def test_find_samples_from_file(self):
"""Find samples defined in file with empty lines and erroneous names"""
with open(os.path.join(j_doe_00_05, "P001_101_index3-bcbb-config.yaml"), "w") as fh:
fh.write("\n")
flist = find_samples(j_doe_00_05, sample=os.path.join(j_doe_00_05, "samples.txt"))
validate_sample_directories(flist, j_doe_00_05)
self.assertEqual(len(flist),2)
os.unlink(os.path.join(j_doe_00_05, "P001_101_index3-bcbb-config.yaml"))
def run(self):
if not self._check_pargs(["project"]):
return
if self.pargs.post_process:
self.pargs.post_process = os.path.abspath(self.pargs.post_process)
basedir = os.path.abspath(os.path.join(self.app.controller._meta.root_path, self.app.controller._meta.path_id))
if self.pargs.from_ssheet:
[
samplesheet_csv_to_yaml(fn)
for fn in find_samples(basedir, pattern="SampleSheet.csv$", **vars(self.pargs))
]
flist = find_samples(basedir, **vars(self.pargs))
# Add filtering on flowcell if necessary
self._meta.pattern = ".*"
flist = [x for x in flist if self._filter_fn(x)]
if self.pargs.merged:
## Setup merged samples and append to flist if new list longer
flist = setup_merged_samples(flist, **vars(self.pargs))
if not len(flist) > 0:
self.log.info("No sample configuration files found")
return
if len(flist) > 0 and not query_yes_no(
"Going to start {} jobs... Are you sure you want to continue?".format(len(flist)), force=self.pargs.force
):
return
# Make absolutely sure analysis directory is a *subdirectory* of the working directory
validate_sample_directories(flist, basedir)
orig_dir = os.path.abspath(os.getcwd())
for run_info in flist:
os.chdir(os.path.abspath(os.path.dirname(run_info)))
setup_sample(run_info, **vars(self.pargs))
os.chdir(orig_dir)
if self.pargs.only_setup:
return
if self.pargs.only_failed:
status = {x: self._sample_status(x) for x in flist}
flist = [x for x in flist if self._sample_status(x) == "FAIL"]
## Here process files again, removing if requested, and running the pipeline
for run_info in flist:
self.app.log.info("Running analysis defined by config file {}".format(run_info))
os.chdir(os.path.abspath(os.path.dirname(run_info)))
if self.app.cmd.monitor(work_dir=os.path.dirname(run_info)):
self.app.log.warn("Not running job")
continue
if self.pargs.restart:
self.app.log.info("Removing old analysis files in {}".format(os.path.dirname(run_info)))
remove_files(run_info, **vars(self.pargs))
(cl, platform_args) = run_bcbb_command(run_info, **vars(self.pargs))
self.app.cmd.command(
cl, **{"platform_args": platform_args, "saveJobId": True, "workingDirectory": os.path.dirname(run_info)}
)
os.chdir(orig_dir)
def test_find_samples_from_file(self):
"""Find samples defined in file with empty lines and erroneous names"""
with open(
os.path.join(j_doe_00_05, "P001_101_index3-bcbb-config.yaml"),
"w") as fh:
fh.write("\n")
flist = find_samples(j_doe_00_05,
sample=os.path.join(j_doe_00_05, "samples.txt"))
validate_sample_directories(flist, j_doe_00_05)
self.assertEqual(len(flist), 2)
os.unlink(os.path.join(j_doe_00_05,
"P001_101_index3-bcbb-config.yaml"))
def run(self):
if not self._check_pargs(["project"]):
return
if self.pargs.post_process:
self.pargs.post_process = os.path.abspath(self.pargs.post_process)
basedir = os.path.abspath(
os.path.join(self.app.controller._meta.root_path,
self.app.controller._meta.path_id))
if self.pargs.from_ssheet:
[
samplesheet_csv_to_yaml(fn) for fn in find_samples(
basedir, pattern="SampleSheet.csv$", **vars(self.pargs))
]
flist = find_samples(basedir, **vars(self.pargs))
# Add filtering on flowcell if necessary
self._meta.pattern = ".*"
flist = [x for x in flist if self._filter_fn(x)]
if self.pargs.merged:
## Setup merged samples and append to flist if new list longer
flist = setup_merged_samples(flist, **vars(self.pargs))
if not len(flist) > 0:
self.log.info("No sample configuration files found")
return
if len(flist) > 0 and not query_yes_no(
"Going to start {} jobs... Are you sure you want to continue?".
format(len(flist)),
force=self.pargs.force):
return
# Make absolutely sure analysis directory is a *subdirectory* of the working directory
validate_sample_directories(flist, basedir)
orig_dir = os.path.abspath(os.getcwd())
for run_info in flist:
os.chdir(os.path.abspath(os.path.dirname(run_info)))
setup_sample(run_info, **vars(self.pargs))
os.chdir(orig_dir)
if self.pargs.only_setup:
return
if self.pargs.only_failed:
status = {x: self._sample_status(x) for x in flist}
flist = [x for x in flist if self._sample_status(x) == "FAIL"]
## Here process files again, removing if requested, and running the pipeline
for run_info in flist:
self.app.log.info(
"Running analysis defined by config file {}".format(run_info))
os.chdir(os.path.abspath(os.path.dirname(run_info)))
if self.app.cmd.monitor(work_dir=os.path.dirname(run_info)):
self.app.log.warn("Not running job")
continue
if self.pargs.restart:
self.app.log.info("Removing old analysis files in {}".format(
os.path.dirname(run_info)))
remove_files(run_info, **vars(self.pargs))
(cl, platform_args) = run_bcbb_command(run_info,
**vars(self.pargs))
self.app.cmd.command(
cl, **{
'platform_args': platform_args,
'saveJobId': True,
'workingDirectory': os.path.dirname(run_info)
})
os.chdir(orig_dir)
