HPO releases with ODK and github

Running the release pipeline

Preparation

• get and install docker + set docker memory to ~8GB

Step 1

• lock hp (via mailinglist)

• docker pull obolibrary/odkfull

• git pull in hpo folder

• cd src/ontology

• sh run.sh make prepare_release hpo_diff -B >> log.txt

Step 2

... wait ...

Step 3

if something goes wrong. panic and call seb or nico.

Step 4

• Semantic diff: sh run.sh robot diff --left ../../hp.owl --right-iri http://purl.obolibrary.org/obo/hp.owl -o hp_robot_diff.txt

Step 5

Push the generated files to github. ONLY DO THIS IF YOU REALLY WANT TO RELEASE! (the purl directs to the master branch)

Step 6

run the HPO-annotation jobs locally (because jenkins isn't working anymore)

Step 7

make the release on github web interface

!!Append the annotation files from step 6 to the github release!!

Step 8

announce:

• monarch-list
• hpo-list
• twitter
• hpo-web

---

Notes:

Implemented a system which allows bypassing of mirroring and imports using parameters.

you can now use:

sh run.sh make IMP=false prepare_release

to prevent both import and mirror generation and

sh run.sh make MIR=false prepare_release

to prevent mirror generation (but still recreated the imports).

From Nico:

First, make sure that you have the latest ODK installed:

docker pull obolibrary/odkfull To run the full release pipeline (this includes imports):

cd src/ontology sh run.sh make prepare_release This command will produce hp.owl and hp.obo and copy it onto the top level of the hp repository.

To reduce avoid imports being recreated, you can and a parameter as follows:

cd src/ontology sh run.sh make IMP=false prepare_release If you instead want to merely avoid the dependent ontologies to be downloaded again, you can run:

cd src/ontology sh run.sh make MIR=false prepare_release Using IMP=false implies MIR=false.

Running the test pipeline locally (not the release pipeline):

cd src/ontology sh run.sh make test Note that this does not execute the full Travis test pipeline (which involves many more custom checks).