Merge pull request #486 from monarch-initiative/evidence_count

Uses 2.0 closurizer and gets monarch-py from a branch to bring in the evidence_count field
monarch-initiative · Jul 7, 2023 · 7bd91ab · 7bd91ab
2 parents ecfe984 + ed13bfc
commit 7bd91ab
Show file tree

Hide file tree

Showing 3 changed files with 36 additions and 28 deletions.
diff --git a/poetry.lock b/poetry.lock
diff --git a/pyproject.toml b/pyproject.toml
@@ -19,8 +19,9 @@ python = "^3.10"
 kghub-downloader = "^0.3.2"
 koza = "^0.3.0"
 cat-merge = "^0.1.18"
-closurizer = "^0.1.7"
-monarch-py = "^0.12.3"
+closurizer = "^0.2.0"
+#monarch-py = "^0.12.3"
+monarch-py = {git = "https://github.com/monarch-initiative/monarch-app.git", branch = "evidence_count", subdirectory = "backend"}
 kgx = "^2.1.0"
 multi-indexer = "*"
 biolink-model = "3.5.0"

diff --git a/src/monarch_ingest/cli_utils.py b/src/monarch_ingest/cli_utils.py
@@ -323,7 +323,8 @@ def apply_closure(
                         'frequency_qualifier',
                         'onset_qualifier',
                         'sex_qualifier',
-                        'stage_qualifier'])
+                        'stage_qualifier'],
+                evidence_fields=['has_evidence', 'publications', 'primary_knowledge_source', 'provided_by'])
     sh.gzip(output_file, force=True)
 
 def load_sqlite():