Merge remote-tracking branch 'origin/main' into process-isa-json-afte…

…r-biosamples

mars-cli/generate_config.py

@@ -32,8 +32,10 @@ def create_settings_file(settings_dir):
     config["ena"] = {
         "development-url": "https://wwwdev.ebi.ac.uk/ena/submit/webin-v2/",
         "development-submission-url": "https://wwwdev.ebi.ac.uk/ena/submit/drop-box/submit/?auth=ENA",
+        "development-data-submission-url": "webin2.ebi.ac.uk",
         "production-url": "https://www.ebi.ac.uk/ena/submit/webin-v2/",
         "production-submission-url": "https://www.ebi.ac.uk/ena/submit/drop-box/submit/?auth=ENA",
+        "production-data-submission-url": "webin2.ebi.ac.uk",
     }
 
     config["biosamples"] = {

mars-cli/mars_cli.py

@@ -63,6 +63,11 @@
                 "development-submission-url",
                 fallback="https://wwwdev.ebi.ac.uk/biosamples/samples/submit",
             ),
+            "DATA-SUBMISSION": config.get(
+                "ena",
+                "development-data-submission-url",
+                fallback="webin2.ebi.ac.uk",
+            ),
         },
         "WEBIN": {
             "SERVICE": config.get(
@@ -101,6 +106,11 @@
                 "production-submission-url",
                 fallback="https://www.ebi.ac.uk/ena/submit/drop-box/submit/?auth=ENA",
             ),
+            "DATA-SUBMISSION": config.get(
+                "ena",
+                "development-data-submission-url",
+                fallback="webin2.ebi.ac.uk",
+            ),
         },
         "WEBIN": {
             "SERVICE": config.get(
@@ -173,6 +183,23 @@ def cli(ctx, development):
     help="Submit to BioSamples.",
 )
 @click.option("--submit-to-ena", type=click.BOOL, default=True, help="Submit to ENA.")
+@click.option(
+    "--file-transfer",
+    type=click.STRING,
+    help="provide the name of a file transfer solution, like ftp or aspera",
+)
+@click.option(
+    "--data-files",
+    type=click.File("r"),
+    multiple=True,
+    help="Path of files to upload",
+)
+# @click.option(
+#     "--data-submit-to-ena",
+#     type=click.BOOL,
+#     default=False,
+#     help="Submit data files to ENA.",
+# )
 @click.option(
     "--submit-to-metabolights",
     type=click.BOOL,
@@ -196,6 +223,8 @@ def submit(
     submit_to_ena,
     submit_to_metabolights,
     investigation_is_root,
+    file_transfer,
+    data_files,
 ):
     """Start a submission to the target repositories."""
     target_repositories = []
@@ -214,6 +243,9 @@ def submit(
     )
 
     urls_dict = ctx.obj["FILTERED_URLS"]
+
+    data_file_paths = [f.name for f in data_files] if file_transfer else []
+
     try:
         submission(
             credential_service_name,
@@ -223,6 +255,8 @@ def submit(
             target_repositories,
             investigation_is_root,
             urls_dict,
+            file_transfer,
+            data_file_paths,
         )
     except requests.RequestException as err:
         tb = sys.exc_info()[2]  # Traceback value

mars-cli/mars_lib/ftp_upload.py

@@ -0,0 +1,59 @@
+import ftplib
+import os
+from pathlib import Path
+from typing import List
+
+from retry import retry
+from mars_lib.logging import print_and_log
+
+
+class PatchFTP_TLS(ftplib.FTP_TLS):
+    """
+    Modification from https://stackoverflow.com/questions/14659154/ftpes-session-reuse-required
+    to work around bug in Python standard library: https://bugs.python.org/issue19500
+    Explicit FTPS, with shared TLS session
+    """
+
+    def ntransfercmd(self, cmd, rest=None):
+        conn, size = ftplib.FTP.ntransfercmd(self, cmd, rest)
+        if self._prot_p:
+            conn = self.context.wrap_socket(
+                conn, server_hostname=self.host, session=self.sock.session
+            )  # this is the fix
+        return conn, size
+
+
+class FTPUploader:
+    def __init__(self, ftp_host: str, username: str, password: str):
+        self.ftp_host = ftp_host
+        self.username = username
+        self.password = password
+
+    @retry(exceptions=ftplib.all_errors, tries=3, delay=2, backoff=1.2, jitter=(1, 3))
+    def upload(self, file_paths: List[Path], target_location: str = "/") -> bool:
+        # Heuristic to set the expected timeout assuming 10Mb/s upload speed but no less than 30 sec
+        # and no more than an hour
+        max_file_size = max([os.path.getsize(f) for f in file_paths])
+        timeout = min(max(int(max_file_size / 10000000), 30), 3600)
+        with PatchFTP_TLS() as ftps:
+            ftps.context.set_ciphers("HIGH:!DH:!aNULL")
+            ftps.connect(self.ftp_host, port=21, timeout=timeout)
+            ftps.login(self.username, self.password)
+            ftps.prot_p()
+
+            ftps.cwd(target_location)
+            previous_content = ftps.nlst()
+            for file_to_upload in file_paths:
+                file_name = os.path.basename(file_to_upload)
+                if file_name in previous_content and ftps.size(
+                    file_name
+                ) == os.path.getsize(file_to_upload):
+                    print_and_log(
+                        f"{file_name} already exists and has the same size on the FTP, skipping"
+                    )
+                    continue
+                print_and_log(f"Uploading {file_name} to FTP")
+                with open(file_to_upload, "rb") as open_file:
+                    ftps.storbinary("STOR %s" % file_name, open_file)
+
+        return True

mars-cli/mars_lib/submit.py

@@ -24,6 +24,10 @@
 from mars_lib.logging import print_and_log
 from pydantic import ValidationError
 
+from mars_lib.ftp_upload import FTPUploader
+from pathlib import Path
+from typing import List
+
 
 def save_step_to_file(time_stamp: float, filename: str, isa_json: IsaJson):
     dir_path = f"tmp/{str(time_stamp)}"
@@ -44,6 +48,8 @@ def submission(
     target_repositories: list[str],
     investigation_is_root: bool,
     urls: dict[str, Any],
+    file_transfer: str,
+    data_file_paths=None,
 ):
     # If credential manager info found:
     # Get password from the credential manager
@@ -82,7 +88,17 @@ def submission(
     ):
         raise ValueError("No target repository selected.")
 
-    if TargetRepository.BIOSAMPLES in target_repositories:
+    if (
+        TargetRepository.ENA in target_repositories
+        and data_file_paths
+        and file_transfer
+    ):
+        upload_to_ena(
+            file_paths=data_file_paths,
+            user_credentials=user_credentials,
+            submission_url=urls["ENA"]["DATA-SUBMISSION"],
+            file_transfer=file_transfer,
+        )
         # Submit to Biosamples
         biosamples_result = submit_to_biosamples(
             isa_json=isa_json,
@@ -202,6 +218,26 @@ def submit_to_ena(
     return result
 
 
+def upload_to_ena(
+    file_paths: List[Path],
+    user_credentials: dict[str, str],
+    submission_url: str,
+    file_transfer: str,
+):
+    ALLOWED_FILE_TRANSFER_SOLUTIONS = {"ftp", "aspera"}
+    file_transfer = file_transfer.lower()
+
+    if file_transfer not in ALLOWED_FILE_TRANSFER_SOLUTIONS:
+        raise ValueError(f"Unsupported transfer protocol: {file_transfer}")
+    if file_transfer == "ftp":
+        uploader = FTPUploader(
+            submission_url,
+            user_credentials["username"],
+            user_credentials["password"],
+        )
+        uploader.upload(file_paths)
+
+
 def create_external_references(
     biosamples_credentials: dict[str, str],
     biosamples_externalReferences: dict[str, Any],

mars-cli/requirements.txt

@@ -3,3 +3,4 @@ jsonschema
 keyring
 pydantic
 click
+retry

mars-cli/tests/test_ftp_upload.py

@@ -0,0 +1,22 @@
+import json
+
+import pytest
+from pathlib import Path
+import ftplib
+
+from mars_lib.ftp_upload import FTPUploader
+
+
+def test_upload_login_failure():
+    uploader = FTPUploader("webin2.ebi.ac.uk", "junk", "more junk")
+    with pytest.raises(ftplib.error_perm, match="530 Login incorrect."):
+        uploader.upload([Path("./tests/fixtures/not_a_json_file.txt")])
+
+
+@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")])

repository-services/repository-api.md

@@ -2,7 +2,7 @@
 This document is to define the interface between the broker and the target repository services.
 This applies to all repositories, including BioSamples.
 
-At present, only a single API endpoint is required, `submit`. Authentication and data transfer are not covered in this document, but some assumptions are laid out below.
+There is one required endpoint, `submit`, as well as a submission status endpoint recommended for long-running submission processing. Authentication and data transfer are not covered in this document, but some assumptions are laid out below.
 
 ## Authentication
 If the repository requires authentication to submit data, the submit endpoint must allow authentication via an authorization header.
@@ -35,24 +35,33 @@ The response must be JSON in the following format:
     "errors": [ 
         // error objects
     ],
+    "status": {
+      // status object
+    },
     "info": [ 
         // info objects
     ]
 }
 ```
 where:
 * `targetRepository` is the identifier used to annotate the ISA-JSON and should take values from [identifiers.org](http://identifiers.org/)
-* Either [`accessions`](#accession-object) OR [`errors`](#error-object), but not both, must be present as a list of objects of the form described below. Presence of this field indicates whether the submission was a success or a failure.
-* (optional) [`info`](#info-object) is a list of objects of the form described below. This allows additional repository-specific information to be returned in the response.
+* Exactly one of the following:
+  * `accessions`: list of objects defined [here](#accession-object)
+  * `errors`: list of objects defined [here](#error-object)
+  * `status`: object defined [here](#status-object)
+* Presence of `accession`, `errors`, or `status` indicates whether the submission was a success, failure, or is still pending (asynchronous response).
+* (optional) `info` is a list of objects of the form described [below](#info-object). This allows additional repository-specific information to be returned in the response.
+
+This object is frequently referred to as the "receipt" or the "MARS receipt".
 
 #### Accession object
 The accession object looks like the following:
 ```jsonc
 {
     "path": [
-        {"key": "studies", "where": {"key": "X", "value": "Y"}},
-	    {"key": "materials"}
-	    // further path objects as needed
+      {"key": "studies", "where": {"key": "X", "value": "Y"}},
+      {"key": "materials"}
+      // further path objects as needed
     ],
     "value": "REPO_123"
 }
@@ -88,6 +97,20 @@ The error objects being returned by the repository may be used by developers to
 
 Besides this error reporting, the service should employ other HTTP error codes as usual (e.g. 401).
 
+#### Status object
+The status object looks like the following:
+```jsonc
+{
+  "statusUrl": "...",
+  "id": "...",
+  "percentComplete": 0.25,
+}
+```
+where:
+* `statusUrl` is a URL that can be queried to determine the completion status of the submission (see [status endpoint](#submission-status-endpoint) section below)
+* (optional) `id` is an identifier for the submission
+* (optional) `percentComplete` is a number between 0 and 1 indicating the approximate percentage of the processing by the repository that is complete
+
 #### Info object
 The info object looks like the following:
 ```jsonc
@@ -96,10 +119,21 @@ The info object looks like the following:
     "message": "..."
 }
 ```
-where `name` and `message` are strings at the repository’s discretion.
+where `name` (optional) and `message` are strings at the repository’s discretion.
 
 This can be used to provide any additional information back to the user, not relating to accessions or errors. For example, it could include the submission date and when the data will be made public. This will not be processed further by the broker but will only be presented to the user.
 
+## Submission status endpoint
+`GET /{submission_id}/status`
+
+(The endpoint path is only a suggestion, the actual path can differ as long as it is accurately returned in the `status` field of the receipt.)
+
+This endpoint is used to poll for the status of a previous submission. It should be used whenever the time from data and metadata submission until the issuing of accessions exceeds a reasonable duration, and it must be returned in the `status` field of the receipt.
+
+### Response
+
+The response must be the same format as for the submit endpoint (i.e. the [MARS receipt](#response)), again indicating whether the submission is complete and successful, complete with errors, or still pending.
+
 ## Examples
 
 ### Submission request
@@ -219,3 +253,14 @@ For illustration only.
  ]
 }
 ```
+
+### Status response
+```json
+{
+  "targetRepository": "eva",
+  "status": {
+    "id": "123-456",
+    "statusUrl": "https://ebi.ac.uk/eva/submission/123-456/status"
+  }
+}
+```