def find_31(): if (('wpa.dbl.bak' in datastore.SYSTEMROOT_FILE_SET) or ('sslkey.exe' in datastore.SYSTEMROOT_FILE_SET)): return True if ('WindowsUpdate.old' in datastore.SYSPATH_FILE_SET): return True if utils.file_exists(('%s\\temp' % datastore.SYSPATH_STR), '~MS1E.tmp'): return True if utils.file_exists(('%s\\temp' % datastore.SYSPATH_STR), '~FMIFEN.tmp'): return True (cmdStatus, cmdId) = dsz.cmd.RunEx( 'registryquery -hive L -key "Software\\Microsoft\\Windows\\CurrentVersion\\Explorer\\Streams\\Desktop"', dsz.RUN_FLAG_RECORD) if (not cmdStatus): return False try: subkeys = set( dsz.cmd.data.Get('key::subkey::name', dsz.TYPE_STRING, cmdId)) except: subkeys = None if (subkeys is not None): search_set = set(('Default Statusbar Sign', 'Default MenuBars Sign', 'Default Taskbar Sign', 'Default Zone')) if (not subkeys.isdisjoint(search_set)): return True return False
def dump_database(): dumpfile = os.path.join(dconf.DB_DUMP_DIR, dconf.DB_NAME + '.dump') if dconf.DB_TYPE == 'oracle': if not dconf.ORACLE_FLASH_BACK and file_exists(dumpfile): LOG.info('%s already exists ! ', dumpfile) return False else: if file_exists(dumpfile): LOG.info('%s already exists ! ', dumpfile) return False if dconf.ORACLE_FLASH_BACK: LOG.info('create restore point %s for database %s in %s', dconf.RESTORE_POINT, dconf.DB_NAME, dconf.RECOVERY_FILE_DEST) else: LOG.info('Dump database %s to %s', dconf.DB_NAME, dumpfile) if dconf.DB_TYPE == 'oracle': if dconf.ORACLE_FLASH_BACK: run_sql_script('createRestore.sh', dconf.RESTORE_POINT, dconf.RECOVERY_FILE_DEST_SIZE, dconf.RECOVERY_FILE_DEST) else: run_sql_script('dumpOracle.sh', dconf.DB_USER, dconf.DB_PASSWORD, dconf.DB_NAME, dconf.DB_DUMP_DIR) elif dconf.DB_TYPE == 'postgres': run('PGPASSWORD={} pg_dump -U {} -h {} -F c -d {} > {}'.format( dconf.DB_PASSWORD, dconf.DB_USER, dconf.DB_HOST, dconf.DB_NAME, dumpfile)) else: raise Exception("Database Type {} Not Implemented !".format( dconf.DB_TYPE)) return True
def find_21(): if utils.file_exists(('%s\\temp' % datastore.SYSPATH_STR), 'temp56273.pdf'): return True for ud in datastore.USER_DIRS_LIST: if utils.file_exists(('%s\\%s\\Local Settings\\History\\cache' % (datastore.PROFILE_PATH, ud)), 'iecache.dll'): return True return False
def process_file(file_path): utils.file_exists(file_path) filename, mod_time = utils.get_file_metadata(file_path) file_hash = utils.get_file_hash(filename, mod_time) if data.logic.file_already_proccessed(file_hash): log.info('The file {} has been already processed') else: log.info('Start processing {}'.format(filename)) data.logic.create_file_processed(file_hash, filename, mod_time) input_records = utils.parse_csv(file_path) records_with_candidates = data.logic.infer_candidates(input_records) process_rows(file_hash, records_with_candidates) log.info('Finished processing {}'.format(filename))
def build_gradle_file_exists(package_path): ''' From a given package path, searches for "build.gradle" file (groovy) or "build.kts" file (kotlin). Returns True if exists, Otherwise, returns False ''' if file_exists(package_path, "build.gradle") is True: return True elif file_exists(package_path, "build.gradle.kts") is True: return True else: return False
def backup(version): if not utils.file_exists(db_file): log.info("ERROR: unable to find the database at " + db_file) exit() backup_db_file = conf["constants"]["tmp_dir"] + "/dump.rdb_" + str(version) log.info("Backing up the database " + db_file + " into " + backup_db_file) run_command("cp -f " + db_file + " " + backup_db_file) if utils.file_exists(conf["constants"]["config_file"]): backup_config_file = conf["constants"][ "tmp_dir"] + "/config.json_" + str(version) log.info("Backing up the configuration file " + conf["constants"]["config_file"] + " into " + backup_config_file) run_command("cp -f " + conf["constants"]["config_file"] + " " + backup_config_file)
async def main(): call_args = get_args() config_env(call_args.random_seed, call_args.log_level) # Kaggle stores compressed files with ".zip" suffix dataset_file_path: Path = call_args.storage_path / (DATASET_FILE + ".zip") await load_dataset( ds_name=call_args.dataset_name, ds_file_name=DATASET_FILE, ds_file_path=dataset_file_path, ) embeddings_arch = call_args.storage_path / "glove.840B.300d.zip" emb_file_path = await get_embeddings(emb_arch_path=embeddings_arch) # Check if preprocessing could be skipped checksum_key = ( f"{dataset_file_path.name}_{DATASET_SIZE}_{emb_file_path.name}_{call_args.train_size}_{call_args.random_seed}" ) need_rerun = True if CHECKSUMS.get(checksum_key, None): need_rerun = False for f_name, checksum in CHECKSUMS.get(checksum_key).items(): f_path = call_args.work_store_path / f_name if not file_exists(f_path) or not verify_checksum(f_path, checksum): need_rerun = True break if need_rerun: objects_to_save = preprocess_data(dataset_file_path, DATASET_SIZE, emb_file_path, call_args.train_size) dump(dump_root=call_args.work_store_path, objects=objects_to_save) else: logging.info(f"All checksums match run configuration, skipping preprocessing.")
def _move_data(self): dens_orig = os.path.join(__class__._config['tmp_density_dir'], self.molID + '.wb97x') ddsc_orig = os.path.join(__class__._config['tmp_density_dir'], self.molID + '.ddsc') while True: time.sleep(__class__._config['dormi_short']) allfile = True for filep in [dens_orig, ddsc_orig]: try: file_exists(filep) except FileNotFoundError: allfile = False if allfile: break shutil.move(dens_orig, self._wb97x_saves) shutil.move(ddsc_orig, self._ddsc_saves)
def gradlew_file_exists(package_path): ''' From a given package path, searches for "gradlew" file. Returns True if exists. Otherwise, returns False ''' return file_exists(package_path, "gradlew")
def restore_database(): dumpfile = os.path.join(dconf.DB_DUMP_DIR, dconf.DB_NAME + '.dump') if not dconf.ORACLE_FLASH_BACK and not file_exists(dumpfile): raise FileNotFoundError( "Database dumpfile '{}' does not exist!".format(dumpfile)) LOG.info('Start restoring database') if dconf.DB_TYPE == 'oracle': if dconf.ORACLE_FLASH_BACK: run_sql_script('flashBack.sh', dconf.RESTORE_POINT) clean_recovery() else: drop_user() create_user() run_sql_script('restoreOracle.sh', dconf.DB_USER, dconf.DB_NAME) elif dconf.DB_TYPE == 'postgres': drop_database() create_database() run('PGPASSWORD={} pg_restore -U {} -h {} -n public -j 8 -F c -d {} {}' .format(dconf.DB_PASSWORD, dconf.DB_USER, dconf.DB_HOST, dconf.DB_NAME, dumpfile)) else: raise Exception("Database Type {} Not Implemented !".format( dconf.DB_TYPE)) LOG.info('Finish restoring database')
def install(self): posix_file = os.path.join(self.inst_dir, 'bin/vtkpython') nt_file = os.path.join(self.inst_dir, 'bin', 'vtkpython.exe') if utils.file_exists(posix_file, nt_file): utils.output("VTK already installed. Skipping build step.") else: # python 2.5.2 setup.py complains that this does not exist # with VTK PV-3-2-1. This is only on installations with # EasyInstall / Python Eggs, then the VTK setup.py uses # EasyInstall and not standard distutils. gah! if not os.path.exists(config.VTK_PYTHON): os.makedirs(config.VTK_PYTHON) os.chdir(self.build_dir) # we save, set and restore the PP env variable, else # stupid setuptools complains save_env = os.environ.get('PYTHONPATH', '') os.environ['PYTHONPATH'] = config.VTK_PYTHON ret = utils.make_command('VTK.sln', install=True) os.environ['PYTHONPATH'] = save_env if ret != 0: utils.error("Could not install VTK. Fix and try again.")
def find_22(): if utils.file_exists(('%s\\etc' % datastore.DRIVERPATH_STR), 'network.ics'): return True if ('acelpvc.dll' in datastore.SYSTEMROOT_FILE_SET): return True (cmdStatus, cmdId) = dsz.cmd.RunEx( 'registryquery -hive L -key "Software\\Sun\\1.1.2"', dsz.RUN_FLAG_RECORD) if (not cmdStatus): return False try: subkeys = dsz.cmd.data.Get('key::subkey::name', dsz.TYPE_STRING, cmdId) except RuntimeError: subkeys = None if (subkeys is not None): if (('AppleTlk' in subkeys) or ('IsoTp' in subkeys)): return True try: values = dsz.cmd.data.Get('key::value::name', dsz.TYPE_STRING, cmdId) except RuntimeError: values = None if (values is not None): if (('AppleTlk' in values) or ('IsoTp' in values)): return True return False
def move_temp_assets(self): """ Moves any temporary assets to the project directory :return: """ import ntpath from shutil import copyfile import os from utils import file_exists script = self.get_script_instance() targets = script.get_targets() model_id = script.model_id client = self.client project_path = self.path for t in targets: target_col = t['column'] model_filepath = get_model_filepath(client, model_id, target_col) model_filename = ntpath.basename(model_filepath) model_source = get_local_model_source(model_filepath) dest_model_path = os.path.join(project_path, model_filename) if model_source.exists(): # We copy the model to our project dir model_source.copy_to(dest_model_path) # Pipeline pipeline_file = get_pipeline_latest('tpot', target_col, client) if pipeline_file is not None: pipeline_filename = ntpath.basename(pipeline_file) dest_pipeline_file = os.path.join(project_path, pipeline_filename) if file_exists(pipeline_file): copyfile(pipeline_file, dest_pipeline_file)
def bower_json_exists(package_path): ''' From a given package path, searches for "bower.json" file. Returns True if exists, Otherwise, returns False ''' return file_exists(package_path, "bower.json")
def prep_r2_with_barcode(fq1, fq2, out_file): safe_makedir(os.path.dirname(out_file)) if file_exists(out_file): print ("%s and %s have already been barcode-prepped, skipping." % (fq1, fq2)) return out_file with open_fastq(fq1) as r1_file, open_fastq(fq2) as r2_file: with file_transaction(out_file) as tx_out_file: out_handle = open(tx_out_file, "w") read_count = 0 buf = list() r1_r2 = itertools.izip(r1_file, r2_file) for header1, header2 in r1_r2: seq1, seq2 = r1_r2.next() plus1, plus2 = r1_r2.next() qual1, qual2 = r1_r2.next() read_name1, read_name2 = header1.split()[0][1:], header2.split()[0][1:] assert read_name1 == read_name2, "FASTQ files may be out of order." seq2, qual2 = seq2.rstrip(), qual2.rstrip() barcode, seq, qual = mask(seq1[0:6], qual1[0:6], min_qual=10) + \ mask(seq1[6:], qual1[6:]), seq2, qual2 barcoded_name = ":".join([read_name2, barcode]) print(format_fastq([barcoded_name, seq, qual]), file=out_handle) out_handle.close() return out_file
def main() -> None: try: # Raises an HTTPError exception if moodle is not properly up get_moodlepage().raise_for_status() # Create a .env file if it doesn't exist if not file_exists(".env"): create_default_env_file() log_with_time("The '.env' file has been created") # Get our session set up user_credentials = get_env_netname_credentials() session = get_session(user_credentials) # Get the fetch_and_notify function running repeatedly log_with_time("Starting scheduler") scheduler = sched.scheduler() scheduler.enter(0, 1, fetch_and_notify, (session, scheduler)) scheduler.run() except HTTPError as e: log_with_time(f"HTTPError occured (status code is 4xx or 5xx):\n{e}") except (ConnectionError, Timeout) as e: log_with_time( f"Moodle website appears to be down (ConnectionError or Timeout):\n{e}" ) except Exception as e: log_with_time(f"Exception:\n{e}") log_with_time( f"Rescheduling the main method to run in {get_scheduler_delay()} seconds" ) scheduler = sched.scheduler() scheduler.enter(get_scheduler_delay(), 1, main) scheduler.run()
def calculate_rel_blast_matrix(self): file_name = '{}-{}-{}_scores.npy'.format(self.org1.org_id, self.org2.org_id, 'rel_blast') if utils.file_exists(file_name, path_name=cs.NP_PATH): message = 'using saved relative blast from {}'.format(file_name) utils.print_log(message) self.blast_sim_n_rel = utils.load_np(self.np_file) self.blast_sim = utils.load_np(self.raw_np_file) # self.blast_sim = interface.blast_xml_to_matrix(self) else: # blast similarity measure blast_sim = interface.blast_xml_to_matrix(self) self.blast_sim = blast_sim blast_1 = interface.self_blast_xml_to_vec(self.org1) blast_1[blast_1 == 0] = 1 blast_1 = np.array([blast_1]).repeat(self.org2.node_count, axis=0).T blast_2 = interface.self_blast_xml_to_vec(self.org2) blast_2[blast_2 == 0] = 1 blast_2 = np.array([blast_2]).repeat(self.org1.node_count, axis=0) blast_sim = blast_sim.reshape(self.org1.node_count, self.org2.node_count) blast_sim = blast_sim / np.power((blast_1 * blast_2), 0.5) blast_sim = blast_sim.reshape(self.dim_sim) # normalize blast matrix self.blast_sim_n_rel = utils.normalize(blast_sim) np_file = utils.join_path(cs.NP_PATH, file_name) utils.write_np(self.blast_sim_n_rel, np_file)
def install(self): config.WRAPITK_TOPLEVEL = self.inst_dir # this dir contains the WrapITK cmake config (WrapITKConfig.cmake) config.WRAPITK_DIR = os.path.join( self.inst_dir, 'lib', 'InsightToolkit', 'WrapITK') # contains all WrapITK shared objects / libraries config.WRAPITK_LIB = os.path.join(config.WRAPITK_DIR, 'lib') # contains itk.py config.WRAPITK_PYTHON = os.path.join(config.WRAPITK_DIR, 'Python') # subsequent wrapitk components will need this config.WRAPITK_SOURCE_DIR = self.source_dir posix_file = os.path.join( config.WRAPITK_LIB, '_RegistrationPython.so') nt_file = os.path.join( config.WRAPITK_LIB, '_RegistrationPython' + config.PYE_EXT) if utils.file_exists(posix_file, nt_file): utils.output("WrapITK already installed, skipping step.") else: os.chdir(self.build_dir) ret = utils.make_command('WrapITK.sln', install=True) if ret != 0: utils.error( "Could not install WrapITK. Fix and try again.")
def package_lock_json_exists(package_path): ''' From a given package path, searches for "package-lock.json" file. Returns True if exists, Otherwise, returns False ''' return file_exists(package_path, "package-lock.json")
def make_dataset(classlist): filename = '/tmp/folderlist.pkl' if utils.file_exists(filename): print("loading from cache") pickle_load = pickle.load(open(filename, "rb")) images = pickle_load["images"] labels = pickle_load["labels"] else: print("cache not found, generating cache, this will take a while") images = [] labels = [] classes = utils.readtextfile(classlist) classes = [x.rstrip('\n') for x in classes] classes.sort() for index in range(len(classes)): for fname in os.listdir(classes[index]): if is_image_file(fname): fname = os.path.join(classes[index], fname) images.append(fname) labels.append(index) pickle_save = {"images": images, "labels": labels} pickle.dump(pickle_save, open(filename, "wb")) return images, labels
def npm_shrinkwrap_json_exists(package_path): ''' From a given package path, searches for "npm-shrinkwrap.json" file. Returns True if exists, Otherwise, returns False ''' return file_exists(package_path, "npm-shrinkwrap.json")
def yarn_lock_exists(package_path): ''' From a given package path, searches for "package.json" file. Returns True if exists, Otherwise, returns False ''' return file_exists(package_path, "yarn.lock")
def pom_xml_exists(package_path): ''' From a given package path, searches for "pom.xml" file. Returns True if exists. Otherwise, returns False ''' return file_exists(package_path, "pom.xml")
def find_04(): if ('$NtUninstallQ817473$' in datastore.SYSPATH_FILE_SET): return True for f in ['Hd1', 'Hd2', 'IdeDrive1', 'IdeDrive2']: if utils.file_exists('\\\\.', (f + '\\')): return True return False
def __init__(self, filep): uts.file_exists(filep) self.config = dict(basis_set='6-31G') self.atoms = [] self.x = [] self.y = [] self.z = [] self.charge = '' self.multiplicity = '' self.title = 'Should be setted!' self._template() self._basis_set_conversion(self.config['basis_set']) self._read_xyz(filep)
def _move_data(self): dens_orig = os.path.join(config['temporary_densities_repo'], self.molID + '.wb97x') ddsc_orig = os.path.join(config['temporary_densities_repo'], self.molID + '.ddsc') while True: time.sleep(config['wait_to_recheck']) allfile = True for filep in [dens_orig, ddsc_orig]: try: file_exists(filep) except FileNotFoundError: allfile = False if allfile: break shutil.move(dens_orig, self._wb97x_saves) shutil.move(ddsc_orig, self._ddsc_saves)
def find_28(): for ud in datastore.USER_DIRS_LIST: if utils.file_exists( ('%s\\%s\\Local Settings\\Application Data' % (datastore.PROFILE_PATH, ud)), 'S-1-5-31-1286970278978-5713669491-166975984-320'): return True return False
def find_08(): if ('s7otbxsx.dll' in datastore.SYSTEMROOT_FILE_SET): return True if ('mrxcls' in datastore.SERVICE_NAME_SET): return True if utils.file_exists(('%s\\inf' % datastore.SYSPATH_STR), 'mdmcpq3.pnf'): return True return False
def download_file(file_url, dest_dir, md5, aspera): if utils.file_exists(file_url, dest_dir, md5): return success = attempt_file_download(file_url, dest_dir, md5, aspera) if not success: success = attempt_file_download(file_url, dest_dir, md5, aspera) if not success: print 'Failed to download file after two attempts'
def on_epoch_end(self, epoch, logs=None): # Saving training history # Check if directory exists directory_path = settings.TRAINED_MODELS_PATH + self.model_name if not file_exists(directory_path): create_dir(directory_path) # Word level history if self.word_level: hist_path = settings.TRAINED_MODELS_PATH + self.model_name + "/" + self.model_name + "word.pkl" average_accuracy = 0 if file_exists(hist_path): acc_loss_history = load_pickle_data(hist_path) else: acc_loss_history = dict() acc_loss_history["accuracy"] = [] acc_loss_history["loss"] = [] # Average accuracy for i in range(0, 6): accuracy = "decoder_dense" + str(i) + "_acc" average_accuracy += logs[accuracy] average_accuracy = float(average_accuracy) / float(6) acc_loss_history["accuracy"].append(average_accuracy) acc_loss_history["loss"].append(logs["loss"]) # Character level history else: hist_path = settings.TRAINED_MODELS_PATH + self.model_name + "/" + self.model_name + "char.pkl" if file_exists(hist_path): acc_loss_history = load_pickle_data(hist_path) else: acc_loss_history = dict() acc_loss_history["accuracy"] = [] acc_loss_history["loss"] = [] acc_loss_history["accuracy"].append(logs["acc"]) acc_loss_history["loss"].append(logs["loss"]) generate_pickle_file(acc_loss_history, hist_path) plot_train_loss_acc(hist_path, self.word_level) self.model.save(self.model_path)
def find_44(): filesinsys32 = ['rasmgr.dll', 'raseap.dll'] otherfiles = ['%windir%\\AppPatch\\rasmain.sdb'] results = [] for f in filesinsys32: results.append((f in datastore.SYSPATH_FILE_SET)) for f in otherfiles: results.append(file_exists(*os.path.split(f))) return any(results)
def load_local_dataset(): if file_exists(TRAIN_PERSIST_PATH): print('Loading dataset from npy file') return load_data(), get_speakers() else: print('Reading and tranforming dataset') train = read_dataset_dir(DATASET_TRAIN_PATH) save_data(train) return train, get_speakers()
def deserialize(self): """ Deserialize the client object from storage. """ if utils.file_exists(self._storage): glbl.LOG.debug( ('deserializing user from `{}` ...').format(self._storage)) self.__dict__.update( pickle.load(open(self._storage, 'rb')).__dict__)
def test_convert_audio_failure(): desired_format = 'ttt' try: convert_audio(ffmpeg_binary, input_file, desired_format, output_file) except ConvertAudioException: pass new_file_exists = file_exists(output_file) assert (new_file_exists == False)
def count_umi(sam_file, gtf_file, barcode_to_well, multimappers=False): """ stripped down implementation of the HTSeq algorithm for counting """ base, _ = os.path.splitext(sam_file) out_file = base + ".counts" out_umi_file = base + ".counts_umi.gz" out_umi_pos_file = base + ".counts_umi_pos.gz" if file_exists(out_file): return out_file wells = sorted(barcode_to_well.values()) seen_umi = defaultdict(set) seen_umi_list = defaultdict(Counter) seen_umi_pos_list = defaultdict(Counter) exons = HTSeq.GenomicArrayOfSets("auto", stranded=False) gtf_handle = HTSeq.GFF_Reader(gtf_file) for feature in gtf_handle: if feature.type == "exon": exons[feature.iv] += feature.attr["gene_id"] sam_handle = HTSeq.SAM_Reader(sam_file) for read in sam_handle: if not read.aligned: continue if not multimappers: try: if read.optional_field("NH") > 1: continue except KeyError: pass iv_seq = (co.ref_iv for co in read.cigar if co.type == "M" and co.size > 0) fs = set() for iv in iv_seq: for iv2, fs2 in exons[iv].steps(): if not fs: fs = fs2.copy() else: fs = fs.intersection(fs2) if len(fs) == 1: fields = read.original_sam_line.split("\t") position = "%s:%s" % (fields[2], fields[3]) barcode, umi = get_barcode_and_umi(read) if barcode not in barcode_to_well: continue seen_umi[(list(fs)[0], barcode_to_well[barcode])].add(umi) seen_umi_list[(list(fs)[0], barcode_to_well[barcode])][umi] += 1 seen_umi_pos_list[(position, barcode_to_well[barcode], list(fs)[0])][umi] += 1 write_extensive_summary(seen_umi_list, out_umi_file) write_extensive_summary_by_pos(seen_umi_pos_list, out_umi_pos_file) with file_transaction(out_file) as tx_out_file: with open(tx_out_file, "w") as out_handle: print("\t".join(["feature"] + wells), file=out_handle) for feature in get_feature_names(gtf_file): counts = [len(seen_umi[(feature, well)]) for well in wells] print("\t".join([feature] + map(str, counts)), file=out_handle)
def OkPressed(self): from utils import file_exists from alert import ErrorDialog fileName = self.GetFileName() if file_exists(fileName) == 0: str = 'File ' + fileName + ' not found.' errorDlg = ErrorDialog(self.top, str) errorDlg.Show() errorDlg.DialogCleanup() return FileDialog.OkPressed(self)
def install(self): posix_file = os.path.join(self.inst_dir, 'bin/ErGUI') nt_file = os.path.join(self.inst_dir, 'bin', 'ErGUI.exe') if utils.file_exists(posix_file, nt_file): utils.output("Template Workbench already installed. Skipping install step.") else: ret = utils.make_command('ErGUI.sln', install=True) if ret != 0: utils.error("Could not install Template Workbench. Fix and try again.")
def OkPressed(self): from utils import file_exists from alert import WarningDialog fileName = self.GetFileName() if file_exists(fileName) == 1: str = 'File ' + fileName + ' exists.\nDo you wish to overwrite it?' warningDlg = WarningDialog(self.top, str) if warningDlg.Show() == 0: warningDlg.DialogCleanup() return warningDlg.DialogCleanup() FileDialog.OkPressed(self)
def deserialize(self): """ Deserialize the client object from storage. """ if utils.file_exists(self._storage): glbl.LOG.debug(( 'deserializing user from `{}` ...' ).format(self._storage)) self.__dict__.update( pickle.load(open(self._storage, 'rb')).__dict__ )
def build(self): posix_file = os.path.join(self.build_dir, "lib/_ItkVtkGluePython.so") nt_file = os.path.join(self.build_dir, "lib", config.BUILD_TARGET, "_ItkVtkGluePython" + config.PYE_EXT) if utils.file_exists(posix_file, nt_file): utils.output("ItkVtkGlue already built. Skipping build step.") else: os.chdir(self.build_dir) ret = utils.make_command("ItkVtkGlue.sln") if ret != 0: utils.error("Could not build ItkVtkGlue. Fix and try again.")
def build(self): bin_path = os.path.join(self.build_dir, 'apps', 'tighten', 'RelWithDebInfo') if utils.file_exists(bin_path, bin_path): utils.output("%s already built. Skipping build step." % BASENAME) else: os.chdir(self.build_dir) ret = utils.make_command('VispackMorphsmooth.sln') if ret != 0: utils.error("Could not build %s. Fix and try again." % BASENAME)
def build(self): posix_file = os.path.join(config.QT_BUILD_BIN, 'libQtCore4.so') #TODO: nt_file = os.path.join(config.QT_BUILD_BIN, 'QtCore4.dll') if utils.file_exists(posix_file, nt_file): utils.output("%s already built. Skipping build step." % BASENAME) return os.chdir(self.build_dir) ret = utils.execute_in_vs_environment('nmake') if ret != 0: utils.error("Could not build %s. Fix and try again." % BASENAME)
def build(self): bin_path = os.path.join(self.build_dir, 'bin') if utils.file_exists(bin_path, bin_path): utils.output("teem already built. Skipping build step.") else: os.chdir(self.build_dir) ret = utils.make_command('teem.sln') if ret != 0: utils.error("Could not build teem. Fix and try again.")
def build(self): bin_path = os.path.join(self.build_dir,'src','multisurfaces','run-particle-system','optimize-particle-system.dir') if utils.file_exists(bin_path, bin_path): utils.output("%s already built. Skipping build step." % BASENAME) else: os.chdir(self.build_dir) ret = utils.make_command('Project.sln') if ret != 0: utils.error("Could not build %s. Fix and try again." % BASENAME)
def build(self): posix_file = os.path.join(self.build_dir,'bin','RelWithDebInfo','volume.o') nt_file = os.path.join(self.build_dir,'bin','RelWithDebInfo','volume.lib') if utils.file_exists(posix_file, nt_file): utils.output("%s already built. Skipping build step." % BASENAME) else: os.chdir(self.build_dir) ret = utils.make_command('%s.sln' % BASENAME) if ret != 0: utils.error("Could not build %s. Fix and try again." % BASENAME)
def build(self): posix_file = os.path.join(self.build_dir, "bin/libvtkgdcmPython.so") nt_file = os.path.join(self.build_dir, "bin", config.BUILD_TARGET, "vtkgdcmPythonD.dll") if utils.file_exists(posix_file, nt_file): utils.output("GDCM already built. Skipping build step.") else: os.chdir(self.build_dir) ret = utils.make_command("GDCM.sln") if ret != 0: utils.error("Could not build GDCM. Fix and try again.")
def build(self): nt_file = os.path.join(self.build_dir, 'vtkTeemInit.cxx') if utils.file_exists(nt_file, nt_file): utils.output("vtkTeem already built. Skipping build step.") else: os.chdir(self.build_dir) ret = utils.make_command('vtkTeem.sln') if ret != 0: utils.error("Could not build vtkTeem. Fix and try againn.")
def bwa_align(fastq_path, reference_prefix, out_file, cores=1): edit_distance = MAX_EDIT_DISTANCE if file_exists(out_file): print ("%s has already been aligned, skipping." % (fastq_path)) return out_file with file_transaction(out_file) as tx_out_file: cmd = ("bwa aln -n {edit_distance} -l 24 {reference_prefix} " "{fastq_path} -t {cores} | bwa samse {reference_prefix} - {fastq_path} " "> {tx_out_file}").format(**locals()) subprocess.check_call(cmd, shell=True) return out_file
def build(self): posix_file = os.path.join(self.build_dir, 'bin/libvtkWidgetsPython.so') nt_file = os.path.join(self.build_dir, 'bin', config.BUILD_TARGET, 'vtkWidgetsPythonD.dll') if utils.file_exists(posix_file, nt_file): utils.output("VTK already built. Skipping build step.") else: os.chdir(self.build_dir) ret = utils.make_command('VTK.sln') if ret != 0: utils.error("Error building VTK. Fix and try again.")
def configure_deluge(): # sudo cp $HOME/src/raspi-config/deluge/logrotate.d_deluge /etc/logrotate.d/deluge with settings(warn_only=True): sudo("cp /home/pi/src/raspi-config/deluge/deluge.conf /etc/init/") sudo("cp /home/pi/src/raspi-config/deluge/deluge-webui.conf /etc/init/") sudo("mkdir -p /var/log/deluge && sudo chown -R pi:pi /var/log/deluge && sudo chmod -R 750 /var/log/deluge") sudo("cp /home/pi/src/raspi-config/deluge/logrotate.d_deluge /etc/logrotate.d/deluge") run("ln -sf /media/RaspiHD/torrent/completo/ /home/pi/runtime/") run("ln -sf /media/RaspiHD/torrent/download/ /home/pi/runtime/") run("ln -sf /media/RaspiHD/torrent/tv_shows.cache /home/pi/runtime/") sudo("start deluge") sudo("stop deluge") if file_exists('/media/RaspiHD/backup/backup.deluge.tar.gz'): run('python $HOME/src/raspi-config/scripts/backup.py restore /media/RaspiHD/backup/ deluge')
def build(self): posix_file = os.path.join(self.build_dir, config.BUILD_TARGET, 'libvtkErCorePython.so') #TODO: check whether this is the correct file to test on nt_file = os.path.join(self.build_dir, config.BUILD_TARGET, 'vtkErCorePythonD.dll') if utils.file_exists(posix_file, nt_file): utils.output("Template Workbench already built. Skipping build step.") else: os.chdir(self.build_dir) ret = utils.make_command('ErGUI.sln') if ret != 0: utils.error("Error building Template Workbench. Fix and try again.")
def checker(request, path): if not file_exists(path, ad_path): return HttpResponseNotFound('<h1>Page not found</h1>') #checkers = ['now', 'true', 'rand', 'rand', 'false'] checkers = ['now', 'true', 'rand', 'rand', 'rand'] t = loader.get_template('checker.html') c = Context({ 'name': path, 'checkers': ','.join(checkers), }) return HttpResponse(t.render(c))
def star_align(fastq_path, reference_prefix, out_prefix, cores=1): max_best = MAX_BEST out_file = out_prefix + "Aligned.out.sam" if file_exists(out_file): print ("%s has already been aligned, skipping." % (fastq_path)) return out_file cmd = ("STAR --genomeDir {reference_prefix} --readFilesIn {fastq_path} " "--runThreadN {cores} --outFileNamePrefix {out_prefix} " "--outFilterMultimapNmax {max_best} " "--outSAMattributes NH HI NM MD AS " "--outSAMstrandField intronMotif").format(**locals()) subprocess.check_call(cmd, shell=True) return out_file
def remove(args): """ Runs the full removal process after ensuring the .desktop exists. """ program = args["name"] if not utils.file_exists(DotDesktopModel.INSTALL_DIR+program+".desktop"): print program + ".desktop is not installed." sys.exit() output.line() _run_remove_desktop(program) _run_remove_icon(program) print "Bye!" output.line()
def build(self): posix_file = os.path.join( self.build_dir, 'bin', 'cswig') nt_file = os.path.join( self.build_dir, 'bin', config.BUILD_TARGET, 'cswig.exe') if utils.file_exists(posix_file, nt_file): utils.output("CableSwig already built. Skipping build step.") else: os.chdir(self.build_dir) ret = utils.make_command('CableSwig.sln') if ret != 0: utils.error("Error building CableSwig. Fix and try again.")
def build(self): posix_file = os.path.join(self.build_dir, 'bin/libvtkdevideExternalPython.so') nt_file = os.path.join(self.build_dir, 'bin', config.BUILD_TARGET, 'vtkdevideExternalPython' + config.PYE_EXT) if utils.file_exists(posix_file, nt_file): utils.output("vtkdevide already built. Skipping build step.") else: os.chdir(self.build_dir) ret = utils.make_command('VTKDEVIDE.sln') if ret != 0: utils.error("Could not build vtkdevide. Fix and try again.")
def build(self): posix_file = os.path.join(self.build_dir, 'bin/libvtktudossGraphicsPython.so') nt_file = os.path.join(self.build_dir, 'bin', config.BUILD_TARGET, 'vtktudossGraphicsPythonD.dll') if utils.file_exists(posix_file, nt_file): utils.output("vtktudoss already built. Skipping build step.") else: os.chdir(self.build_dir) ret = utils.make_command('VTKTUDOSS.sln') if ret != 0: utils.error("Could not build vtktudoss. Fix and try again.")
def install(self): posix_file = os.path.join(self.inst_dir, 'bin/vtkpython') nt_file = os.path.join(self.inst_dir, 'bin', 'vtkpython.exe') if utils.file_exists(posix_file, nt_file): utils.output("VTK already installed. Skipping build step.") else: # python 2.5.2 setup.py complains that this does not exist # with VTK PV-3-2-1. This is only on installations with # EasyInstall / Python Eggs, then the VTK setup.py uses # EasyInstall and not standard distutils. gah! # just tested with VTK 5.8.0 and Python 2.7.2 # it indeed installs VTK_PYTHON/VTK-5.8.0-py2.7.egg # but due to the site.py and easy-install.pth magic in there, # adding VTK_PYTHON to the PYTHONPATH still works. We can keep # pip, yay! if not os.path.exists(config.VTK_PYTHON): os.makedirs(config.VTK_PYTHON) os.chdir(self.build_dir) # we save, set and restore the PP env variable, else # stupid setuptools complains save_env = os.environ.get('PYTHONPATH', '') os.environ['PYTHONPATH'] = config.VTK_PYTHON ret = utils.make_command('VTK.sln', install=True) os.environ['PYTHONPATH'] = save_env if ret != 0: utils.error("Could not install VTK. Fix and try again.") # now do some surgery on VTKConfig.cmake and # VTKLibraryDepends.cmake so builds of VTK-dependent libraries # with only the DRE to link with Just Work(tm) # on windows, we need to replace backslash with forward slash # as that's the style used by the config files. On *ix mostly # harmless idp = re.sub(r'\\','/', config.inst_dir) for fn in [os.path.join(config.VTK_DIR, 'VTKConfig.cmake'), os.path.join(config.VTK_DIR, 'VTKLibraryDepends.cmake'), os.path.join(config.VTK_DIR, 'VTKTargets-relwithdebinfo.cmake')]: if os.path.exists(fn): utils.re_sub_filter_file( [(idp, '${VTK_INSTALL_PREFIX}/..')], fn)