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Updated stacky with new metadata manager #509

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Sep 2, 2024
Merged

Updated stacky with new metadata manager #509

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24 changes: 23 additions & 1 deletion ...hon-metadata-tools-layer/metadata_tools_layer/src/metadata_tools/utils/library_helpers.py
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Original file line number Diff line number Diff line change
Expand Up @@ -16,7 +16,7 @@ def get_library_from_library_id(library_id: Union[int | str]) -> Dict:
if isinstance(library_id, str):
# We have an internal id, convert to int
params = {
"internal_id": library_id
"library_id": library_id
}
else:
endpoint = f"{endpoint}/{library_id}"
Expand Down Expand Up @@ -94,6 +94,28 @@ def get_library_workflow(library_id: str) -> Union[str | None]:
return library.get("workflow")


def get_library_project_owner(library_id: str) -> Union[str | None]:
"""
Given a library id, collect the library project owner
:param library_id:
:return:
"""
library = get_library_from_library_id(library_id)

return library.get("project_owner")
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@williamputraintan williamputraintan Aug 21, 2024 •
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On the casing end, I suppose this get will take value directly from the results JSON? (From #502) the metadata now has a middleware to translate snake_case to camelCase aligning with other microservices, so this might not get project_owner properly.

In terms of query params, the API may still support snake_case filters, but would recommend using the camelCase if you can as this is what the Swagger documents it.

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I guess this is the same for library_id/Id and subject_id/Id too?

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Yes, the response will be in camelCase



def get_library_project_name(library_id: str) -> Union[str | None]:
"""
Given a library id, collect the library workflow
:param library_id:
:return:
"""
library = get_library_from_library_id(library_id)

return library.get("project_name")


def get_all_libraries() -> List[Dict]:
"""
Collect all libraries from the database
Expand Down
2 changes: 1 addition & 1 deletion ...on-metadata-tools-layer/metadata_tools_layer/src/metadata_tools/utils/specimen_helpers.py
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Expand Up @@ -27,7 +27,7 @@ def get_specimen_from_specimen_id(specimen_id: Union[str, int]) -> Dict:
if isinstance(specimen_id, str):
# We have an internal id, convert to int
params = {
"internal_id": specimen_id
"specimen_id": specimen_id
}
else:
endpoint = f"{endpoint}/{specimen_id}"
Expand Down
2 changes: 1 addition & 1 deletion ...hon-metadata-tools-layer/metadata_tools_layer/src/metadata_tools/utils/subject_helpers.py
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Expand Up @@ -24,7 +24,7 @@ def get_subject_from_subject_id(subject_id: Union[str, int]) -> Dict:
if isinstance(subject_id, str):
# We have an internal id, convert to int
params = {
"internal_id": subject_id
"subject_id": subject_id
}
else:
endpoint = f"{endpoint}/{subject_id}"
Expand Down
21 changes: 11 additions & 10 deletions ...esheet-event-shower/lambdas/generate_event_data_objects_py/generate_event_data_objects.py
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Expand Up @@ -16,12 +16,11 @@

def generate_subject_event_data_object_from_subject(subject_obj: Dict, instrument_run_id: str) -> Dict:
return {
"id": subject_obj.get("id"),
"event_data": {
"instrumentRunId": instrument_run_id,
"subject": {
"id": subject_obj.get("id"),
"internalId": subject_obj.get("internal_id")
"orcabusId": subject_obj.get("orcabus_id"),
"subjectId": subject_obj.get("subject_id")
}
}
}
Expand Down Expand Up @@ -66,7 +65,7 @@ def get_library_bclconvert_rows(library_obj: Dict, bclconvert_data: List[Dict])
"""
return list(
filter(
lambda bclconvert_row: bclconvert_row.get("sample_id") == library_obj.get("internal_id"),
lambda bclconvert_row: bclconvert_row.get("sample_id") == library_obj.get("library_id"),
bclconvert_data
)
)
Expand All @@ -90,21 +89,23 @@ def generate_library_event_data_object_from_library_specimen_and_subject(
"""

library_event_obj = {
"id": library_obj.get("id"),
"internalId": library_obj.get("internal_id"),
"orcabusId": library_obj.get("orcabus_id"),
"libraryId": library_obj.get("library_id"),
"phenotype": library_obj.get("phenotype", None),
"workflow": library_obj.get("workflow", None),
"quality": library_obj.get("quality", None),
"type": library_obj.get("type", None),
"assay": library_obj.get("assay", None),
"coverage": library_obj.get("coverage", None),
"projectOwner": library_obj.get("project_owner", None),
"projectName": library_obj.get("project_name", None),
"specimen": {
"id": specimen_obj.get("id"),
"internalId": specimen_obj.get("internal_id")
"orcabusId": specimen_obj.get("orcabus_id"),
"specimenId": specimen_obj.get("specimen_id")
},
"subject": {
"id": subject_obj.get("id"),
"internalId": subject_obj.get("internal_id")
"orcabusId": subject_obj.get("orcabus_id"),
"subjectId": subject_obj.get("subject_id")
}
}

Expand Down
22 changes: 11 additions & 11 deletions ...heet-event-shower/step_functions_templates/samplesheet_event_shower_sfn_template.asl.json
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Expand Up @@ -175,8 +175,8 @@
"Type": "Map",
"ItemsPath": "$.generate_event_objects_step.subject_event_data_list",
"ItemSelector": {
"subject_id.$": "$$.Map.Item.Value.event_data.subject.internalId",
"subject_metadata_db_id.$": "$$.Map.Item.Value.id",
"subject_id.$": "$$.Map.Item.Value.event_data.subject.subjectId",
"subject_orcabus_id.$": "$$.Map.Item.Value.subject.orcabusId",
"subject_event_data.$": "$$.Map.Item.Value.event_data",
"instrument_run_id.$": "$$.Map.Item.Value.event_data.instrumentRunId"
},
Expand Down Expand Up @@ -228,10 +228,10 @@
"id_type": {
"S": "${__subject_table_partition_name__}"
},
"metadata_db_id": {
"N.$": "States.Format('{}', $.subject_metadata_db_id)"
"orcabus_id": {
"S.$": "$.subject_orcabus_id"
},
"internal_id": {
"subject_id": {
"S.$": "$.subject_id"
},
"instrument_run_id_set": {
Expand Down Expand Up @@ -298,8 +298,8 @@
"Type": "Map",
"ItemsPath": "$.generate_event_objects_step.library_event_data_list",
"ItemSelector": {
"library_id.$": "$$.Map.Item.Value.event_data.library.internalId",
"library_metadata_db_id.$": "$$.Map.Item.Value.id",
"library_id.$": "$$.Map.Item.Value.event_data.library.libraryId",
"library_orcabus_id.$": "$$.Map.Item.Value.library.orcabusId",
"library_event_data.$": "$$.Map.Item.Value.event_data",
"instrument_run_id.$": "$$.Map.Item.Value.event_data.instrumentRunId"
},
Expand Down Expand Up @@ -370,11 +370,11 @@
"id_type": {
"S": "${__library_table_partition_name__}"
},
"metadata_db_id": {
"N.$": "States.Format('{}', $.library_metadata_db_id)"
"orcabus_id": {
"S.$": "$.library_orcabus_id"
},
"internal_id": {
"S.$": "$.library_event_data.library.internalId"
"library_id": {
"S.$": "$.library_event_data.library.libraryId"
},
"instrument_run_id_set": {
"SS.$": "States.Array($.instrument_run_id)"
Expand Down
14 changes: 7 additions & 7 deletions ...-library-dbs/step_functions_templates/initialise_cttsov2_library_db_sfn_template.asl.json
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Expand Up @@ -16,7 +16,7 @@
"ItemSelector": {
"bclconvert_data_row.$": "$$.Map.Item.Value",
"instrument_run_id.$": "$.input_payload_data.instrumentRunId",
"library_id.$": "$.input_payload_data.library.internalId"
"library_id.$": "$.input_payload_data.library.libraryId"
},
"ItemProcessor": {
"ProcessorConfig": {
Expand Down Expand Up @@ -63,7 +63,7 @@
"UpdateExpression": "ADD library_set :library_set, fastq_list_row_id_set :fastq_list_row_id_set",
"ExpressionAttributeValues": {
":library_set": {
"SS.$": "States.Array($.input_payload_data.library.internalId)"
"SS.$": "States.Array($.input_payload_data.library.libraryId)"
},
":fastq_list_row_id_set": {
"SS.$": "$.bclconvert_and_fastq_list_row_id_inputs[*].fastq_list_row_id"
Expand All @@ -84,16 +84,16 @@
"TableName": "${__table_name__}",
"Item": {
"id": {
"S.$": "$.input_payload_data.library.internalId"
"S.$": "$.input_payload_data.library.libraryId"
},
"id_type": {
"S": "${__library_partition_name__}"
},
"metadata_db_id": {
"N.$": "States.Format('{}', $.input_payload_data.library.id)"
"orcabus_id": {
"S.$": "$.input_payload_data.library.orcabusId"
},
"internal_id": {
"S.$": "$.input_payload_data.library.internalId"
"library_id": {
"S.$": "$.input_payload_data.library.libraryId"
},
"fastq_list_row_id_set": {
"SS.$": "$.bclconvert_and_fastq_list_row_id_inputs[*].fastq_list_row_id"
Expand Down
4 changes: 2 additions & 2 deletions ...plates/fastq_list_row_shower_complete_event_to_cttsov2_draft_events_sfn_template.asl.json
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Expand Up @@ -56,7 +56,7 @@
},
"ResultPath": "$.get_fastq_list_row_ids_step",
"ResultSelector": {
"internal_id.$": "$.Item.internal_id.S",
"library_id.$": "$.Item.library_id.S",
"fastq_list_row_id_list.$": "$.Item.fastq_list_row_id_set.SS"
},
"Next": "For each FastqListRowID"
Expand Down Expand Up @@ -186,7 +186,7 @@
}
],
"ResultSelector": {
"sample_id.$": "$[0].get_fastq_list_row_ids_step.internal_id",
"sample_id.$": "$[0].get_fastq_list_row_ids_step.library_id",
"samplesheet.$": "$[0].generate_samplesheet_step.samplesheet",
"fastq_list_rows.$": "$[0].get_fastq_list_row_values_step.fastq_list_rows",
"fastq_list_row_ids.$": "$[0].get_fastq_list_row_ids_step.fastq_list_row_id_list",
Expand Down
16 changes: 8 additions & 8 deletions ...gts-library-dbs/step_functions_templates/initialise_wgts_library_db_sfn_template.asl.json
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Expand Up @@ -16,7 +16,7 @@
"ItemSelector": {
"bclconvert_data_row.$": "$$.Map.Item.Value",
"instrument_run_id.$": "$.input_payload_data.instrumentRunId",
"library_id.$": "$.input_payload_data.library.internalId"
"library_id.$": "$.input_payload_data.library.libraryId"
},
"ItemProcessor": {
"ProcessorConfig": {
Expand Down Expand Up @@ -62,7 +62,7 @@
"UpdateExpression": "ADD library_set :library_set, fastq_list_row_id_set :fastq_list_row_id_set",
"ExpressionAttributeValues": {
":library_set": {
"SS.$": "States.Array($.input_payload_data.library.internalId)"
"SS.$": "States.Array($.input_payload_data.library.libraryId)"
},
":fastq_list_row_id_set": {
"SS.$": "$.bclconvert_and_fastq_list_row_id_inputs[*].fastq_list_row_id"
Expand All @@ -83,16 +83,16 @@
"TableName": "${__table_name__}",
"Item": {
"id": {
"S.$": "$.input_payload_data.library.internalId"
"S.$": "$.input_payload_data.library.libraryId"
},
"id_type": {
"S": "${__library_partition_name__}"
},
"metadata_db_id": {
"N.$": "States.Format('{}', $.input_payload_data.library.id)"
"orcabus_id": {
"S.$": "$.input_payload_data.library.orcabusId"
},
"internal_id": {
"S.$": "$.input_payload_data.library.internalId"
"library_id": {
"S.$": "$.input_payload_data.library.libraryId"
},
"sample_type": {
"S.$": "$.input_payload_data.library.type"
Expand All @@ -114,7 +114,7 @@
"ItemsPath": "$.bclconvert_and_fastq_list_row_id_inputs",
"ItemSelector": {
"fastq_list_row_id.$": "$$.Map.Item.Value.fastq_list_row_id",
"library_id.$": "$.input_payload_data.library.internalId",
"library_id.$": "$.input_payload_data.library.libraryId",
"instrument_run_id.$": "$.input_payload_data.instrumentRunId"
},
"ItemProcessor": {
Expand Down
4 changes: 2 additions & 2 deletions ...unctions_templates/fastq_list_rows_shower_complete_to_wgts_qc_draft_sfn_template.asl.json
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Expand Up @@ -51,7 +51,7 @@
"Next": "For each FastqListRowID",
"ResultPath": "$.get_fastq_list_row_ids_step",
"ResultSelector": {
"internal_id.$": "$.Item.internal_id.S",
"library_id.$": "$.Item.library_id.S",
"sample_type.$": "$.Item.sample_type.S",
"fastq_list_row_id_list.$": "$.Item.fastq_list_row_id_set.SS"
}
Expand All @@ -62,7 +62,7 @@
"ItemSelector": {
"fastq_list_row_id.$": "$$.Map.Item.Value",
"sample_type.$": "$.get_fastq_list_row_ids_step.sample_type",
"library_id.$": "$.get_fastq_list_row_ids_step.internal_id",
"library_id.$": "$.get_fastq_list_row_ids_step.library_id",
"instrument_run_id.$": "$.instrument_run_id"
},
"ItemProcessor": {
Expand Down
8 changes: 4 additions & 4 deletions ...se-tn-subject-dbs/step_functions_templates/initialise_tn_subject_db_sfn_template.asl.json
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Expand Up @@ -15,7 +15,7 @@
"Parameters": {
"TableName": "${__table_name__}",
"Key": {
"id.$": "$.payload_data.subject.internalId",
"id.$": "$.payload_data.subject.subjectId",
"id_type": "${__subject_partition_name__}"
}
},
Expand Down Expand Up @@ -44,10 +44,10 @@
"Parameters": {
"TableName": "${__table_name__}",
"Item": {
"id.$": "$.payload_data.subject.internalId",
"id.$": "$.payload_data.subject.subjectId",
"id_type": "${__subject_partition_name__}",
"metadata_db_id": {
"N.$": "States.Format('{}', $.payload_data.subject.id)"
"orcabus_id": {
"S.$": "$.payload_data.subject.orcabusId"
}
}
},
Expand Down
16 changes: 8 additions & 8 deletions ...se-tn-library-dbs/step_functions_templates/initialise_tn_library_db_sfn_template.asl.json
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Expand Up @@ -15,7 +15,7 @@
"Parameters": {
"TableName": "${__table_name__}",
"Key": {
"id.$": "$.payload_data.library.internalId",
"id.$": "$.payload_data.library.libraryId",
"id_type": "${__library_partition_name__}"
}
},
Expand All @@ -34,13 +34,13 @@
"Parameters": {
"TableName": "${__table_name__}",
"Key": {
"id.$": "$.payload_data.library.subject.internalId",
"id.$": "$.payload_data.library.subject.subjectId",
"id_type": "${__subject_partition_name__}"
},
"UpdateExpression": "ADD library_set :library_set",
"ExpressionAttributeValues": {
":library_set": {
"SS.$": "States.Array($.payload_data.library.internalId)"
"SS.$": "States.Array($.payload_data.library.libraryId)"
}
}
},
Expand Down Expand Up @@ -70,10 +70,10 @@
"Parameters": {
"TableName": "${__table_name__}",
"Item": {
"id.$": "$.payload_data.library.internalId",
"id.$": "$.payload_data.library.libraryId",
"id_type": "${__library_partition_name__}",
"metadata_db_id": {
"N.$": "States.Format('{}', $.payload_data.library.id)"
"orcabus_id": {
"S.$": "$.payload_data.library.orcabusId"
},
"phenotype": {
"S.$": "$.payload_data.library.phenotype"
Expand All @@ -88,7 +88,7 @@
"S.$": "$.payload_data.library.assay"
},
"subject_id": {
"S.$": "$.payload_data.library.subject.internalId"
"S.$": "$.payload_data.library.subject.subjectId"
}
}
},
Expand All @@ -112,7 +112,7 @@
"ItemSelector": {
"bclconvert_data_row.$": "$$.Map.Item.Value",
"instrument_run_id.$": "$.payload_data.instrumentRunId",
"library_id.$": "$.payload_data.library.internalId"
"library_id.$": "$.payload_data.library.libraryId"
},
"ItemProcessor": {
"ProcessorConfig": {
Expand Down
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