Support s3 uris and bump wrapica to 2.27.1

lib/workload/components/dynamodb-icav2-ready-event-handler-sfn/icav2_launch_pipeline_lambda_py/requirements.txt

@@ -1,2 +1,2 @@
-wrapica>=2.27.0.post20240714154223,<2.28.0
+wrapica>=2.27.1.post20240803214221,<2.28.0
 boto3>=1.28

lib/workload/components/icav2-copy-files/check_or_launch_job_lambda_py/check_or_launch_job_lambda.py

@@ -36,7 +36,7 @@
 
 # Wrapica imports
 from wrapica.job import get_job
-from wrapica.project_data import convert_icav2_uri_to_project_data_obj, project_data_copy_batch_handler
+from wrapica.project_data import convert_uri_to_project_data_obj, project_data_copy_batch_handler
 
 if typing.TYPE_CHECKING:
  from mypy_boto3_ssm import SSMClient
@@ -112,7 +112,7 @@ def submit_copy_job(dest_uri: str, source_uris: List[str]) -> str:
  # Rerun copy batch process
  source_data_ids = list(
  map(
- lambda source_uri_iter: convert_icav2_uri_to_project_data_obj(
+ lambda source_uri_iter: convert_uri_to_project_data_obj(
  source_uri_iter
  ).data.id,
  source_uris

lib/workload/components/icav2-copy-files/check_or_launch_job_lambda_py/requirements.txt

@@ -1,2 +1,2 @@
-wrapica==2.27.0
+wrapica==2.27.1
 boto3>=1.34

lib/workload/stateless/stacks/bclconvert-interop-qc-pipeline-manager/lambdas/set_outputs_json_py/requirements.txt

@@ -1,2 +1,2 @@
-wrapica==2.27.0
+wrapica==2.27.1
 boto3>=1.34.0

lib/workload/stateless/stacks/bclconvert-interop-qc-pipeline-manager/lambdas/set_outputs_json_py/set_outputs_json.py

@@ -33,10 +33,10 @@
  from mypy_boto3_secretsmanager.client import SecretsManagerClient
 
 # ICA imports
-from wrapica.enums import DataType
+from wrapica.enums import DataType, UriType
 from wrapica.libica_models import ProjectData
 from wrapica.project_data import (
- convert_icav2_uri_to_project_data_obj, convert_project_data_obj_to_icav2_uri,
+ convert_uri_to_project_data_obj, convert_project_data_obj_to_uri,
  list_project_data_non_recursively
 )
 
@@ -78,7 +78,7 @@ def handler(events, context):
  analysis_uri = events.get("analysis_output_uri")
 
  # Convert analysis uri to project folder object
- analysis_project_data_obj = convert_icav2_uri_to_project_data_obj(analysis_uri)
+ analysis_project_data_obj = convert_uri_to_project_data_obj(analysis_uri)
 
  # Analysis list
  analysis_top_level_data_list = list_project_data_non_recursively(
@@ -128,9 +128,9 @@ def handler(events, context):
  )
 
  return {
- "interop_output_dir": convert_project_data_obj_to_icav2_uri(interop_data_obj),
- "multiqc_html_report": convert_project_data_obj_to_icav2_uri(multiqc_html_data_obj),
- "multiqc_output_dir": convert_project_data_obj_to_icav2_uri(multiqc_data_obj)
+ "interop_output_dir": convert_project_data_obj_to_uri(interop_data_obj, uri_type=UriType.S3),
+ "multiqc_html_report": convert_project_data_obj_to_uri(multiqc_html_data_obj, uri_type=UriType.S3),
+ "multiqc_output_dir": convert_project_data_obj_to_uri(multiqc_data_obj, uri_type=UriType.S3)
  }
 
 

lib/workload/stateless/stacks/bclconvert-interop-qc-pipeline-manager/layers/pyproject.toml

@@ -19,7 +19,7 @@ boto3 = "^1.28"
 botocore = "^1.31"
 aws_requests_auth = "^0.4.3"
 v2_samplesheet_maker = "^4.2.4"
-wrapica = "2.27.0"
+wrapica = "2.27.1"
 uuid6 = "^2024.1.12"
 
 [tool.poetry.group.dev]

lib/workload/stateless/stacks/bclconvert-manager/deps/requirements.txt

@@ -1,6 +1,6 @@
 uuid6>=2024.1.12
 v2-samplesheet-maker>=4.2.4.post20240528161300
-wrapica==2.27.0
+wrapica==2.27.1
 xmltodict==0.13.0
 mypy_boto3_ssm>=1.16.0
 mypy_boto3_secretsmanager>=1.16.0

lib/workload/stateless/stacks/bs-runs-upload-manager/layers/pyproject.toml

@@ -23,7 +23,7 @@ aws_requests_auth = "^0.4.3"
 xmltodict = "^0.13.0"
 pandas = "^2.2.0"
 v2_samplesheet_maker = "^4.2.4"
-wrapica = "2.27.0"
+wrapica = "2.27.1"
 
 [tool.poetry.group.dev]
 optional = true

lib/workload/stateless/stacks/bssh-icav2-fastq-copy-manager/lambdas/query_bclconvert_outputs_handler_py/query_bclconvert_outputs_handler.py

@@ -29,16 +29,16 @@
 from typing import Dict
 from urllib.parse import urlparse
 import pandas as pd
-from wrapica.enums import DataType
 import logging
 
 # Wrapica imports
+from wrapica.enums import DataType
 from wrapica.libica_models import ProjectData
 from wrapica.project_data import (
  get_project_data_obj_by_id,
  read_icav2_file_contents_to_string,
  get_project_data_folder_id_from_project_id_and_path,
- convert_project_id_and_data_path_to_icav2_uri
+ convert_project_id_and_data_path_to_uri
 )
 
 # Local imports
@@ -179,7 +179,7 @@ def handler(event, context):
  # Generate the manifest output for all files in the output directory
  # to link to the standard output path from the run id
  logger.info("Generating the run manifest file")
- run_root_uri = convert_project_id_and_data_path_to_icav2_uri(
+ run_root_uri = convert_project_id_and_data_path_to_uri(
  project_id,
  bcl_convert_output_path,
  DataType.FOLDER
@@ -237,13 +237,13 @@ def handler(event, context):
  interops_as_uri = dict(
  map(
  lambda interop_iter: (
- convert_project_id_and_data_path_to_icav2_uri(
+ convert_project_id_and_data_path_to_uri(
  project_id,
  Path(interop_iter.data.details.path),
  data_type=DataType.FILE
  ),
  [
- convert_project_id_and_data_path_to_icav2_uri(
+ convert_project_id_and_data_path_to_uri(
  dest_project_id,
  (
  dest_folder_path /
@@ -275,21 +275,23 @@ def handler(event, context):
  )
  except StopIteration:
  # Add 'IndexMetricsOut.bin' from reports directory to the interop files
- index_metrics_uri = convert_project_id_and_data_path_to_icav2_uri(
+ index_metrics_uri = convert_project_id_and_data_path_to_uri(
  project_id,
  Path(bcl_convert_output_obj.data.details.path) / "Reports" / "IndexMetricsOut.bin",
  data_type=DataType.FILE
  )
 
  # Append InterOp directory to list of outputs for IndexMetricsOut.bin
  run_manifest[index_metrics_uri].append(
- convert_project_id_and_data_path_to_icav2_uri(
+ convert_project_id_and_data_path_to_uri(
  dest_project_id,
  dest_folder_path / "InterOp",
  data_type=DataType.FOLDER
  )
  )
 
+ logger.info("Outputting the manifest and fastq list rows")
+
  return {
  "manifest_b64gz": compress_dict(run_manifest),
  "fastq_list_rows_b64gz": compress_dict(fastq_list_rows_df_list),
@@ -302,8 +304,8 @@ def handler(event, context):
 # handler(
 # {
 # "project_id": "a7c67a80-c8f2-4348-adec-3a5a073d1d55",
-# "analysis_id": "2800e302-4a12-4bf0-9028-f74e4a83479f",
-# "output_uri": "icav2://ea19a3f5-ec7c-4940-a474-c31cd91dbad4/primary_data/240424_A01052_0193_BH7JMMDRX5/202406066dd81cc9/"
+# "analysis_id": "47936e52-21fd-457b-a1dc-97139d571441",
+# "output_uri": "icav2://development/primary_data/240424_A01052_0193_BH7JMMDRX5/202406066dd81cc9/"
 # },
 # None
 # ),
@@ -312,6 +314,6 @@ def handler(event, context):
 # )
 #
 # # {
-# # "manifest_b64gz": "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", # pragma: allowlist secret
-# # "fastq_list_rows_b64gz": "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" # pragma: allowlist secret
+# # "manifest_b64gz": "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", # pragma: allowlist secret
+# # "fastq_list_rows_b64gz": "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" # pragma: allowlist secret
 # # }

lib/workload/stateless/stacks/bssh-icav2-fastq-copy-manager/layers/pyproject.toml

@@ -23,7 +23,7 @@ aws_requests_auth = "^0.4.3"
 xmltodict = "^0.13.0"
 pandas = "^2.2.0"
 v2_samplesheet_maker = "^4.2.4"
-wrapica = "2.27.0"
+wrapica = "2.27.1"
 
 [tool.poetry.group.dev]
 optional = true

lib/workload/stateless/stacks/bssh-icav2-fastq-copy-manager/layers/src/bssh_manager_tools/utils/manifest_helper.py

@@ -11,7 +11,9 @@
 
 # Wrapica imports
 from wrapica.libica_models import ProjectData
-from wrapica.project_data import convert_project_data_obj_to_icav2_uri
+from wrapica.project_data import convert_project_data_obj_to_uri
+from wrapica.storage_configuration import convert_icav2_uri_to_s3_uri
+from wrapica.enums import UriType
 
 
 def get_destination_uri_path(
@@ -35,7 +37,7 @@ def get_destination_uri_path(
  # Get the output path (which is the parent directory)
  dest_uri_path = str(
  urlunparse((
- "icav2",
+ UriType.ICAV2.value,
  output_project_id,
  str(output_folder_path.joinpath(relative_file_path).absolute().parent) + "/",
  None, None, None
@@ -66,14 +68,14 @@ def get_dest_uri_from_src_uri(
  # Get the output path (which is the parent directory)
  dest_uri_path = str(
  urlunparse((
- "icav2",
+ UriType.ICAV2.value,
  dest_project_id,
  str(dest_folder_path.joinpath(relative_file_path).absolute().parent) + "/",
  None, None, None
  ))
  )
 
- return dest_uri_path
+ return convert_icav2_uri_to_s3_uri(dest_uri_path)
 
 
 def generate_run_manifest(
@@ -100,7 +102,9 @@ def generate_run_manifest(
  for file_obj_iter in project_data_list:
 
  # Get the source file uri
- source_file_uri = convert_project_data_obj_to_icav2_uri(file_obj_iter)
+ # The source file uri is the path to the file in the input project
+ # The source file will not be on byob storage.
+ source_file_uri = convert_project_data_obj_to_uri(file_obj_iter, uri_type=UriType.ICAV2)
 
  # Get the output path (which is the parent directory)
  dest_uri_path = get_destination_uri_path(
@@ -110,6 +114,9 @@ def generate_run_manifest(
  file_path=file_obj_iter.data.details.path
  )
 
+ # However we convert the dest uri path to an s3 path
+ dest_uri_path = convert_icav2_uri_to_s3_uri(dest_uri_path)
+
  # Add the source file uri to the run manifest dictionary
  run_manifest_dict[source_file_uri] = [
  dest_uri_path

lib/workload/stateless/stacks/bssh-icav2-fastq-copy-manager/layers/src/bssh_manager_tools/utils/sample_helper.py

@@ -6,9 +6,9 @@
 from pathlib import Path
 
 # Wrapica imports
-from wrapica.enums import DataType
+from wrapica.enums import DataType, UriType
 from wrapica.project_data import (
- convert_project_id_and_data_path_to_icav2_uri
+ convert_project_id_and_data_path_to_uri
 )
 
 
@@ -250,19 +250,21 @@ def get_fastq_list_paths_from_bssh_output_and_fastq_list_csv(
 
  # Update the fastqs to contain the full path
  fastq_list_pd["Read1FileUriSrc"] = fastq_list_pd.apply(
- lambda row: convert_project_id_and_data_path_to_icav2_uri(
- project_id,
- run_output_path / row["sample_prefix"] / row["Read1File"],
- DataType.FILE
+ lambda row: convert_project_id_and_data_path_to_uri(
+ project_id=project_id,
+ data_path=run_output_path / row["sample_prefix"] / row["Read1File"],
+ data_type=DataType.FILE,
+ uri_type=UriType.ICAV2
  ),
  axis="columns"
  )
 
  fastq_list_pd["Read2FileUriSrc"] = fastq_list_pd.apply(
- lambda row: convert_project_id_and_data_path_to_icav2_uri(
- project_id,
- run_output_path / row["sample_prefix"] / row["Read2File"],
- DataType.FILE
+ lambda row: convert_project_id_and_data_path_to_uri(
+ project_id=project_id,
+ data_path=run_output_path / row["sample_prefix"] / row["Read2File"],
+ data_type=DataType.FILE,
+ uri_type=UriType.ICAV2
  ),
  axis="columns"
  )

lib/workload/stateless/stacks/cttso-v2-pipeline-manager/lambdas/compress_icav2_vcf/compress_icav2_vcf.py

@@ -18,7 +18,7 @@
 
 from wrapica.project_data import (
  write_icav2_file_contents, read_icav2_file_contents,
- convert_icav2_uri_to_project_data_obj, delete_project_data
+ convert_uri_to_project_data_obj, delete_project_data
 )
 
 if typing.TYPE_CHECKING:
@@ -83,7 +83,7 @@ def write_icav2_vcf_file_to_compressed_output(icav2_uri: str, output_path: Path)
  :return:
  """
  # Download decompressed file
- project_data_obj = convert_icav2_uri_to_project_data_obj(icav2_uri)
+ project_data_obj = convert_uri_to_project_data_obj(icav2_uri)
 
  # Write to output file
  read_icav2_file_contents(project_data_obj.project_id, project_data_obj.data.id, output_path.with_suffix(''))
@@ -128,7 +128,7 @@ def compress_icav2_vcf_and_upload(icav2_uri):
  :param icav2_uri:
  :return:
  """
- project_data_obj = convert_icav2_uri_to_project_data_obj(icav2_uri)
+ project_data_obj = convert_uri_to_project_data_obj(icav2_uri)
 
  with TemporaryDirectory() as temp_dir:
  # Initialise parameters

lib/workload/stateless/stacks/cttso-v2-pipeline-manager/lambdas/delete_cache_uri_py/delete_cache_uri.py

@@ -15,9 +15,8 @@
 
 """
 from wrapica.enums import DataType
-from wrapica.libica_exceptions import ApiException
 from wrapica.project_data import (
- convert_icav2_uri_to_project_data_obj, list_project_data_non_recursively, delete_project_data
+ convert_uri_to_project_data_obj, list_project_data_non_recursively, delete_project_data
 )
 from cttso_v2_pipeline_manager_tools.utils.aws_ssm_helpers import set_icav2_env_vars
 import logging
@@ -52,7 +51,7 @@ def handler(event, context):
 
  # Part 1 - check that in the cache uri, only the sample_id directory exists along with the file SampleSheet.csv
  try:
- cache_obj = convert_icav2_uri_to_project_data_obj(cache_uri)
+ cache_obj = convert_uri_to_project_data_obj(cache_uri)
  except NotADirectoryError as e:
  logger.info("Cache directory has already been deleted")
  return None