Merge pull request #79 from meaningfy-ws/feature/TED-295

Feature/ted 295

dags/worker_single_notice_process_orchestrator.py

@@ -4,13 +4,17 @@
 from dags.dags_utils import pull_dag_upstream, push_dag_downstream
 from ted_sws import config
 from ted_sws.core.model.notice import NoticeStatus
+from ted_sws.data_manager.adapters.mapping_suite_repository import MappingSuiteRepositoryMongoDB
 from ted_sws.data_manager.adapters.notice_repository import NoticeRepository
 from ted_sws.metadata_normaliser.services.metadata_normalizer import normalise_notice_by_id
 
 from airflow.decorators import dag
 from airflow.operators.python import get_current_context, BranchPythonOperator, PythonOperator
 
 from dags import DEFAULT_DAG_ARGUMENTS
+from ted_sws.notice_eligibility.services.notice_eligibility import notice_eligibility_checker_by_id
+from ted_sws.notice_transformer.adapters.rml_mapper import RMLMapper
+from ted_sws.notice_transformer.services.notice_transformer import transform_notice_by_id
 
 NOTICE_ID = "notice_id"
 MAPPING_SUITE_ID = "mapping_suite_id"
@@ -37,22 +41,39 @@ def _normalise_notice_metadata():
 
     def _check_eligibility_for_transformation():
         notice_id = pull_dag_upstream(NOTICE_ID)
-        notice_id = notice_id + "_checked"
+        mongodb_client = MongoClient(config.MONGO_DB_AUTH_URL)
+        notice_repository = NoticeRepository(mongodb_client=mongodb_client)
+        mapping_suite_repository = MappingSuiteRepositoryMongoDB(mongodb_client=mongodb_client)
+        notice_id, mapping_suite_id = notice_eligibility_checker_by_id(notice_id=notice_id,
+                                                                       notice_repository=notice_repository,
+                                                                       mapping_suite_repository=mapping_suite_repository)
         push_dag_downstream(NOTICE_ID, notice_id)
-        push_dag_downstream(MAPPING_SUITE_ID, "mapping_suite_id")
+        push_dag_downstream(MAPPING_SUITE_ID, mapping_suite_id)
 
     def _preprocess_xml_manifestation():
         notice_id = pull_dag_upstream(NOTICE_ID)
         mapping_suite_id = pull_dag_upstream(MAPPING_SUITE_ID)
-        notice_id = notice_id + "_preprocessed"
+        mongodb_client = MongoClient(config.MONGO_DB_AUTH_URL)
+        notice_repository = NoticeRepository(mongodb_client=mongodb_client)
+        notice = notice_repository.get(reference=notice_id)
+        notice.update_status_to(new_status=NoticeStatus.PREPROCESSED_FOR_TRANSFORMATION)
+        notice_repository.update(notice=notice)
         push_dag_downstream(NOTICE_ID, notice_id)
-        pull_dag_upstream(MAPPING_SUITE_ID, mapping_suite_id)
+        push_dag_downstream(MAPPING_SUITE_ID, mapping_suite_id)
 
     def _transform_notice():
         notice_id = pull_dag_upstream(NOTICE_ID)
         mapping_suite_id = pull_dag_upstream(MAPPING_SUITE_ID)
-        notice_id = notice_id + "_transformed"
+        mongodb_client = MongoClient(config.MONGO_DB_AUTH_URL)
+        notice_repository = NoticeRepository(mongodb_client=mongodb_client)
+        mapping_suite_repository = MappingSuiteRepositoryMongoDB(mongodb_client=mongodb_client)
+        rml_mapper = RMLMapper(rml_mapper_path=config.RML_MAPPER_PATH)
+        transform_notice_by_id(notice_id=notice_id, mapping_suite_id=mapping_suite_id,
+                               notice_repository=notice_repository, mapping_suite_repository=mapping_suite_repository,
+                               rml_mapper=rml_mapper
+                               )
         push_dag_downstream(NOTICE_ID, notice_id)
+        push_dag_downstream(MAPPING_SUITE_ID, mapping_suite_id)
 
     def _resolve_entities_in_the_rdf_manifestation():
         notice_id = pull_dag_upstream(NOTICE_ID)
@@ -90,9 +111,17 @@ def _fail_on_state():
 
     def _check_notice_state_before_transform():
         notice_id = pull_dag_upstream(NOTICE_ID)
+        mapping_suite_id = pull_dag_upstream(MAPPING_SUITE_ID)
+        mongodb_client = MongoClient(config.MONGO_DB_AUTH_URL)
+        notice_repository = NoticeRepository(mongodb_client=mongodb_client)
+        notice = notice_repository.get(reference=notice_id)
         push_dag_downstream(NOTICE_ID, notice_id)
-        status = NoticeStatus.ELIGIBLE_FOR_TRANSFORMATION
-        if status == NoticeStatus.ELIGIBLE_FOR_TRANSFORMATION:
+        push_dag_downstream(MAPPING_SUITE_ID, mapping_suite_id)
+        print(notice.status)
+        print(NoticeStatus.ELIGIBLE_FOR_TRANSFORMATION)
+        print(notice.status == NoticeStatus.ELIGIBLE_FOR_TRANSFORMATION)
+        if notice.status == NoticeStatus.ELIGIBLE_FOR_TRANSFORMATION:
+            print("Go to preprocess_xml_manifestation")
             return "preprocess_xml_manifestation"
         else:
             return "fail_on_state"

ted_sws/core/model/notice.py

@@ -150,9 +150,8 @@ class Notice(WorkExpression):
     _status: NoticeStatus = NoticeStatus.RAW  # PrivateAttr(default=NoticeStatus.RAW)
     ted_id: str = Field(..., allow_mutation=False)
     original_metadata: Optional[TEDMetadata] = None
-    _normalised_metadata: Optional[NormalisedMetadata] = None
-
     xml_manifestation: XMLManifestation = Field(..., allow_mutation=False)
+    _normalised_metadata: Optional[NormalisedMetadata] = None
     _preprocessed_xml_manifestation: Optional[XMLManifestation] = None
     _distilled_rdf_manifestation: Optional[RDFManifestation] = None
     _rdf_manifestation: Optional[RDFManifestation] = None
@@ -178,8 +177,7 @@ def rdf_manifestation(self) -> RDFManifestation:
     def mets_manifestation(self) -> METSManifestation:
         return self._mets_manifestation
 
-    @property
-    def rdf_validation(self) -> RDFValidationManifestation:
+    def get_rdf_validation(self) -> RDFValidationManifestation:
         if not self.rdf_manifestation:
             return None
 

ted_sws/data_manager/adapters/notice_repository.py

@@ -1,8 +1,10 @@
 import logging
-from typing import Iterator
+from typing import Iterator, Union
 from pymongo import MongoClient
 
 from ted_sws import config
+from ted_sws.core.model.manifestation import XMLManifestation, RDFManifestation, METSManifestation
+from ted_sws.core.model.metadata import NormalisedMetadata
 from ted_sws.data_manager.adapters.repository_abc import NoticeRepositoryABC
 from ted_sws.core.model.notice import Notice, NoticeStatus
 
@@ -23,6 +25,32 @@ def __init__(self, mongodb_client: MongoClient, database_name: str = _database_n
         notice_db = mongodb_client[self._database_name]
         self.collection = notice_db[self._collection_name]
 
+
+    @staticmethod
+    def _create_notice_from_repository_result(notice_dict: dict) -> Union[Notice, None]:
+        """
+
+        :param notice_dict:
+        :return:
+        """
+
+        def init_object_from_dict(object_class, key):
+            if notice_dict[key]:
+                return object_class(**notice_dict[key])
+            return None
+
+        if notice_dict:
+            del notice_dict["_id"]
+            notice = Notice(**notice_dict)
+            notice._status = NoticeStatus(notice_dict["status"])
+            notice._normalised_metadata= init_object_from_dict(NormalisedMetadata,"normalised_metadata")
+            notice._preprocessed_xml_manifestation = init_object_from_dict(XMLManifestation,"preprocessed_xml_manifestation")
+            notice._distilled_rdf_manifestation = init_object_from_dict(RDFManifestation,"distilled_rdf_manifestation")
+            notice._rdf_manifestation =  init_object_from_dict(RDFManifestation,"rdf_manifestation")
+            notice._mets_manifestation = init_object_from_dict(METSManifestation,"mets_manifestation")
+            return notice
+        return None
+
     def add(self, notice: Notice):
         """
             This method allows you to add notice objects to the repository.
@@ -50,7 +78,7 @@ def get(self, reference) -> Notice:
         :return: Notice
         """
         result_dict = self.collection.find_one({"ted_id": reference})
-        return Notice(**result_dict) if result_dict else None
+        return NoticeRepository._create_notice_from_repository_result(result_dict)
 
     def get_notice_by_status(self, notice_status: NoticeStatus) -> Iterator[Notice]:
         """
@@ -59,12 +87,12 @@ def get_notice_by_status(self, notice_status: NoticeStatus) -> Iterator[Notice]:
         :return:
         """
         for result_dict in self.collection.find({"status": notice_status}):
-            yield Notice(**result_dict)
+            yield NoticeRepository._create_notice_from_repository_result(result_dict)
 
     def list(self) -> Iterator[Notice]:
         """
             This method allows all records to be retrieved from the repository.
         :return: list of notices
         """
         for result_dict in self.collection.find():
-            yield Notice(**result_dict)
+            yield NoticeRepository._create_notice_from_repository_result(result_dict)

ted_sws/notice_eligibility/services/notice_eligibility.py

@@ -72,5 +72,6 @@ def notice_eligibility_checker_by_id(notice_id: str, notice_repository: NoticeRe
     notice = notice_repository.get(reference=notice_id)
     if notice is None:
         raise ValueError(f'Notice, with {notice_id} id, was not found')
-
-    return notice_eligibility_checker(notice=notice, mapping_suite_repository=mapping_suite_repository)
+    result = notice_eligibility_checker(notice=notice, mapping_suite_repository=mapping_suite_repository)
+    notice_repository.update(notice=notice)
+    return result

ted_sws/notice_transformer/services/notice_transformer.py

@@ -10,12 +10,13 @@
 from ted_sws.core.model.notice import Notice, NoticeStatus
 from ted_sws.core.model.transform import MappingSuite, FileResource
 from ted_sws.data_manager.adapters.mapping_suite_repository import MappingSuiteRepositoryInFileSystem
+from ted_sws.data_manager.adapters.repository_abc import NoticeRepositoryABC, MappingSuiteRepositoryABC
 from ted_sws.notice_transformer.adapters.rml_mapper import RMLMapperABC, SerializationFormat as RMLSerializationFormat
 
 DATA_SOURCE_PACKAGE = "data"
 
 
-def transform_notice(notice: Notice, mapping_suite: MappingSuite, rml_mapper: RMLMapperABC):
+def transform_notice(notice: Notice, mapping_suite: MappingSuite, rml_mapper: RMLMapperABC) -> Notice:
     """
         This function allows the XML content of a Notice to be transformed into RDF,
          using the mapping rules in mapping_suite and the rml_mapper mapping adapter.
@@ -27,6 +28,30 @@ def transform_notice(notice: Notice, mapping_suite: MappingSuite, rml_mapper: RM
     return NoticeTransformer(mapping_suite=mapping_suite, rml_mapper=rml_mapper).transform_notice(notice=notice)
 
 
+def transform_notice_by_id(notice_id: str, mapping_suite_id: str, notice_repository: NoticeRepositoryABC,
+                           mapping_suite_repository: MappingSuiteRepositoryABC, rml_mapper: RMLMapperABC):
+    """
+        This function allows the XML content of a Notice to be transformed into RDF,
+         using the mapping rules in mapping_suite and the rml_mapper mapping adapter.
+    :param notice_id:
+    :param mapping_suite_id:
+    :param notice_repository:
+    :param mapping_suite_repository:
+    :param rml_mapper:
+    :return:
+    """
+    notice = notice_repository.get(reference=notice_id)
+    mapping_suite = mapping_suite_repository.get(reference=mapping_suite_id)
+    if notice is None:
+        raise ValueError(f'Notice, with {notice_id} id, was not found')
+
+    if mapping_suite is None:
+        raise ValueError(f'Mapping suite, with {mapping_suite_id} id, was not found')
+
+    result_notice = transform_notice(notice=notice, mapping_suite=mapping_suite, rml_mapper=rml_mapper)
+    notice_repository.update(notice=result_notice)
+
+
 def transform_test_data(mapping_suite: MappingSuite, rml_mapper: RMLMapperABC, output_path: Path,
                         loggable: bool = False):
     """

tests/features/model/test_notice_operations.py

@@ -144,7 +144,7 @@ def step_impl(raw_notice):
 
 @then("notice contains no RDF validation")
 def step_impl(transformation_eligible_notice):
-    assert transformation_eligible_notice.rdf_validation is None
+    assert transformation_eligible_notice.get_rdf_validation() is None
 
 
 @then("notice contains no METS manifestation")
@@ -210,7 +210,7 @@ def step_impl(transformation_eligible_notice, rdf_validation):
 
 @then("the notice object contains the RDF validation report")
 def step_impl(transformation_eligible_notice):
-    assert transformation_eligible_notice.rdf_validation is not None
+    assert transformation_eligible_notice.get_rdf_validation() is not None
 
 
 @then("the notice status is VALIDATED")

tests/unit/notice_transformer/conftest.py

@@ -1,3 +1,5 @@
+import mongomock
+import pymongo
 import pytest
 
 from ted_sws.data_manager.adapters.mapping_suite_repository import MappingSuiteRepositoryInFileSystem
@@ -45,3 +47,8 @@ def fake_mapping_suite(fake_repository_path, fake_mapping_suite_id) -> MappingSu
     repository_path = fake_repository_path
     mapping_suite_repository = MappingSuiteRepositoryInFileSystem(repository_path=repository_path)
     return mapping_suite_repository.get(reference=fake_mapping_suite_id)
+
+@pytest.fixture
+@mongomock.patch(servers=(('server.example.com', 27017),))
+def mongodb_client():
+    return pymongo.MongoClient('server.example.com')

tests/unit/notice_transformer/test_notice_transformer.py

@@ -2,9 +2,12 @@
 import tempfile
 from collections import Counter
 
+import pytest
+
 from ted_sws.core.model.notice import NoticeStatus
+from ted_sws.data_manager.adapters.mapping_suite_repository import MappingSuiteRepositoryMongoDB
 from ted_sws.notice_transformer.services.notice_transformer import NoticeTransformer, transform_notice, \
-    transform_test_data
+    transform_test_data, transform_notice_by_id
 
 
 def test_notice_transformer(fake_rml_mapper, fake_mapping_suite, notice_2018):
@@ -20,6 +23,32 @@ def test_notice_transformer_function(fake_rml_mapper, fake_mapping_suite, notice
     assert result_notice.status == NoticeStatus.TRANSFORMED
 
 
+def test_notice_transformer_by_id_function(fake_rml_mapper, mongodb_client, fake_mapping_suite, notice_2018,
+                                           notice_repository):
+    notice_2018._status = NoticeStatus.PREPROCESSED_FOR_TRANSFORMATION
+    notice_repository.add(notice=notice_2018)
+    notice_id = notice_2018.ted_id
+    mapping_suite_repository = MappingSuiteRepositoryMongoDB(mongodb_client=mongodb_client)
+    mapping_suite_repository.add(mapping_suite=fake_mapping_suite)
+    transform_notice_by_id(notice_id, fake_mapping_suite.identifier, notice_repository, mapping_suite_repository,
+                           fake_rml_mapper)
+    result_notice = notice_repository.get(reference=notice_id)
+    assert result_notice.status == NoticeStatus.TRANSFORMED
+
+
+def test_notice_transformer_by_id_function_with_invalid_ids(fake_rml_mapper, mongodb_client, fake_mapping_suite,
+                                                            notice_2018,
+                                                            notice_repository):
+    notice_2018._status = NoticeStatus.PREPROCESSED_FOR_TRANSFORMATION
+    notice_id = notice_2018.ted_id
+    mapping_suite_repository = MappingSuiteRepositoryMongoDB(mongodb_client=mongodb_client)
+    with pytest.raises(Exception) as e_info:
+        transform_notice_by_id(notice_id, fake_mapping_suite.identifier, notice_repository, mapping_suite_repository,
+                               fake_rml_mapper)
+    result_notice = notice_repository.get(reference=notice_id)
+    assert result_notice is None
+
+
 def test_transform_test_data(fake_rml_mapper, fake_mapping_suite):
     notice_transformer = NoticeTransformer(mapping_suite=fake_mapping_suite, rml_mapper=fake_rml_mapper)
     with tempfile.TemporaryDirectory() as d: