def __prepare_local_ensembl_repository(self):
"""
This helper makes sure that the local folder structure for receiving Ensembl data is available.
:return: no return value
"""
self._get_logger().debug(
"Preparing local Ensembl repository, root folder - '{}'".format(
self.get_local_path_root_ensembl_repo()))
general.check_create_folders([self.get_local_path_root_ensembl_repo()])
self._get_logger().debug(
"Local path for Ensembl Release - '{}'".format(
self.get_local_path_ensembl_release()))
if self._get_configuration_manager(
).is_rewrite_local_path_ensembl_repo():
self._get_logger().debug(
"Creating folder in 'OVERWRITE' mode - '{}'".format(
self.get_local_path_ensembl_release()))
general.check_create_folders_overwrite(
[self.get_local_path_ensembl_release()])
else:
self._get_logger().debug(
"Creating folder if it doesn't exist - '{}'".format(
self.get_local_path_ensembl_release()))
general.check_create_folders(
[self.get_local_path_ensembl_release()])
def _prepare_trackhub_destination_folder(self, trackhub_exporter):
if not self.__trackhub_destination_folder:
# Check if anything was specified
if self._get_configuration_manager(
).get_folder_pride_cluster_trackhubs():
# The destination folder will be a subfolder there
self.__trackhub_destination_folder = os.path.join(
self._get_configuration_manager(
).get_folder_pride_cluster_trackhubs(),
self._get_configuration_manager().
get_cluster_file_exporter_version_parameter())
else:
# Set the default trackhub destination folder by default
self.__trackhub_destination_folder = os.path.join(
trackhub_exporter.track_hub_destination_folder,
self._get_configuration_manager().
get_cluster_file_exporter_version_parameter())
# Make sure the destination folder is there
general_toolbox.check_create_folders(
[self.__trackhub_destination_folder])
general_toolbox.create_latest_symlink_overwrite(
self.__trackhub_destination_folder)
# Set the destination folder for the exporter of the trackhub
trackhub_exporter.track_hub_destination_folder = self.__trackhub_destination_folder
self._get_logger().info(
"PRIDE Cluster trackhub destination folder at '{}'")
return self.__trackhub_destination_folder
def __init__(self, configuration_object, configuration_file):
super(AppConfigManager, self).__init__(configuration_object,
configuration_file)
global _log_level
global _logger_formatters
# Session ID
hpc_service = None
try:
hpc_service = HpcServiceFactory.get_hpc_service()
except HpcServiceFactoryException as e:
pass
lsf_jobid = ''
if hpc_service:
try:
lsf_jobid = "-{}-".format(hpc_service.get_current_job_id())
except HpcServiceException as e:
lsf_jobid = "-NO_JOB_ID-"
self.__session_id = time.strftime('%Y.%m.%d_%H.%M') \
+ lsf_jobid + "-" \
+ str(uuid.uuid4()) \
+ "-" \
+ get_pipeline_name()
# TODO config, folder_run, etc.
self.__session_working_dir = os.path.abspath(
os.path.join(self.get_folder_run(), self.get_session_id()))
# TODO check and create folders (if needed)
folders_to_check = [
self.get_folder_bin(),
self.get_folder_logs(),
self.get_folder_resources(),
self.get_folder_run(),
self.get_session_working_dir(),
]
general.check_create_folders(folders_to_check)
# Prepare Logging subsystem
if "loglevel" in configuration_object["logger"]:
_log_level = configuration_object["logger"]["loglevel"]
if "formatters" in configuration_object["logger"]["formatters"]:
_logger_formatters = configuration_object["logger"]["formatters"]
self.__log_handlers = []
log_handlers_prefix = self.get_session_id() + '-'
log_handlers_extension = '.log'
self.__logger = logging.getLogger(__name__)
self.__logger.setLevel(getattr(logging, _log_level))
# TODO fix this code
self.__log_files = []
for llevel, lformat in _logger_formatters.items():
logfile = os.path.join(
self.get_folder_logs(),
log_handlers_prefix + llevel.lower() + log_handlers_extension)
lformatter = logging.Formatter(lformat)
lhandler = logging.FileHandler(logfile, mode='w')
lhandler.setLevel(getattr(logging, llevel))
lhandler.setFormatter(lformatter)
self.__log_handlers.append(lhandler)
# Add the handlers to my own logger
self.__logger.addHandler(lhandler)
# Keep the path to the log file
self.__log_files.append(logfile)
self._get_logger().debug("Logging system initialized")
def __init__(self, configuration_object, configuration_file):
super().__init__(configuration_object, configuration_file)
global _log_level
global _logger_formatters
# Session ID
self.__session_id = time.strftime('%Y.%m.%d_%H.%M') \
+ "-{}".format(str(uuid.uuid4())) \
+ "-session"
# TODO config, folder_run, etc.
self.__session_working_dir = os.path.abspath(
os.path.join(self.get_folder_run(), self.get_session_id()))
# TODO check and create folders (if needed)
folders_to_check = [
self.get_folder_bin(),
self.get_folder_logs(),
self.get_folder_resources(),
self.get_folder_run(),
self.get_session_working_dir(),
]
general.check_create_folders(folders_to_check)
# Prepare Logging subsystem
if "loglevel" in configuration_object["logger"]:
_log_level = configuration_object["logger"]["loglevel"]
if "formatters" in configuration_object["logger"]["formatters"]:
_logger_formatters = configuration_object["logger"]["formatters"]
self.__log_handlers = []
log_handlers_prefix = self.get_session_id() + '-'
log_handlers_extension = '.log'
self._logger = logging.getLogger("{}.{}".format(
__name__,
type(self).__name__))
self._logger.setLevel(getattr(logging, _log_level))
# TODO fix this code
# for llevel, lformat in _logger_formatters.items():
# logfile = os.path.join(self.get_folder_logs(),
# log_handlers_prefix + llevel.lower() + log_handlers_extension)
# lformatter = logging.Formatter(lformat)
# lhandler = logging.FileHandler(logfile, mode='w')
# lhandler.setLevel(getattr(logging, llevel))
# lhandler.setFormatter(lformatter)
# self.__log_handlers.append(lhandler)
# # Add the handlers to my own logger
# self._logger.addHandler(lhandler)
if is_show_logs_on_console():
lhandler = logging.StreamHandler(stream=sys.stdout)
lhandler.setLevel(getattr(logging, _console_log_level))
lformatter = logging.Formatter(
_logger_formatters[_console_log_level])
lhandler.setFormatter(lformatter)
self.__log_handlers.append(lhandler)
# Add the handlers to my own logger
self._logger.addHandler(lhandler)
self._logger.debug("Logging system initialized")
def get_cluster_file_exporter_destination_folder(self):
"""
Get the destination folder for the cluster file exporter result files, it will typically be a subfolder of the
current running session working directory.
This is computed here just in case I want to make it either a configuration parameter or a command line argument
in the near future
:return: destination folder for pride cluster-file-exporter result files
"""
destination_folder = os.path.join(
config_manager.get_app_config_manager().get_session_working_dir(),
self._CONFIG_CLUSTER_FILE_EXPORTER_WORKING_SUBDIR)
# Make sure the folder is there
general_toolbox.check_create_folders([destination_folder])
return destination_folder
def get_browser_instance():
logger = config_manager.get_app_config_manager().get_logger_for(
"{}.{}".format(__name__, "get_browser_instance"))
folder_prefix = os.path.join(
config_manager.get_app_config_manager().get_session_working_dir(),
"browser_profile_no")
profile_folder = "{}{}".format(folder_prefix, uuid.uuid4())
general_toolbox.check_create_folders([profile_folder])
logger.debug("Creating Browser instance, profile folder at '{}'".format(
profile_folder))
chrome_options = webdriver.ChromeOptions()
chrome_options.add_argument("--headless")
chrome_options.add_argument('--ignore-certificate-errors')
chrome_options.add_argument("user-data-dir={}".format(profile_folder))
browser = webdriver.Chrome(
executable_path=config_manager.get_app_config_manager(
).get_path_chrome_driver(),
chrome_options=chrome_options)
browser.implicitly_wait(3)
return browser
def __prepare_local_ensembl_repository(self):
self._get_logger().debug(
"Preparing local Ensembl repository, root folder - '{}'".format(
self.get_local_path_root_ensembl_repo()))
general.check_create_folders([self.get_local_path_root_ensembl_repo()])
self._get_logger().debug(
"Local path for Ensembl Release - '{}'".format(
self.get_local_path_ensembl_release()))
if self._get_configuration_manager(
).is_rewrite_local_path_ensembl_repo():
self._get_logger().debug(
"Creating folder in 'OVERWRITE' mode - '{}'".format(
self.get_local_path_ensembl_release()))
general.check_create_folders_overwrite(
[self.get_local_path_ensembl_release()])
else:
self._get_logger().debug(
"Creating folder if it doesn't exist - '{}'".format(
self.get_local_path_ensembl_release()))
general.check_create_folders(
[self.get_local_path_ensembl_release()])
general.create_latest_symlink_overwrite(
self.get_local_path_ensembl_release())
def export_simple_trackhub(self, trackhub_builder):
file_trackhub_descriptor = os.path.join(self.track_hub_destination_folder, 'hub.txt')
self.export_summary.track_hub_root_folder = self.track_hub_destination_folder
self.export_summary.track_hub_descriptor_file_path = file_trackhub_descriptor
# TODO - Tell clients when you're not exporting anything
if os.path.isfile(file_trackhub_descriptor):
error_message = "Trackhub Export to '{}' ABORTED, there already is a trackhub there"\
.format(self.track_hub_destination_folder)
self.logger.warning(error_message)
self.export_summary.errors.append(error_message)
else:
self.logger.info("Export Simple TrackHub to '{}'".format(self.track_hub_destination_folder))
# Check / Create destination folder
general.check_create_folders([self.track_hub_destination_folder])
# Create hub.txt file
with open(file_trackhub_descriptor, 'w') as wf:
wf.write("{}\n".format(str(trackhub_builder.track_hub)))
self.logger.info("TrackHub descriptor file at '{}'".format(file_trackhub_descriptor))
# Per assembly
# TODO - I should also have an assembly collector and refactor TrackHubGenomeAssembly accordingly, but I'm
# TODO - cutting some corners here to get the first iteration up and running as soon as possible. Supporting
# TODO - more complex genomes.txt files is not as critical as getting the 'tracks' the right way
assembly_mapping = {}
for assembly in trackhub_builder.assemblies:
tracks_with_non_empty_bed_files = \
self.__get_tracks_with_non_empty_bed_files(assembly,
trackhub_builder.assemblies[assembly].track_collector)
if not tracks_with_non_empty_bed_files:
self.logger.warning("Assembly '{}' contains ALL EMPTY BIG DATA FILE TRACKS -- SKIPPED --"
.format(assembly))
continue
assembly_folder = os.path.join(self.track_hub_destination_folder, assembly)
# Create the folder for the assembly
general.check_create_folders([assembly_folder])
self.logger.info("For Assembly '{}', trackhub folder created at '{}'".format(assembly, assembly_folder))
# Per track in its track collector, we'll process only those tracks with non-empty big data files
for track in tracks_with_non_empty_bed_files:
# Copy track file to assembly folder
# TODO - source of this
big_data_file_name = os.path.basename(track.get_big_data_url())
destination_file_path = os.path.join(assembly_folder, big_data_file_name)
shutil.copy(track.get_big_data_url(), destination_file_path)
# Modify the track (irreversible) to point to the big data file relative to the trackDB.txt file
# path
new_big_data_url = big_data_file_name
track.set_big_data_url(new_big_data_url)
self.logger.info(
"Assembly '{}' ---> Data for track '{}' prepared, track information updated"
.format(assembly, track.get_track()))
# Export trackDB.txt with the current set of 'valid' tracks
trackdb_file_path = os.path.join(assembly_folder, 'trackDb.txt')
track_collector_exporter = TrackCollectorFileExporter(trackdb_file_path)
track_collector_exporter.export_from_track_collection(tracks_with_non_empty_bed_files)
# Add assembly entry to genomes.txt files within trackhub root folder
assembly_mapping[assembly] = os.path.join(os.path.basename(os.path.dirname(trackdb_file_path)),
os.path.basename(trackdb_file_path))
self.logger.info("Assembly data collected and exported to its corresponding subfolders")
# Export data to genomes.txt file
genomes_file_path = os.path.join(self.track_hub_destination_folder, 'genomes.txt')
with open(genomes_file_path, 'w') as wf:
for assembly in assembly_mapping:
wf.write("genome {}\n"
"trackDb {}\n"
.format(assembly, assembly_mapping[assembly]))
self.logger.info("Genomes file with per-assembly data exported to '{}'".format(genomes_file_path))
# Prepare summary object
self.export_summary.export_performed = True
self.logger.info("Trackhub export summary prepared")
return self.export_summary
def get_genome_reference_for_species(self, taxonomy_id):
"""
This method will make sure the GTF files are available locally, before returning the result map
that contains the file names and their local paths
:param taxonomy_id: Taxonomy ID for which we want the GTF files
:return: the list of GTF file names with their local paths or None in case the taxonomy has not
been found on Ensembl
"""
# Work out the file names for the data to retrieve from Ensembl
file_names = self._get_genome_reference_ensembl_file_name_for_species(
taxonomy_id)
if not file_names:
return None
self._get_logger().debug(
"Working with Ensembl GTF file names for taxonomy ID '{}' - '{}'".
format(taxonomy_id, str(file_names)))
# Work out their path in the local repository
gtf_files_local_path = self._get_genome_reference_file_path_local(
taxonomy_id, file_names)
self._get_logger().debug(
"Local Ensembl Repo GTF paths for taxonomy ID '{}', file paths '{}'"
.format(taxonomy_id, str(gtf_files_local_path)))
# Check if they already exist locally
missing_files = [
(missing_file_name, missing_file_path)
for missing_file_name, missing_file_path in gtf_files_local_path
if not os.path.exists(missing_file_path)
]
if missing_files:
# If not, work out their remote path on Ensembl FTP
self._get_logger() \
.debug("There are {} GTF files missing from the local repository for taxonomy ID '{}': {}"
.format(len(missing_files),
taxonomy_id,
"[{}]".format(",".join(["'{} -> {}'".format(
missing_file_name, missing_file_path)
for missing_file_name, missing_file_path
in missing_files]))))
# Retrieve the files
download_information = self._get_genome_reference_file_path_remote(
[file_entry[0] for file_entry in missing_files], taxonomy_id)
destination_folder = self._get_genome_reference_file_destination_path_local(
taxonomy_id)
# Make sure that the destination folder exists
general.check_create_folders([destination_folder])
download_urls = [url for file_name, url in download_information]
self._get_logger().info(
"GTF files to download to '{}': '{}'".format(
destination_folder, ",".join(download_urls)))
download_manager = DownloadManager(download_urls,
destination_folder,
self._get_logger())
download_manager.start_downloads()
download_manager.wait_all()
if not download_manager.is_success():
self._get_logger().error(
"ERROR Downloading files from Ensembl !!!")
# TODO - Should I raise an exception here? See how the code goes and take a decission later
# Once the files have been downloaded, we know they come compressed from Ensembl, with .gz extension
# Uncompress the files
# I have their local paths in 'missin_files' second component of the pairs in the list, I just need to add
# the '.gz' extension for them, as they come gzipped from Ensembl
errors = general.gunzip_files([
"{}.gz".format(file_local_path)
for file_name, file_local_path in missing_files
])
# Deal with possible errors
if errors:
msg = "An ERROR occurred while obtaining the following GTF files for taxonomy ID '{}' -> '{}'" \
.format(taxonomy_id,
"\n".join(["File '{}', ERROR '{}'"
.format(file, error) for file, error in errors]
))
self._get_logger().error(msg)
# I just found out that Ensembl does not have files for all the taxonomies using all the suffixes in a
# uniform way, thus, if some of the files where not found, I WILL NOT raise an exception, I will do the
# "Windows" here by keeping it quiet ^_^
# raise EnsemblDownloadManagerException(msg)
# Return the .gtf file names and their local paths for the given ncbi taxonomy id. Return only those file that
# were successfuly downloaded.
# TODO - I need to review this return value in the future
return [(file_name, file_path)
for file_name, file_path in gtf_files_local_path
if os.path.isfile(file_path)]
def export_simple_trackhub(self, trackhub_builder):
"""
When exporting a simple trackhub from a (simple) trackhub builder, those tracks with empty .bed files will be
skipped
:param trackhub_builder: a TrackhubBuilder that holds all the trackhub parts together
:return: a report of the export process as a TrackHubExportSummary
"""
file_trackhub_descriptor = os.path.join(
self.track_hub_destination_folder, 'hub.txt')
self.export_summary.track_hub_root_folder = self.track_hub_destination_folder
self.export_summary.track_hub_descriptor_file_path = file_trackhub_descriptor
# TODO - Tell clients when you're not exporting anything
if os.path.isfile(file_trackhub_descriptor):
error_message = "Trackhub Export to '{}' ABORTED, there already is a trackhub there" \
.format(self.track_hub_destination_folder)
self.logger.warning(error_message)
self.export_summary.errors.append(error_message)
else:
self.logger.info("Export Simple TrackHub to '{}'".format(
self.track_hub_destination_folder))
# Check / Create destination folder
general.check_create_folders([self.track_hub_destination_folder])
# Create hub.txt file
with open(file_trackhub_descriptor, 'w') as wf:
wf.write("{}\n".format(str(trackhub_builder.track_hub)))
self.logger.info("TrackHub descriptor file at '{}'".format(
file_trackhub_descriptor))
# Per assembly
# TODO - I should also have an assembly collector and refactor TrackHubGenomeAssembly accordingly, but I'm
# TODO - cutting some corners here to get the first iteration up and running as soon as possible. Supporting
# TODO - more complex genomes.txt files is not as critical as getting the 'tracks' the right way
assembly_mapping = {}
assembly_mapping_service = AssemblyMappingServiceFactory.get_assembly_mapping_service(
)
ensembl_species_service = ensembl.service.get_service(
).get_species_data_service()
for assembly in dict(trackhub_builder.assemblies):
try:
ucsc_assembly = assembly_mapping_service \
.get_ucsc_assembly_for_ensembl_assembly_accession(ensembl_species_service
.get_species_entry_for_assembly(assembly)
.get_assembly_accession())
except AssemblyMappingServiceException as e:
message = "ERROR while mapping Ensembl Assembly '{}' - SKIPPING THIS ASSEMBLY - xxx> '{}'"\
.format(assembly, e.value)
self.export_summary.warnings.append(message)
self.logger.error(message)
trackhub_builder.invalidate_assembly(assembly)
continue
self.logger.info(
"Ensembl Assembly '{}' --- mapped_to ---> UCSC Assembly '{}'"
.format(assembly, ucsc_assembly))
tracks_with_non_empty_bed_files = \
self.__get_tracks_with_non_empty_bed_files(assembly,
trackhub_builder.assemblies[assembly].track_collector)
if not tracks_with_non_empty_bed_files:
message = "Assembly '{} ({})' contains ALL EMPTY BIG DATA FILE TRACKS -- SKIPPED --"\
.format(assembly,ucsc_assembly)
self.export_summary.warnings.append(message)
self.logger.warning(message)
trackhub_builder.invalidate_assembly(assembly)
continue
assembly_folder = os.path.join(
self.track_hub_destination_folder, ucsc_assembly)
# Create the folder for the assembly
general.check_create_folders([assembly_folder])
self.logger.info(
"For Assembly '{} ({})', trackhub folder created at '{}'".
format(assembly, ucsc_assembly, assembly_folder))
# Per track in its track collector, we'll process only those tracks with non-empty big data files
# The following map will contain the tracks that are ready for being added to the collector. If a track
# has no converter associated, then it can be added with no problem, but if it has a converter, we need
# to wait for it to finish the conversion process before we can add the track to the collector
# TODO - Apparently, there's usually just a couple of tracks per assembly (without PTMs and with PTMs),
# TODO - this part can be parallelized even further by making a map <assembly, <track, converter>> that
# TODO - will contain all the processed tracks for all the assemblies, so all the conversions happen in
# TODO - parallel. Then, iterating over this would produce the final genomes.txt file
track_converter_map = {}
for track in tracks_with_non_empty_bed_files:
# Copy track file to assembly folder
# TODO - source of this
# Instead of copying the file, if it is a BED file, perform conversion -
# Get the original big data url
big_data_file_name = os.path.basename(
track.get_big_data_url())
# Default destination for the big data file is just copying it
destination_file_path = os.path.join(
assembly_folder, big_data_file_name)
# if track type is BED, workout the destination file as bigbed and do not copy the data, convert it
converter = None
if (track.get_type() == BaseTrack.TRACK_TYPE_BED) \
and track.taxonomy_id:
destination_file_path = \
os.path.join(assembly_folder,
"{}.bb".format(big_data_file_name[:big_data_file_name.rfind(".")]))
# The new name for the big data file
big_data_file_name = os.path.basename(
destination_file_path)
# Convert the file
converter = DataFormatConverterFactory.get_bed_to_bigbed_converter(
track.taxonomy_id, track.get_big_data_url(),
destination_file_path)
# We start the converter
converter.start()
else:
shutil.copy(track.get_big_data_url(),
destination_file_path)
# Update the big data url with either the copied file or the newly built .bb (bigBed) file
# Modify the track (irreversible) to point to the big data file relative to the trackDB.txt file
# path
new_big_data_url = big_data_file_name
track.set_big_data_url(new_big_data_url)
self.logger.info(
"Assembly '{} ({})' ---> Data for track '{}' prepared, track information updated"
.format(assembly, ucsc_assembly, track.get_track()))
# Apparently, 'blank spaces' are not allowed in the track names (UCSC)
track.set_track(track.get_track().replace(' ', '_'))
# Add the track to the map
track_converter_map[track] = converter
# Export trackDB.txt with the current set of 'valid' tracks
trackdb_file_path = os.path.join(assembly_folder,
'trackDb.txt')
track_collector_exporter = TrackCollectorFileExporter(
trackdb_file_path)
# Add successful tracks
successful_tracks = []
for track, converter in track_converter_map.items():
if converter:
converter.wait()
if not converter.is_conversion_ok():
message = "SKIP TRACK for Assembly '{} ({})' " \
"---> Track '{}' Big Data File FAILED conversion process " \
"- STDOUT '{}', STDERR '{}'".format(assembly,
ucsc_assembly,
track.get_track(),
converter.get_conversion_output(),
converter.get_conversion_output_error())
self.export_summary.warnings.append(message)
self.logger.error(message)
# Skip this track
continue
# Add the track to the successful tracks list
successful_tracks.append(track)
track_collector_exporter.export_from_track_collection(
successful_tracks)
# Add assembly entry to genomes.txt files within trackhub root folder
assembly_mapping[ucsc_assembly] = os.path.join(
os.path.basename(os.path.dirname(trackdb_file_path)),
os.path.basename(trackdb_file_path))
if not assembly_mapping:
message = "ALL Assemblies in this project are INVALID"
self.export_summary.errors.append(message)
self.logger.error(message)
self.logger.info(
"Assembly data collected and exported to its corresponding subfolders"
)
# Export data to genomes.txt file
genomes_file_path = os.path.join(self.track_hub_destination_folder,
'genomes.txt')
with open(genomes_file_path, 'w') as wf:
for assembly in assembly_mapping:
wf.write("genome {}\n"
"trackDb {}\n\n".format(
assembly, assembly_mapping[assembly]))
self.logger.info(
"Genomes file with per-assembly data exported to '{}'".format(
genomes_file_path))
# Prepare summary object
self.export_summary.export_performed = True
self.logger.info("Trackhub export summary prepared")
return self.export_summary
