Merge pull request #7 from monarch-initiative/branch-review

Branch review code for node obsoletion

.gitignore

@@ -135,5 +135,7 @@ tests/input/example-relation-graph.tsv.gz
 .vscode/*
 **/__pycache__/**
 tmp/*
+reports/*
+
 !tmp/.keep
 !tmp/mondo_validate*

Makefile

@@ -22,7 +22,13 @@ tmp/mondo_edit.obo:
 tmp/mondo.owl: tmp/mondo_edit.obo
 	robot convert -i $< --output $@
 
-tmp/mondo.db: tmp/mondo.owl
+tmp/mondo-relaxed-branchreview.owl: tmp/mondo_edit.obo
+	robot merge -i $< -i $< relax -o $@
+
+tmp/mondo-reasoned-branchreview.owl: tmp/mondo_edit.obo
+	robot merge -i $< -i $< reason -o $@
+
+tmp/mondo%.db: tmp/mondo%.owl
 	$(RUN) semsql make $@
 	rm -f .template.db
 	rm -f tmp/mondo-relation-graph.tsv.gz
@@ -36,7 +42,15 @@ tmp/mondo_validate_full.tsv: tmp/mondo.db
 tmp/mondo_validate.tsv: tmp/mondo_validate_full.tsv
 	$(RUN) mondoqc validate $< -o $@
 
+obsoletion-tables: tmp/mondo-relaxed-branchreview.db  tmp/mondo-reasoned-branchreview.db
+	for id in $(shell cat src/mondolib/config/branch_ids.tsv); do \
+        $(RUN) mondoqc create-review-table -i tmp/mondo-reasoned-branchreview.db -o tmp/mondo-reasoned-branch-$$id-review.tsv -f src/mondolib/config/obsoletion_terms.tsv -b $$id;\
+		$(RUN) mondoqc create-review-table -i tmp/mondo-relaxed-branchreview.db -o tmp/mondo-relaxed-branch-$$id-review.tsv -f src/mondolib/config/obsoletion_terms.tsv -b $$id;\
+		$(RUN) mondoqc relax-and-reason -i tmp/mondo-reasoned-branch-$$id-review.tsv -i tmp/mondo-relaxed-branch-$$id-review.tsv -r tmp/mondo-relaxed-branchreview.db   -f src/mondolib/config/obsoletion_terms.tsv -o reports/mondo-combined-branch-$$id-review.tsv;\
+    done
+
 lexmatch: tmp/mondo_lexmatch.sssom.tsv
 validate: tmp/mondo_validate.tsv
+
 clear-tmp:
 	rm -rf tmp/*

pyproject.toml

@@ -42,6 +42,7 @@ target-version = ["py38", "py39", "py310"]
 extend-ignore = [
     "D211",  # `no-blank-line-before-class`
     "D212",  # `multi-line-summary-first-line`
+    "B005",  # Using `.strip()` with multi-character strings is misleading the reader
     ]
 exclude = [
     "src/mondolib/datamodels/*"

src/mondolib/cli.py

@@ -4,7 +4,7 @@
 import click
 
 from mondolib import __version__
-from mondolib.main import validate
+from mondolib.main import create_review_table, relax_and_reason, validate
 
 __all__ = [
     "main",
@@ -42,5 +42,34 @@ def click_validate(input: str, output: str):
     validate(input, output)
 
 
+@main.command("create-review-table")
+@click.option("-i", "--input", help="DB source file.")
+@click.option("-b", "--branch-id", help="Branch ID")
+@click.option("-B", "--branch-id-file", help="TSV with one column of obsoletion CURIEs")
+@click.option(
+    "-f",
+    "--obsoletion-candidates-file",
+    help="TSV with one column of obsoletion CURIEs",
+)
+@click.option("-o", "--output-file", help="Path to report file")
+def click_create_review_table(branch_id, branch_id_file, obsoletion_candidates_file, output_file, input):
+    """Create review table."""
+    create_review_table(branch_id, branch_id_file, obsoletion_candidates_file, output_file, input)
+
+
+@main.command("relax-and-reason")
+@click.option("-i", "--input", help="branch review files to be combined.", multiple=True)
+@click.option(
+    "-f",
+    "--obsoletion-candidates-file",
+    help="TSV with one column of obsoletion CURIEs",
+)
+@click.option("-o", "--output-file", help="Path to report file")
+@click.option("-r", "--relaxed-resource", help="DB source file.")
+def click_relax_and_reason(input, obsoletion_candidates_file, output_file, relaxed_resource):
+    """Create final output takinf `reason` and `relax` output of resource via robot."""
+    relax_and_reason(input, obsoletion_candidates_file, output_file, relaxed_resource)
+
+
 if __name__ == "__main__":
     main()

src/mondolib/config/branch_ids.tsv

@@ -0,0 +1,39 @@
+MONDO:0002409
+MONDO:0002657
+MONDO:0045024
+MONDO:0004995
+MONDO:0019040
+MONDO:0003900
+MONDO:0004335
+MONDO:0021147
+MONDO:0002022
+MONDO:0024458
+MONDO:0005151
+MONDO:0005570
+MONDO:0003847
+MONDO:0043543
+MONDO:0700007
+MONDO:0005046
+MONDO:0005550
+MONDO:0021166
+MONDO:0002051
+MONDO:0005066
+MONDO:0044970
+MONDO:0006858
+MONDO:0002081
+MONDO:0005071
+MONDO:0005137
+MONDO:0700003
+MONDO:0100366
+MONDO:0024623
+MONDO:0100086
+MONDO:0029000
+MONDO:0021669
+MONDO:0002025
+MONDO:0043459
+MONDO:0005039
+MONDO:0005087
+MONDO:0002254
+MONDO:0043839
+MONDO:0044991
+MONDO:0002118