bam-masterdata 0.6.0__tar.gz → 0.6.2__tar.gz

bam_masterdata-0.6.2/.github/release.yml

@@ -0,0 +1,30 @@
+changelog:
+  exclude:
+    authors: [github-actions, pre-commit-ci]
+  categories:
+    - title: 💥 Breaking Changes
+      labels: [breaking]
+    - title: 🎉 New Features
+      labels: [feature]
+    - title: 🛠 Enhancements
+      labels: [enhancement, DX, UX]
+    - title: 🐛 Bug Fixes
+      labels: [fix]
+    - title: 📖 Documentation
+      labels: [docs]
+    - title: 🚀 Performance
+      labels: [performance]
+    - title: 🚧 CI
+      labels: [ci]
+    - title: 💡 Refactoring
+      labels: [refactor]
+    - title: 🧪 Tests
+      labels: [tests]
+    - title: 🔒 Security Fixes
+      labels: [security]
+    - title: 🏥 Package Health
+      labels: [pkg]
+    - title: 📦 Dependencies
+      labels: [dependencies, outdated]
+    - title: 🤷‍♂️ Other Changes
+      labels: ['*']

{bam_masterdata-0.6.0 → bam_masterdata-0.6.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: bam-masterdata
-Version: 0.6.0
+Version: 0.6.2
 Summary: The BAM Data Store utility tools and masterdata models wrapped in a Python package with a front-end web interface.
 Author-email: BAM Data Store <datastore@bam.de>
 Maintainer-email: "Jose M. Pizarro" <jose.pizarro-blanco@bam.de>

{bam_masterdata-0.6.0 → bam_masterdata-0.6.2}/bam_masterdata/_version.py

@@ -17,5 +17,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.6.0'
-__version_tuple__ = version_tuple = (0, 6, 0)
+__version__ = version = '0.6.2'
+__version_tuple__ = version_tuple = (0, 6, 2)

{bam_masterdata-0.6.0 → bam_masterdata-0.6.2}/bam_masterdata/cli/cli.py

@@ -59,6 +59,7 @@ def cli():
 @click.option(
     "--export-dir",
     type=str,
+    default="./bam_masterdata/datamodel",
     required=False,
     help="The directory where the Masterdata will be exported to.",
 )
@@ -619,18 +620,26 @@ def run_parser(
             f"Space {openbis.username} does not exist in openBIS. Please create it first."
         )
         return
-    project = space.new_project(
-        code=project_name,
-        description="New project created via automated parsing with `bam_masterdata`.",
-    )
+    if project_name.upper() in [p.code for p in space.get_projects()]:
+        project = space.get_project(project_name)
+    else:
+        project = space.new_project(
+            code=project_name,
+            description="New project created via automated parsing with `bam_masterdata`.",
+        )
     project.save()
 
     # Create a new pybis `COLLECTION` to store the generated objects
-    collection_openbis = openbis.new_collection(
-        code=collection_name,
-        type="COLLECTION",
-        project=project,
-    )
+    if collection_name.upper() in [c.code for c in project.get_collections()]:
+        collection_openbis = space.get_collection(
+            f"/{openbis.username}/{project_name}/{collection_name}".upper()
+        )
+    else:
+        collection_openbis = openbis.new_collection(
+            code=collection_name,
+            type="COLLECTION",
+            project=project,
+        )
     collection_openbis.save()
 
     # Create a bam_masterdata CollectionType instance for storing parsed results
@@ -658,11 +667,21 @@ def run_parser(
             props=obj_props,
         )
         object_openbis.save()
+
         # save local and openbis IDs to map parent-child relationships
         openbis_id_map[object_id] = object_openbis.identifier
         click.echo(
             f"Object {obj_props.get('$name')} stored in openBIS collection {collection_name}."
         )
+    for _, files in files_parser.items():
+        # Upload the file to openBIS
+        dataset = openbis.new_dataset(
+            type="RAW_DATA",
+            files=files,
+            collection=collection_openbis,
+        )
+        dataset.save()
+        click.echo(f"Files uploaded to openBIS collection {collection_name}.")
 
     # Map parent-child relationships
     for parent_id, child_id in collection.relationships.values():

{bam_masterdata-0.6.0 → bam_masterdata-0.6.2}/bam_masterdata/cli/entities_to_excel.py

@@ -52,7 +52,7 @@ def entities_to_excel(
         worksheet.append(header_values)
 
         # Properties assignment for ObjectType, DatasetType, and CollectionType
-        if obj_instance.cls_name in ["ObjectType", "DatasetType", "CollectionType"]:
+        if obj_instance.base_name in ["ObjectType", "DatasetType", "CollectionType"]:
             if not obj_instance.properties:
                 continue
             worksheet.append(
@@ -68,7 +68,7 @@ def entities_to_excel(
                     row.append(val)
                 worksheet.append(row)
         # Terms assignment for VocabularyType
-        elif obj_instance.cls_name == "VocabularyType":
+        elif obj_instance.base_name == "VocabularyType":
             if not obj_instance.terms:
                 continue
             worksheet.append(list(obj_instance.terms[0].excel_headers_map.values()))