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Update store/synapse.updateDB to take sg and se #1291

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merged 2 commits into from
Oct 10, 2023
Merged

Update store/synapse.updateDB to take sg and se #1291

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7a2badd
update updateDB to take sg and se
mialy-defelice Sep 19, 2023
463cb54
simplify sg ref
mialy-defelice Oct 2, 2023
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68 changes: 37 additions & 31 deletions schematic/store/synapse.py
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Original file line number Diff line number Diff line change
Expand Up @@ -800,7 +800,7 @@ def getProjectManifests(self, projectId: str) -> List[str]:

return manifests

def upload_project_manifests_to_synapse(self, projectId: str) -> List[str]:
def upload_project_manifests_to_synapse(self, sg: SchemaGenerator, se: SchemaExplorer, projectId: str) -> List[str]:
"""Upload all metadata manifest files across all datasets in a specified project as tables in Synapse.

Returns: String of all the manifest_table_ids of all the manifests that have been loaded.
Expand All @@ -822,7 +822,7 @@ def upload_project_manifests_to_synapse(self, projectId: str) -> List[str]:
manifest_name = manifest_info["properties"]["name"]
manifest_path = manifest_info["path"]
manifest_df = load_df(manifest_path)
manifest_table_id = uploadDB(manifest, datasetId, datasetName)
manifest_table_id = uploadDB(sg=sg, se=se, manifest=manifest, datasetId=datasetId, table_name=datasetName)
manifest_loaded.append(datasetName)
return manifest_loaded

Expand Down Expand Up @@ -952,7 +952,8 @@ def get_table_info(self, datasetId: str = None, projectId: str = None) -> List[s

@missing_entity_handler
def uploadDB(self,
sg: SchemaGenerator,
sg: SchemaGenerator,
se: SchemaExplorer,
manifest: pd.DataFrame,
datasetId: str,
table_name: str,
Expand All @@ -964,6 +965,7 @@ def uploadDB(self,
Method to upload a database to an asset store. In synapse, this will upload a metadata table

Args:
sg: schemaGenerator object
se: schemaExplorer object
manifest: pd.Df manifest to upload
datasetId: synID of the dataset for the manifest
Expand All @@ -981,13 +983,13 @@ def uploadDB(self,
"""


col_schema, table_manifest = self.formatDB(sg, manifest, useSchemaLabel)
col_schema, table_manifest = self.formatDB(se=se, manifest=manifest, useSchemaLabel=useSchemaLabel)

manifest_table_id = self.buildDB(datasetId, table_name, col_schema, table_manifest, table_manipulation, sg, restrict,)

return manifest_table_id, manifest, table_manifest

def formatDB(self, sg, manifest, useSchemaLabel):
def formatDB(self, se, manifest, useSchemaLabel):
"""
Method to format a manifest appropriatly for upload as table

Expand All @@ -1010,7 +1012,7 @@ def formatDB(self, sg, manifest, useSchemaLabel):

if useSchemaLabel:
cols = [
sg.se.get_class_label_from_display_name(
se.get_class_label_from_display_name(
str(col)
).translate({ord(x): '' for x in blacklist_chars})
for col in manifest_columns
Expand Down Expand Up @@ -1499,13 +1501,14 @@ def upload_manifest_as_table(
"""
# Upload manifest as a table, get the ID and updated manifest.
manifest_synapse_table_id, manifest, table_manifest = self.uploadDB(
schemaGenerator,
manifest,
datasetId,
table_name,
restrict,
useSchemaLabel,
table_manipulation)
sg=schemaGenerator,
se=se,
manifest=manifest,
datasetId=datasetId,
table_name=table_name,
restrict=restrict,
useSchemaLabel=useSchemaLabel,
table_manipulation=table_manipulation)

manifest = self.add_annotations_to_entities_files(se, schemaGenerator, manifest, manifest_record_type, datasetId, hideBlanks, manifest_synapse_table_id)
# Load manifest to synapse as a CSV File
Expand All @@ -1518,13 +1521,14 @@ def upload_manifest_as_table(

# Update manifest Synapse table with new entity id column.
manifest_synapse_table_id, manifest, table_manifest = self.uploadDB(
schemaGenerator,
manifest,
datasetId,
table_name,
restrict,
sg=schemaGenerator,
se=se,
manifest=manifest,
datasetId=datasetId,
table_name=table_name,
restrict=restrict,
useSchemaLabel=useSchemaLabel,
table_manipulation='update',)
table_manipulation='update')

# Set annotations for the table manifest
manifest_annotations = self.format_manifest_annotations(manifest, manifest_synapse_table_id)
Expand Down Expand Up @@ -1605,13 +1609,14 @@ def upload_manifest_combo(
manifest_synapse_file_id (str): SynID of manifest csv uploaded to synapse.
"""
manifest_synapse_table_id, manifest, table_manifest = self.uploadDB(
se,
manifest,
datasetId,
table_name,
restrict,
sg=schemaGenerator,
se=se,
manifest=manifest,
datasetId=datasetId,
table_name=table_name,
restrict=restrict,
useSchemaLabel=useSchemaLabel,
table_manipulation=table_manipulation,)
table_manipulation=table_manipulation)

manifest = self.add_annotations_to_entities_files(se, schemaGenerator, manifest, manifest_record_type, datasetId, hideBlanks, manifest_synapse_table_id)

Expand All @@ -1625,13 +1630,14 @@ def upload_manifest_combo(

# Update manifest Synapse table with new entity id column.
manifest_synapse_table_id, manifest, table_manifest = self.uploadDB(
se,
manifest,
datasetId,
table_name,
restrict,
sg=schemaGenerator,
se=se,
manifest=manifest,
datasetId=datasetId,
table_name=table_name,
restrict=restrict,
useSchemaLabel=useSchemaLabel,
table_manipulation='update',)
table_manipulation='update')

# Set annotations for the table manifest
manifest_annotations = self.format_manifest_annotations(manifest, manifest_synapse_table_id)
Expand Down