proliferation -Apoptosis suppression" with graphId c21dc -* [http://classic.wikipathways.org/instance/WP4204_r123410](http://classic.wikipathways.org/instance/WP4204_r123410) "G0/G1 transition" with graphId e28db -* [http://classic.wikipathways.org/instance/WP4204_r123410](http://classic.wikipathways.org/instance/WP4204_r123410) "Transcription" with graphId a9540 -* [http://classic.wikipathways.org/instance/WP4204_r123410](http://classic.wikipathways.org/instance/WP4204_r123410) "Transcription" with graphId c6795 - - -More details at [https://www.wikipathways.org/WikiPathwaysCurator/InteractionTests/interactionsWithLabels](https://www.wikipathways.org/WikiPathwaysCurator/InteractionTests/interactionsWithLabels) +Pathways DataNodes with WikiPathways ID that can be converted to have a RoundedRectangle ShapeType so that they become clickable: 3 +``` +http://classic.wikipathways.org/instance/WP4204_r136357 -> c4a7f, WP4249 + http://classic.wikipathways.org/instance/WP4204_r136357 -> e262d, WP428 + http://classic.wikipathways.org/instance/WP4204_r136357 -> f75a5, WP179 + ``` diff --git a/reports/WP5189.md b/reports/WP5189.md index 0119a073..3c6f4285 100644 --- a/reports/WP5189.md +++ b/reports/WP5189.md @@ -65,8 +65,8 @@ The following DataNodes have no identifier: 2 -* [http://classic.wikipathways.org/instance/WP5189_r128212](http://classic.wikipathways.org/instance/WP5189_r128212) http://rdf.wikipathways.org/Pathway/WP5189_r128212/DataNode/cb8d9 (Reductase) -* [http://classic.wikipathways.org/instance/WP5189_r128212](http://classic.wikipathways.org/instance/WP5189_r128212) http://rdf.wikipathways.org/Pathway/WP5189_r128212/DataNode/fbedb (Reductase) +* [http://classic.wikipathways.org/instance/WP5189_r136358](http://classic.wikipathways.org/instance/WP5189_r136358) http://rdf.wikipathways.org/Pathway/WP5189_r136358/DataNode/cb8d9 (Reductase) +* [http://classic.wikipathways.org/instance/WP5189_r136358](http://classic.wikipathways.org/instance/WP5189_r136358) http://rdf.wikipathways.org/Pathway/WP5189_r136358/DataNode/fbedb (Reductase) More details at [https://www.wikipathways.org/WikiPathwaysCurator/DataNodesTests/dataNodesWithoutIdentifier](https://www.wikipathways.org/WikiPathwaysCurator/DataNodesTests/dataNodesWithoutIdentifier) @@ -77,8 +77,8 @@ More details at [https://www.wikipathways.org/WikiPathwaysCurator/DataNodesTests The following DataNodes have Unknown @Type: 2 -* [http://classic.wikipathways.org/instance/WP5189_r128212](http://classic.wikipathways.org/instance/WP5189_r128212) http://rdf.wikipathways.org/Pathway/WP5189_r128212/DataNode/cb8d9 (Reductase) -* [http://classic.wikipathways.org/instance/WP5189_r128212](http://classic.wikipathways.org/instance/WP5189_r128212) http://rdf.wikipathways.org/Pathway/WP5189_r128212/DataNode/fbedb (Reductase) +* [http://classic.wikipathways.org/instance/WP5189_r136358](http://classic.wikipathways.org/instance/WP5189_r136358) http://rdf.wikipathways.org/Pathway/WP5189_r136358/DataNode/cb8d9 (Reductase) +* [http://classic.wikipathways.org/instance/WP5189_r136358](http://classic.wikipathways.org/instance/WP5189_r136358) http://rdf.wikipathways.org/Pathway/WP5189_r136358/DataNode/fbedb (Reductase) More details at [https://www.wikipathways.org/WikiPathwaysCurator/DataNodesTests/unknownTypes](https://www.wikipathways.org/WikiPathwaysCurator/DataNodesTests/unknownTypes) @@ -89,12 +89,12 @@ More details at [https://www.wikipathways.org/WikiPathwaysCurator/DataNodesTests Interactions found that involve Labels: 5 -* [http://classic.wikipathways.org/instance/WP5189_r128212](http://classic.wikipathways.org/instance/WP5189_r128212) "X-linked distal spinal +* [http://classic.wikipathways.org/instance/WP5189_r136358](http://classic.wikipathways.org/instance/WP5189_r136358) "X-linked distal spinal muscular atrophy" with graphId a0156 -* [http://classic.wikipathways.org/instance/WP5189_r128212](http://classic.wikipathways.org/instance/WP5189_r128212) "MEDNIK syndrome" with graphId f1b13 -* [http://classic.wikipathways.org/instance/WP5189_r128212](http://classic.wikipathways.org/instance/WP5189_r128212) "Occipital horn syndrome" with graphId f0f37 -* [http://classic.wikipathways.org/instance/WP5189_r128212](http://classic.wikipathways.org/instance/WP5189_r128212) "Wilson disease" with graphId c84f9 -* [http://classic.wikipathways.org/instance/WP5189_r128212](http://classic.wikipathways.org/instance/WP5189_r128212) "Menkes disease" with graphId dfcfd +* [http://classic.wikipathways.org/instance/WP5189_r136358](http://classic.wikipathways.org/instance/WP5189_r136358) "MEDNIK syndrome" with graphId f1b13 +* [http://classic.wikipathways.org/instance/WP5189_r136358](http://classic.wikipathways.org/instance/WP5189_r136358) "Menkes disease" with graphId dfcfd +* [http://classic.wikipathways.org/instance/WP5189_r136358](http://classic.wikipathways.org/instance/WP5189_r136358) "Occipital horn syndrome" with graphId f0f37 +* [http://classic.wikipathways.org/instance/WP5189_r136358](http://classic.wikipathways.org/instance/WP5189_r136358) "Wilson disease" with graphId c84f9 More details at [https://www.wikipathways.org/WikiPathwaysCurator/InteractionTests/interactionsWithLabels](https://www.wikipathways.org/WikiPathwaysCurator/InteractionTests/interactionsWithLabels) @@ -105,7 +105,7 @@ More details at [https://www.wikipathways.org/WikiPathwaysCurator/InteractionTes Found 1 pathways with zero (PubMed) references -* [http://classic.wikipathways.org/instance/WP5189_r128212](http://classic.wikipathways.org/instance/WP5189_r128212) 'Copper metabolism' in Homo sapiens has zero references; +* [http://classic.wikipathways.org/instance/WP5189_r136358](http://classic.wikipathways.org/instance/WP5189_r136358) 'Copper metabolism' in Homo sapiens has zero references; More details at [https://www.wikipathways.org/WikiPathwaysCurator/ReferencesTests/atLeastOneReference](https://www.wikipathways.org/WikiPathwaysCurator/ReferencesTests/atLeastOneReference)