Skip to content

Remove space check before archiving #489

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
alneberg wants to merge 1 commit into
base: master
Choose a base branch
from
Open

Remove space check before archiving #489

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
57 changes: 0 additions & 57 deletions taca/backup/backup.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -102,61 +102,6 @@ def collect_runs(self, ext=None, filter_by_ext=False):
if self._is_ready_to_archive(run, ext):
self.runs.append(run)

def avail_disk_space(self, path, run):
"""Check the space on file system based on parent directory of the run."""
# not able to fetch runtype use the max size as precaution, size units in GB
run_sizes = {
"novaseq": 1800,
"miseq": 20,
"nextseq": 250,
"NovaSeqXPlus": 3600,
"promethion": 3000,
"minion": 1000,
"aviti": 350,
}
required_size = run_sizes.get(self._get_run_type(run), 900) * 2
# check for any ongoing runs and add up the required size accordingly
for data_dir in self.data_dirs.values():
if not os.path.isdir(data_dir):
continue
for run_dir in os.listdir(data_dir):
if not (
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)
):
continue
if not (
os.path.exists(
os.path.join(data_dir, run_dir, "RTAComplete.txt")
) # Illumina
or os.path.exists(
os.path.join(data_dir, run_dir, ".sync_finished") # ONT
)
or os.path.exists(
os.path.join(data_dir, run_dir, "RunUploaded.json") # Element
)
):
required_size += run_sizes.get(self._get_run_type(run), 900)
# get available free space from the file system
try:
df_proc = sp.Popen(["df", path], stdout=sp.PIPE, stderr=sp.PIPE)
df_out, df_err = df_proc.communicate()
available_size = (
int(df_out.strip().decode("utf-8").split("\n")[-1].strip().split()[3])
/ 1024
/ 1024
)
except Exception as e:
logger.error(f"Evaluation of disk space failed with error {e}")
raise SystemExit
if available_size < required_size:
e_msg = f"Required space for encryption is {required_size}GB, but only {available_size}GB available"
subjt = f"Low space for encryption - {self.host_name}"
logger.error(e_msg)
misc.send_mail(subjt, e_msg, self.mail_recipients)
raise SystemExit

def file_in_pdc(self, src_file, silent=True):
"""Check if the given files exist in PDC."""
# dsmc will return zero/True only when file exists, it returns
Expand Down Expand Up @@ -381,8 +326,6 @@ def encrypt_runs(cls, run, force):
run.dst_key_encrypted = os.path.join(bk.keys_path, run.key_encrypted)
tmp_files = [run.tar_encrypted, run.key_encrypted, run.key, run.flag]
logger.info(f"Encryption of run {run.name} is now started")
# Check if there is enough space and exit if not
bk.avail_disk_space(run.path, run.name)
# Check if the run in demultiplexed
if not force and bk.check_demux:
if not misc.run_is_demuxed(
Expand Down
Loading