From 1cd0c31d05c3c1fcfc1faf7d7c17e8f7941077e4 Mon Sep 17 00:00:00 2001
From: Joe Flack <joeflack4@gmail.com>
Date: Thu, 6 Jun 2024 16:46:55 -0400
Subject: [PATCH] HGNC ROBOT template - Rename: mondo_genes.csv -->
 mondo_genes.robot.tsv

---
 .github/workflows/buid_and_release.yml |  2 +-
 .gitignore                             |  2 +-
 README.md                              | 17 ++++--
 makefile                               | 14 ++++-
 run.sh                                 | 85 ++++++++++++++++++++++++++
 5 files changed, 111 insertions(+), 9 deletions(-)
 create mode 100644 run.sh

diff --git a/.github/workflows/buid_and_release.yml b/.github/workflows/buid_and_release.yml
index 747c4d1..c2a4638 100644
--- a/.github/workflows/buid_and_release.yml
+++ b/.github/workflows/buid_and_release.yml
@@ -40,4 +40,4 @@ jobs:
         files: |
           omim.owl
           omim.sssom.tsv
-          mondo_genes.csv
+          mondo_genes.robot.tsv
diff --git a/.gitignore b/.gitignore
index 00a176d..ae2ebb0 100644
--- a/.gitignore
+++ b/.gitignore
@@ -34,4 +34,4 @@ omim.json
 mondo_exactmatch_omim.sssom.tsv
 mondo_exactmatch_omimps.sssom.tsv
 omim.owl
-mondo_genes.csv
+mondo_genes.robot.tsv
diff --git a/README.md b/README.md
index 48f105d..05bbaae 100644
--- a/README.md
+++ b/README.md
@@ -5,7 +5,7 @@ OMIM stands for "Online Mendelian Inheritance in Man", and is an online
 catalog of human genes and genetic disorders. The official site is: https://omim.org/
 
 This purpose of this repository is for data transformations for ingest into Mondo. Mainly, 
-it is for generating an `omim.ttl` file.
+it is for generating an `omim.ttl` and other release artefacts.
 
 Disclaimer: This repository and its created data artefacts are unnofficial. For 
 official, up-to-date OMIM data, please visit [omim.org](https://omim.org).
@@ -31,10 +31,10 @@ you get an error related to this when installing, ignore it, as it is does not
 seem to be needed to run any of the tools. If however you do get a `psutil` error
 when running anything, please let us know by [creating an issue](https://github.com/monarch-initiative/omim/issues/new).
 
-## Running & creating `omim.ttl`
-Run: `make all`
+## Running & creating release
+Run: `sh run.sh make all`
 
-Running this will create a new `omim.ttl` file in the root directory.
+Running this will create new release artefacts in the root directory.
 
 You can also run `make build` or `python -m omim2obo`. These are all the same 
 command. This will download files from omim.org and run the build.
@@ -44,8 +44,11 @@ If there's an issue downloading the files, or you are offline, or you just want
 to use the cache anyway, you can pass the `--use-cache` flag.
 
 ## Additional tools
+<details><summary>Details</summary>
+<p>
+
 ### Get PMIDs used for OMIM codes from `omim.ttl`
-Command: `make get-pmids`
+Command: `sh run.sh make get-pmids`
 
 ### OMIM Code Web Scraper
 Currently, the only feature is `get_codes_by_yyyy_mm`, which returns a list of 
@@ -86,3 +89,7 @@ from omim2obo.omim_code_scraper import get_codes_by_yyyy_mm
 
 code_tuples = get_codes_by_yyyy_mm('2021/05')
 ```
+
+
+</p>
+</details> 
diff --git a/makefile b/makefile
index 11f3af7..ef8f94b 100644
--- a/makefile
+++ b/makefile
@@ -2,7 +2,7 @@
 
 
 # MAIN COMMANDS / GOALS ------------------------------------------------------------------------------------------------
-all: omim.ttl omim.sssom.tsv omim.owl mondo_genes.csv
+all: omim.ttl omim.sssom.tsv omim.owl mondo_genes.robot.tsv
 
 # build: Create new omim.ttl
 omim.ttl:
@@ -35,8 +35,18 @@ omim.owl: omim.ttl mondo_exactmatch_omim.sssom.owl mondo_exactmatch_omimps.sssom
 		query --update sparql/hgnc_links.ru \
 		convert -f ofn -o $@
 
-mondo_genes.csv: omim.owl
+mondo_genes.robot.tsv: omim.owl
+	# Create a TSV of relational information for gene and disease classes
 	robot query -i omim.owl --query sparql/mondo_genes.sparql $@
+	# Insert the source_code column as the second to last column
+	awk 'BEGIN {FS=OFS="\t"} {if (NR==1) {$$(NF+1)=$$(NF); $$(NF-1)="?source_code";} else {$$(NF+1)=$$(NF); $$(NF-1)="MONDO:OMIM";}} 1' $@ > temp_file && mv temp_file $@
+	# Remove the first character of each field in the header
+	awk 'BEGIN {FS=OFS="\t"} NR==1 {for (i=1; i<=NF; i++) $$i=substr($$i, 2)} {print}' $@ > temp_file && mv temp_file $@
+	# Remove < and > characters from specified columns
+	awk 'BEGIN {FS=OFS="\t"} NR>1 {gsub(/^<|>$$/, "", $$1); gsub(/^<|>$$/, "", $$2); gsub(/^<|>$$/, "", $$5)} {print}' $@ > temp_file && mv temp_file $@
+	# Insert ROBOT subheader
+	robot_subheader="ID\tSC 'has material basis in germline mutation in' some %\t>A oboInOwl:source\t>A oboInOwl:source\t" && \
+	sed 1a"$$robot_subheader" $@ > temp_file && mv temp_file $@
 
 cleanup:
 	@rm -f omim.json
diff --git a/run.sh b/run.sh
new file mode 100644
index 0000000..1f6db72
--- /dev/null
+++ b/run.sh
@@ -0,0 +1,85 @@
+#!/bin/sh
+# Wrapper script for docker.
+#
+# This is used primarily for wrapping the GNU Make workflow.
+# Instead of typing "make TARGET", type "./run.sh make TARGET".
+# This will run the make workflow within a docker container.
+#
+# The assumption is that you are working in the src/ontology folder;
+# we therefore map the whole repo (../..) to a docker volume.
+#
+# To use singularity instead of docker, please issue
+# export USE_SINGULARITY=<any-value>
+# before running this script.
+#
+# See README-editors.md for more details.
+
+if [ -f run.sh.conf ]; then
+    . ./run.sh.conf
+fi
+
+# Look for a GitHub token
+if [ -n "$GH_TOKEN" ]; then
+    :
+elif [ -f ../../.github/token.txt ]; then
+    GH_TOKEN=$(cat ../../.github/token.txt)
+elif [ -f $XDG_CONFIG_HOME/ontology-development-kit/github/token ]; then
+    GH_TOKEN=$(cat $XDG_CONFIG_HOME/ontology-development-kit/github/token)
+elif [ -f "$HOME/Library/Application Support/ontology-development-kit/github/token" ]; then
+    GH_TOKEN=$(cat "$HOME/Library/Application Support/ontology-development-kit/github/token")
+fi
+
+ODK_IMAGE=${ODK_IMAGE:-odkfull}
+TAG_IN_IMAGE=$(echo $ODK_IMAGE | awk -F':' '{ print $2 }')
+if [ -n "$TAG_IN_IMAGE" ]; then
+  # Override ODK_TAG env var if IMAGE already includes a tag
+  ODK_TAG=$TAG_IN_IMAGE
+  ODK_IMAGE=$(echo $ODK_IMAGE | awk -F':' '{ print $1 }')
+fi
+ODK_TAG=${ODK_TAG:-v1.4.3}
+ODK_JAVA_OPTS=${ODK_JAVA_OPTS:--Xmx20G}
+ODK_DEBUG=${ODK_DEBUG:-no}
+
+# Convert OWLAPI_* environment variables to the OWLAPI as Java options
+# See http://owlcs.github.io/owlapi/apidocs_4/org/semanticweb/owlapi/model/parameters/ConfigurationOptions.html
+# for a list of allowed options
+OWLAPI_OPTIONS_NAMESPACE=org.semanticweb.owlapi.model.parameters.ConfigurationOptions
+for owlapi_var in $(env | sed -n s/^OWLAPI_//p) ; do
+    ODK_JAVA_OPTS="$ODK_JAVA_OPTS -D$OWLAPI_OPTIONS_NAMESPACE.${owlapi_var%=*}=${owlapi_var#*=}"
+done
+
+TIMECMD=
+if [ x$ODK_DEBUG = xyes ]; then
+    # If you wish to change the format string, take care of using
+    # non-breaking spaces (U+00A0) instead of normal spaces, to
+    # prevent the shell from tokenizing the format string.
+    echo "Running ${IMAGE} with ${ODK_JAVA_OPTS} of memory for ROBOT and Java-based pipeline steps."
+    TIMECMD="/usr/bin/time -f ### DEBUG STATS ###\nElapsed time: %E\nPeak memory: %M kb"
+fi
+
+VOLUME_BIND=$PWD:/work
+WORK_DIR=/work
+
+if [ -n "$ODK_BINDS" ]; then
+    VOLUME_BIND="$VOLUME_BIND,$ODK_BINDS"
+fi
+
+if [ -n "$USE_SINGULARITY" ]; then
+
+    singularity exec --cleanenv $ODK_SINGULARITY_OPTIONS \
+        --env "ROBOT_JAVA_ARGS=$ODK_JAVA_OPTS,JAVA_OPTS=$ODK_JAVA_OPTS" \
+        --bind $VOLUME_BIND \
+        -W $WORK_DIR \
+        docker://obolibrary/$ODK_IMAGE:$ODK_TAG $TIMECMD "$@"
+else
+    BIND_OPTIONS="-v $(echo $VOLUME_BIND | sed 's/,/ -v /')"
+    docker run $ODK_DOCKER_OPTIONS $BIND_OPTIONS -w $WORK_DIR \
+        -e ROBOT_JAVA_ARGS="$ODK_JAVA_OPTS" -e JAVA_OPTS="$ODK_JAVA_OPTS" \
+        --rm -ti obolibrary/$ODK_IMAGE:$ODK_TAG $TIMECMD "$@"
+fi
+
+case "$@" in
+*update_repo*|*release*)
+    echo "Please remember to update your ODK image from time to time: https://oboacademy.github.io/obook/howto/odk-update/."
+    ;;
+esac
\ No newline at end of file