Merge pull request #64 from elixir-europe/process-isa-json-after-bios…

…amples

Process isa json after biosamples

mars-cli/mars_cli.py

@@ -176,6 +176,12 @@ def cli(ctx, development):
     help="Name of a credentials file",
 )
 @click.argument("isa_json_file", type=click.File("r"))
+@click.option(
+    "--submit-to-biosamples",
+    type=click.BOOL,
+    default=True,
+    help="Submit to BioSamples.",
+)
 @click.option("--submit-to-ena", type=click.BOOL, default=True, help="Submit to ENA.")
 @click.option(
     "--file-transfer",
@@ -200,29 +206,34 @@ def cli(ctx, development):
     type=click.BOOL,
     help="Boolean indicating if the investigation is the root of the ISA JSON. Set this to True if the ISA-JSON does not contain a 'investigation' field.",
 )
+@click.option(
+    "--output",
+    type=click.STRING,
+    default=f"output_{datetime.now().strftime('%Y-%m-%dT%H:%M:%S')}",
+)
 @click.pass_context
 def submit(
     ctx,
     credential_service_name,
     username_credentials,
     credentials_file,
     isa_json_file,
+    submit_to_biosamples,
     submit_to_ena,
     submit_to_metabolights,
     investigation_is_root,
     file_transfer,
+    output,
     data_files,
 ):
     """Start a submission to the target repositories."""
-    target_repositories = [TargetRepository.BIOSAMPLES]
+    target_repositories = []
+
+    if submit_to_biosamples:
+        target_repositories.append(TargetRepository.BIOSAMPLES)
 
     if submit_to_ena:
         target_repositories.append(TargetRepository.ENA)
-        target_repositories.remove(TargetRepository.BIOSAMPLES)
-        print_and_log(
-            f"Skipping {TargetRepository.BIOSAMPLES} repository due to {TargetRepository.ENA} being present in the list of repositories",
-            level="debug",
-        )
 
     if submit_to_metabolights:
         target_repositories.append(TargetRepository.METABOLIGHTS)
@@ -245,6 +256,7 @@ def submit(
             investigation_is_root,
             urls_dict,
             file_transfer,
+            output,
             data_file_paths,
         )
     except requests.RequestException as err:

mars-cli/mars_lib/isa_json.py

@@ -22,21 +22,21 @@
 
 
 def reduce_isa_json_for_target_repo(
-    input_isa_json: Investigation, target_repo: str
-) -> Investigation:
+    input_isa_json: IsaJson, target_repo: str
+) -> IsaJson:
     """
     Filters out assays that are not meant to be sent to the specified target repository.
 
     Args:
-        input_isa_json (Investigation): Input ISA JSON that contains the original information.
+        input_isa_json (IsaJson): Input ISA JSON that contains the original information.
         target_repo (TargetRepository): Target repository as a constant.
 
     Returns:
-        Investigation: Filtered ISA JSON.
+        IsaJson: Filtered ISA JSON.
     """
     filtered_isa_json = input_isa_json.model_copy(deep=True)
     new_studies = []
-    studies = filtered_isa_json.studies
+    studies = filtered_isa_json.investigation.studies
     for study in studies:
         if target_repo == TargetRepository.BIOSAMPLES:
             filtered_assays = []
@@ -51,7 +51,7 @@ def reduce_isa_json_for_target_repo(
         study.assays = filtered_assays
         new_studies.append(study)
 
-    filtered_isa_json.studies = new_studies
+    filtered_isa_json.investigation.studies = new_studies
     return filtered_isa_json
 
 
@@ -64,6 +64,8 @@ def detect_target_repo_comment(comments: List[Comment]) -> Comment:
     Returns:
         Comment: The comment where the name corresponds with the name of the provided target repo.
     """
+    if len(comments) < 1:
+        raise ValueError("No comments found! Not able to detect the target repository!")
     return next(comment for comment in comments if comment.name == TARGET_REPO_KEY)
 
 
@@ -188,13 +190,15 @@ def accession_characteristic_present(
             f"'where' atribute is missing in path {material_type_path.key}."
         )
 
-    accession_characteristics = [
-        char
-        for char in material.characteristics
-        if char.category
-        and char.category.characteristicType
-        and char.category.characteristicType.annotationValue == "accession"
-    ]
+    accession_characteristics = []
+    for char in material.characteristics:
+        if char.category and char.category.characteristicType:
+            if char.category.characteristicType.annotationValue:
+                if char.category.characteristicType.annotationValue == "accession":
+                    accession_characteristics.append(char)
+            else:
+                if char.category.characteristicType == "accession":
+                    accession_characteristics.append(char)
 
     if len(accession_characteristics) > 1:
         raise AttributeError(
@@ -255,17 +259,12 @@ def add_accession_to_node(
     if not updated_material_accession_characteristic:
         raise ValueError("Accession characteristic is not present.")
 
-    if updated_material_accession_characteristic.value and hasattr(
-        updated_material_accession_characteristic.value, "annotationValue"
-    ):
-        accession_ontology_annotation = OntologyAnnotation()
-        accession_ontology_annotation.id = (
-            f"#ontology_annotation/accession_{updated_material.id}"
-        )
-        accession_ontology_annotation.annotationValue = accession_number
-        updated_material_accession_characteristic.value = accession_ontology_annotation
-    else:
-        updated_material_accession_characteristic.value = accession_number
+    accession_ontology_annotation = OntologyAnnotation()
+    accession_ontology_annotation.id = (
+        f"#ontology_annotation/accession_{updated_material.id}"
+    )
+    accession_ontology_annotation.annotationValue = accession_number
+    updated_material_accession_characteristic.value = accession_ontology_annotation
 
     updated_material.characteristics.append(updated_material_accession_characteristic)
     print(f"{updated_material.id}: {updated_material_accession_characteristic.value}.")
@@ -352,20 +351,18 @@ def create_accession_characteristic(
     updated_material.characteristics.append(new_material_attribute_value)
 
 
-def update_investigation(
-    investigation: Investigation, repo_response: RepositoryResponse
-) -> Investigation:
+def update_isa_json(isa_json: IsaJson, repo_response: RepositoryResponse) -> IsaJson:
     """
     Adds the accession to the ISA JSON.
 
     Args:
-        isa_json (Investigation): The ISA JSON to be updated.
+        isa_json (IsaJson): The ISA JSON to be updated.
         repo_response (RepositoryResponse): The response from the repository.
 
     Returns:
-        Investigation: The updated ISA JSON.
+        IsaJson: The updated ISA JSON.
     """
-    updated_investigation = investigation.model_copy(deep=True)
+    investigation = isa_json.investigation
     for accession in repo_response.accessions:
 
         has_assay_in_path = [p for p in accession.path if p.key == "assays"]
@@ -380,7 +377,7 @@ def update_investigation(
         if not study_filter:
             raise ValueError(f"Study filter is not present in {accession.path}.")
 
-        updated_node = apply_filter(study_filter, updated_investigation.studies)
+        updated_node = apply_filter(study_filter, investigation.studies)
 
         if target_level == "assay":
             assay_filter = get_filter_for_accession_key(accession, "assays")
@@ -407,4 +404,5 @@ def update_investigation(
 
         add_accession_to_node(updated_node, accession.value, material_type_path)
 
-    return updated_investigation
+    isa_json.investigation = investigation
+    return isa_json

mars-cli/mars_lib/submit.py

@@ -1,3 +1,5 @@
+import os
+from datetime import datetime
 from io import TextIOWrapper
 import requests
 import json
@@ -11,8 +13,13 @@
     input_json_schema_filepath,
 )
 from mars_lib.credential import CredentialManager
-from mars_lib.isa_json import load_isa_json
+from mars_lib.isa_json import (
+    load_isa_json,
+    reduce_isa_json_for_target_repo,
+    update_isa_json,
+)
 from mars_lib.models.isa_json import IsaJson
+from mars_lib.models.repository_response import RepositoryResponse
 from mars_lib.target_repo import TargetRepository
 from mars_lib.logging import print_and_log
 from pydantic import ValidationError
@@ -22,6 +29,17 @@
 from typing import List
 
 
+def save_step_to_file(time_stamp: float, filename: str, isa_json: IsaJson):
+    dir_path = f"tmp/{datetime.now().strftime('%Y-%m-%dT%H:%M:%S')}"
+    os.makedirs(dir_path, exist_ok=True)
+
+    with open(f"{dir_path}/{filename}.json", "w") as f:
+        f.write(isa_json.model_dump_json(by_alias=True, exclude_none=True))
+
+
+DEBUG = os.getenv("MARS_DEBUG") in ["1", 1]
+
+
 def submission(
     credential_service_name: str,
     username_credentials: str,
@@ -31,8 +49,9 @@ def submission(
     investigation_is_root: bool,
     urls: dict[str, Any],
     file_transfer: str,
+    output: str,
     data_file_paths=None,
-):
+) -> None:
     # If credential manager info found:
     # Get password from the credential manager
     # Else:
@@ -59,6 +78,37 @@ def submission(
         f"ISA JSON with investigation '{isa_json.investigation.title}' is valid."
     )
 
+    time_stamp = datetime.timestamp(datetime.now())
+
+    if DEBUG:
+        save_step_to_file(time_stamp, "0_Initial_ISA_JSON_in_model", isa_json)
+
+    if all(
+        repo not in TargetRepository.available_repositories()
+        for repo in target_repositories
+    ):
+        raise ValueError("No target repository selected.")
+
+    if TargetRepository.BIOSAMPLES in target_repositories:
+        # Submit to Biosamples
+        biosamples_result = submit_to_biosamples(
+            isa_json=isa_json,
+            biosamples_credentials=user_credentials,
+            biosamples_url=urls["BIOSAMPLES"]["SUBMISSION"],
+            webin_token_url=urls["WEBIN"]["TOKEN"],
+        )
+        print_and_log(
+            f"Submission to {TargetRepository.BIOSAMPLES} was successful. Result:\n{biosamples_result.json()}",
+            level="info",
+        )
+        # Update `isa_json`, based on the receipt returned
+        bs_mars_receipt = RepositoryResponse.model_validate(
+            json.loads(biosamples_result.content)
+        )
+        isa_json = update_isa_json(isa_json, bs_mars_receipt)
+        if DEBUG:
+            save_step_to_file(time_stamp, "1_after_biosamples", isa_json)
+
     if TargetRepository.ENA in target_repositories:
         # Step 1 : upload data if file paths are provided
         if data_file_paths and file_transfer:
@@ -68,8 +118,8 @@ def submission(
                 submission_url=urls["ENA"]["DATA-SUBMISSION"],
                 file_transfer=file_transfer,
             )
+
         # Step 2 : submit isa-json to ena
-        # TODO: Filter out other assays
         ena_result = submit_to_ena(
             isa_json=isa_json,
             user_credentials=user_credentials,
@@ -78,40 +128,32 @@ def submission(
         print_and_log(
             f"Submission to {TargetRepository.ENA} was successful. Result:\n{ena_result.json()}"
         )
-        # TODO: Update `isa_json`, based on the receipt returned
+        # Update `isa_json`, based on the receipt returned
+        ena_mars_receipt = RepositoryResponse.from_json(str(ena_result.content))
+        isa_json = update_isa_json(isa_json, ena_mars_receipt)
+        if DEBUG:
+            save_step_to_file(time_stamp, "2_after_ena", isa_json)
 
-    elif TargetRepository.BIOSAMPLES in target_repositories:
-        # Submit to Biosamples
-        biosamples_result = submit_to_biosamples(
-            isa_json=isa_json,
-            biosamples_credentials=user_credentials,
-            biosamples_url=urls["BIOSAMPLES"]["SUBMISSION"],
-            webin_token_url=urls["WEBIN"]["TOKEN"],
-        )
-        print_and_log(
-            f"Submission to {TargetRepository.BIOSAMPLES} was successful. Result:\n{biosamples_result.json()}",
-            level="info",
-        )
-        # TODO: Update `isa_json`, based on the receipt returned
-    elif TargetRepository.METABOLIGHTS in target_repositories:
+    if TargetRepository.METABOLIGHTS in target_repositories:
         # Submit to MetaboLights
         # TODO: Filter out other assays
         print_and_log(
             f"Submission to {TargetRepository.METABOLIGHTS} was successful",
             level="info",
         )
         # TODO: Update `isa_json`, based on the receipt returned
-    elif TargetRepository.EVA in target_repositories:
+
+    if TargetRepository.EVA in target_repositories:
         # Submit to EVA
         # TODO: Filter out other assays
         print_and_log(
             f"Submission to {TargetRepository.EVA} was successful", level="info"
         )
         # TODO: Update `isa_json`, based on the receipt returned
-    else:
-        raise ValueError("No target repository selected.")
 
-    # TODO: Return the updated ISA JSON
+    # Return the updated ISA JSON
+    with open(f"{output}.json", "w") as f:
+        f.write(isa_json.model_dump_json(by_alias=True, exclude_none=True))
 
 
 def submit_to_biosamples(
@@ -130,7 +172,9 @@ def submit_to_biosamples(
         biosamples_url,
         headers=headers,
         params=params,
-        json=isa_json.model_dump(by_alias=True, exclude_none=True),
+        json=reduce_isa_json_for_target_repo(
+            isa_json, TargetRepository.BIOSAMPLES
+        ).model_dump(by_alias=True, exclude_none=True),
     )
 
     if result.status_code != 200:
@@ -158,7 +202,9 @@ def submit_to_ena(
         submission_url,
         headers=headers,
         params=params,
-        json=isa_json.model_dump(by_alias=True, exclude_none=True),
+        json=reduce_isa_json_for_target_repo(isa_json, TargetRepository.ENA).model_dump(
+            by_alias=True, exclude_none=True
+        ),
     )
 
     if result.status_code != 200:

mars-cli/mars_lib/target_repo.py

@@ -13,3 +13,7 @@ class TargetRepository(str, Enum):
     METABOLIGHTS = "metabolights"
     BIOSAMPLES = "biosamples"
     EVA = "eva"
+
+    @classmethod
+    def available_repositories(cls):
+        return {item.value for item in cls}

mars-cli/tests/test_ftp_upload.py

@@ -13,10 +13,17 @@ def test_upload_login_failure():
         uploader.upload([Path("./tests/fixtures/not_a_json_file.txt")])
 
 
-@pytest.mark.skip(reason="Relies on real ENA credentials in test_credentials_example.json")
+@pytest.mark.skip(
+    reason="Relies on real ENA credentials in test_credentials_example.json"
+)
 def test_upload_success():
     # For local testing, add ENA username/password to test_credentials_example.json
     with open("./tests/test_credentials_example.json") as f:
         creds = json.load(f)
     uploader = FTPUploader("webin2.ebi.ac.uk", creds["username"], creds["password"])
-    uploader.upload([Path("../test-data/ENA_TEST2.R1.fastq.gz"), Path("./tests/fixtures/not_a_json_file.txt")])
+    uploader.upload(
+        [
+            Path("../test-data/ENA_TEST2.R1.fastq.gz"),
+            Path("./tests/fixtures/not_a_json_file.txt"),
+        ]
+    )