deciphonctl_s3_url overried

EBI-Metagenomics · Oct 19, 2023 · 9df5ec9 · 9df5ec9
1 parent b2ffda3
commit 9df5ec9
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Showing 3 changed files with 27 additions and 22 deletions.
diff --git a/control/deciphonctl/cli.py b/control/deciphonctl/cli.py
@@ -70,51 +70,51 @@
 @hmm.command("add")
 def hmm_add(hmmfile: HMMFILE, gencode: GENCODE, epsilon: EPSILON = 0.01):
     settings = Settings()
-    sched = Sched(settings.sched_url)
+    sched = Sched(settings.sched_url, settings.s3_url)
     sched.upload(hmmfile, sched.presigned.upload_hmm_post(hmmfile.name))
     sched.hmm_post(HMMFile(name=hmmfile.name), gencode, epsilon)
 
 
 @hmm.command("rm")
 def hmm_rm(hmm_id: HMMID):
     settings = Settings()
-    sched = Sched(settings.sched_url)
+    sched = Sched(settings.sched_url, settings.s3_url)
     sched.hmm_delete(hmm_id)
 
 
 @hmm.command("ls")
 def hmm_ls():
     settings = Settings()
-    sched = Sched(settings.sched_url)
+    sched = Sched(settings.sched_url, settings.s3_url)
     rich.print(sched.hmm_list())
 
 
 @db.command("add")
 def db_add(dbfile: DBFILE, gencode: GENCODE, epsilon: EPSILON = 0.01):
     settings = Settings()
-    sched = Sched(settings.sched_url)
+    sched = Sched(settings.sched_url, settings.s3_url)
     sched.upload(dbfile, sched.presigned.upload_db_post(dbfile.name))
     sched.db_post(DBFile(name=dbfile.name, gencode=gencode, epsilon=epsilon))
 
 
 @db.command("rm")
 def db_rm(db_id: DBID):
     settings = Settings()
-    sched = Sched(settings.sched_url)
+    sched = Sched(settings.sched_url, settings.s3_url)
     sched.db_delete(db_id)
 
 
 @db.command("ls")
 def db_ls():
     settings = Settings()
-    sched = Sched(settings.sched_url)
+    sched = Sched(settings.sched_url, settings.s3_url)
     rich.print(sched.db_list())
 
 
 @job.command("ls")
 def job_ls():
     settings = Settings()
-    sched = Sched(settings.sched_url)
+    sched = Sched(settings.sched_url, settings.s3_url)
     rich.print(sched.job_list())
 
 
@@ -128,57 +128,57 @@ def scan_add(
     settings = Settings()
     seqs = [Seq(name=x.id, data=x.sequence) for x in fasta_reader.Reader(fasta)]
     x = Scan(db_id=db_id, multi_hits=multi_hits, hmmer3_compat=hmmer3_compat, seqs=seqs)
-    sched = Sched(settings.sched_url)
+    sched = Sched(settings.sched_url, settings.s3_url)
     sched.scan_post(x)
 
 
 @scan.command("rm")
 def scan_rm(scan_id: SCANID):
     settings = Settings()
-    sched = Sched(settings.sched_url)
+    sched = Sched(settings.sched_url, settings.s3_url)
     sched.scan_delete(scan_id)
 
 
 @scan.command("ls")
 def scan_ls():
     settings = Settings()
-    sched = Sched(settings.sched_url)
+    sched = Sched(settings.sched_url, settings.s3_url)
     rich.print(sched.scan_list())
 
 
 @seq.command("ls")
 def seq_ls():
     settings = Settings()
-    sched = Sched(settings.sched_url)
+    sched = Sched(settings.sched_url, settings.s3_url)
     rich.print(sched.seq_list())
 
 
 @scan.command("snap-add")
 def snap_add(scan_id: SCANID, snap: SNAPFILE):
     settings = Settings()
-    sched = Sched(settings.sched_url)
+    sched = Sched(settings.sched_url, settings.s3_url)
     sched.snap_post(scan_id, snap)
 
 
 @scan.command("snap-get")
 def snap_get(scan_id: SCANID, output_file: OUTFILE = Path("snap.dcs")):
     settings = Settings()
-    sched = Sched(settings.sched_url)
+    sched = Sched(settings.sched_url, settings.s3_url)
     with open(output_file, "wb") as file:
         file.write(sched.snap_get(scan_id))
 
 
 @scan.command("snap-rm")
 def snap_rm(scan_id: SCANID):
     settings = Settings()
-    sched = Sched(settings.sched_url)
+    sched = Sched(settings.sched_url, settings.s3_url)
     sched.snap_delete(scan_id)
 
 
 @scan.command("snap-view")
 def snap_view(scan_id: SCANID):
     settings = Settings()
-    sched = Sched(settings.sched_url)
+    sched = Sched(settings.sched_url, settings.s3_url)
     print(sched.snap_view(scan_id))
 
 
@@ -191,7 +191,7 @@ def presser_run(num_workers: int = 1, log_level: LOG_LEVEL = LogLevel.info):
     raise_sigint_on_sigterm()
     logger.remove()
     logger.add(sys.stderr, level=log_level.value.upper())
-    sched = Sched(settings.sched_url)
+    sched = Sched(settings.sched_url, settings.s3_url)
     presser_entry(settings, sched, num_workers)
 
 
@@ -203,7 +203,7 @@ def scanner_run(
     raise_sigint_on_sigterm()
     logger.remove()
     logger.add(sys.stderr, level=log_level.value.upper())
-    sched = Sched(settings.sched_url)
+    sched = Sched(settings.sched_url, settings.s3_url)
     scanner_entry(settings, sched, num_workers, num_threads)
 
 

diff --git a/control/deciphonctl/sched.py b/control/deciphonctl/sched.py
@@ -2,7 +2,7 @@
 
 import urllib.parse
 from pathlib import Path
-from typing import Any
+from typing import Any, Optional
 
 import requests
 from deciphon_core.schema import Gencode
@@ -28,9 +28,10 @@ def __init__(self, response):
 
 
 class Sched:
-    def __init__(self, url: HttpUrl):
+    def __init__(self, url: HttpUrl, s3_url: Optional[HttpUrl]):
         logger.info(f"Sched URL: {url}")
         self._url = url
+        self.s3_url = s3_url
 
     def handle_http_response(self, response):
         logger.debug(f"{response.request} {response.request.url} {response}")
@@ -151,11 +152,13 @@ def download_db_url(self, filename: str):
 
     def upload_hmm_post(self, filename: str):
         x = self._request(f"hmms/presigned-upload/{filename}")
-        return UploadPost(url=HttpUrl(x["url"]), fields=x["fields"])
+        url = self._sched.s3_url if self._sched.s3_url else HttpUrl(x["url"])
+        return UploadPost(url=url, fields=x["fields"])
 
     def upload_db_post(self, filename: str):
         x = self._request(f"dbs/presigned-upload/{filename}")
-        return UploadPost(url=HttpUrl(x["url"]), fields=x["fields"])
+        url = self._sched.s3_url if self._sched.s3_url else HttpUrl(x["url"])
+        return UploadPost(url=url, fields=x["fields"])
 
 
 class UploadPost(BaseModel):

diff --git a/control/deciphonctl/settings.py b/control/deciphonctl/settings.py
@@ -1,3 +1,5 @@
+from typing import Optional
+
 from pydantic import HttpUrl
 from pydantic_settings import BaseSettings, SettingsConfigDict
 
@@ -7,7 +9,7 @@ class Settings(BaseSettings):
 
     sched_url: HttpUrl = HttpUrl("http://localhost")
 
-    s3_url: HttpUrl = HttpUrl("http://localhost:9000")
+    s3_url: Optional[HttpUrl] = None
     s3_bucket: str = "deciphon"
 
     mqtt_host: str = "localhost"