Knowledge-Graph-Hub automate-pheno-comparisons issues

Knowledge-Graph-Hub / automate-pheno-comparisons

Jenkins-based automation of phenotype semantic similarity on PHENIO with Semsimian.

BSD 3-Clause "New" or "Revised" License

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issues

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Extra help for yq eval

#42 caufieldjh closed 4 months ago
0
Another attempt to fix bugs re: Groovy

#41 caufieldjh closed 4 months ago
0
Explicitly use local yq, run from local dir

#40 caufieldjh closed 4 months ago
0
Install yq during setup in build

#39 caufieldjh closed 4 months ago
0
Move variable setting into script block

#38 caufieldjh closed 4 months ago
0
Fixing quotes in Jenkinsfile

#37 caufieldjh closed 4 months ago
0
Collect and log ontology versions

#36 caufieldjh closed 4 months ago
0
Populate `ancestor_label`

#35 caufieldjh opened 4 months ago
0
Remove HP vs HP (w/o PHENIO) stages

#34 caufieldjh closed 4 months ago
0
Store output similarity tables on alternative, public location

#33 caufieldjh opened 4 months ago
0
Remove stage `Run similarity for HP vs HP through HP alone`

#32 caufieldjh closed 4 months ago
0
Determine whether PHENIO edges are necessary in calculating HP vs HP semsim

#31 caufieldjh closed 4 months ago
4
Produce log for overall build process

#30 caufieldjh opened 5 months ago
3
Fix incorrect HP vs ZP output filename

#29 caufieldjh closed 5 months ago
0
Another file path issue: HP vs ZP is using incorrect path for joined table output

#28 caufieldjh closed 5 months ago
0
Fix name of HPO_terms.tsv

#27 caufieldjh closed 5 months ago
0
Another file path issue: HP vs MP can't find HP termset TSV

#26 caufieldjh closed 5 months ago
0
Fix name of HP vs HP ontoonly upload

#25 caufieldjh closed 5 months ago
0
Call to s3cmd fails with "nothing to upload"

#24 caufieldjh closed 5 months ago
0
Fix a lingering incorrect filename

#23 caufieldjh closed 5 months ago
0
Fix issues with string parsing

#22 caufieldjh closed 5 months ago
0
Jenkins string replacement and parsing errors

#21 caufieldjh closed 5 months ago
3
Correct path to HPO_terms.tsv

#20 caufieldjh closed 5 months ago
0
Call to duckdb includes incorrect filepath

#19 caufieldjh closed 5 months ago
0
Extract duckdb with python zipfile

#18 caufieldjh closed 5 months ago
0
Install `unzip`

#17 caufieldjh closed 5 months ago
0
unzip: not found

#16 caufieldjh closed 5 months ago
2
Adjustments for debugging and ease of use

#15 caufieldjh closed 5 months ago
1
Consider adding HP associations when doing HPvMP and HPvZP comparisons

#14 caufieldjh opened 5 months ago
0
Include metadata along with each table

#13 caufieldjh opened 5 months ago
1
Handle cases of CURIEs in closure but not in IC map

#12 caufieldjh opened 5 months ago
0
Add HTML file to enable browser-based viewing

#11 caufieldjh opened 5 months ago
0
Test use_custom_ic on Jenkins

#10 caufieldjh closed 5 months ago
1
Updates to produce new, better phenotype comparisons

#9 caufieldjh closed 5 months ago
17
Update to use semsimian's custom IC maps

#8 caufieldjh closed 5 months ago
2
Log the memory peak

#7 caufieldjh opened 9 months ago
0
Align with monarch-initiative/monarch-semantic-similarity-profiles

#6 matentzn opened 1 year ago
0
Update Jenkins build for most recent oaklib and semsimian

#5 caufieldjh closed 1 year ago
0
Produce smaller output

#4 caufieldjh closed 1 year ago
0
Compress the output

#3 caufieldjh closed 1 year ago
0
Omit labels from output

#2 caufieldjh closed 1 year ago
0
Duplicate prefix breaks run

#1 caufieldjh closed 1 year ago
7