Working inside the odk container

Intro

A little guidance on how to quickly set up an OBO-compliant ontology development environment using the INCATools Ontology Development Kit.

Boot

Pull the odkfull instance from dockerhub. You only need to do this when you need a new dockerfile or you need updates.

docker pull obolibrary/odkfull

Run a bash terminal in the container interactively with enough memory to handle CHEBI and NCBITaxon.

docker run --cpus 4 --memory="6g" -it obolibrary/odkfull /bin/bash

You'll get a swapiness error, but the containerised bash should load with a bash-#.# prompt

Perform Makefile-driven and memory-hogging task

Clone the ontology repo you want to work with and get into the src directory

git clone https://github.com/EnvironmentOntology/biorealm.git
cd biorealm/src/ontology/

MAKE SURE YOU'RE ON THE BRANCH YOU WANT TO BE ON You'll be on master by default.

If this is a freshly spun up container, you'll need to refresh your git user ID variables:

git config --global user.email "[YOUR EMAIL]"
git config --global user.name "[YOUR GITHUB USER NAME]"

Let's attempt a CHEBI min-graph import...

  make imports/chebi_import.owl
``

Here's the abbreviated trace:

  make imports/chebi_import.owl
wget --no-check-certificate http://purl.obolibrary.org/obo/chebi.owl -O
mirror/chebi-local.owl && touch mirror/chebi-local.owl
--2019-09-04 09:23:59--  http://purl.obolibrary.org/obo/chebi.owl
Resolving purl.obolibrary.org... 52.3.123.63
Connecting to purl.obolibrary.org|52.3.123.63|:80... connected.
HTTP request sent, awaiting response... 302 Found
Location: ftp://ftp.ebi.ac.uk/pub/databases/chebi/ontology/chebi.owl
[following]
--2019-09-04 09:23:59--
ftp://ftp.ebi.ac.uk/pub/databases/chebi/ontology/chebi.owl
            => 'mirror/chebi-local.owl'
Resolving ftp.ebi.ac.uk... 193.62.197.74
Connecting to ftp.ebi.ac.uk|193.62.197.74|:21... connected.
Logging in as anonymous ... Logged in!
==> SYST ... done.    ==> PWD ... done.
==> TYPE I ... done.  ==> CWD (1) /pub/databases/chebi/ontology ... done.
==> SIZE chebi.owl ... 497796725
==> PASV ... done.    ==> RETR chebi.owl ... done.
Length: 497796725 (475M) (unauthoritative)

chebi.owl
100%[====================================================================================================================>]
474.74M  90.2MB/s    in 5.5s

2019-09-04 09:24:05 (86.8 MB/s) - 'mirror/chebi-local.owl' saved [497796725]

owltools --no-debug mirror/chebi-local.owl --log-debug
--remove-annotation-assertions -l --remove-dangling-annotations
--make-subset-by-properties -f BFO:0000050 BFO:0000051 RO:0002202
immediate_transformation_of RO:0002176 IAO:0000136  -o mirror/chebi.owl
2019-09-04 09:24:56,750 INFO  (CommandRunner:1219) Number of annotation
assertion axioms:1785995
2019-09-04 09:24:56,752 INFO  (CommandRunner:1220) Axioms to preserve:151506
2019-09-04 09:24:56,807 INFO  (CommandRunner:1222) Number of annotation
assertion axioms being removed:1634489
2019-09-04 09:24:56,808 INFO  (CommandRunner:1231) Total number of
axioms being removed, including annotation properties:1634522
2019-09-04 09:25:00,567 INFO  (Sim2CommandRunner:211) Removing 0 axioms

[...]

robot annotate --input modules/entity_quality_location.tmp.owl -O
http://purl.obolibrary.org/obo/envo/modules/entity_quality_location.owl
--output modules/entity_quality_location.owl && rm
modules/entity_quality_location.tmp.owl
owltools --catalog-xml catalog-v001.xml envo-edit.owl
--merge-imports-closure --export-table imports/seed.tsv.tmp && cut -f1
imports/seed.tsv.tmp | grep purl.obolib | sort -u > imports/seed.tsv
cut -f1 imports/chebi_terms.txt imports/seed.tsv | sort -u >
imports/chebi_combined_seed.tsv
robot extract -i mirror/chebi.owl -T imports/chebi_combined_seed.tsv -m
BOT -O http://purl.obolibrary.org/obo/envo/imports/chebi_import.owl -o
imports/chebi_import.owl.tmp.owl && mv imports/chebi_import.owl.tmp.owl
imports/chebi_import.owl
rm imports/chebi_combined_seed.tsv

Push changes back to ontology repo

Let's push the changes. You'll likely need to declare the git user variables the first time you run the container (or if it updates)

bash-4.4# git status
On branch master
Your branch is up to date with 'origin/master'.

Changes not staged for commit:
   (use "git add <file>..." to update what will be committed)
   (use "git checkout -- <file>..." to discard changes in working directory)

         modified:   imports/chebi_import.owl

Untracked files:
   (use "git add <file>..." to include in what will be committed)

         dosdp-tools.log
         imports/seed.tsv

no changes added to commit (use "git add" and/or "git commit -a")

bash-4.4# git add -u
bash-4.4# git commit -m 'updated CHEBI import'

*** Please tell me who you are.

Run

   git config --global user.email "[email protected]"
   git config --global user.name "Your Name"

to set your account's default identity.
Omit --global to set the identity only in this repository.

fatal: unable to auto-detect email address (got 'root@7e6002aeea91.(none)')


bash-4.4# git config --global user.email "[YOUR EMAIL]"
bash-4.4# git config --global user.name "[YOUR GITHUB USERNAME]"
bash-4.4# git commit -m 'updated CHEBI import'
[master a637c36] updated CHEBI import
  1 file changed, 11 insertions(+), 2 deletions(-)
bash-4.4# git push

Enumerating objects: 11, done.
Counting objects: 100% (11/11), done.
Delta compression using up to 40 threads
Compressing objects: 100% (6/6), done.
Writing objects: 100% (6/6), 599 bytes | 599.00 KiB/s, done.
Total 6 (delta 4), reused 0 (delta 0)
remote: Resolving deltas: 100% (4/4), completed with 4 local objects.
To https://github.com/EnvironmentOntology/envo.git
    6c707c3..a637c36  master -> master

Profit