Merge branch 'dev' of github.com:AAFC-BICoE/dina-py into dev

README.md

@@ -14,6 +14,12 @@ Python access to the DINA API
     - Storage Unit
     - Form Template
     - Split Configuration
+    - Metagenomics Batch
+    - Metagenomics Batch Item
+    - Molecular Analysis Result
+    - Molecular Analysis Run
+    - Molecular Analysis Run Item
+    - Project
 #### DINA APIs
 - Currently supported APIs:
     - Agent API
@@ -26,12 +32,18 @@ Python access to the DINA API
       - SplitConfiguration
       - MaterialSample
       - Organism
+      - Project
     - Object Store API
       - Any Object Store API endpoint using ObjectStoreApi's CRUD methods 
     - SeqDB API
       - PCR Batch
       - PCR Batch Item
       - SEQ Reaction
+      - Metagenomics Batch
+      - Metagenomics Batch Item
+      - Molecular Analysis Result
+      - Molecular Analysis Run
+      - Molecular Analysis Run Item
     - Export API
       - Any Export API endpoint using DinaExportApi's CRUD methods 
 
@@ -84,6 +96,12 @@ Python access to the DINA API
    - Person
    - Split Configuration
    - Storage Unit Usage
+   - Metagenomics Batch
+   - Metagenomics Batch Item
+   - Molecular Analysis Result
+   - Molecular Analysis Run
+   - Molecular Analysis Run Item
+   - Project
 
 ## Installation Instructions
 ### Local Install

dinapy/apis/collectionapi/project_api.py

@@ -0,0 +1,9 @@
+"""Class that extracts common functionality for Project entity"""
+
+from .collectionapi import CollectionModuleApi
+
+class ProjectAPI(CollectionModuleApi):
+
+	def __init__(self, config_path: str = None, base_url: str = None) -> None:
+		super().__init__(config_path, base_url)
+		self.base_url += "collecting-event"

dinapy/entities/Project.py

@@ -0,0 +1,103 @@
+class ProjectDTO:
+    def __init__(self, id = None, type = 'project', attributes = None, relationships = 'undefined'):
+        self.id = id
+        self.type = type
+        self.attributes = attributes
+        self.relationships = relationships
+
+    def get_id(self):
+        return self.id
+
+    def get_type(self):
+        return self.type
+
+class ProjectDTOBuilder:
+    def __init__(self):
+        self._id = None
+        self._type = 'project'
+        self._attributes = None
+        self._relationships = None
+
+    def attributes(self, attributes):
+        self._attributes = attributes
+        return self
+
+    def relationships(self, relationships):
+        self._relationships = relationships
+        return self
+
+    def build(self):
+        return ProjectDTO(self._id, self._type, self._attributes, self._relationships)
+
+class ProjectAttributesDTO:
+    def __init__(self, createdOn = 'undefined', createdBy = 'undefined', group = 'undefined', name = 'undefined', startDate = 'undefined', endDate = 'undefined', status = 'undefined', multilingualDescription = 'undefined', extensionValues = 'undefined'):
+        self.createdOn = createdOn
+        self.createdBy = createdBy
+        self.group = group
+        self.name = name
+        self.startDate = startDate
+        self.endDate = endDate
+        self.status = status
+        self.multilingualDescription = multilingualDescription
+        self.extensionValues = extensionValues
+
+class ProjectAttributesDTOBuilder:
+    def __init__(self):
+        self._createdOn = 'undefined'
+        self._createdBy = 'undefined'
+        self._group = 'undefined'
+        self._name = 'undefined'
+        self._startDate = 'undefined'
+        self._endDate = 'undefined'
+        self._status = 'undefined'
+        self._multilingualDescription = 'undefined'
+        self._extensionValues = 'undefined'
+
+    def createdOn(self, createdOn):
+        self._createdOn = createdOn
+        return self
+
+    def createdBy(self, createdBy):
+        self._createdBy = createdBy
+        return self
+
+    def group(self, group):
+        self._group = group
+        return self
+
+    def name(self, name):
+        self._name = name
+        return self
+
+    def startDate(self, startDate):
+        self._startDate = startDate
+        return self
+
+    def endDate(self, endDate):
+        self._endDate = endDate
+        return self
+
+    def status(self, status):
+        self._status = status
+        return self
+
+    def multilingualDescription(self, multilingualDescription):
+        self._multilingualDescription = multilingualDescription
+        return self
+
+    def extensionValues(self, extensionValues):
+        self._extensionValues = extensionValues
+        return self
+
+    def build(self):
+        return ProjectAttributesDTO(
+        self._createdOn,
+        self._createdBy,
+        self._group,
+        self._name,
+        self._startDate,
+        self._endDate,
+        self._status,
+        self._multilingualDescription,
+        self._extensionValues
+        )

dinapy/schemas/molecular_analysis_result_schema.py

@@ -9,7 +9,7 @@
 
 class Attachment(BaseSchema):
     class Meta:
-        type_ = 'attacment'
+        type_ = 'attachment'
 
 class MolecularAnalysisResultSchema(Schema):
     id = fields.Str(load_only=True)

dinapy/schemas/project_schema.py

@@ -0,0 +1,61 @@
+# This file holds schemas for serializing and deserializing Project entities
+# using the JSON API format. It utilizes the marshmallow_jsonapi library.
+from marshmallow import post_load
+from marshmallow_jsonapi import Schema, fields
+from dinapy.schemas.materialsampleschema import *
+from dinapy.entities.Project import ProjectDTO
+from .customFields import SkipUndefinedField
+from .BaseSchema import *
+
+class Attachment(BaseSchema):
+    class Meta:
+        type_ = 'attachment'
+
+class ProjectSchema(Schema):
+    id = fields.Str(load_only=True)
+    createdBy = SkipUndefinedField(fields.Str,attribute="attributes.createdBy")
+    createdOn = SkipUndefinedField(fields.DateTime,load_only=True,attribute="attributes.createdOn")
+    group = SkipUndefinedField(fields.Str,attribute="attributes.group")
+    name = SkipUndefinedField(fields.Str,required=True,attribute="attributes.name")
+    startDate = SkipUndefinedField(fields.Str,allow_none=True,attribute="attributes.startDate")
+    endDate = SkipUndefinedField(fields.Str,allow_none=True,attribute="attributes.endDate")
+    status = SkipUndefinedField(fields.Str,allow_none=True,attribute="attributes.status")
+    multilingualDescription = SkipUndefinedField(fields.Dict,allow_none=True,attribute="attributes.multilingualDescription")
+    extensionValues = SkipUndefinedField(fields.Dict,allow_none=True,attribute="attributes.extensionValues")
+
+    attachment = create_relationship("project","attachment")
+
+    meta = fields.DocumentMeta()
+
+    class Meta: 
+        type_ = "project"
+
+    @post_dump
+    def remove_skipped_fields(self, data, many, **kwargs):
+        # Remove fields with the special marker value
+        return {key: value for key, value in data.items() if value is not SkipUndefinedField(fields.Field).SKIP_MARKER}
+
+    @post_dump
+    def remove_meta(self, data, many, **kwargs):
+        if 'meta' in data:
+            del(data['meta'])
+        return data
+
+    @post_load
+    def set_none_to_undefined(self, data, **kwargs):
+        for attr in data.attributes:
+            if data.attributes[attr] is None:
+                data.attributes[attr] = 'undefined'
+        return data
+
+    @post_load
+    def object_deserialization(self, data, **kwargs):
+        if 'meta' in data:
+            del data['meta']
+        return ProjectDTO(**data)
+
+    def dump(self, obj, many=None, *args, **kwargs):
+        data = super().dump(obj, many=many, *args, **kwargs)
+        if 'meta' in data:
+            del data['meta']
+        return data

examples/external-resource-import-demo/README.md

@@ -18,4 +18,6 @@ Copy the .txt file containing the External URLs to be uploaded into the current
 Then modify (as needed) and run the **external_resource_importer.py** script.
 
 An output file called **external_url_uuids.txt** should have been created containing the generated UUIDs for each External Resource.
-A similar file called material_sample_uuids.txt should also appear for the created Material Samples.
+A similar file called **material_sample_uuids.txt** should also appear for the created Material Samples.
+
+Optionally, you can also link all creted Material Samples using **link_samples_to_project.py** which reads **material_sample_uuids.txt** and links them to a Project in DINA through a given Project UUID.

tests/project_schema_test.py

@@ -0,0 +1,79 @@
+# This file contains tests relating to ProjectAPI.
+# Currently only contains tests for the ProjectSchema (serialization and deserialization tests).
+# API mock call tests should be added.
+
+import unittest
+from marshmallow.exceptions import ValidationError
+
+import sys
+import os
+
+# Add the root directory of the project to the Python path
+project_root = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
+sys.path.insert(0, project_root)
+
+# Import modules from the dinaapi package
+from dinapy.schemas.project_schema import ProjectSchema
+from dinapy.entities.Project import *
+
+VALID_PROJECT_DATA = {
+    "data": {
+        "id": "01939377-b15d-75f6-b405-54d9e719a509",
+        "type": "project",
+        "attributes": {
+            "createdOn": "2024-12-04T20:58:35.237491Z",
+            "createdBy": "dina-admin",
+            "group": "aafc",
+            "name": "test project",
+            "startDate": "2024-05-01",
+            "endDate": "2025-12-04",
+            "status": "Open",
+            "multilingualDescription": {
+                "descriptions": [
+                    {
+                        "lang": "en",
+                        "desc": "test decription"
+                    }
+                ]
+            },
+            "extensionValues": {}
+        },
+        "relationships": {}
+    }
+}
+
+class ProjectSchemaTest(unittest.TestCase):
+    def test_deserialize_project(self):
+        schema = ProjectSchema()
+        try:
+            result = schema.load(VALID_PROJECT_DATA)
+            print(result.__dict__)
+            self.assertIsInstance(result, ProjectDTO)
+        except ValidationError as e:
+            self.fail(f"Validation failed with error: {e.messages}")
+
+    def test_serialize_project(self):
+        schema = ProjectSchema()
+        project_attributes = ProjectAttributesDTOBuilder(
+            ).name("test project").group("aafc").build()
+        project = ProjectDTOBuilder().attributes(project_attributes).build()
+
+        try:
+            serialized_project = schema.dump(project)
+            expected = {
+                "data": {
+                    "type": "project",
+                    "attributes": {
+                        "name": "test project",
+                        "group": "aafc"
+                    }
+                }
+            }
+            print(serialized_project)
+            self.assertIsInstance(serialized_project, dict)
+            self.assertDictEqual(serialized_project, expected)
+        except ValidationError as e:
+            self.fail(f"Validation failed with error: {e.messages}")
+
+if __name__ == "__main__":
+    unittest.main()