Update cellPartOfAnatomicalEntity.yaml

[dosumis]

Add back xrefs.

[dosumis]

I don't remember why they were removed in the first place.. Probably needs to check whether it works as well.

Should work (and should be on all patterns on CL & Uberon - probably more generally. I'll run a test to check.

[github-actions[bot]]

This PR has not seen any activity in the past month; if nobody comments or reviews it in the next week, the PR editor will be allowed to proceed with merging without explicit approval, should they wish to do so.

[ghost]

@matentzn, @dosumis, this PR has been approved, but not yet merged. Last action Oct 2021. Can we merge or close? Will also add to the "DOS" board.

[matentzn]

@bvarner-ebi if you merge master in to this branch and run:

sh run.sh make ../patterns/definitions.owl -B

We will know for sure if it works.

[ghost]

% sh run.sh make ../patterns/definitions.owl -B
if [ true  = true ] && [ "cellCapableOfBiologicalProcess cellPartOfAnatomicalEntity" ]; then dosdp-tools generate --catalog=catalog-v001.xml \
    --infile=../patterns/data/default/ --template=../patterns/dosdp-patterns --batch-patterns="cellCapableOfBiologicalProcess cellPartOfAnatomicalEntity" \
    --ontology=cl-edit.owl --obo-prefixes=true --outfile=../patterns/data/default; fi
2022-08-25 08:19:03.239Z  warn [] [context: command=generate;pattern=../patterns/dosdp-patterns/cellCapableOfBiologicalProcess.yaml;input=../patterns/data/default//cellCapableOfBiologicalProcess.tsv;output=../patterns/data/default/cellCapableOfBiologicalProcess.ofn] Input ../patterns/data/default//cellCapableOfBiologicalProcess.tsv for pattern ../patterns/dosdp-patterns/cellCapableOfBiologicalProcess.yaml is missing column for pattern variable <cell>
2022-08-25 08:19:03.253Z  warn [] [context: command=generate;pattern=../patterns/dosdp-patterns/cellCapableOfBiologicalProcess.yaml;input=../patterns/data/default//cellCapableOfBiologicalProcess.tsv;output=../patterns/data/default/cellCapableOfBiologicalProcess.ofn] Input ../patterns/data/default//cellCapableOfBiologicalProcess.tsv for pattern ../patterns/dosdp-patterns/cellCapableOfBiologicalProcess.yaml is missing column for pattern variable <biological_process>
2022-08-25 08:19:03.700Z error [] [context: command=generate;pattern=../patterns/dosdp-patterns/cellPartOfAnatomicalEntity.yaml;input=../patterns/data/default//cellPartOfAnatomicalEntity.tsv;output=../patterns/data/default/cellPartOfAnatomicalEntity.ofn] JSON does not conform to DOS-DP schema for pattern file at ../patterns/dosdp-patterns/cellPartOfAnatomicalEntity.yaml:
String: DownField(xrefs),DownField(def)
2022-08-25 08:19:03.710Z error [] [context: ] JSON does not conform to DOS-DP schema for pattern file at ../patterns/dosdp-patterns/cellPartOfAnatomicalEntity.yaml
make: *** [Makefile:544: ../patterns/data/default/cellCapableOfBiologicalProcess.ofn] Error 1

[matentzn]

Yeah, @rays22 can help you with that

[github-actions[bot]]

Here's a diff of how these changes impact the classified ontology (on -simple file):

Ontologies are identical

[github-actions[bot]]

Here's a diff of your edit file (unreasoned)

Ontologies are identical

[rays22]

2022-08-25 08:19:03.700Z error [] [context: command=generate;pattern=../patterns/dosdp-patterns/cellPartOfAnatomicalEntity.yaml;input=../patterns/data/default//cellPartOfAnatomicalEntity.tsv;output=../patterns/data/default/cellPartOfAnatomicalEntity.ofn] JSON does not conform to DOS-DP schema for pattern file at ../patterns/dosdp-patterns/cellPartOfAnatomicalEntity.yaml: String: DownField(xrefs),DownField(def) 2022-08-25 08:19:03.710Z error [] [context: ] JSON does not conform to DOS-DP schema for pattern file at ../patterns/dosdp-patterns/cellPartOfAnatomicalEntity.yaml make: *** [Makefile:544: ../patterns/data/default/cellCapableOfBiologicalProcess.ofn] Error 1

I think I have fixed the String: DownField(xrefs),DownField(def) error, but running

sh run.sh make ../patterns/definitions.owl -B

seems to take ages.

[ghost]

I think I have fixed it, but running

sh run.sh make ../patterns/definitions.owl -B

seems to take ages.

Thank you, @rays22. I ran it, and it took a couple of minutes.

I still get missing column messages:

ontology % sh run.sh make ../patterns/definitions.owl -B
if [ true  = true ] && [ "cellCapableOfBiologicalProcess cellPartOfAnatomicalEntity" ]; then dosdp-tools generate --catalog=catalog-v001.xml \
    --infile=../patterns/data/default/ --template=../patterns/dosdp-patterns --batch-patterns="cellCapableOfBiologicalProcess cellPartOfAnatomicalEntity" \
    --ontology=cl-edit.owl --obo-prefixes=true --outfile=../patterns/data/default; fi
2022-08-26 11:31:57.101Z  warn [] [context: command=generate;pattern=../patterns/dosdp-patterns/cellCapableOfBiologicalProcess.yaml;input=../patterns/data/default//cellCapableOfBiologicalProcess.tsv;output=../patterns/data/default/cellCapableOfBiologicalProcess.ofn] Input ../patterns/data/default//cellCapableOfBiologicalProcess.tsv for pattern ../patterns/dosdp-patterns/cellCapableOfBiologicalProcess.yaml is missing column for pattern variable <cell>
2022-08-26 11:31:57.115Z  warn [] [context: command=generate;pattern=../patterns/dosdp-patterns/cellCapableOfBiologicalProcess.yaml;input=../patterns/data/default//cellCapableOfBiologicalProcess.tsv;output=../patterns/data/default/cellCapableOfBiologicalProcess.ofn] Input ../patterns/data/default//cellCapableOfBiologicalProcess.tsv for pattern ../patterns/dosdp-patterns/cellCapableOfBiologicalProcess.yaml is missing column for pattern variable <biological_process>
2022-08-26 11:31:57.566Z  warn [] [context: command=generate;pattern=../patterns/dosdp-patterns/cellPartOfAnatomicalEntity.yaml;input=../patterns/data/default//cellPartOfAnatomicalEntity.tsv;output=../patterns/data/default/cellPartOfAnatomicalEntity.ofn] Input ../patterns/data/default//cellPartOfAnatomicalEntity.tsv for pattern ../patterns/dosdp-patterns/cellPartOfAnatomicalEntity.yaml is missing column for pattern variable <cell>
2022-08-26 11:31:57.566Z  warn [] [context: command=generate;pattern=../patterns/dosdp-patterns/cellPartOfAnatomicalEntity.yaml;input=../patterns/data/default//cellPartOfAnatomicalEntity.tsv;output=../patterns/data/default/cellPartOfAnatomicalEntity.ofn] Input ../patterns/data/default//cellPartOfAnatomicalEntity.tsv for pattern ../patterns/dosdp-patterns/cellPartOfAnatomicalEntity.yaml is missing column for pattern variable <anatomical_entity>
2022-08-26 11:31:57.566Z  warn [] [context: command=generate;pattern=../patterns/dosdp-patterns/cellPartOfAnatomicalEntity.yaml;input=../patterns/data/default//cellPartOfAnatomicalEntity.tsv;output=../patterns/data/default/cellPartOfAnatomicalEntity.ofn] Input ../patterns/data/default//cellPartOfAnatomicalEntity.tsv for pattern ../patterns/dosdp-patterns/cellPartOfAnatomicalEntity.yaml is missing column for pattern variable <pubs>
if [ true  = true ] && [ "cellCapableOfBiologicalProcess cellPartOfAnatomicalEntity" ]; then dosdp-tools generate --catalog=catalog-v001.xml \
    --infile=../patterns/data/default/ --template=../patterns/dosdp-patterns --batch-patterns="cellCapableOfBiologicalProcess cellPartOfAnatomicalEntity" \
    --ontology=cl-edit.owl --obo-prefixes=true --outfile=../patterns/data/default; fi
2022-08-26 11:32:23.442Z  warn [] [context: command=generate;pattern=../patterns/dosdp-patterns/cellCapableOfBiologicalProcess.yaml;input=../patterns/data/default//cellCapableOfBiologicalProcess.tsv;output=../patterns/data/default/cellCapableOfBiologicalProcess.ofn] Input ../patterns/data/default//cellCapableOfBiologicalProcess.tsv for pattern ../patterns/dosdp-patterns/cellCapableOfBiologicalProcess.yaml is missing column for pattern variable <cell>
2022-08-26 11:32:23.455Z  warn [] [context: command=generate;pattern=../patterns/dosdp-patterns/cellCapableOfBiologicalProcess.yaml;input=../patterns/data/default//cellCapableOfBiologicalProcess.tsv;output=../patterns/data/default/cellCapableOfBiologicalProcess.ofn] Input ../patterns/data/default//cellCapableOfBiologicalProcess.tsv for pattern ../patterns/dosdp-patterns/cellCapableOfBiologicalProcess.yaml is missing column for pattern variable <biological_process>
2022-08-26 11:32:23.886Z  warn [] [context: command=generate;pattern=../patterns/dosdp-patterns/cellPartOfAnatomicalEntity.yaml;input=../patterns/data/default//cellPartOfAnatomicalEntity.tsv;output=../patterns/data/default/cellPartOfAnatomicalEntity.ofn] Input ../patterns/data/default//cellPartOfAnatomicalEntity.tsv for pattern ../patterns/dosdp-patterns/cellPartOfAnatomicalEntity.yaml is missing column for pattern variable <cell>
2022-08-26 11:32:23.887Z  warn [] [context: command=generate;pattern=../patterns/dosdp-patterns/cellPartOfAnatomicalEntity.yaml;input=../patterns/data/default//cellPartOfAnatomicalEntity.tsv;output=../patterns/data/default/cellPartOfAnatomicalEntity.ofn] Input ../patterns/data/default//cellPartOfAnatomicalEntity.tsv for pattern ../patterns/dosdp-patterns/cellPartOfAnatomicalEntity.yaml is missing column for pattern variable <anatomical_entity>
2022-08-26 11:32:23.887Z  warn [] [context: command=generate;pattern=../patterns/dosdp-patterns/cellPartOfAnatomicalEntity.yaml;input=../patterns/data/default//cellPartOfAnatomicalEntity.tsv;output=../patterns/data/default/cellPartOfAnatomicalEntity.ofn] Input ../patterns/data/default//cellPartOfAnatomicalEntity.tsv for pattern ../patterns/dosdp-patterns/cellPartOfAnatomicalEntity.yaml is missing column for pattern variable <pubs>
if [ true  = true ] && [ "cellCapableOfBiologicalProcess" ]; then dosdp-tools generate --catalog=catalog-v001.xml \
    --infile=../patterns/data/clustering --template=../patterns/dosdp-patterns/ --batch-patterns="cellCapableOfBiologicalProcess" \
    --ontology=cl-edit.owl --obo-prefixes=true --outfile=../patterns/data/clustering; fi
2022-08-26 11:32:49.361Z  warn [] [context: command=generate;pattern=../patterns/dosdp-patterns//cellCapableOfBiologicalProcess.yaml;input=../patterns/data/clustering/cellCapableOfBiologicalProcess.tsv;output=../patterns/data/clustering/cellCapableOfBiologicalProcess.ofn] Input ../patterns/data/clustering/cellCapableOfBiologicalProcess.tsv for pattern ../patterns/dosdp-patterns//cellCapableOfBiologicalProcess.yaml is missing column for pattern variable <cell>
2022-08-26 11:32:49.378Z  warn [] [context: command=generate;pattern=../patterns/dosdp-patterns//cellCapableOfBiologicalProcess.yaml;input=../patterns/data/clustering/cellCapableOfBiologicalProcess.tsv;output=../patterns/data/clustering/cellCapableOfBiologicalProcess.ofn] Input ../patterns/data/clustering/cellCapableOfBiologicalProcess.tsv for pattern ../patterns/dosdp-patterns//cellCapableOfBiologicalProcess.yaml is missing column for pattern variable <biological_process>
if [ true  = true ] && [ "cellCapableOfBiologicalProcess cellPartOfAnatomicalEntity" ]   || [ "cellCapableOfBiologicalProcess" ] && [ true  = true ]; then robot --catalog catalog-v001.xml merge -i ../patterns/data/default/cellCapableOfBiologicalProcess.ofn -i ../patterns/data/default/cellPartOfAnatomicalEntity.ofn -i ../patterns/data/clustering/cellCapableOfBiologicalProcess.ofn \
	annotate --ontology-iri http://purl.obolibrary.org/obo/cl/patterns/definitions.owl  --version-iri http://purl.obolibrary.org/obo/cl/releases/2022-08-26/patterns/definitions.owl \
      --annotation owl:versionInfo 2022-08-26 -o definitions.ofn && mv definitions.ofn ../patterns/definitions.owl; fi

[matentzn]

You could make a dosdp tools issue https://github.com/INCATools/dosdp-tools/issues

Linking to this PR, saying that

Redundant missing column message if table is empty

It seems like if the dosdp table has no data, dosdp-tools erroneously believes that it is missing a column

[shawntanzk]

@bvarner-ebi - assigning this to you, and @rays22 can help if you need any. Thanks

[ghost]

@bvarner-ebi - assigning this to you, and @rays22 can help if you need any. Thanks

Not sure what needs to be done here... I tried to close this PR, but unclear to me what the background is as there is no linked issue. I opened a ticket per @matentzn's direction, but next steps are not clear to me.

As this has been a pending PR since 2021 with sparse follow up, I'm inclined to close this PR without merging.

[matentzn]

@bvarner-ebi can you confirm that @dosumis comments where addressed, if so, just merge it! Its a totally fine PR!

[rays22]

Not sure what needs to be done here... I tried to close this PR, but unclear to me what the background is as there is no linked issue. I opened a ticket per @matentzn's direction, but next steps are not clear to me.

As this has been a pending PR since 2021 with sparse follow up, I'm inclined to close this PR without merging.

@bvarner-ebi , I think I know what is left to be done for this PR. I will update the src/patterns/dosdp-patterns/cellPartOfAnatomicalEntity.yaml DOS-DP template and take care of merging the PR.