def check_days(site, days, config):
"""Check if 'days' given while running command. If not take the default threshold
from config file (which should exist). Also when 'days' given on the command line
raise a check to make sure it was really meant to do so
:param str site: site to be cleaned and relevent date to pick
:param int days: number of days to check, will be None if '-d' not used
:param dict config: config file parsed and saved as dictionary
"""
try:
default_days = config["cleanup"][site]["days"]
except KeyError:
raise
if not days:
return default_days
elif days >= default_days:
return days
else:
if misc.query_yes_no(
"Seems like given days({}) is less than the "
" default({}), are you sure to proceed ?".format(days, default_days),
default="no",
):
return days
else:
return None
def check_default(site, seconds, config):
"""Check if time(as seconds) given while running command. If not take the default threshold
from config file (which should exist). Also when 'days' given on the command line
raise a check to make sure it was really meant to do so
:param str site: site to be cleaned and relevent date to pick
:param int seconds: Days/hours converted as seconds to check
:param dict config: config file parsed and saved as dictionary
"""
try:
default_days = config['cleanup']['milou'][site]['days']
default_seconds = misc.to_seconds(days=default_days)
except KeyError:
raise
if not seconds:
return default_seconds
elif seconds >= default_seconds:
return seconds
else:
if misc.query_yes_no(
"Seems like given time is less than the "
" default({}) days, are you sure to proceed ?".format(
default_days),
default="no"):
return seconds
else:
return None
def check_default(site, seconds, config):
"""Check if time(as seconds) given while running command. If not take the default threshold
from config file (which should exist). Also when 'days' given on the command line
raise a check to make sure it was really meant to do so
:param str site: site to be cleaned and relevent date to pick
:param int seconds: Days/hours converted as seconds to check
:param dict config: config file parsed and saved as dictionary
"""
try:
default_days = config['cleanup']['milou'][site]['days']
default_seconds = misc.to_seconds(days=default_days)
except KeyError:
raise
if not seconds:
return default_seconds
elif seconds >= default_seconds:
return seconds
else:
if misc.query_yes_no("Seems like given time is less than the "
" default({}) days, are you sure to proceed ?"
.format(default_days), default="no"):
return seconds
else:
return None
def check_days(site, days, config):
"""Check if 'days' given while running command. If not take the default threshold
from config file (which should exist). Also when 'days' given on the command line
raise a check to make sure it was really meant to do so
:param str site: site to be cleaned and relevent date to pick
:param int days: number of days to check, will be None if '-d' not used
:param dict config: config file parsed and saved as dictionary
"""
try:
default_days = config['cleanup'][site]['days']
except KeyError:
raise
if not days:
return default_days
elif days >= default_days:
return days
else:
if misc.query_yes_no("Seems like given days({}) is less than the "
" default({}), are you sure to proceed ?"
.format(days,default_days), default="no"):
return days
else:
return None
def cleanup_irma(days_fastq,
days_analysis,
only_fastq,
only_analysis,
clean_undetermined,
status_db_config,
exclude_projects,
list_only,
date,
dry_run=False):
"""Remove fastq/analysis data for projects that have been closed more than given
days (as days_fastq/days_analysis) from the given 'irma' cluster
:param int days_fastq: Days to consider to remove fastq files for project
:param int days_analysis: Days to consider to remove analysis data for project
:param bool only_fastq: Remove only fastq files for closed projects
:param bool only_analysis: Remove only analysis data for closed projects
:param bool dry_run: Will summarize what is going to be done without really doing it
Example for mat for config file
cleanup:
irma:
flowcell:
##this path is nothing but incoming directory, can given multiple paths
root:
- path/to/flowcells_dir
relative_project_source: Demultiplexing
undet_file_pattern: "Undetermined_*.fastq.gz"
##this is path where projects are organized
data_dir: path/to/data_dir
analysis:
##directory where analysis are perfoemed for projects
root: path/to/analysis_dir
#should be exactly same as the qc folder name and files wished to be removed
files_to_remove:
piper_ngi:
- "*.bam"
"""
try:
config = CONFIG['cleanup']['irma']
flowcell_dir_root = config['flowcell']['root']
flowcell_project_source = config['flowcell']['relative_project_source']
flowcell_undet_files = config['flowcell']['undet_file_pattern']
data_dir = config['data_dir']
analysis_dir = config['analysis']['root']
analysis_data_to_remove = config['analysis']['files_to_remove']
if date:
date = datetime.strptime(date, '%Y-%m-%d')
except KeyError as e:
logger.error(
"Config file is missing the key {}, make sure it have all required information"
.format(str(e)))
raise SystemExit
except ValueError as e:
logger.error(
"Date given with '--date' option is not in required format, see help for more info"
)
raise SystemExit
# make a connection for project db #
pcon = statusdb.ProjectSummaryConnection(conf=status_db_config)
assert pcon, "Could not connect to project database in StatusDB"
# make exclude project list if provided
exclude_list = []
if exclude_projects:
if os.path.isfile(exclude_projects):
with open(exclude_projects, 'r') as in_file:
exclude_list.extend([p.strip() for p in in_file.readlines()])
else:
exclude_list.extend(exclude_projects.split(','))
# sanity check for mentioned project to exculde or valid
invalid_projects = filter(
lambda p: p not in pcon.id_view.keys() and p not in pcon.name_view.
keys(), exclude_list)
if invalid_projects:
logger.error(
"'--exclude_projects' was called with some invalid projects '{}', "
"provide valid project name/id".format(
",".join(invalid_projects)))
raise SystemExit
#compile list for project to delete
project_clean_list, project_processed_list = ({}, [])
if not list_only and not clean_undetermined:
logger.info("Building initial project list for removing data..")
if only_fastq:
logger.info(
"Option 'only_fastq' is given, so will not look for analysis data")
elif only_analysis:
logger.info(
"Option 'only_analysis' is given, so will not look for fastq data")
if clean_undetermined:
all_undet_files = []
for flowcell_dir in flowcell_dir_root:
for fc in [
d for d in os.listdir(flowcell_dir)
if re.match(filesystem.RUN_RE, d)
]:
fc_abs_path = os.path.join(flowcell_dir, fc)
with filesystem.chdir(fc_abs_path):
if not os.path.exists(flowcell_project_source):
logger.warn(
"Flowcell {} do not contain a '{}' direcotry".
format(fc, flowcell_project_source))
continue
projects_in_fc = [d for d in os.listdir(flowcell_project_source) \
if re.match(r'^[A-Z]+[_\.]+[A-Za-z]+_\d\d_\d\d$',d) and \
not os.path.exists(os.path.join(flowcell_project_source, d, "cleaned"))]
# the above check looked for project directories and also that are not cleaned
# so if it could not find any project, means there is no project diretory at all
# or all the project directory is already cleaned. Then we can remove the undet
if len(projects_in_fc) > 0:
continue
fc_undet_files = glob(
os.path.join(flowcell_project_source,
flowcell_undet_files))
if fc_undet_files:
logger.info(
"All projects was cleaned for FC {}, found {} undeterminded files"
.format(fc, len(fc_undet_files)))
all_undet_files.extend(
map(os.path.abspath, fc_undet_files))
if all_undet_files:
undet_size = _def_get_size_unit(
sum(map(os.path.getsize, all_undet_files)))
if misc.query_yes_no(
"In total found {} undetermined files which are {} in size, delete now ?"
.format(len(all_undet_files), undet_size),
default="no"):
removed = _remove_files(all_undet_files)
return
elif only_analysis:
for pid in [d for d in os.listdir(analysis_dir) if re.match(r'^P\d+$', d) and \
not os.path.exists(os.path.join(analysis_dir, d, "cleaned"))]:
proj_abs_path = os.path.join(analysis_dir, pid)
proj_info = get_closed_proj_info(
pid, pcon.get_entry(pid, use_id_view=True), date)
if proj_info and proj_info['closed_days'] >= days_analysis:
# move on if this project has to be excluded
if proj_info['name'] in exclude_list or proj_info[
'pid'] in exclude_list:
continue
analysis_data, analysis_size = collect_analysis_data_irma(
pid, analysis_dir, analysis_data_to_remove)
proj_info['analysis_to_remove'] = analysis_data
proj_info['analysis_size'] = analysis_size
proj_info['fastq_to_remove'] = "not_selected"
proj_info['fastq_size'] = 0
project_clean_list[proj_info['name']] = proj_info
else:
for flowcell_dir in flowcell_dir_root:
for fc in [
d for d in os.listdir(flowcell_dir)
if re.match(filesystem.RUN_RE, d)
]:
fc_abs_path = os.path.join(flowcell_dir, fc)
with filesystem.chdir(fc_abs_path):
if not os.path.exists(flowcell_project_source):
logger.warn(
"Flowcell {} do not contain a '{}' direcotry".
format(fc, flowcell_project_source))
continue
projects_in_fc = [d for d in os.listdir(flowcell_project_source) \
if re.match(r'^[A-Z]+[_\.]+[A-Za-z0-9]+_\d\d_\d\d$',d) and \
not os.path.exists(os.path.join(flowcell_project_source, d, "cleaned"))]
for _proj in projects_in_fc:
proj = re.sub(r'_+', '.', _proj, 1)
# if a project is already processed no need of fetching it again from status db
if proj in project_processed_list:
# if the project is closed more than threshold days collect the fastq files from FC
# no need of looking for analysis data as they would have been collected in the first time
if proj in project_clean_list and project_clean_list[
proj]['closed_days'] >= days_fastq:
fc_fq_files, fq_size = collect_fastq_data_irma(
fc_abs_path,
os.path.join(flowcell_project_source,
_proj))
project_clean_list[proj]['fastq_to_remove'][
'flowcells'][fc] = fc_fq_files[
'flowcells'][fc]
project_clean_list[proj][
'fastq_size'] += fq_size
continue
project_processed_list.append(proj)
#by default assume all projects are not old enough for delete
fastq_data, analysis_data = ("young", "young")
fastq_size, analysis_size = (0, 0)
proj_info = get_closed_proj_info(
proj, pcon.get_entry(proj), date)
if proj_info:
# move on if this project has to be excluded
if proj_info['name'] in exclude_list or proj_info[
'pid'] in exclude_list:
continue
# if project not old enough for fastq files and only fastq files selected move on to next project
if proj_info['closed_days'] >= days_fastq:
fastq_data, fastq_size = collect_fastq_data_irma(
fc_abs_path,
os.path.join(flowcell_project_source,
_proj), data_dir,
proj_info['pid'])
if not only_fastq:
# if project is old enough for fastq files and not 'only_fastq' try collect analysis files
if proj_info['closed_days'] >= days_analysis:
analysis_data, analysis_size = collect_analysis_data_irma(
proj_info['pid'], analysis_dir,
analysis_data_to_remove)
# if both fastq and analysis files are not old enough move on
if (analysis_data == fastq_data) or (
(not analysis_data or analysis_data
== "cleaned") and fastq_data == "young"):
continue
elif fastq_data == "young":
continue
else:
analysis_data = "not_selected"
proj_info['fastq_to_remove'] = fastq_data
proj_info['fastq_size'] = fastq_size
proj_info['analysis_to_remove'] = analysis_data
proj_info['analysis_size'] = analysis_size
project_clean_list[proj] = proj_info
if not project_clean_list:
logger.info("There are no projects to clean")
return
# list only the project and exit if 'list_only' option is selected
if list_only:
print "Project ID\tProject Name\tBioinfo resp.\tClosed Days\tClosed Date\tFastq size\tAnalysis size"
for p_info in sorted(project_clean_list.values(),
key=lambda d: d['closed_days'],
reverse=True):
print "\t".join([
p_info['name'], p_info['pid'], p_info['bioinfo_responsible'],
str(p_info['closed_days']), p_info['closed_date'],
_def_get_size_unit(p_info['fastq_size']),
_def_get_size_unit(p_info['analysis_size'])
])
raise SystemExit
logger.info("Initial list is built with {} projects {}".format(
len(project_clean_list), get_files_size_text(project_clean_list)))
if misc.query_yes_no("Interactively filter projects for cleanup ?",
default="yes"):
filtered_project, proj_count = ([], 0)
#go through complied project list and remove files
for proj, info in project_clean_list.iteritems():
proj_count += 1
if not misc.query_yes_no(
"{}Delete files for this project ({}/{})".format(
get_proj_meta_info(info, days_fastq), proj_count,
len(project_clean_list)),
default="no"):
logger.info(
"Will not remove files for project {}".format(proj))
filtered_project.append(proj)
# remove projects that were decided not to delete
map(project_clean_list.pop, filtered_project)
logger.info("Removed {}/{} projects from initial list".format(
len(filtered_project), proj_count))
if not project_clean_list:
logger.info("There are no projects to clean after filtering")
return
logger.info("Final list is created with {} projects {}".format(
len(project_clean_list), get_files_size_text(project_clean_list)))
if not misc.query_yes_no("Proceed with cleanup ?", default="no"):
logger.info("Aborting cleanup")
return
logger.info("Will start cleaning up project now")
for proj, info in project_clean_list.iteritems():
fastq_info = info.get('fastq_to_remove')
if fastq_info and isinstance(fastq_info, dict):
logger.info("Cleaning fastq files for project {}".format(proj))
fastq_fc = fastq_info.get('flowcells', {})
removed_fc = []
for fc, fc_info in fastq_fc.iteritems():
proj_fc_root = fc_info['proj_root']
logger.info(
"Removing fastq files from {}".format(proj_fc_root))
if not dry_run:
if _remove_files(fc_info['fq_files']):
logger.info(
"Removed fastq files from FC {} for project {}, marking it as cleaned"
.format(fc, proj))
_touch_cleaned(proj_fc_root)
removed_fc.append(fc)
if len(fastq_fc) == len(removed_fc):
try:
proj_data_root = fastq_info['proj_data']['proj_data_root']
logger.info(
"All flowcells cleaned for this project, marking it as cleaned in {}"
.format(proj_data_root))
_touch_cleaned(proj_data_root)
except:
pass
analysis_info = info.get('analysis_to_remove')
if analysis_info and isinstance(analysis_info, dict):
proj_analysis_root = analysis_info['proj_analysis_root']
logger.info("cleaning analysis data for project {}".format(proj))
removed_qc = []
for qc, files in analysis_info['analysis_files'].iteritems():
logger.info("Removing files of '{}' from {}".format(
qc, proj_analysis_root))
if not dry_run:
if _remove_files(files):
removed_qc.append(qc)
else:
logger.warn(
"Couldn't remove some files in qc directory '{}'".
format(qc))
map(analysis_info['analysis_files'].pop, removed_qc)
if len(analysis_info['analysis_files']) == 0:
logger.info(
"Removed analysis data for project {}, marking it cleaned".
format(proj))
_touch_cleaned(proj_analysis_root)
def cleanup_irma(days_fastq, days_analysis, only_fastq, only_analysis, clean_undetermined, status_db_config, exclude_projects, list_only, date, dry_run=False):
"""Remove fastq/analysis data for projects that have been closed more than given
days (as days_fastq/days_analysis) from the given 'irma' cluster
:param int days_fastq: Days to consider to remove fastq files for project
:param int days_analysis: Days to consider to remove analysis data for project
:param bool only_fastq: Remove only fastq files for closed projects
:param bool only_analysis: Remove only analysis data for closed projects
:param bool dry_run: Will summarize what is going to be done without really doing it
Example for mat for config file
cleanup:
irma:
flowcell:
##this path is nothing but incoming directory, can given multiple paths
root:
- path/to/flowcells_dir
relative_project_source: Demultiplexing
undet_file_pattern: "Undetermined_*.fastq.gz"
##this is path where projects are organized
data_dir: path/to/data_dir
analysis:
##directory where analysis are perfoemed for projects
root: path/to/analysis_dir
#should be exactly same as the qc folder name and files wished to be removed
files_to_remove:
piper_ngi:
- "*.bam"
"""
try:
config = CONFIG['cleanup']['irma']
flowcell_dir_root = config['flowcell']['root']
flowcell_project_source = config['flowcell']['relative_project_source']
flowcell_undet_files = config['flowcell']['undet_file_pattern']
data_dir = config['data_dir']
analysis_dir = config['analysis']['root']
analysis_data_to_remove = config['analysis']['files_to_remove']
if date:
date = datetime.strptime(date, '%Y-%m-%d')
except KeyError as e:
logger.error("Config file is missing the key {}, make sure it have all required information".format(str(e)))
raise SystemExit
except ValueError as e:
logger.error("Date given with '--date' option is not in required format, see help for more info")
raise SystemExit
# make a connection for project db #
pcon = statusdb.ProjectSummaryConnection(conf=status_db_config)
assert pcon, "Could not connect to project database in StatusDB"
# make exclude project list if provided
exclude_list = []
if exclude_projects:
if os.path.isfile(exclude_projects):
with open(exclude_projects, 'r') as in_file:
exclude_list.extend([p.strip() for p in in_file.readlines()])
else:
exclude_list.extend(exclude_projects.split(','))
# sanity check for mentioned project to exculde or valid
invalid_projects = filter(lambda p: p not in pcon.id_view.keys() and p not in pcon.name_view.keys(), exclude_list)
if invalid_projects:
logger.error("'--exclude_projects' was called with some invalid projects '{}', "
"provide valid project name/id".format(",".join(invalid_projects)))
raise SystemExit
#compile list for project to delete
project_clean_list, project_processed_list = ({}, [])
if not list_only and not clean_undetermined:
logger.info("Building initial project list for removing data..")
if only_fastq:
logger.info("Option 'only_fastq' is given, so will not look for analysis data")
elif only_analysis:
logger.info("Option 'only_analysis' is given, so will not look for fastq data")
if clean_undetermined:
all_undet_files = []
for flowcell_dir in flowcell_dir_root:
for fc in [d for d in os.listdir(flowcell_dir) if re.match(filesystem.RUN_RE,d)]:
fc_abs_path = os.path.join(flowcell_dir, fc)
with filesystem.chdir(fc_abs_path):
if not os.path.exists(flowcell_project_source):
logger.warn("Flowcell {} do not contain a '{}' direcotry".format(fc, flowcell_project_source))
continue
projects_in_fc = [d for d in os.listdir(flowcell_project_source) \
if re.match(r'^[A-Z]+[_\.]+[A-Za-z]+_\d\d_\d\d$',d) and \
not os.path.exists(os.path.join(flowcell_project_source, d, "cleaned"))]
# the above check looked for project directories and also that are not cleaned
# so if it could not find any project, means there is no project diretory at all
# or all the project directory is already cleaned. Then we can remove the undet
if len(projects_in_fc) > 0:
continue
fc_undet_files = glob(os.path.join(flowcell_project_source,flowcell_undet_files))
if fc_undet_files:
logger.info("All projects was cleaned for FC {}, found {} undeterminded files".format(fc,len(fc_undet_files)))
all_undet_files.extend(map(os.path.abspath, fc_undet_files))
if all_undet_files:
undet_size = _def_get_size_unit(sum(map(os.path.getsize, all_undet_files)))
if misc.query_yes_no("In total found {} undetermined files which are {} in size, delete now ?".format(len(all_undet_files),
undet_size), default="no"):
removed = _remove_files(all_undet_files)
return
elif only_analysis:
for pid in [d for d in os.listdir(analysis_dir) if re.match(r'^P\d+$', d) and \
not os.path.exists(os.path.join(analysis_dir, d, "cleaned"))]:
proj_abs_path = os.path.join(analysis_dir, pid)
proj_info = get_closed_proj_info(pid, pcon.get_entry(pid, use_id_view=True), date)
if proj_info and proj_info['closed_days'] >= days_analysis:
# move on if this project has to be excluded
if proj_info['name'] in exclude_list or proj_info['pid'] in exclude_list:
continue
analysis_data, analysis_size = collect_analysis_data_irma(pid, analysis_dir, analysis_data_to_remove)
proj_info['analysis_to_remove'] = analysis_data
proj_info['analysis_size'] = analysis_size
proj_info['fastq_to_remove'] = "not_selected"
proj_info['fastq_size'] = 0
project_clean_list[proj_info['name']] = proj_info
else:
for flowcell_dir in flowcell_dir_root:
for fc in [d for d in os.listdir(flowcell_dir) if re.match(filesystem.RUN_RE,d)]:
fc_abs_path = os.path.join(flowcell_dir, fc)
with filesystem.chdir(fc_abs_path):
if not os.path.exists(flowcell_project_source):
logger.warn("Flowcell {} do not contain a '{}' direcotry".format(fc, flowcell_project_source))
continue
projects_in_fc = [d for d in os.listdir(flowcell_project_source) \
if re.match(r'^[A-Z]+[_\.]+[A-Za-z0-9]+_\d\d_\d\d$',d) and \
not os.path.exists(os.path.join(flowcell_project_source, d, "cleaned"))]
for _proj in projects_in_fc:
proj = re.sub(r'_+', '.', _proj, 1)
# if a project is already processed no need of fetching it again from status db
if proj in project_processed_list:
# if the project is closed more than threshold days collect the fastq files from FC
# no need of looking for analysis data as they would have been collected in the first time
if proj in project_clean_list and project_clean_list[proj]['closed_days'] >= days_fastq:
fc_fq_files, fq_size = collect_fastq_data_irma(fc_abs_path, os.path.join(flowcell_project_source, _proj))
project_clean_list[proj]['fastq_to_remove']['flowcells'][fc] = fc_fq_files['flowcells'][fc]
project_clean_list[proj]['fastq_size'] += fq_size
continue
project_processed_list.append(proj)
#by default assume all projects are not old enough for delete
fastq_data, analysis_data = ("young", "young")
fastq_size, analysis_size = (0, 0)
proj_info = get_closed_proj_info(proj, pcon.get_entry(proj), date)
if proj_info:
# move on if this project has to be excluded
if proj_info['name'] in exclude_list or proj_info['pid'] in exclude_list:
continue
# if project not old enough for fastq files and only fastq files selected move on to next project
if proj_info['closed_days'] >= days_fastq:
fastq_data, fastq_size = collect_fastq_data_irma(fc_abs_path, os.path.join(flowcell_project_source, _proj),
data_dir, proj_info['pid'])
if not only_fastq:
# if project is old enough for fastq files and not 'only_fastq' try collect analysis files
if proj_info['closed_days'] >= days_analysis:
analysis_data, analysis_size = collect_analysis_data_irma(proj_info['pid'], analysis_dir, analysis_data_to_remove)
# if both fastq and analysis files are not old enough move on
if (analysis_data == fastq_data) or ((not analysis_data or analysis_data == "cleaned") and fastq_data == "young"):
continue
elif fastq_data == "young":
continue
else:
analysis_data = "not_selected"
proj_info['fastq_to_remove'] = fastq_data
proj_info['fastq_size'] = fastq_size
proj_info['analysis_to_remove'] = analysis_data
proj_info['analysis_size'] = analysis_size
project_clean_list[proj] = proj_info
if not project_clean_list:
logger.info("There are no projects to clean")
return
# list only the project and exit if 'list_only' option is selected
if list_only:
print "Project ID\tProject Name\tBioinfo resp.\tClosed Days\tClosed Date\tFastq size\tAnalysis size"
for p_info in sorted(project_clean_list.values(), key=lambda d: d['closed_days'], reverse=True):
print "\t".join([p_info['name'], p_info['pid'], p_info['bioinfo_responsible'],
str(p_info['closed_days']), p_info['closed_date'],
_def_get_size_unit(p_info['fastq_size']), _def_get_size_unit(p_info['analysis_size'])])
raise SystemExit
logger.info("Initial list is built with {} projects {}".format(len(project_clean_list), get_files_size_text(project_clean_list)))
if misc.query_yes_no("Interactively filter projects for cleanup ?", default="yes"):
filtered_project, proj_count = ([], 0)
#go through complied project list and remove files
for proj, info in project_clean_list.iteritems():
proj_count += 1
if not misc.query_yes_no("{}Delete files for this project ({}/{})".format(get_proj_meta_info(info, days_fastq),
proj_count, len(project_clean_list)), default="no"):
logger.info("Will not remove files for project {}".format(proj))
filtered_project.append(proj)
# remove projects that were decided not to delete
map(project_clean_list.pop, filtered_project)
logger.info("Removed {}/{} projects from initial list".format(len(filtered_project), proj_count))
if not project_clean_list:
logger.info("There are no projects to clean after filtering")
return
logger.info("Final list is created with {} projects {}".format(len(project_clean_list), get_files_size_text(project_clean_list)))
if not misc.query_yes_no("Proceed with cleanup ?", default="no"):
logger.info("Aborting cleanup")
return
logger.info("Will start cleaning up project now")
for proj, info in project_clean_list.iteritems():
fastq_info = info.get('fastq_to_remove')
if fastq_info and isinstance(fastq_info, dict):
logger.info("Cleaning fastq files for project {}".format(proj))
fastq_fc = fastq_info.get('flowcells', {})
removed_fc = []
for fc, fc_info in fastq_fc.iteritems():
proj_fc_root = fc_info['proj_root']
logger.info("Removing fastq files from {}".format(proj_fc_root))
if not dry_run:
if _remove_files(fc_info['fq_files']):
logger.info("Removed fastq files from FC {} for project {}, marking it as cleaned".format(fc, proj))
_touch_cleaned(proj_fc_root)
removed_fc.append(fc)
if len(fastq_fc) == len(removed_fc):
try:
proj_data_root = fastq_info['proj_data']['proj_data_root']
logger.info("All flowcells cleaned for this project, marking it as cleaned in {}".format(proj_data_root))
_touch_cleaned(proj_data_root)
except:
pass
analysis_info = info.get('analysis_to_remove')
if analysis_info and isinstance(analysis_info, dict):
proj_analysis_root = analysis_info['proj_analysis_root']
logger.info("cleaning analysis data for project {}".format(proj))
removed_qc = []
for qc, files in analysis_info['analysis_files'].iteritems():
logger.info("Removing files of '{}' from {}".format(qc, proj_analysis_root))
if not dry_run:
if _remove_files(files):
removed_qc.append(qc)
else:
logger.warn("Couldn't remove some files in qc directory '{}'".format(qc))
map(analysis_info['analysis_files'].pop, removed_qc)
if len(analysis_info['analysis_files']) == 0:
logger.info("Removed analysis data for project {}, marking it cleaned".format(proj))
_touch_cleaned(proj_analysis_root)
def cleanup_irma(days_fastq, days_analysis, only_fastq, only_analysis, status_db_config, dry_run=False):
"""Remove fastq/analysis data for projects that have been closed more than given
days (as days_fastq/days_analysis) from the given 'irma' cluster
:param int days_fastq: Days to consider to remove fastq files for project
:param int days_analysis: Days to consider to remove analysis data for project
:param bool only_fastq: Remove only fastq files for closed projects
:param bool only_analysis: Remove only analysis data for closed projects
:param bool dry_run: Will summarize what is going to be done without really doing it
Example for mat for config file
cleanup:
irma:
flowcell:
##this path is nothing but incoming directory, can given multiple paths
root:
- path/to/flowcells_dir
relative_project_source: Demultiplexing
##this is path where projects are organized
data_dir: path/to/data_dir
analysis:
##directory where analysis are perfoemed for projects
root: path/to/analysis_dir
#should be exactly same as the qc folder name and files wished to be removed
files_to_remove:
piper_ngi:
- "*.bam"
"""
try:
config = CONFIG['cleanup']['irma']
flowcell_dir_root = config['flowcell']['root']
flowcell_project_source = config['flowcell']['relative_project_source']
data_dir = config['data_dir']
analysis_dir = config['analysis']['root']
analysis_data_to_remove = config['analysis']['files_to_remove']
except KeyError as e:
logger.error("Config file is missing the key {}, make sure it have all required information".format(str(e)))
raise SystemExit
# make a connection for project db #
pcon = statusdb.ProjectSummaryConnection(conf=status_db_config)
assert pcon, "Could not connect to project database in StatusDB"
#compile list for project to delete
project_clean_list, project_processed_list = ({}, [])
logger.info("Building initial project list for removing data..")
if only_fastq:
logger.info("Option 'only_fastq' is given, so will not look for analysis data")
elif only_analysis:
logger.info("Option 'only_analysis' is given, so will not look for fastq data")
if only_analysis:
for pid in [d for d in os.listdir(analysis_dir) if re.match(r'^P\d+$', d) and \
not os.path.exists(os.path.join(analysis_dir, d, "cleaned"))]:
proj_abs_path = os.path.join(analysis_dir, pid)
proj_info = get_closed_proj_info(pid, pcon.get_entry(pid, use_id_view=True))
if proj_info and proj_info['closed_days'] >= days_analysis:
analysis_data, analysis_size = collect_analysis_data_irma(pid, analysis_dir, analysis_data_to_remove)
proj_info['analysis_to_remove'] = analysis_data
proj_info['analysis_size'] = analysis_size
proj_info['fastq_to_remove'] = "not_selected"
proj_info['fastq_size'] = 0
project_clean_list[proj_info['name']] = proj_info
else:
for flowcell_dir in flowcell_dir_root:
for fc in [d for d in os.listdir(flowcell_dir) if re.match(filesystem.RUN_RE,d)]:
fc_abs_path = os.path.join(flowcell_dir, fc)
with filesystem.chdir(fc_abs_path):
projects_in_fc = [d for d in os.listdir(flowcell_project_source) \
if re.match(r'^[A-Z]+[_\.]+[A-Za-z]+_\d\d_\d\d$',d) and \
not os.path.exists(os.path.join(flowcell_project_source, d, "cleaned"))]
for _proj in projects_in_fc:
proj = re.sub(r'_+', '.', _proj, 1)
# if a project is already processed no need of fetching it again from status db
if proj in project_processed_list:
# if the project is closed more than threshold days collect the fastq files from FC
# no need of looking for analysis data as they would have been collected in the first time
if proj in project_clean_list and project_clean_list[proj]['closed_days'] >= days_fastq:
fc_fq_files, fq_size = collect_fastq_data_irma(fc_abs_path, os.path.join(flowcell_project_source, _proj))
project_clean_list[proj]['fastq_to_remove']['flowcells'][fc] = fc_fq_files['flowcells'][fc]
project_clean_list[proj]['fastq_size'] += fq_size
continue
project_processed_list.append(proj)
#by default assume all projects are not old enough for delete
fastq_data, analysis_data = ("young", "young")
fastq_size, analysis_size = (0, 0)
proj_info = get_closed_proj_info(proj, pcon.get_entry(proj))
if proj_info:
# if project not old enough for fastq files and only fastq files selected move on to next project
if proj_info['closed_days'] >= days_fastq:
fastq_data, fastq_size = collect_fastq_data_irma(fc_abs_path, os.path.join(flowcell_project_source, _proj),
data_dir, proj_info['pid'])
if not only_fastq:
# if project is old enough for fastq files and not 'only_fastq' try collect analysis files
if proj_info['closed_days'] >= days_analysis:
analysis_data, analysis_size = collect_analysis_data_irma(proj_info['pid'], analysis_dir, analysis_data_to_remove)
# if both fastq and analysis files are not old enough move on
if (analysis_data == fastq_data) or ((not analysis_data or analysis_data == "cleaned") and fastq_data == "young"):
continue
elif fastq_data == "young":
continue
else:
analysis_data = "not_selected"
proj_info['fastq_to_remove'] = fastq_data
proj_info['fastq_size'] = fastq_size
proj_info['analysis_to_remove'] = analysis_data
proj_info['analysis_size'] = analysis_size
project_clean_list[proj] = proj_info
if not project_clean_list:
logger.info("There are no projects to clean")
return
get_files_size_text(project_clean_list)
logger.info("Initial list is built with {} projects {}".format(len(project_clean_list), get_files_size_text(project_clean_list)))
if misc.query_yes_no("Interactively filter projects for cleanup ?", default="yes"):
filtered_project, proj_count = ([], 0)
#go through complied project list and remove files
for proj, info in project_clean_list.iteritems():
proj_count += 1
if not misc.query_yes_no("{}Delete files for this project ({}/{})".format(get_proj_meta_info(info, days_fastq),
proj_count, len(project_clean_list)), default="no"):
logger.info("Will not remove files for project {}".format(proj))
filtered_project.append(proj)
# remove projects that were decided not to delete
map(project_clean_list.pop, filtered_project)
logger.info("Removed {}/{} projects from initial list".format(len(filtered_project), proj_count))
if not project_clean_list:
logger.info("There are no projects to clean after filtering")
return
logger.info("Final list is created with {} projects {}".format(len(project_clean_list), get_files_size_text(project_clean_list)))
if not misc.query_yes_no("Proceed with cleanup ?", default="no"):
logger.info("Aborting cleanup")
return
logger.info("Will start cleaning up project now")
for proj, info in project_clean_list.iteritems():
fastq_info = info.get('fastq_to_remove')
if fastq_info and isinstance(fastq_info, dict):
logger.info("Cleaning fastq files for project {}".format(proj))
fastq_fc = fastq_info.get('flowcells', {})
removed_fc = []
for fc, fc_info in fastq_fc.iteritems():
proj_fc_root = fc_info['proj_root']
logger.info("Removing fastq files from {}".format(proj_fc_root))
if not dry_run:
if _remove_files(fc_info['fq_files']):
logger.info("Removed fastq files from FC {} for project {}, marking it as cleaned".format(fc, proj))
_touch_cleaned(proj_fc_root)
removed_fc.append(fc)
if len(fastq_fc) == len(removed_fc):
try:
proj_data_root = fastq_info['proj_data']['proj_data_root']
logger.info("All flowcells cleaned for this project, marking it as cleaned in {}".format(proj_data_root))
_touch_cleaned(proj_data_root)
except:
pass
analysis_info = info.get('analysis_to_remove')
if analysis_info and isinstance(analysis_info, dict):
proj_analysis_root = analysis_info['proj_analysis_root']
logger.info("cleaning analysis data for project {}".format(proj))
removed_qc = []
for qc, files in analysis_info['analysis_files'].iteritems():
logger.info("Removing files of '{}' from {}".format(qc, proj_analysis_root))
if not dry_run:
if _remove_files(files):
removed_qc.append(qc)
else:
logger.warn("Couldn't remove some files in qc directory '{}'".format(qc))
map(analysis_info['analysis_files'].pop, removed_qc)
if len(analysis_info['analysis_files']) == 0:
logger.info("Removed analysis data for project {}, marking it cleaned".format(proj))
_touch_cleaned(proj_analysis_root)
def test_query_yes_no_false(self, mock_raw_input):
"""Return False from answer no."""
response = misc.query_yes_no('Some question')
self.assertFalse(response)
def test_query_yes_no_true(self, mock_raw_input):
"""Return True from answer yes."""
response = misc.query_yes_no('Some question')
self.assertTrue(response)
