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Allow backup of aviti teton runs to PDC #499

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Merged
ssjunnebo merged 4 commits into from
Nov 28, 2025
Merged

Allow backup of aviti teton runs to PDC #499

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3d0365b
Backup teton runs to PDC
ssjunnebo Nov 24, 2025
0fc0f53
Also log when uploaded
ssjunnebo Nov 24, 2025
0f3a1eb
Merge branch 'master' of https://github.com/NationalGenomicsInfrastru…
ssjunnebo Nov 27, 2025
ccccad2
Versioning
ssjunnebo Nov 27, 2025
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4 changes: 4 additions & 0 deletions VERSIONLOG.md
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Original file line number Diff line number Diff line change
@@ -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
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2 changes: 1 addition & 1 deletion taca/__init__.py
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Original file line number Diff line number Diff line change
@@ -1,3 +1,3 @@
"""Main TACA module"""

__version__ = "1.6.13"
__version__ = "1.6.14"
11 changes: 9 additions & 2 deletions taca/backup/backup.py
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Expand Up @@ -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
Expand All @@ -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]
Expand Down Expand Up @@ -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 (
Expand Down Expand Up @@ -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 = ""
Expand Down Expand Up @@ -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"
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1 change: 1 addition & 0 deletions taca/utils/filesystem.py
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Expand Up @@ -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
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