From 281902a0a3bbde6a0e0c897620374fd35d90c2be Mon Sep 17 00:00:00 2001
From: hunterckx <118154470+hunterckx@users.noreply.github.com>
Date: Mon, 26 May 2025 12:18:32 -0700
Subject: [PATCH 1/8] refactor: move catalog build package to be directly under
 catalog directory (#540)

---
 .../py/{build-files-from-ncbi.py => build_files_from_ncbi.py}   | 2 +-
 .../{build/py/package => py_package}/catalog_build/__init__.py  | 0
 catalog/{build/py/package => py_package}/catalog_build/build.py | 0
 catalog/{build/py/package => py_package}/setup.py               | 0
 package.json                                                    | 2 +-
 5 files changed, 2 insertions(+), 2 deletions(-)
 rename catalog/build/py/{build-files-from-ncbi.py => build_files_from_ncbi.py} (96%)
 rename catalog/{build/py/package => py_package}/catalog_build/__init__.py (100%)
 rename catalog/{build/py/package => py_package}/catalog_build/build.py (100%)
 rename catalog/{build/py/package => py_package}/setup.py (100%)

diff --git a/catalog/build/py/build-files-from-ncbi.py b/catalog/build/py/build_files_from_ncbi.py
similarity index 96%
rename from catalog/build/py/build-files-from-ncbi.py
rename to catalog/build/py/build_files_from_ncbi.py
index 30c70f6e..279a84e6 100644
--- a/catalog/build/py/build-files-from-ncbi.py
+++ b/catalog/build/py/build_files_from_ncbi.py
@@ -1,4 +1,4 @@
-from package.catalog_build import build_files
+from ...py_package.catalog_build import build_files
 
 ASSEMBLIES_PATH = "catalog/source/assemblies.yml"
 ORGANISMS_PATH = "catalog/source/organisms.yml"
diff --git a/catalog/build/py/package/catalog_build/__init__.py b/catalog/py_package/catalog_build/__init__.py
similarity index 100%
rename from catalog/build/py/package/catalog_build/__init__.py
rename to catalog/py_package/catalog_build/__init__.py
diff --git a/catalog/build/py/package/catalog_build/build.py b/catalog/py_package/catalog_build/build.py
similarity index 100%
rename from catalog/build/py/package/catalog_build/build.py
rename to catalog/py_package/catalog_build/build.py
diff --git a/catalog/build/py/package/setup.py b/catalog/py_package/setup.py
similarity index 100%
rename from catalog/build/py/package/setup.py
rename to catalog/py_package/setup.py
diff --git a/package.json b/package.json
index fa913355..4083e02a 100644
--- a/package.json
+++ b/package.json
@@ -15,7 +15,7 @@
     "prepare": "husky",
     "test": "jest --runInBand",
     "build-brc-db": "esrun catalog/build/ts/build-catalog.ts",
-    "build-files-from-ncbi": "python3 ./catalog/build/py/build-files-from-ncbi.py",
+    "build-files-from-ncbi": "python3 -m catalog.build.py.build_files_from_ncbi",
     "iwc-manifest-to-workflows-yaml": "python3 ./catalog/build/py/iwc_manifest_to_workflows_yaml.py --exclude-other",
     "gen-schema": "./catalog/schema/scripts/gen-schema.sh",
     "test-gen-python": "./catalog/schema/scripts/test-gen-python.sh",

From a5cb1ef98a92b0ee332c3c02edce7f48f14ff780 Mon Sep 17 00:00:00 2001
From: hunterckx <118154470+hunterckx@users.noreply.github.com>
Date: Mon, 26 May 2025 12:38:52 -0700
Subject: [PATCH 2/8] refactor: move schema source files to catalog build
 package (#540)

---
 .../{ => py_package/catalog_build}/schema/assemblies.yaml   | 2 +-
 .../catalog_build}/schema/enums/organism_ploidy.yaml        | 2 +-
 .../catalog_build}/schema/enums/outbreak_priority.yaml      | 2 +-
 .../catalog_build}/schema/enums/outbreak_resource_type.yaml | 2 +-
 .../catalog_build}/schema/enums/workflow_category_id.yaml   | 2 +-
 .../schema/enums/workflow_parameter_variable.yaml           | 2 +-
 .../catalog_build}/schema/enums/workflow_ploidy.yaml        | 2 +-
 .../{ => py_package/catalog_build}/schema/organisms.yaml    | 2 +-
 .../{ => py_package/catalog_build}/schema/outbreaks.yaml    | 2 +-
 catalog/{ => py_package/catalog_build}/schema/schema.yaml   | 2 +-
 .../catalog_build}/schema/workflow_categories.yaml          | 2 +-
 .../{ => py_package/catalog_build}/schema/workflows.yaml    | 2 +-
 catalog/schema/scripts/gen-schema.sh                        | 6 +++---
 catalog/schema/scripts/test-gen-python.sh                   | 2 +-
 catalog/schema/scripts/validate-catalog.sh                  | 2 +-
 15 files changed, 17 insertions(+), 17 deletions(-)
 rename catalog/{ => py_package/catalog_build}/schema/assemblies.yaml (91%)
 rename catalog/{ => py_package/catalog_build}/schema/enums/organism_ploidy.yaml (78%)
 rename catalog/{ => py_package/catalog_build}/schema/enums/outbreak_priority.yaml (80%)
 rename catalog/{ => py_package/catalog_build}/schema/enums/outbreak_resource_type.yaml (81%)
 rename catalog/{ => py_package/catalog_build}/schema/enums/workflow_category_id.yaml (87%)
 rename catalog/{ => py_package/catalog_build}/schema/enums/workflow_parameter_variable.yaml (81%)
 rename catalog/{ => py_package/catalog_build}/schema/enums/workflow_ploidy.yaml (79%)
 rename catalog/{ => py_package/catalog_build}/schema/organisms.yaml (93%)
 rename catalog/{ => py_package/catalog_build}/schema/outbreaks.yaml (97%)
 rename catalog/{ => py_package/catalog_build}/schema/schema.yaml (84%)
 rename catalog/{ => py_package/catalog_build}/schema/workflow_categories.yaml (94%)
 rename catalog/{ => py_package/catalog_build}/schema/workflows.yaml (98%)

diff --git a/catalog/schema/assemblies.yaml b/catalog/py_package/catalog_build/schema/assemblies.yaml
similarity index 91%
rename from catalog/schema/assemblies.yaml
rename to catalog/py_package/catalog_build/schema/assemblies.yaml
index 30122042..c2e3d9b0 100644
--- a/catalog/schema/assemblies.yaml
+++ b/catalog/py_package/catalog_build/schema/assemblies.yaml
@@ -1,4 +1,4 @@
-id: https://github.com/galaxyproject/brc-analytics/blob/main/catalog/schema/assemblies.yaml#
+id: https://github.com/galaxyproject/brc-analytics/blob/main/catalog/py_package/catalog_build/schema/assemblies.yaml#
 name: assemblies
 description: Schema for source assembly list.
 
diff --git a/catalog/schema/enums/organism_ploidy.yaml b/catalog/py_package/catalog_build/schema/enums/organism_ploidy.yaml
similarity index 78%
rename from catalog/schema/enums/organism_ploidy.yaml
rename to catalog/py_package/catalog_build/schema/enums/organism_ploidy.yaml
index 7d5f4ce2..807d3cd5 100644
--- a/catalog/schema/enums/organism_ploidy.yaml
+++ b/catalog/py_package/catalog_build/schema/enums/organism_ploidy.yaml
@@ -1,4 +1,4 @@
-id: https://github.com/galaxyproject/brc-analytics/blob/main/catalog/schema/enums/organism_ploidy.yaml#
+id: https://github.com/galaxyproject/brc-analytics/blob/main/catalog/py_package/catalog_build/schema/enums/organism_ploidy.yaml#
 name: enums_organism_ploidy
 
 enums:
diff --git a/catalog/schema/enums/outbreak_priority.yaml b/catalog/py_package/catalog_build/schema/enums/outbreak_priority.yaml
similarity index 80%
rename from catalog/schema/enums/outbreak_priority.yaml
rename to catalog/py_package/catalog_build/schema/enums/outbreak_priority.yaml
index 7dc944ef..60346a40 100644
--- a/catalog/schema/enums/outbreak_priority.yaml
+++ b/catalog/py_package/catalog_build/schema/enums/outbreak_priority.yaml
@@ -1,4 +1,4 @@
-id: https://github.com/galaxyproject/brc-analytics/blob/main/catalog/schema/enums/outbreak_priority.yaml#
+id: https://github.com/galaxyproject/brc-analytics/blob/main/catalog/py_package/catalog_build/schema/enums/outbreak_priority.yaml#
 name: enums_outbreak_priority
 
 enums:
diff --git a/catalog/schema/enums/outbreak_resource_type.yaml b/catalog/py_package/catalog_build/schema/enums/outbreak_resource_type.yaml
similarity index 81%
rename from catalog/schema/enums/outbreak_resource_type.yaml
rename to catalog/py_package/catalog_build/schema/enums/outbreak_resource_type.yaml
index bc5ade2a..23d09198 100644
--- a/catalog/schema/enums/outbreak_resource_type.yaml
+++ b/catalog/py_package/catalog_build/schema/enums/outbreak_resource_type.yaml
@@ -1,4 +1,4 @@
-id: https://github.com/galaxyproject/brc-analytics/blob/main/catalog/schema/enums/outbreak_resource_type.yaml#
+id: https://github.com/galaxyproject/brc-analytics/blob/main/catalog/py_package/catalog_build/schema/enums/outbreak_resource_type.yaml#
 name: enums_outbreak_resource_type
 
 enums:
diff --git a/catalog/schema/enums/workflow_category_id.yaml b/catalog/py_package/catalog_build/schema/enums/workflow_category_id.yaml
similarity index 87%
rename from catalog/schema/enums/workflow_category_id.yaml
rename to catalog/py_package/catalog_build/schema/enums/workflow_category_id.yaml
index 473193e2..18cd25fd 100644
--- a/catalog/schema/enums/workflow_category_id.yaml
+++ b/catalog/py_package/catalog_build/schema/enums/workflow_category_id.yaml
@@ -1,4 +1,4 @@
-id: https://github.com/galaxyproject/brc-analytics/blob/main/catalog/schema/enums/workflow_type.yaml#
+id: https://github.com/galaxyproject/brc-analytics/blob/main/catalog/py_package/catalog_build/schema/enums/workflow_type.yaml#
 name: enums_workflow_category_id
 description: Definition of the workflow category ID enum.
 
diff --git a/catalog/schema/enums/workflow_parameter_variable.yaml b/catalog/py_package/catalog_build/schema/enums/workflow_parameter_variable.yaml
similarity index 81%
rename from catalog/schema/enums/workflow_parameter_variable.yaml
rename to catalog/py_package/catalog_build/schema/enums/workflow_parameter_variable.yaml
index 5261d2d3..ae1bb3fd 100644
--- a/catalog/schema/enums/workflow_parameter_variable.yaml
+++ b/catalog/py_package/catalog_build/schema/enums/workflow_parameter_variable.yaml
@@ -1,4 +1,4 @@
-id: https://github.com/galaxyproject/brc-analytics/blob/main/catalog/schema/enums/workflow_parameter_variable.yaml#
+id: https://github.com/galaxyproject/brc-analytics/blob/main/catalog/py_package/catalog_build/schema/enums/workflow_parameter_variable.yaml#
 name: enums_workflow_parameter_variable
 
 enums:
diff --git a/catalog/schema/enums/workflow_ploidy.yaml b/catalog/py_package/catalog_build/schema/enums/workflow_ploidy.yaml
similarity index 79%
rename from catalog/schema/enums/workflow_ploidy.yaml
rename to catalog/py_package/catalog_build/schema/enums/workflow_ploidy.yaml
index 48d699b0..8177b53f 100644
--- a/catalog/schema/enums/workflow_ploidy.yaml
+++ b/catalog/py_package/catalog_build/schema/enums/workflow_ploidy.yaml
@@ -1,4 +1,4 @@
-id: https://github.com/galaxyproject/brc-analytics/blob/main/catalog/schema/enums/workflow_ploidy.yaml#
+id: https://github.com/galaxyproject/brc-analytics/blob/main/catalog/py_package/catalog_build/schema/enums/workflow_ploidy.yaml#
 name: enums_workflow_ploidy
 
 enums:
diff --git a/catalog/schema/organisms.yaml b/catalog/py_package/catalog_build/schema/organisms.yaml
similarity index 93%
rename from catalog/schema/organisms.yaml
rename to catalog/py_package/catalog_build/schema/organisms.yaml
index 80dcdc55..f4161b68 100644
--- a/catalog/schema/organisms.yaml
+++ b/catalog/py_package/catalog_build/schema/organisms.yaml
@@ -1,4 +1,4 @@
-id: https://github.com/galaxyproject/brc-analytics/blob/main/catalog/schema/organisms.yaml#
+id: https://github.com/galaxyproject/brc-analytics/blob/main/catalog/py_package/catalog_build/schema/organisms.yaml#
 name: organisms
 description: Schema for source organism info.
 
diff --git a/catalog/schema/outbreaks.yaml b/catalog/py_package/catalog_build/schema/outbreaks.yaml
similarity index 97%
rename from catalog/schema/outbreaks.yaml
rename to catalog/py_package/catalog_build/schema/outbreaks.yaml
index 8903a84c..cb2db45d 100644
--- a/catalog/schema/outbreaks.yaml
+++ b/catalog/py_package/catalog_build/schema/outbreaks.yaml
@@ -1,4 +1,4 @@
-id: https://github.com/galaxyproject/brc-analytics/blob/main/catalog/schema/outbreaks.yaml#
+id: https://github.com/galaxyproject/brc-analytics/blob/main/catalog/py_package/catalog_build/schema/outbreaks.yaml#
 name: outbreaks
 description: Schema for source outbreak info.
 
diff --git a/catalog/schema/schema.yaml b/catalog/py_package/catalog_build/schema/schema.yaml
similarity index 84%
rename from catalog/schema/schema.yaml
rename to catalog/py_package/catalog_build/schema/schema.yaml
index 0b342712..dffb5a39 100644
--- a/catalog/schema/schema.yaml
+++ b/catalog/py_package/catalog_build/schema/schema.yaml
@@ -1,4 +1,4 @@
-id: https://github.com/galaxyproject/brc-analytics/blob/main/catalog/schema/schema.yaml#
+id: https://github.com/galaxyproject/brc-analytics/blob/main/catalog/py_package/catalog_build/schema/schema.yaml#
 name: schema
 description: Combined source data schemas.
 
diff --git a/catalog/schema/workflow_categories.yaml b/catalog/py_package/catalog_build/schema/workflow_categories.yaml
similarity index 94%
rename from catalog/schema/workflow_categories.yaml
rename to catalog/py_package/catalog_build/schema/workflow_categories.yaml
index 54472d3c..7b4aca8c 100644
--- a/catalog/schema/workflow_categories.yaml
+++ b/catalog/py_package/catalog_build/schema/workflow_categories.yaml
@@ -1,4 +1,4 @@
-id: https://github.com/galaxyproject/brc-analytics/blob/main/catalog/schema/workflow_categories.yaml#
+id: https://github.com/galaxyproject/brc-analytics/blob/main/catalog/py_package/catalog_build/schema/workflow_categories.yaml#
 name: workflow_categories
 description: Schema for source workflow categories list.
 
diff --git a/catalog/schema/workflows.yaml b/catalog/py_package/catalog_build/schema/workflows.yaml
similarity index 98%
rename from catalog/schema/workflows.yaml
rename to catalog/py_package/catalog_build/schema/workflows.yaml
index 37c9cd91..e4ea274e 100644
--- a/catalog/schema/workflows.yaml
+++ b/catalog/py_package/catalog_build/schema/workflows.yaml
@@ -1,4 +1,4 @@
-id: https://github.com/galaxyproject/brc-analytics/blob/main/catalog/schema/workflows.yaml#
+id: https://github.com/galaxyproject/brc-analytics/blob/main/catalog/py_package/catalog_build/schema/workflows.yaml#
 name: workflows
 description: Schema for source workflows list.
 
diff --git a/catalog/schema/scripts/gen-schema.sh b/catalog/schema/scripts/gen-schema.sh
index 74195e92..f066f6c4 100755
--- a/catalog/schema/scripts/gen-schema.sh
+++ b/catalog/schema/scripts/gen-schema.sh
@@ -3,13 +3,13 @@
 source ./catalog/schema/scripts/source-file-schema-names.sh
 
 # Generate Pydantic models for all source data types
-gen-pydantic ./catalog/schema/schema.yaml > ./catalog/build/py/generated_schema/schema.py
+gen-pydantic ./catalog/py_package/catalog_build/schema/schema.yaml > ./catalog/build/py/generated_schema/schema.py
 
 # Generate TypeScript definitions for all source data types
-python3 ./catalog/schema/scripts/gen-typescript.py ./catalog/schema/schema.yaml > ./catalog/schema/generated/schema.ts
+python3 ./catalog/schema/scripts/gen-typescript.py ./catalog/py_package/catalog_build/schema/schema.yaml > ./catalog/schema/generated/schema.ts
 
 # Generate a JSON schema for each source file
 for name in ${SOURCE_FILE_SCHEMA_NAMES[@]}
 do
-  gen-json-schema "./catalog/schema/$name.yaml" > "./catalog/schema/generated/$name.json"
+  gen-json-schema "./catalog/py_package/catalog_build/schema/$name.yaml" > "./catalog/schema/generated/$name.json"
 done
diff --git a/catalog/schema/scripts/test-gen-python.sh b/catalog/schema/scripts/test-gen-python.sh
index 6a8e3d22..dbf0dd27 100755
--- a/catalog/schema/scripts/test-gen-python.sh
+++ b/catalog/schema/scripts/test-gen-python.sh
@@ -6,7 +6,7 @@ validation_failed=false
 
 for name in schema ${SOURCE_FILE_SCHEMA_NAMES[@]}
 do
-  gen-python "./catalog/schema/$name.yaml" > /dev/null
+  gen-python "./catalog/py_package/catalog_build/schema/$name.yaml" > /dev/null
   if [ $? -ne 0 ]; then
     validation_failed=true
   fi
diff --git a/catalog/schema/scripts/validate-catalog.sh b/catalog/schema/scripts/validate-catalog.sh
index 434da4bc..2f8432e2 100755
--- a/catalog/schema/scripts/validate-catalog.sh
+++ b/catalog/schema/scripts/validate-catalog.sh
@@ -7,7 +7,7 @@ validation_failed=false
 for name in ${SOURCE_FILE_SCHEMA_NAMES[@]}
 do
   echo "$name:"
-  linkml-validate -s "./catalog/schema/$name.yaml" "./catalog/source/$name.yml"
+  linkml-validate -s "./catalog/py_package/catalog_build/schema/$name.yaml" "./catalog/source/$name.yml"
   if [ $? -ne 0 ]; then
     validation_failed=true
   fi

From 278459cc485fae8cb225113b244204642c2d9886 Mon Sep 17 00:00:00 2001
From: hunterckx <118154470+hunterckx@users.noreply.github.com>
Date: Mon, 26 May 2025 14:25:17 -0700
Subject: [PATCH 3/8] feat: move validation script logic to package (#540)

---
 .../schema_utils/validate_catalog.py          | 48 +++++++++++++++++++
 catalog/schema/scripts/validate-catalog.sh    | 17 +------
 2 files changed, 49 insertions(+), 16 deletions(-)
 create mode 100644 catalog/py_package/catalog_build/schema_utils/validate_catalog.py

diff --git a/catalog/py_package/catalog_build/schema_utils/validate_catalog.py b/catalog/py_package/catalog_build/schema_utils/validate_catalog.py
new file mode 100644
index 00000000..eff0a959
--- /dev/null
+++ b/catalog/py_package/catalog_build/schema_utils/validate_catalog.py
@@ -0,0 +1,48 @@
+import os.path
+import sys
+from argparse import ArgumentParser
+
+from linkml.validator import (
+    JsonschemaValidationPlugin,
+    Validator,
+    default_loader_for_file,
+)
+from linkml.validator.report import Severity
+
+SCHEMA_DIR = os.path.join(os.path.dirname(os.path.realpath(__file__)), "../schema")
+
+
+def validate_catalog(source_dir, source_types):
+    source_dir = os.path.abspath(source_dir)
+    found_errors = False
+    for name in source_types:
+        print(f"{name}:")
+        validator = Validator(
+            os.path.join(SCHEMA_DIR, f"{name}.yaml"),
+            validation_plugins=[JsonschemaValidationPlugin(closed=True)],
+        )
+        loader = default_loader_for_file(os.path.join(source_dir, f"{name}.yml"))
+        severities = set()
+        for result in validator.iter_results_from_source(loader):
+            severities.add(result.severity)
+            print(f"[{result.severity.value}] {result.message}")
+        if not severities:
+            print("No issues found")
+        elif Severity.ERROR in severities:
+            found_errors = True
+        print("")
+    if found_errors:
+        print("Validation failed for one or more schemas.")
+        sys.exit(1)
+
+
+def cli():
+    parser = ArgumentParser()
+    parser.add_argument("source_dir")
+    parser.add_argument("source_type", nargs="+")
+    args = parser.parse_args()
+    validate_catalog(args.source_dir, args.source_type)
+
+
+if __name__ == "__main__":
+    cli()
diff --git a/catalog/schema/scripts/validate-catalog.sh b/catalog/schema/scripts/validate-catalog.sh
index 2f8432e2..5eee3f4a 100755
--- a/catalog/schema/scripts/validate-catalog.sh
+++ b/catalog/schema/scripts/validate-catalog.sh
@@ -2,19 +2,4 @@
 
 source ./catalog/schema/scripts/source-file-schema-names.sh
 
-validation_failed=false
-
-for name in ${SOURCE_FILE_SCHEMA_NAMES[@]}
-do
-  echo "$name:"
-  linkml-validate -s "./catalog/py_package/catalog_build/schema/$name.yaml" "./catalog/source/$name.yml"
-  if [ $? -ne 0 ]; then
-    validation_failed=true
-  fi
-  echo ""
-done
-
-if [ "$validation_failed" = true ]; then
-  echo "Validation failed for one or more schemas."
-  exit 1
-fi
+python3 -m catalog.py_package.catalog_build.schema_utils.validate_catalog "./catalog/source" "${SOURCE_FILE_SCHEMA_NAMES[@]}"

From 129eb0ed040e79176bc49615365b4c1cfb2c654f Mon Sep 17 00:00:00 2001
From: hunterckx <118154470+hunterckx@users.noreply.github.com>
Date: Mon, 26 May 2025 17:00:52 -0700
Subject: [PATCH 4/8] feat: move schema generation logic to package (#540)

---
 catalog/build/py/generated_schema/schema.py   | 34 ++++----
 .../catalog_build/schema_utils/gen_schema.py  | 81 +++++++++++++++++++
 .../schema_utils/gen_typescript.py}           |  3 +-
 catalog/schema/generated/assemblies.json      |  2 +-
 catalog/schema/generated/organisms.json       |  2 +-
 catalog/schema/generated/outbreaks.json       |  2 +-
 .../schema/generated/workflow_categories.json |  2 +-
 catalog/schema/generated/workflows.json       |  2 +-
 catalog/schema/scripts/gen-schema.sh          | 15 +---
 9 files changed, 109 insertions(+), 34 deletions(-)
 create mode 100644 catalog/py_package/catalog_build/schema_utils/gen_schema.py
 rename catalog/{schema/scripts/gen-typescript.py => py_package/catalog_build/schema_utils/gen_typescript.py} (90%)

diff --git a/catalog/build/py/generated_schema/schema.py b/catalog/build/py/generated_schema/schema.py
index 36611da4..ed9fc1db 100644
--- a/catalog/build/py/generated_schema/schema.py
+++ b/catalog/build/py/generated_schema/schema.py
@@ -44,9 +44,9 @@ def __contains__(self, key: str) -> bool:
 
 linkml_meta = LinkMLMeta(
     {
-        "default_prefix": "https://github.com/galaxyproject/brc-analytics/blob/main/catalog/schema/schema.yaml#",
+        "default_prefix": "https://github.com/galaxyproject/brc-analytics/blob/main/catalog/py_package/catalog_build/schema/schema.yaml#",
         "description": "Combined source data schemas.",
-        "id": "https://github.com/galaxyproject/brc-analytics/blob/main/catalog/schema/schema.yaml#",
+        "id": "https://github.com/galaxyproject/brc-analytics/blob/main/catalog/py_package/catalog_build/schema/schema.yaml#",
         "imports": [
             "./assemblies",
             "./organisms",
@@ -61,7 +61,7 @@ def __contains__(self, key: str) -> bool:
                 "prefix_reference": "https://w3id.org/linkml/",
             }
         },
-        "source_file": "./catalog/schema/schema.yaml",
+        "source_file": "/Users/hunter/git-repos/brc-analytics/catalog/py_package/catalog_build/schema_utils/../schema/schema.yaml",
     }
 )
 
@@ -146,7 +146,7 @@ class Assemblies(ConfiguredBaseModel):
 
     linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta(
         {
-            "from_schema": "https://github.com/galaxyproject/brc-analytics/blob/main/catalog/schema/assemblies.yaml#",
+            "from_schema": "https://github.com/galaxyproject/brc-analytics/blob/main/catalog/py_package/catalog_build/schema/assemblies.yaml#",
             "tree_root": True,
         }
     )
@@ -167,7 +167,7 @@ class Assembly(ConfiguredBaseModel):
 
     linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta(
         {
-            "from_schema": "https://github.com/galaxyproject/brc-analytics/blob/main/catalog/schema/assemblies.yaml#"
+            "from_schema": "https://github.com/galaxyproject/brc-analytics/blob/main/catalog/py_package/catalog_build/schema/assemblies.yaml#"
         }
     )
 
@@ -187,7 +187,7 @@ class Organisms(ConfiguredBaseModel):
 
     linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta(
         {
-            "from_schema": "https://github.com/galaxyproject/brc-analytics/blob/main/catalog/schema/organisms.yaml#",
+            "from_schema": "https://github.com/galaxyproject/brc-analytics/blob/main/catalog/py_package/catalog_build/schema/organisms.yaml#",
             "tree_root": True,
         }
     )
@@ -208,7 +208,7 @@ class Organism(ConfiguredBaseModel):
 
     linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta(
         {
-            "from_schema": "https://github.com/galaxyproject/brc-analytics/blob/main/catalog/schema/organisms.yaml#"
+            "from_schema": "https://github.com/galaxyproject/brc-analytics/blob/main/catalog/py_package/catalog_build/schema/organisms.yaml#"
         }
     )
 
@@ -238,7 +238,7 @@ class Outbreaks(ConfiguredBaseModel):
 
     linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta(
         {
-            "from_schema": "https://github.com/galaxyproject/brc-analytics/blob/main/catalog/schema/outbreaks.yaml#",
+            "from_schema": "https://github.com/galaxyproject/brc-analytics/blob/main/catalog/py_package/catalog_build/schema/outbreaks.yaml#",
             "tree_root": True,
         }
     )
@@ -259,7 +259,7 @@ class Outbreak(ConfiguredBaseModel):
 
     linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta(
         {
-            "from_schema": "https://github.com/galaxyproject/brc-analytics/blob/main/catalog/schema/outbreaks.yaml#"
+            "from_schema": "https://github.com/galaxyproject/brc-analytics/blob/main/catalog/py_package/catalog_build/schema/outbreaks.yaml#"
         }
     )
 
@@ -333,7 +333,7 @@ class OutbreakResource(ConfiguredBaseModel):
 
     linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta(
         {
-            "from_schema": "https://github.com/galaxyproject/brc-analytics/blob/main/catalog/schema/outbreaks.yaml#"
+            "from_schema": "https://github.com/galaxyproject/brc-analytics/blob/main/catalog/py_package/catalog_build/schema/outbreaks.yaml#"
         }
     )
 
@@ -370,7 +370,7 @@ class MarkdownFileReference(ConfiguredBaseModel):
 
     linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta(
         {
-            "from_schema": "https://github.com/galaxyproject/brc-analytics/blob/main/catalog/schema/outbreaks.yaml#"
+            "from_schema": "https://github.com/galaxyproject/brc-analytics/blob/main/catalog/py_package/catalog_build/schema/outbreaks.yaml#"
         }
     )
 
@@ -402,7 +402,7 @@ class WorkflowCategories(ConfiguredBaseModel):
 
     linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta(
         {
-            "from_schema": "https://github.com/galaxyproject/brc-analytics/blob/main/catalog/schema/workflow_categories.yaml#",
+            "from_schema": "https://github.com/galaxyproject/brc-analytics/blob/main/catalog/py_package/catalog_build/schema/workflow_categories.yaml#",
             "tree_root": True,
         }
     )
@@ -426,7 +426,7 @@ class WorkflowCategory(ConfiguredBaseModel):
 
     linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta(
         {
-            "from_schema": "https://github.com/galaxyproject/brc-analytics/blob/main/catalog/schema/workflow_categories.yaml#"
+            "from_schema": "https://github.com/galaxyproject/brc-analytics/blob/main/catalog/py_package/catalog_build/schema/workflow_categories.yaml#"
         }
     )
 
@@ -476,7 +476,7 @@ class Workflows(ConfiguredBaseModel):
 
     linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta(
         {
-            "from_schema": "https://github.com/galaxyproject/brc-analytics/blob/main/catalog/schema/workflows.yaml#",
+            "from_schema": "https://github.com/galaxyproject/brc-analytics/blob/main/catalog/py_package/catalog_build/schema/workflows.yaml#",
             "tree_root": True,
         }
     )
@@ -497,7 +497,7 @@ class Workflow(ConfiguredBaseModel):
 
     linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta(
         {
-            "from_schema": "https://github.com/galaxyproject/brc-analytics/blob/main/catalog/schema/workflows.yaml#"
+            "from_schema": "https://github.com/galaxyproject/brc-analytics/blob/main/catalog/py_package/catalog_build/schema/workflows.yaml#"
         }
     )
 
@@ -569,7 +569,7 @@ class WorkflowParameter(ConfiguredBaseModel):
 
     linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta(
         {
-            "from_schema": "https://github.com/galaxyproject/brc-analytics/blob/main/catalog/schema/workflows.yaml#"
+            "from_schema": "https://github.com/galaxyproject/brc-analytics/blob/main/catalog/py_package/catalog_build/schema/workflows.yaml#"
         }
     )
 
@@ -610,7 +610,7 @@ class WorkflowUrlSpec(ConfiguredBaseModel):
 
     linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta(
         {
-            "from_schema": "https://github.com/galaxyproject/brc-analytics/blob/main/catalog/schema/workflows.yaml#"
+            "from_schema": "https://github.com/galaxyproject/brc-analytics/blob/main/catalog/py_package/catalog_build/schema/workflows.yaml#"
         }
     )
 
diff --git a/catalog/py_package/catalog_build/schema_utils/gen_schema.py b/catalog/py_package/catalog_build/schema_utils/gen_schema.py
new file mode 100644
index 00000000..95b86d86
--- /dev/null
+++ b/catalog/py_package/catalog_build/schema_utils/gen_schema.py
@@ -0,0 +1,81 @@
+import os.path
+from argparse import ArgumentParser
+
+from linkml.generators import JsonSchemaGenerator, PydanticGenerator
+
+from .gen_typescript import TypescriptGeneratorFixed
+
+SCHEMA_DIR = os.path.join(os.path.dirname(os.path.realpath(__file__)), "../schema")
+
+# Mapping from name to tuple of generator class and output file extension
+GENERATOR_TYPES = {
+    "Pydantic": (PydanticGenerator, "py"),
+    "TypeScript": (TypescriptGeneratorFixed, "ts"),
+    "JSON Schema": (JsonSchemaGenerator, "json"),
+}
+
+
+def gen_schema_type(type_name, out_dir, schema_names, default_schema_names):
+    if out_dir is None:
+        if schema_names is not None:
+            print(f"No output path specified for {type_name} generator\n")
+        return
+
+    if not schema_names:
+        if not default_schema_names:
+            print(f"No schemas specified for {type_name} generator\n")
+            return
+        schema_names = default_schema_names
+
+    print(f"Generating {type_name}")
+
+    generator, extension = GENERATOR_TYPES[type_name]
+
+    for name in schema_names:
+        result_text = generator(os.path.join(SCHEMA_DIR, f"{name}.yaml")).serialize()
+        out_path = os.path.join(out_dir, f"{name}.{extension}")
+        with open(out_path, "w") as file:
+            file.write(result_text + "\n")
+            print(f"Wrote to {out_path}")
+
+    print("")
+
+
+def gen_schema(
+    default_schema_names,
+    *,
+    py_path=None,
+    py_names=None,
+    ts_path=None,
+    ts_names=None,
+    json_path=None,
+    json_names=None,
+):
+    gen_schema_type("Pydantic", py_path, py_names, default_schema_names)
+    gen_schema_type("TypeScript", ts_path, ts_names, default_schema_names)
+    gen_schema_type("JSON Schema", json_path, json_names, default_schema_names)
+
+
+def cli():
+    parser = ArgumentParser()
+    parser.add_argument("schema_name", nargs="*")
+    parser.add_argument("--py-path")
+    parser.add_argument("--py-name", action="append")
+    parser.add_argument("--ts-path")
+    parser.add_argument("--ts-name", action="append")
+    parser.add_argument("--json-path")
+    parser.add_argument("--json-name", action="append")
+    args = parser.parse_args()
+    gen_schema(
+        args.schema_name,
+        py_path=args.py_path,
+        py_names=args.py_name,
+        ts_path=args.ts_path,
+        ts_names=args.ts_name,
+        json_path=args.json_path,
+        json_names=args.json_name,
+    )
+
+
+if __name__ == "__main__":
+    cli()
diff --git a/catalog/schema/scripts/gen-typescript.py b/catalog/py_package/catalog_build/schema_utils/gen_typescript.py
similarity index 90%
rename from catalog/schema/scripts/gen-typescript.py
rename to catalog/py_package/catalog_build/schema_utils/gen_typescript.py
index 6ebe7041..91a5ea75 100644
--- a/catalog/schema/scripts/gen-typescript.py
+++ b/catalog/py_package/catalog_build/schema_utils/gen_typescript.py
@@ -24,4 +24,5 @@ def range(self, slot):
         return base_result if slot.required else f"{base_result} | null"
 
 
-print(TypescriptGeneratorFixed(sys.argv[1]).serialize())
+if __name__ == "__main__":
+    print(TypescriptGeneratorFixed(sys.argv[1]).serialize())
diff --git a/catalog/schema/generated/assemblies.json b/catalog/schema/generated/assemblies.json
index b991ac72..a57b0d01 100644
--- a/catalog/schema/generated/assemblies.json
+++ b/catalog/schema/generated/assemblies.json
@@ -34,7 +34,7 @@
             "type": "object"
         }
     },
-    "$id": "https://github.com/galaxyproject/brc-analytics/blob/main/catalog/schema/assemblies.yaml#",
+    "$id": "https://github.com/galaxyproject/brc-analytics/blob/main/catalog/py_package/catalog_build/schema/assemblies.yaml#",
     "$schema": "https://json-schema.org/draft/2019-09/schema",
     "additionalProperties": true,
     "description": "Object containing list of assemblies.",
diff --git a/catalog/schema/generated/organisms.json b/catalog/schema/generated/organisms.json
index ef4cf5a3..9ba0ed2e 100644
--- a/catalog/schema/generated/organisms.json
+++ b/catalog/schema/generated/organisms.json
@@ -52,7 +52,7 @@
             "type": "object"
         }
     },
-    "$id": "https://github.com/galaxyproject/brc-analytics/blob/main/catalog/schema/organisms.yaml#",
+    "$id": "https://github.com/galaxyproject/brc-analytics/blob/main/catalog/py_package/catalog_build/schema/organisms.yaml#",
     "$schema": "https://json-schema.org/draft/2019-09/schema",
     "additionalProperties": true,
     "description": "Object containing list of organisms.",
diff --git a/catalog/schema/generated/outbreaks.json b/catalog/schema/generated/outbreaks.json
index 3e9795bf..d4d099f7 100644
--- a/catalog/schema/generated/outbreaks.json
+++ b/catalog/schema/generated/outbreaks.json
@@ -139,7 +139,7 @@
             "type": "object"
         }
     },
-    "$id": "https://github.com/galaxyproject/brc-analytics/blob/main/catalog/schema/outbreaks.yaml#",
+    "$id": "https://github.com/galaxyproject/brc-analytics/blob/main/catalog/py_package/catalog_build/schema/outbreaks.yaml#",
     "$schema": "https://json-schema.org/draft/2019-09/schema",
     "additionalProperties": true,
     "description": "Object containing list of outbreaks.",
diff --git a/catalog/schema/generated/workflow_categories.json b/catalog/schema/generated/workflow_categories.json
index fc1ec740..dc182646 100644
--- a/catalog/schema/generated/workflow_categories.json
+++ b/catalog/schema/generated/workflow_categories.json
@@ -64,7 +64,7 @@
             "type": "string"
         }
     },
-    "$id": "https://github.com/galaxyproject/brc-analytics/blob/main/catalog/schema/workflow_categories.yaml#",
+    "$id": "https://github.com/galaxyproject/brc-analytics/blob/main/catalog/py_package/catalog_build/schema/workflow_categories.yaml#",
     "$schema": "https://json-schema.org/draft/2019-09/schema",
     "additionalProperties": true,
     "description": "Object containing list of workflow categories.",
diff --git a/catalog/schema/generated/workflows.json b/catalog/schema/generated/workflows.json
index a5d20190..bd99bbea 100644
--- a/catalog/schema/generated/workflows.json
+++ b/catalog/schema/generated/workflows.json
@@ -192,7 +192,7 @@
             "type": "object"
         }
     },
-    "$id": "https://github.com/galaxyproject/brc-analytics/blob/main/catalog/schema/workflows.yaml#",
+    "$id": "https://github.com/galaxyproject/brc-analytics/blob/main/catalog/py_package/catalog_build/schema/workflows.yaml#",
     "$schema": "https://json-schema.org/draft/2019-09/schema",
     "additionalProperties": true,
     "description": "Object containing list of workflows.",
diff --git a/catalog/schema/scripts/gen-schema.sh b/catalog/schema/scripts/gen-schema.sh
index f066f6c4..57e2ff65 100755
--- a/catalog/schema/scripts/gen-schema.sh
+++ b/catalog/schema/scripts/gen-schema.sh
@@ -2,14 +2,7 @@
 
 source ./catalog/schema/scripts/source-file-schema-names.sh
 
-# Generate Pydantic models for all source data types
-gen-pydantic ./catalog/py_package/catalog_build/schema/schema.yaml > ./catalog/build/py/generated_schema/schema.py
-
-# Generate TypeScript definitions for all source data types
-python3 ./catalog/schema/scripts/gen-typescript.py ./catalog/py_package/catalog_build/schema/schema.yaml > ./catalog/schema/generated/schema.ts
-
-# Generate a JSON schema for each source file
-for name in ${SOURCE_FILE_SCHEMA_NAMES[@]}
-do
-  gen-json-schema "./catalog/py_package/catalog_build/schema/$name.yaml" > "./catalog/schema/generated/$name.json"
-done
+python3 -m catalog.py_package.catalog_build.schema_utils.gen_schema "${SOURCE_FILE_SCHEMA_NAMES[@]}" \
+  --json-path ./catalog/schema/generated \
+  --py-path ./catalog/build/py/generated_schema --py-name schema \
+  --ts-path ./catalog/schema/generated --ts-name schema

From 09e6e30a44b1dccf777fe0703def13d5e38569f2 Mon Sep 17 00:00:00 2001
From: hunterckx <118154470+hunterckx@users.noreply.github.com>
Date: Mon, 26 May 2025 17:19:02 -0700
Subject: [PATCH 5/8] feat: add iwc workflows script to package (#540)

---
 .../catalog_build}/generated_schema/schema.py |  0
 .../iwc_manifest_to_workflows_yaml.py         | 27 ++++++++++---------
 catalog/schema/scripts/gen-schema.sh          |  2 +-
 package.json                                  |  2 +-
 4 files changed, 17 insertions(+), 14 deletions(-)
 rename catalog/{build/py => py_package/catalog_build}/generated_schema/schema.py (100%)
 rename catalog/{build/py => py_package/catalog_build}/iwc_manifest_to_workflows_yaml.py (90%)

diff --git a/catalog/build/py/generated_schema/schema.py b/catalog/py_package/catalog_build/generated_schema/schema.py
similarity index 100%
rename from catalog/build/py/generated_schema/schema.py
rename to catalog/py_package/catalog_build/generated_schema/schema.py
diff --git a/catalog/build/py/iwc_manifest_to_workflows_yaml.py b/catalog/py_package/catalog_build/iwc_manifest_to_workflows_yaml.py
similarity index 90%
rename from catalog/build/py/iwc_manifest_to_workflows_yaml.py
rename to catalog/py_package/catalog_build/iwc_manifest_to_workflows_yaml.py
index 37dc927c..2e87bdbc 100644
--- a/catalog/build/py/iwc_manifest_to_workflows_yaml.py
+++ b/catalog/py_package/catalog_build/iwc_manifest_to_workflows_yaml.py
@@ -6,7 +6,8 @@
 
 import requests
 import yaml
-from generated_schema.schema import (
+
+from .generated_schema.schema import (
     Workflow,
     WorkflowCategoryId,
     WorkflowParameter,
@@ -15,7 +16,6 @@
 )
 
 URL = "https://iwc.galaxyproject.org/workflow_manifest.json"
-WORKFLOWS_PATH = "catalog/source/workflows.yml"
 DOCKSTORE_COLLECTION_TO_CATEGORY = {
     "Variant Calling": WorkflowCategoryId.VARIANT_CALLING,
     "Transcriptomics": WorkflowCategoryId.TRANSCRIPTOMICS,
@@ -31,9 +31,9 @@
 )
 
 
-def read_existing_yaml():
-    if os.path.exists(WORKFLOWS_PATH):
-        with open(WORKFLOWS_PATH) as fh:
+def read_existing_yaml(workflows_path):
+    if os.path.exists(workflows_path):
+        with open(workflows_path) as fh:
             workflows = Workflows.model_validate(yaml.safe_load(fh)).workflows
     else:
         # start from scratch
@@ -116,8 +116,8 @@ def generate_current_workflows():
     return by_trs_id
 
 
-def merge_into_existing():
-    existing = read_existing_yaml()
+def merge_into_existing(workflows_path):
+    existing = read_existing_yaml(workflows_path)
     current = generate_current_workflows()
     merged: Dict[str, Workflow] = {}
     for versionless_trs_id, current_workflow_input in current.items():
@@ -144,8 +144,8 @@ def merge_into_existing():
     return merged
 
 
-def to_workflows_yaml(exclude_other: bool):
-    by_trs_id = merge_into_existing()
+def to_workflows_yaml(workflows_path: str, exclude_other: bool):
+    by_trs_id = merge_into_existing(workflows_path)
     # sort by trs id, should play nicer with git diffs
     sorted_workflows = list(dict(sorted(by_trs_id.items())).values())
     if exclude_other:
@@ -160,7 +160,7 @@ def to_workflows_yaml(exclude_other: bool):
             final_workflows.append(workflow)
         sorted_workflows = final_workflows
     final_workflows = sorted_workflows
-    with open(WORKFLOWS_PATH, "w") as out:
+    with open(workflows_path, "w") as out:
         yaml.safe_dump(
             Workflows(workflows=final_workflows).model_dump(exclude_none=True),
             out,
@@ -168,17 +168,20 @@ def to_workflows_yaml(exclude_other: bool):
             sort_keys=False,
         )
     # Turns out the YAML style prettier likes is really hard to create in python ...
-    subprocess.run(["npx", "prettier", "--write", WORKFLOWS_PATH])
+    subprocess.run(["npx", "prettier", "--write", workflows_path])
 
 
 if __name__ == "__main__":
     parser = argparse.ArgumentParser(
         description="Build workflows.yaml file from latest IWC JSON manifest."
     )
+    parser.add_argument(
+        "workflows_path", help="Path of workflows YAML file to read/write."
+    )
     parser.add_argument(
         "--exclude-other",
         action="store_true",
         help="Exclude other items from processing.",
     )
     args = parser.parse_args()
-    to_workflows_yaml(exclude_other=args.exclude_other)
+    to_workflows_yaml(args.workflows_path, exclude_other=args.exclude_other)
diff --git a/catalog/schema/scripts/gen-schema.sh b/catalog/schema/scripts/gen-schema.sh
index 57e2ff65..91420e7c 100755
--- a/catalog/schema/scripts/gen-schema.sh
+++ b/catalog/schema/scripts/gen-schema.sh
@@ -4,5 +4,5 @@ source ./catalog/schema/scripts/source-file-schema-names.sh
 
 python3 -m catalog.py_package.catalog_build.schema_utils.gen_schema "${SOURCE_FILE_SCHEMA_NAMES[@]}" \
   --json-path ./catalog/schema/generated \
-  --py-path ./catalog/build/py/generated_schema --py-name schema \
+  --py-path ./catalog/py_package/catalog_build/generated_schema --py-name schema \
   --ts-path ./catalog/schema/generated --ts-name schema
diff --git a/package.json b/package.json
index 4083e02a..d4dac911 100644
--- a/package.json
+++ b/package.json
@@ -16,7 +16,7 @@
     "test": "jest --runInBand",
     "build-brc-db": "esrun catalog/build/ts/build-catalog.ts",
     "build-files-from-ncbi": "python3 -m catalog.build.py.build_files_from_ncbi",
-    "iwc-manifest-to-workflows-yaml": "python3 ./catalog/build/py/iwc_manifest_to_workflows_yaml.py --exclude-other",
+    "iwc-manifest-to-workflows-yaml": "python3 -m catalog.py_package.catalog_build.iwc_manifest_to_workflows_yaml ./catalog/source/workflows.yml --exclude-other",
     "gen-schema": "./catalog/schema/scripts/gen-schema.sh",
     "test-gen-python": "./catalog/schema/scripts/test-gen-python.sh",
     "validate-catalog": "./catalog/schema/scripts/validate-catalog.sh"

From 4a77baf65ea1b84843ec46fe302103ba4fd70951 Mon Sep 17 00:00:00 2001
From: hunterckx <118154470+hunterckx@users.noreply.github.com>
Date: Mon, 26 May 2025 17:44:32 -0700
Subject: [PATCH 6/8] docs: update readmes to reflect new directory structure
 (#540)

---
 README.md         | 2 +-
 catalog/README.md | 3 ++-
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/README.md b/README.md
index 413c1db2..cde310f0 100644
--- a/README.md
+++ b/README.md
@@ -75,7 +75,7 @@ These values will be substituted with assembly-specific values at runtime.
 
 ## Editing the LinkML schemas
 
-If the LinkML schemas in `catalog/schema` are edited, the derived JSON schemas and TypeScript definitions should be
+If the LinkML schemas in `catalog/py_package/catalog_build/schema` are edited, the derived JSON schemas and TypeScript definitions should be
 updated
 as follows:
 
diff --git a/catalog/README.md b/catalog/README.md
index 5a21158d..e273b2d6 100644
--- a/catalog/README.md
+++ b/catalog/README.md
@@ -7,5 +7,6 @@ This directory provides the catalog data (information on genome assemblies, orga
   - `py` - Python scripts.
   - `ts` - Typescript scripts.
 - `output` - JSON files output by the catalog build process, to be consumed by the app.
-- `schema` - LinkML schemas for source files.
+- `py_package` - Python package used to share catalog features, such as the schemas and build process, with other projects.
+- `schema` - Schema-related scripts and derived models.
 - `source` - YAML files providing data used as input for building the catalog.

From 0211191db16212214bf2b5ccf93e5dc2b2a5c938 Mon Sep 17 00:00:00 2001
From: hunterckx <118154470+hunterckx@users.noreply.github.com>
Date: Mon, 26 May 2025 17:52:19 -0700
Subject: [PATCH 7/8] fix: update linting in checks workflow for new directory
 structure (#540)

---
 .github/workflows/run-checks.yml | 2 +-
 package.json                     | 1 +
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/run-checks.yml b/.github/workflows/run-checks.yml
index 7d4bad63..f45f7872 100644
--- a/.github/workflows/run-checks.yml
+++ b/.github/workflows/run-checks.yml
@@ -33,7 +33,7 @@ jobs:
         run: pip install -r ./catalog/build/py/requirements.txt
       - name: Run linkml-lint
         # Run linting on the LinkML schemas, to enforce conventions such as in naming, and to catch simple errors.
-        run: linkml-lint ./catalog/schema --validate --verbose
+        run: npm run lint-schema
       - name: Test LinkML Python generation
         # Generate Python code from the main LinkML schemas, discarding the output; this will catch more subtle errors such as references to nonexistent elements.
         run: npm run test-gen-python
diff --git a/package.json b/package.json
index d4dac911..4b2b5c3f 100644
--- a/package.json
+++ b/package.json
@@ -17,6 +17,7 @@
     "build-brc-db": "esrun catalog/build/ts/build-catalog.ts",
     "build-files-from-ncbi": "python3 -m catalog.build.py.build_files_from_ncbi",
     "iwc-manifest-to-workflows-yaml": "python3 -m catalog.py_package.catalog_build.iwc_manifest_to_workflows_yaml ./catalog/source/workflows.yml --exclude-other",
+    "lint-schema": "linkml-lint ./catalog/py_package/catalog_build/schema --validate --verbose",
     "gen-schema": "./catalog/schema/scripts/gen-schema.sh",
     "test-gen-python": "./catalog/schema/scripts/test-gen-python.sh",
     "validate-catalog": "./catalog/schema/scripts/validate-catalog.sh"

From b749ad34e4a6ac1bfe7e20c92f118a03ac985134 Mon Sep 17 00:00:00 2001
From: hunterckx <118154470+hunterckx@users.noreply.github.com>
Date: Mon, 26 May 2025 18:41:57 -0700
Subject: [PATCH 8/8] docs: add descriptions to schema scripts' arguments
 (#540)

---
 .../catalog_build/schema_utils/gen_schema.py  | 36 +++++++++++++++----
 .../schema_utils/validate_catalog.py          |  8 +++--
 2 files changed, 35 insertions(+), 9 deletions(-)

diff --git a/catalog/py_package/catalog_build/schema_utils/gen_schema.py b/catalog/py_package/catalog_build/schema_utils/gen_schema.py
index 95b86d86..ab550b8c 100644
--- a/catalog/py_package/catalog_build/schema_utils/gen_schema.py
+++ b/catalog/py_package/catalog_build/schema_utils/gen_schema.py
@@ -58,13 +58,35 @@ def gen_schema(
 
 def cli():
     parser = ArgumentParser()
-    parser.add_argument("schema_name", nargs="*")
-    parser.add_argument("--py-path")
-    parser.add_argument("--py-name", action="append")
-    parser.add_argument("--ts-path")
-    parser.add_argument("--ts-name", action="append")
-    parser.add_argument("--json-path")
-    parser.add_argument("--json-name", action="append")
+    parser.add_argument(
+        "schema_name",
+        nargs="*",
+        help="name of a default schema to generate from if generator-specific schemas aren't specified",
+    )
+    parser.add_argument(
+        "--py-path", help="path of directory to output pydantic files to"
+    )
+    parser.add_argument(
+        "--py-name",
+        action="append",
+        help="name of a schema to generate pydantic models from",
+    )
+    parser.add_argument(
+        "--ts-path", help="path of directory to output typescript files to"
+    )
+    parser.add_argument(
+        "--ts-name",
+        action="append",
+        help="name of a schema to generate typescript definitions from",
+    )
+    parser.add_argument(
+        "--json-path", help="path of directory to output json schema files to"
+    )
+    parser.add_argument(
+        "--json-name",
+        action="append",
+        help="name of a schema to generate json schema from",
+    )
     args = parser.parse_args()
     gen_schema(
         args.schema_name,
diff --git a/catalog/py_package/catalog_build/schema_utils/validate_catalog.py b/catalog/py_package/catalog_build/schema_utils/validate_catalog.py
index eff0a959..e9fde2d5 100644
--- a/catalog/py_package/catalog_build/schema_utils/validate_catalog.py
+++ b/catalog/py_package/catalog_build/schema_utils/validate_catalog.py
@@ -38,8 +38,12 @@ def validate_catalog(source_dir, source_types):
 
 def cli():
     parser = ArgumentParser()
-    parser.add_argument("source_dir")
-    parser.add_argument("source_type", nargs="+")
+    parser.add_argument(
+        "source_dir", help="path of directory to validate catalog source files from"
+    )
+    parser.add_argument(
+        "source_type", nargs="+", help="name of a schema/entity type to validate"
+    )
     args = parser.parse_args()
     validate_catalog(args.source_dir, args.source_type)