Merge pull request #60 from apriltuesday/ftp-upload

Add FTP upload

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(
@@ -167,6 +177,23 @@ def cli(ctx, development):
 )
 @click.argument("isa_json_file", type=click.File("r"))
 @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,
@@ -189,6 +216,8 @@ def submit(
     submit_to_ena,
     submit_to_metabolights,
     investigation_is_root,
+    file_transfer,
+    data_files,
 ):
     """Start a submission to the target repositories."""
     target_repositories = [TargetRepository.BIOSAMPLES]
@@ -209,6 +238,9 @@ 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,
@@ -218,6 +250,8 @@ 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

@@ -17,6 +17,10 @@
 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 submission(
     credential_service_name: str,
@@ -26,6 +30,8 @@ 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
@@ -53,7 +59,18 @@ def submission(
         f"ISA JSON with investigation '{isa_json.investigation.title}' is valid."
     )
 
-    if TargetRepository.ENA 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,
+        )
+    elif TargetRepository.ENA in target_repositories:
         # TODO: Filter out other assays
         ena_result = submit_to_ena(
             isa_json=isa_json,
@@ -64,6 +81,7 @@ def submission(
             f"Submission to {TargetRepository.ENA} was successful. Result:\n{ena_result.json()}"
         )
         # TODO: Update `isa_json`, based on the receipt returned
+
     elif TargetRepository.BIOSAMPLES in target_repositories:
         # Submit to Biosamples
         biosamples_result = submit_to_biosamples(
@@ -158,6 +176,26 @@ 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")])