def setup_cdm_corpus(self) -> CdmCorpusDefinition:
corpus = CdmCorpusDefinition()
corpus.default_namespace = 'local'
corpus.storage.mount(
'cdm', LocalAdapter(TestHelper.sample_schema_folder_path))
corpus.storage.mount(
'local',
LocalAdapter(
AdlsModelJsonTestHelper.get_actual_sub_folder_path(
self.tests_subpath, self.test_name,
AdlsModelJsonTestHelper.input_folder_name)))
corpus.storage.mount(
'adls',
AdlsTestHelper.create_adapter_with_client_id(
self.root_relative_path))
return corpus
async def main():
# Make a corpus, the corpus is the collection of all documents and folders created or discovered while navigating
# objects and paths.
cdm_corpus = CdmCorpusDefinition()
cdm_corpus.ctx.update_logging_options(level='ERROR')
print('configure storage adapters')
cdm_corpus.storage.mount('local', LocalAdapter(root='..'))
# Local is our default. So any paths that start out navigating without a device tag will assume local.
cdm_corpus.default_namespace = 'local'
# Fake cdm, normally use the github adapter.
cdm_corpus.storage.mount('cdm', LocalAdapter(root='../../example-public-standards'))
# This sample is going to simulate the steps a tool would follow in order to create a new manifest document in some user
# Storage folder when the shapes of the entities in that folder are all taken from some public standards with no
# extensions or additions
# The steps are:
# 1. Create a temporary 'manifest' object at the root of the corpus that contains a list of the selected entities.
# 2. Each selected entity points at an 'abstract' schema defintion in the public standards. These entity docs are too
# hard to deal with because of abstractions and inheritence, etc. So to make things concrete, we want to make a
# 'resolved' version of each entity doc in our local folder. To do this, we call create_resolved_manifest on our
# starting manifest. this will resolve everything and find all of the relationships between entities for us.
# 3. Save the new documents.
print('make placeholder manifest')
# Make the temp manifest and add it to the root of the local documents in the corpus.
manifest_abstract = cdm_corpus.make_object(CdmObjectType.MANIFEST_DEF, 'temp_abstract') # type: CdmManifestDefinition
# Add each declaration, this example is about medical appointments and care plans.
ent_dec = cdm_corpus.make_object(CdmObjectType.LOCAL_ENTITY_DECLARATION_DEF, 'Account') # type: CdmLocalEntityDeclarationDefinition
ent_dec.entity_path = 'cdm:/core/applicationCommon/foundationCommon/crmCommon/accelerators/healthCare/electronicMedicalRecords/Account.cdm.json/Account'
manifest_abstract.entities.add(ent_dec)
ent_dec = cdm_corpus.make_object(CdmObjectType.LOCAL_ENTITY_DECLARATION_DEF, 'Address')
ent_dec.entity_path = 'cdm:/core/applicationCommon/foundationCommon/crmCommon/accelerators/healthCare/electronicMedicalRecords/Address.cdm.json/Address'
manifest_abstract.entities.add(ent_dec)
ent_dec = cdm_corpus.make_object(CdmObjectType.LOCAL_ENTITY_DECLARATION_DEF, 'CarePlan')
ent_dec.entity_path = 'cdm:/core/applicationCommon/foundationCommon/crmCommon/accelerators/healthCare/electronicMedicalRecords/CarePlan.cdm.json/CarePlan'
manifest_abstract.entities.add(ent_dec)
ent_dec = cdm_corpus.make_object(CdmObjectType.LOCAL_ENTITY_DECLARATION_DEF, 'CodeableConcept')
ent_dec.entity_path = 'cdm:/core/applicationCommon/foundationCommon/crmCommon/accelerators/healthCare/electronicMedicalRecords/CodeableConcept.cdm.json/CodeableConcept'
manifest_abstract.entities.add(ent_dec)
ent_dec = cdm_corpus.make_object(CdmObjectType.LOCAL_ENTITY_DECLARATION_DEF, 'Contact')
ent_dec.entity_path = 'cdm:/core/applicationCommon/foundationCommon/crmCommon/accelerators/healthCare/electronicMedicalRecords/Contact.cdm.json/Contact'
manifest_abstract.entities.add(ent_dec)
ent_dec = cdm_corpus.make_object(CdmObjectType.LOCAL_ENTITY_DECLARATION_DEF, 'Device')
ent_dec.entity_path = 'cdm:/core/applicationCommon/foundationCommon/crmCommon/accelerators/healthCare/electronicMedicalRecords/Device.cdm.json/Device'
manifest_abstract.entities.add(ent_dec)
ent_dec = cdm_corpus.make_object(CdmObjectType.LOCAL_ENTITY_DECLARATION_DEF, 'EmrAppointment')
ent_dec.entity_path = 'cdm:/core/applicationCommon/foundationCommon/crmCommon/accelerators/healthCare/electronicMedicalRecords/EmrAppointment.cdm.json/EmrAppointment'
manifest_abstract.entities.add(ent_dec)
ent_dec = cdm_corpus.make_object(CdmObjectType.LOCAL_ENTITY_DECLARATION_DEF, 'Encounter')
ent_dec.entity_path = 'cdm:/core/applicationCommon/foundationCommon/crmCommon/accelerators/healthCare/electronicMedicalRecords/Encounter.cdm.json/Encounter'
manifest_abstract.entities.add(ent_dec)
ent_dec = cdm_corpus.make_object(CdmObjectType.LOCAL_ENTITY_DECLARATION_DEF, 'EpisodeOfCare')
ent_dec.entity_path = 'cdm:/core/applicationCommon/foundationCommon/crmCommon/accelerators/healthCare/electronicMedicalRecords/EpisodeOfCare.cdm.json/EpisodeOfCare'
manifest_abstract.entities.add(ent_dec)
ent_dec = cdm_corpus.make_object(CdmObjectType.LOCAL_ENTITY_DECLARATION_DEF, 'Location')
ent_dec.entity_path = 'cdm:/core/applicationCommon/foundationCommon/crmCommon/accelerators/healthCare/electronicMedicalRecords/Location.cdm.json/Location'
manifest_abstract.entities.add(ent_dec)
# Add the temp manifest to the root of the local documents in the corpus.
local_root = cdm_corpus.storage.fetch_root_folder('local')
local_root.add_document('temp_abstract.manifest.cdm.json', manifest_abstract)
# Create the resolved version of everything in the root folder too.
print('resolve the placeholder')
manifest_resolved = await manifest_abstract.create_resolved_manifest_async('default', '')
# Add an import to the foundations doc so the traits about partitons will resolve nicely.
manifest_resolved.add_import('cdm:/foundations.cdm.json', '')
print('save the docs')
for e_def in manifest_resolved.entities:
# Get the entity being pointed at.
local_e_def = cast(CdmLocalEntityDeclarationDefinition, e_def)
# Turns a relative path from manifest_resolved into an absolute path.
ent_def = cast(CdmEntityDefinition, await cdm_corpus.fetch_object_async(local_e_def.entity_path, manifest_resolved))
# Make a fake partition, just to demo that.
part = cdm_corpus.make_object(CdmObjectType.DATA_PARTITION_DEF, '{}-data-description'.format(ent_def.entity_name)) # type: CdmDataPartitionDefinition
local_e_def.data_partitions.add(part)
part.explanation = 'not real data, just for demo'
# Define the location of the partition, relative to the manifest
local_location = 'local:/{}/partition-data.csv'.format(ent_def.entity_name)
part.location = cdm_corpus.storage.create_relative_corpus_path(local_location, manifest_resolved)
# Add trait to partition for csv params.
csv_trait = part.add_exhibited_trait('is.partition.format.CSV', False)
csv_trait.add_argument('columnHeaders', 'true')
csv_trait.add_argument('delimiter', ',')
# Get the actual location of the partition file from the corpus.
part_path = cdm_corpus.storage.corpus_path_to_adapter_path(location)
# Make a fake file with nothing but header for columns.
header = ','.join([att.name for att in ent_def.has_attributes])
os.makedirs(cdm_corpus.storage.corpus_path_to_adapter_path('local:/{}'.format(ent_def.entity_name)), exist_ok=True)
with open(part_path, 'w') as file:
file.write(header)
await manifest_resolved.save_as_async('{}.manifest.cdm.json'.format(manifest_resolved.manifest_name), True)
# 2. The model_json_root constant points to the location of the model.json file
# 3. ADLSg2 adapter configuration is updated according to your env setup
# 4. The partition location in model.json file is specifying the same ADLSg2 account and file-system settings
# 5. Ensure the Azure user object is assigned "Storage Blob Data Contributor" role in the ADLSg2 access management page
# ---------------------------------------------------------------------------------------------
model_json_root = './4-read-local-save-adls/sample-data'
# ---------------------------------------------------------------------------------------------
# Instantiate corpus and set it to use default namespace 'adls'
corpus = CdmCorpusDefinition()
# set callback to receive error and warning logs.
corpus.set_event_callback(event_callback, CdmStatusLevel.WARNING)
corpus.default_namespace = 'local'
# ---------------------------------------------------------------------------------------------
# Set up a local, remote and adls adapters
# Fake cdm, normaly use the CDM Standards adapter
# Mount it as the 'cdm' device, not the default so must use "cdm:/folder" to get there
corpus.storage.mount(
'cdm',
LocalAdapter(
root=os.path.join(ROOT_PATH, '../../example-public-standards')))
corpus.storage.mount('local', LocalAdapter(root=model_json_root))
# Example how to mount to the ADLS - make sure the hostname and root entered here are also changed
# in the example.model.json file we load in the next section
corpus.storage.mount(
'adls',
#
# IMPORTANT: Before running this sample, make sure following is satisfied:
# 1. The OM library is available in the execution scope of this sample
# 2. The model_json_root constant points to the location of the model.json file
# 3. ADLSg2 adapter configuration is updated according to your env setup
# 4. The partition location in model.json file is specifying the same ADLSg2 account and file-system settings
# 5. Ensure the Azure user object is assigned "Storage Blob Data Contributor" role in the ADLSg2 access management page
# ---------------------------------------------------------------------------------------------
model_json_root = '<<<INPUT_PATH>>>'
# ---------------------------------------------------------------------------------------------
# Instantiate corpus and set it to use default namespace 'adls'
corpus = CdmCorpusDefinition()
corpus.default_namespace = 'adls'
# The context is set up to log messages to console
corpus.ctx.update_logging_options(level='INFO')
# ---------------------------------------------------------------------------------------------
# Set up a local, remote and adls adapters
corpus.storage.mount('local', LocalAdapter(root=model_json_root))
corpus.storage.mount('remote',
RemoteAdapter(hosts={'contoso': 'http://contoso.com'}))
corpus.storage.mount(
'adls',
AdlsAdapter(
root='/<FILESYSTEM_NAME>', # Container name
hostname='<ACCOUNT_NAME>.dfs.core.windows.net', # Blob endpoint
