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Merged
merged 2 commits into from
May 19, 2021
Merged

test release on 2021-05-14 #1164

merged 2 commits into from
May 19, 2021

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wdduncan
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@cmungall @pbuttigieg @kaiiam @turbomam
I ran make release, and a number of subsets were changed (see log).

Also the robot report produced the following:

robot --catalog catalog-v001.xml report -p reports/report_profile_edit.txt -l true -i envo-edit.owl --fail-on ERROR --print 5 -o reports/envo-edit-robot-report.tsv
Violations: 471
-----------------
ERROR:      0
WARN:       394
INFO:       77
tsv!
First 5 violations:
WARN	annotation_whitespace	nest of ant	has_exact_synonym	ant's nest	
WARN	annotation_whitespace	autoclaved sand	rdfs:comment	Requested in Issue 116 as part of the annotation of metagenomic submissions present in the European Nucleotide Archive.

WARN	annotation_whitespace	tropical mixed broadleaf forest	rdfs:comment	This class corresponds to  the \"Tropical Mixed needleleaf / broadleaf forest\" category of the updated Global Forest Map classification (GFM 2000). To reconstruct the original class, an aggregate class with this and the \"tropical mixed needleleaf forest\" class can be made.

WARN	missing_label	poly(vinyl chloride)	rdfs:label	
WARN	missing_label	poly(propylene)	rdfs:label	
robot --catalog catalog-v001.xml report -l true -i envo-base.owl --fail-on NONE --print 5 -o reports/envo-base-robot-report.tsv
Violations: 607
-----------------
ERROR:      6
WARN:       387
INFO:       214
tsv!
First 5 violations:
ERROR	missing_label	CHEBI:53243	rdfs:label	
ERROR	missing_label	CHEBI:53550	rdfs:label	
ERROR	missing_label	CHEBI:60034	rdfs:label	
ERROR	missing_label	CHEBI:60737	rdfs:label	
ERROR	missing_label	CHEBI:61452	rdfs:label	
robot --catalog catalog-v001.xml report -l true -i envo-edit-module-merged.owl --fail-on NONE --print 5 -o reports/envo-src-robot-report.tsv
Violations: 607
-----------------
ERROR:      6
WARN:       387
INFO:       214
tsv!
First 5 violations:
ERROR	missing_label	poly(vinyl chloride)	rdfs:label	
ERROR	missing_label	poly(propylene)	rdfs:label	
ERROR	missing_label	polyethylene polymer	rdfs:label	
ERROR	missing_label	polyurethane polymer	rdfs:label	
ERROR	missing_label	poly(ethylene terephthalate) polymer	rdfs:label	
cp -pr catalog-v001.xml envo.obo envo.owl envo.json envo-base.owl subsets mappings imports ../..
rm imports/foodon_combined_seed.tsv imports/fao_combined_seed.tsv imports/chebi_combined_seed.tsv imports/pato_combined_seed.tsv imports/go_combined_seed.tsv imports/pco_combined_seed.tsv imports/po_combined_seed.tsv imports/ro_combined_seed.tsv imports/ncbitaxon_combined_seed.tsv imports/uberon_combined_seed.tsv imports/iao_combined_seed.tsv imports/obi_combined_seed.tsv

I've attached a zipped text file of the full output of the make process.
test-release-2021-05-14-output.txt.gz

@wdduncan
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Here is a list of changed files after running git status:

modified:   ../../envo-base.owl
	modified:   ../../envo.json
	modified:   ../../envo.obo
	modified:   ../../envo.owl
	modified:   ../../imports/chebi_import.obo
	modified:   ../../imports/chebi_import.owl
	modified:   ../../imports/foodon_import.obo
	modified:   ../../imports/foodon_import.owl
	modified:   ../../imports/go_import.obo
	modified:   ../../imports/go_import.owl
	modified:   ../../imports/iao_import.owl
	modified:   ../../imports/ncbitaxon_import.obo
	modified:   ../../imports/ncbitaxon_import.owl
	modified:   ../../imports/obi_import.owl
	modified:   ../../imports/pato_import.obo
	modified:   ../../imports/pato_import.owl
	modified:   ../../imports/pco_import.obo
	modified:   ../../imports/pco_import.owl
	modified:   ../../imports/ro_import.obo
	modified:   ../../imports/ro_import.owl
	modified:   ../../imports/uberon_import.obo
	modified:   ../../imports/uberon_import.owl
	modified:   envo-simple.owl
	modified:   envo.json
	modified:   envo.obo
	modified:   envo.owl
	modified:   imports/chebi_import.obo
	modified:   imports/chebi_import.owl
	modified:   imports/foodon_import.owl
	modified:   imports/go_import.obo
	modified:   imports/iao_import.owl
	modified:   imports/ncbitaxon_import.obo
	modified:   imports/ncbitaxon_import.owl
	modified:   imports/obi_import.owl
	modified:   imports/pato_import.obo
	modified:   imports/pco_import.obo
	modified:   imports/pco_import.owl
	modified:   imports/uberon_import.obo
	modified:   imports/uberon_import.owl
	modified:   reports/envo-basicReport.tsv
	modified:   reports/envo-edges.tsv
	modified:   reports/envo-stats.tsv
	modified:   reports/envo-subsetTable.tsv
	modified:   reports/envo-tags.tsv
	modified:   reports/envo-termTable.tsv
	modified:   subsets/EnvO-Lite-GSC.json
	modified:   subsets/EnvO-Lite-GSC.obo
	modified:   subsets/EnvO-Lite-GSC.owl
	modified:   subsets/EnvO-Lite-GSC.tsv
	modified:   subsets/biome-hierarchy.json
	modified:   subsets/biome-hierarchy.obo
	modified:   subsets/biome-hierarchy.owl
	modified:   subsets/biome-hierarchy.tsv
	modified:   subsets/environmental_hazards.json
	modified:   subsets/environmental_hazards.obo
	modified:   subsets/environmental_hazards.owl
	modified:   subsets/environmental_hazards.tsv
	modified:   subsets/envo-basic.json
	modified:   subsets/envo-basic.obo
	modified:   subsets/envo-basic.owl
	modified:   subsets/envo-basic.tsv
	modified:   subsets/envoAstro.json
	modified:   subsets/envoAstro.obo
	modified:   subsets/envoAstro.owl
	modified:   subsets/envoAstro.tsv
	modified:   subsets/envoCesab.json
	modified:   subsets/envoCesab.obo
	modified:   subsets/envoCesab.owl
	modified:   subsets/envoCesab.tsv
	modified:   subsets/envoEmpo.json
	modified:   subsets/envoEmpo.obo
	modified:   subsets/envoEmpo.owl
	modified:   subsets/envoOmics.json
	modified:   subsets/envoOmics.obo
	modified:   subsets/envoOmics.owl
	modified:   subsets/envoPolar.json
	modified:   subsets/envoPolar.obo
	modified:   subsets/envoPolar.owl
	modified:   subsets/envoPolar.tsv
	modified:   subsets/material-hierarchy.json
	modified:   subsets/material-hierarchy.obo
	modified:   subsets/material-hierarchy.owl
	modified:   subsets/material-hierarchy.tsv
	modified:   subsets/process-hierarchy.json
	modified:   subsets/process-hierarchy.obo
	modified:   subsets/process-hierarchy.owl
	modified:   subsets/process-hierarchy.tsv
	modified:   ../../subsets/EnvO-Lite-GSC.json
	modified:   ../../subsets/EnvO-Lite-GSC.obo
	modified:   ../../subsets/EnvO-Lite-GSC.owl
	modified:   ../../subsets/EnvO-Lite-GSC.tsv
	modified:   ../../subsets/astronomical-body-part-hierarchy.json
	modified:   ../../subsets/astronomical-body-part-hierarchy.obo
	modified:   ../../subsets/astronomical-body-part-hierarchy.owl
	modified:   ../../subsets/astronomical-body-part-hierarchy.tsv
	modified:   ../../subsets/biome-hierarchy.json
	modified:   ../../subsets/biome-hierarchy.obo
	modified:   ../../subsets/biome-hierarchy.owl
	modified:   ../../subsets/biome-hierarchy.tsv
	modified:   ../../subsets/environmental_hazards.json
	modified:   ../../subsets/environmental_hazards.obo
	modified:   ../../subsets/environmental_hazards.owl
	modified:   ../../subsets/environmental_hazards.tsv
	modified:   ../../subsets/envo-basic.json
	modified:   ../../subsets/envo-basic.obo
	modified:   ../../subsets/envo-basic.owl
	modified:   ../../subsets/envo-basic.tsv
	modified:   ../../subsets/envoAstro.json
	modified:   ../../subsets/envoAstro.obo
	modified:   ../../subsets/envoAstro.owl
	modified:   ../../subsets/envoAstro.tsv
	modified:   ../../subsets/envoCesab.json
	modified:   ../../subsets/envoCesab.obo
	modified:   ../../subsets/envoCesab.owl
	modified:   ../../subsets/envoCesab.tsv
	modified:   ../../subsets/envoEmpo.json
	modified:   ../../subsets/envoEmpo.obo
	modified:   ../../subsets/envoEmpo.owl
	modified:   ../../subsets/envoOmics.json
	modified:   ../../subsets/envoOmics.obo
	modified:   ../../subsets/envoOmics.owl
	modified:   ../../subsets/envoPolar.json
	modified:   ../../subsets/envoPolar.obo
	modified:   ../../subsets/envoPolar.owl
	modified:   ../../subsets/envoPolar.tsv
	modified:   ../../subsets/material-hierarchy.json
	modified:   ../../subsets/material-hierarchy.obo
	modified:   ../../subsets/material-hierarchy.owl
	modified:   ../../subsets/material-hierarchy.tsv
	modified:   ../../subsets/process-hierarchy.json
	modified:   ../../subsets/process-hierarchy.obo
	modified:   ../../subsets/process-hierarchy.owl
	modified:   ../../subsets/process-hierarchy.tsv

@kaiiam
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kaiiam commented May 17, 2021

Build checks have now passed after fixing the merge conflicts. @wdduncan was able to get CHEBI to run along with all other files (which was what @pbuttigieg had asked me to do) so I think we’re good to proceed with this?

I guess the next steps would be to merge and draft a release on github? Perhaps also running that script to get the list of new terms? Do we also want/need to add descriptions?

Maybe we should write all the required and supplementary steps down in a new envo github wiki page?

pbuttigieg
pbuttigieg approved these changes May 18, 2021
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As discussed in our editors' Slack - this looks good overall, but we're wondering why the envoPlastics subset wasn't made as part of this release. @raissameyer confirmed it was being made locally (#1092)

We also note that there were some stragglers from #970 that are still in the editors' version only here, but they'll be incorporated in the next release along with more EOV terms.

We'll create a follow up issue and sort that out for the next release, but let's get the current state out there.

@pbuttigieg pbuttigieg modified the milestone: summerRelease May 18, 2021
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kaiiam commented May 19, 2021

Let's do this!

@kaiiam kaiiam merged commit 529e242 into master May 19, 2021
@kaiiam kaiiam deleted the test-release-2021-05-14 branch May 19, 2021 11:51
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@pbuttigieg pbuttigieg pbuttigieg approved these changes

@cmungall cmungall Awaiting requested review from cmungall

@kaiiam kaiiam Awaiting requested review from kaiiam

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