Merge pull request #499 from ssjunnebo/teton_backup_pdc

Allow backup of aviti teton runs to PDC

Author: ssjunnebo

VERSIONLOG.md

@@ -1,5 +1,9 @@
 # TACA Version Log
 
+##20251127.1
+
+Enable archiving of Aviti Teton runs to PDC
+
 ##20251121.1
 
 Exclude pod5 from delivery by default

taca/__init__.py

@@ -1,3 +1,3 @@
 """Main TACA module"""
 
-__version__ = "1.6.13"
+__version__ = "1.6.14"

taca/backup/backup.py

@@ -72,6 +72,7 @@ def collect_runs(self, ext=None, filter_by_ext=False):
                 re.match(filesystem.RUN_RE_ILLUMINA, run.name)
                 or re.match(filesystem.RUN_RE_ONT, run.name)
                 or re.match(filesystem.RUN_RE_ELEMENT, run.name)
+                or re.match(filesystem.RUN_RE_TETON, run.name)
             ):
                 logger.error(f"Given run {self.run} did not match a FC pattern")
                 raise SystemExit
@@ -95,6 +96,7 @@ def collect_runs(self, ext=None, filter_by_ext=False):
                         re.match(filesystem.RUN_RE_ILLUMINA, item)
                         or re.match(filesystem.RUN_RE_ONT, item)
                         or re.match(filesystem.RUN_RE_ELEMENT, item)
+                        or re.match(filesystem.RUN_RE_TETON, item)
                     ) and item not in self.runs:
                         run_type = self._get_run_type(item)
                         archive_path = self.archive_dirs[run_type]
@@ -124,6 +126,7 @@ def avail_disk_space(self, path, run):
                     re.match(filesystem.RUN_RE_ILLUMINA, run_dir)
                     or re.match(filesystem.RUN_RE_ONT, run_dir)
                     or re.match(filesystem.RUN_RE_ELEMENT, run_dir)
+                    or re.match(filesystem.RUN_RE_TETON, run_dir)
                 ):
                     continue
                 if not (
@@ -196,7 +199,9 @@ def _get_run_type(self, run):
                 "^(\d{8})_(\d{4})_([1-3][A-H])_([0-9a-zA-Z]+)_([0-9a-zA-Z]+)$", run
             ):
                 run_type = "promethion"
-            elif re.match(filesystem.RUN_RE_ELEMENT, run):
+            elif re.match(filesystem.RUN_RE_ELEMENT, run) or re.match(
+                filesystem.RUN_RE_TETON, run
+            ):
                 run_type = "aviti"
             else:
                 run_type = ""
@@ -276,7 +281,9 @@ def _clean_tmp_files(self, files):
 
     def _log_pdc_statusdb(self, run):
         """Log the time stamp in statusDB if a file is succussfully sent to PDC."""
-        if re.match(filesystem.RUN_RE_ELEMENT, run):
+        if re.match(filesystem.RUN_RE_ELEMENT, run) or re.match(
+            filesystem.RUN_RE_TETON, run
+        ):
             try:
                 element_db_connection = statusdb.ElementRunsConnection(
                     self.couch_info, dbname="element_runs"

taca/utils/filesystem.py

@@ -7,6 +7,7 @@
 RUN_RE_ILLUMINA = r"^\d{6,8}_[a-zA-Z\d\-]+_\d{2,}_[AB0][A-Z\d\-]+$"
 RUN_RE_ONT = r"^(\d{8})_(\d{4})_([0-9a-zA-Z]+)_([0-9a-zA-Z]+)_([0-9a-zA-Z]+)$"
 RUN_RE_ELEMENT = r"^\d{8}_AV\d{6}_[AB]\d{10}$"
+RUN_RE_TETON = r"^\d{8}_AV\d{6}_[AB]P\d{5}$"
 
 
 @contextlib.contextmanager