[FIX] if no test webin upload fixed -test parameter

ETH-NEXUS · Dec 17, 2024 · 96f42a2 · 96f42a2
1 parent 4699d71
commit 96f42a2
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Showing 4 changed files with 34 additions and 17 deletions.
diff --git a/api/app/core/ena_helpers.py b/api/app/core/ena_helpers.py
@@ -230,20 +230,35 @@ def webin_upload(job: AnalysisJob):
         mf.write(job.manifest.encode("utf-8"))
         mf.close()
         try:
-            out = webin(
-                "-context",
-                "genome",
-                "-username",
-                settings.ENA_USERNAME,
-                "-password",
-                settings.ENA_PASSWORD,
-                "-manifest",
-                mf.name,
-                "-submit",
-                "-ascp",
-                "-test" if settings.ENA_USE_DEV_ENDPOINT else "",
-                _err_to_out=True,
-            )
+            if settings.ENA_USE_DEV_ENDPOINT:
+                out = webin(
+                    "-context",
+                    "genome",
+                    "-username",
+                    settings.ENA_USERNAME,
+                    "-password",
+                    settings.ENA_PASSWORD,
+                    "-manifest",
+                    mf.name,
+                    "-submit",
+                    "-ascp",
+                    "-test",
+                    _err_to_out=True,
+                )
+            else:
+                out = webin(
+                    "-context",
+                    "genome",
+                    "-username",
+                    settings.ENA_USERNAME,
+                    "-password",
+                    settings.ENA_PASSWORD,
+                    "-manifest",
+                    mf.name,
+                    "-submit",
+                    "-ascp",
+                    _err_to_out=True,
+                )
             log.debug(f"Submission output: {out}")
             accession = re.findall("ERZ[0-9]+", out, flags=re.MULTILINE)
             log.debug(f"Accessions: {accession}")

diff --git a/api/app/ena_upload_ms/settings.py b/api/app/ena_upload_ms/settings.py
@@ -294,3 +294,8 @@
 ENA_UPLOAD_FREQ_SECS = int(environ.get("ENA_UPLOAD_FREQ_SECS", 5))
 TEMPLATE_DIR = "/templates"
 DATA_DIR = "/data"
+
+###
+# Proxy support
+###
+ENA_PROXY_PREFIX = environ.get("ENA_PROXY_PREFIX", "")
diff --git a/docker-compose.dev.yml b/docker-compose.dev.yml
@@ -1,5 +1,3 @@
-version: "3"
-
 services:
   api:
     environment:

diff --git a/docker-compose.yml b/docker-compose.yml
@@ -1,4 +1,3 @@
-version: "3"
 volumes:
   pg_data:
 services: