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How to use rand_name method in tempest
Best Python code snippet using tempest_python
datagen.py
Source:datagen.py 
...73 :param image_id: image id or name74 :returns: BayModelEntity with generated data75 """76 data = {77 "name": data_utils.rand_name('bay'),78 "coe": "kubernetes",79 "tls_disabled": False,80 "network_driver": None,81 "volume_driver": None,82 "labels": {},83 "public": False,84 "dns_nameserver": "8.8.8.8",85 "flavor_id": data_utils.rand_name('bay'),86 "master_flavor_id": data_utils.rand_name('bay'),87 "external_network_id": config.Config.nic_id,88 "keypair_id": data_utils.rand_name('bay'),89 "image_id": data_utils.rand_name('bay')90 }91 data.update(kwargs)92 model = baymodel_model.BayModelEntity.from_dict(data)93 return model94def baymodel_replace_patch_data(path, value=data_utils.rand_name('bay')):95 """Generates random baymodel patch data96 :param path: path to replace97 :param value: value to replace in patch98 :returns: BayModelPatchCollection with generated data99 """100 data = [{101 "path": path,102 "value": value,103 "op": "replace"104 }]105 return baymodelpatch_model.BayModelPatchCollection.from_dict(data)106def baymodel_remove_patch_data(path):107 """Generates baymodel patch data by removing value108 :param path: path to remove109 :returns: BayModelPatchCollection with generated data110 """111 data = [{112 "path": path,113 "op": "remove"114 }]115 return baymodelpatch_model.BayModelPatchCollection.from_dict(data)116def baymodel_data_with_valid_keypair_image_flavor():117 """Generates random baymodel data with valid keypair,image and flavor118 :returns: BayModelEntity with generated data119 """120 return baymodel_data(keypair_id=config.Config.keypair_name,121 image_id=config.Config.image_id,122 flavor_id=config.Config.flavor_id,123 master_flavor_id=config.Config.master_flavor_id)124def baymodel_data_with_missing_image():125 """Generates random baymodel data with missing image126 :returns: BayModelEntity with generated data127 """128 return baymodel_data(keypair_id=config.Config.keypair_name,129 flavor_id=config.Config.flavor_id,130 master_flavor_id=config.Config.master_flavor_id)131def baymodel_data_with_missing_flavor():132 """Generates random baymodel data with missing flavor133 :returns: BayModelEntity with generated data134 """135 return baymodel_data(keypair_id=config.Config.keypair_name,136 image_id=config.Config.image_id)137def baymodel_data_with_missing_keypair():138 """Generates random baymodel data with missing keypair139 :returns: BayModelEntity with generated data140 """141 return baymodel_data(image_id=config.Config.image_id,142 flavor_id=config.Config.flavor_id,143 master_flavor_id=config.Config.master_flavor_id)144def baymodel_valid_data_with_specific_coe(coe):145 """Generates random baymodel data with valid keypair and image146 :param coe: coe147 :returns: BayModelEntity with generated data148 """149 return baymodel_data(keypair_id=config.Config.keypair_name,150 image_id=config.Config.image_id, coe=coe)151def valid_kubernetes_baymodel(is_public=False):152 """Generates a valid kubernetes baymodel with valid data153 :returns: BayModelEntity with generated data154 """155 return baymodel_data(image_id=config.Config.image_id,156 flavor_id=config.Config.flavor_id, public=is_public,157 dns_nameserver=config.Config.dns_nameserver,158 master_flavor_id=config.Config.master_flavor_id,159 keypair_id=config.Config.keypair_name,160 coe="kubernetes",161 cluster_distro=None,162 external_network_id=config.Config.nic_id,163 http_proxy=None, https_proxy=None, no_proxy=None,164 network_driver=None, volume_driver=None, labels={},165 tls_disabled=False)166def bay_data(name=data_utils.rand_name('bay'),167 baymodel_id=data_utils.rand_uuid(),168 node_count=random_int(1, 5), discovery_url=gen_random_ip(),169 bay_create_timeout=random_int(1, 30),170 master_count=random_int(1, 5)):171 """Generates random bay data172 BayModel_id cannot be random for the bay to be valid due to173 validations for the presence of baymodel prior to baymodel174 creation.175 :param name: bay name (must be unique)176 :param baymodel_id: baymodel unique id (must already exist)177 :param node_count: number of agents for bay178 :param discovery_url: url provided for node discovery179 :param bay_create_timeout: timeout in minutes for bay create180 :param master_count: number of master nodes for the bay181 :returns: BayEntity with generated data182 """183 data = {184 "name": name,185 "baymodel_id": baymodel_id,186 "node_count": node_count,187 "discovery_url": None,188 "bay_create_timeout": bay_create_timeout,189 "master_count": master_count190 }191 model = bay_model.BayEntity.from_dict(data)192 return model193def valid_bay_data(baymodel_id, name=data_utils.rand_name('bay'), node_count=1,194 master_count=1, bay_create_timeout=None):195 """Generates random bay data with valid196 :param baymodel_id: baymodel unique id that already exists197 :param name: bay name (must be unique)198 :param node_count: number of agents for bay199 :returns: BayEntity with generated data200 """201 return bay_data(baymodel_id=baymodel_id, name=name,202 master_count=master_count, node_count=node_count,203 bay_create_timeout=bay_create_timeout)204def bay_name_patch_data(name=data_utils.rand_name('bay')):205 """Generates random baymodel patch data206 :param name: name to replace in patch207 :returns: BayPatchCollection with generated data208 """209 data = [{210 "path": "/name",211 "value": name,212 "op": "replace"213 }]214 return baypatch_model.BayPatchCollection.from_dict(data)215def bay_api_addy_patch_data(address='0.0.0.0'):216 """Generates random bay patch data217 :param name: name to replace in patch218 :returns: BayPatchCollection with generated data219 """220 data = [{221 "path": "/api_address",222 "value": address,223 "op": "replace"224 }]225 return baypatch_model.BayPatchCollection.from_dict(data)226def bay_node_count_patch_data(node_count=2):227 """Generates random bay patch data228 :param name: name to replace in patch229 :returns: BayPatchCollection with generated data230 """231 data = [{232 "path": "/node_count",233 "value": node_count,234 "op": "replace"235 }]236 return baypatch_model.BayPatchCollection.from_dict(data)237def cert_data(cluster_uuid, csr_data):238 data = {239 "cluster_uuid": cluster_uuid,240 "csr": csr_data}241 model = cert_model.CertEntity.from_dict(data)242 return model243def cluster_template_data(**kwargs):244 """Generates random cluster_template data245 Keypair and image id cannot be random for the cluster_template to be valid246 due to validations for the presence of keypair and image id prior to247 cluster_template creation.248 :param keypair_id: keypair name249 :param image_id: image id or name250 :returns: ClusterTemplateEntity with generated data251 """252 data = {253 "name": data_utils.rand_name('cluster'),254 "coe": "kubernetes",255 "tls_disabled": False,256 "network_driver": None,257 "volume_driver": None,258 "labels": {},259 "public": False,260 "dns_nameserver": "8.8.8.8",261 "flavor_id": data_utils.rand_name('cluster'),262 "master_flavor_id": data_utils.rand_name('cluster'),263 "external_network_id": config.Config.nic_id,264 "keypair_id": data_utils.rand_name('cluster'),265 "image_id": data_utils.rand_name('cluster')266 }267 data.update(kwargs)268 model = cluster_template_model.ClusterTemplateEntity.from_dict(data)269 return model270def cluster_template_replace_patch_data(path,271 value=data_utils.rand_name('cluster')):272 """Generates random ClusterTemplate patch data273 :param path: path to replace274 :param value: value to replace in patch275 :returns: ClusterTemplatePatchCollection with generated data276 """277 data = [{278 "path": path,279 "value": value,280 "op": "replace"281 }]282 collection = cluster_templatepatch_model.ClusterTemplatePatchCollection283 return collection.from_dict(data)284def cluster_template_remove_patch_data(path):285 """Generates ClusterTemplate patch data by removing value286 :param path: path to remove287 :returns: ClusterTemplatePatchCollection with generated data288 """289 data = [{290 "path": path,291 "op": "remove"292 }]293 collection = cluster_templatepatch_model.ClusterTemplatePatchCollection294 return collection.from_dict(data)295def cluster_template_name_patch_data(name=data_utils.rand_name('cluster')):296 """Generates random cluster_template patch data297 :param name: name to replace in patch298 :returns: ClusterTemplatePatchCollection with generated data299 """300 data = [{301 "path": "/name",302 "value": name,303 "op": "replace"304 }]305 collection = cluster_templatepatch_model.ClusterTemplatePatchCollection306 return collection.from_dict(data)307def cluster_template_flavor_patch_data(flavor=data_utils.rand_name('cluster')):308 """Generates random cluster_template patch data309 :param flavor: flavor to replace in patch310 :returns: ClusterTemplatePatchCollection with generated data311 """312 data = [{313 "path": "/flavor_id",314 "value": flavor,315 "op": "replace"316 }]317 collection = cluster_templatepatch_model.ClusterTemplatePatchCollection318 return collection.from_dict(data)319def cluster_template_data_with_valid_keypair_image_flavor():320 """Generates random clustertemplate data with valid data321 :returns: ClusterTemplateEntity with generated data322 """323 master_flavor = config.Config.master_flavor_id324 return cluster_template_data(keypair_id=config.Config.keypair_name,325 image_id=config.Config.image_id,326 flavor_id=config.Config.flavor_id,327 master_flavor_id=master_flavor)328def cluster_template_data_with_missing_image():329 """Generates random cluster_template data with missing image330 :returns: ClusterTemplateEntity with generated data331 """332 return cluster_template_data(333 keypair_id=config.Config.keypair_name,334 flavor_id=config.Config.flavor_id,335 master_flavor_id=config.Config.master_flavor_id)336def cluster_template_data_with_missing_flavor():337 """Generates random cluster_template data with missing flavor338 :returns: ClusterTemplateEntity with generated data339 """340 return cluster_template_data(keypair_id=config.Config.keypair_name,341 image_id=config.Config.image_id)342def cluster_template_data_with_missing_keypair():343 """Generates random cluster_template data with missing keypair344 :returns: ClusterTemplateEntity with generated data345 """346 return cluster_template_data(347 image_id=config.Config.image_id,348 flavor_id=config.Config.flavor_id,349 master_flavor_id=config.Config.master_flavor_id)350def cluster_template_valid_data_with_specific_coe(coe):351 """Generates random cluster_template data with valid keypair and image352 :param coe: coe353 :returns: ClusterTemplateEntity with generated data354 """355 return cluster_template_data(keypair_id=config.Config.keypair_name,356 image_id=config.Config.image_id, coe=coe)357def valid_cluster_template(is_public=False):358 """Generates a valid swarm-mode cluster_template with valid data359 :returns: ClusterTemplateEntity with generated data360 """361 master_flavor_id = config.Config.master_flavor_id362 return cluster_template_data(363 image_id=config.Config.image_id,364 flavor_id=config.Config.flavor_id,365 public=is_public,366 dns_nameserver=config.Config.dns_nameserver,367 master_flavor_id=master_flavor_id,368 coe=config.Config.coe,369 cluster_distro=None,370 external_network_id=config.Config.nic_id,371 http_proxy=None, https_proxy=None,372 no_proxy=None, network_driver=config.Config.network_driver,373 volume_driver=None, labels={},374 docker_storage_driver=config.Config.docker_storage_driver,375 tls_disabled=False)376def cluster_data(name=data_utils.rand_name('cluster'),377 cluster_template_id=data_utils.rand_uuid(),378 node_count=random_int(1, 5), discovery_url=gen_random_ip(),379 create_timeout=None,380 master_count=random_int(1, 5)):381 """Generates random cluster data382 cluster_template_id cannot be random for the cluster to be valid due to383 validations for the presence of clustertemplate prior to clustertemplate384 creation.385 :param name: cluster name (must be unique)386 :param cluster_template_id: clustertemplate unique id (must already exist)387 :param node_count: number of agents for cluster388 :param discovery_url: url provided for node discovery389 :param create_timeout: timeout in minutes for cluster create390 :param master_count: number of master nodes for the cluster391 :returns: ClusterEntity with generated data392 """393 timeout = create_timeout or config.Config.cluster_creation_timeout394 data = {395 "name": name,396 "cluster_template_id": cluster_template_id,397 "keypair": config.Config.keypair_name,398 "node_count": node_count,399 "discovery_url": None,400 "create_timeout": timeout,401 "master_count": master_count402 }403 model = cluster_model.ClusterEntity.from_dict(data)404 return model405def valid_cluster_data(cluster_template_id,406 name=data_utils.rand_name('cluster'),407 node_count=1, master_count=1, create_timeout=None):408 """Generates random cluster data with valid409 :param cluster_template_id: clustertemplate unique id that already exists410 :param name: cluster name (must be unique)411 :param node_count: number of agents for cluster412 :returns: ClusterEntity with generated data413 """414 return cluster_data(cluster_template_id=cluster_template_id, name=name,415 master_count=master_count, node_count=node_count,416 create_timeout=create_timeout)417def cluster_name_patch_data(name=data_utils.rand_name('cluster')):418 """Generates random clustertemplate patch data419 :param name: name to replace in patch420 :returns: ClusterPatchCollection with generated data421 """422 data = [{423 "path": "/name",424 "value": name,425 "op": "replace"426 }]427 return clusterpatch_model.ClusterPatchCollection.from_dict(data)428def cluster_api_addy_patch_data(address='0.0.0.0'):429 """Generates random cluster patch data430 :param name: name to replace in patch431 :returns: ClusterPatchCollection with generated data...
ccbr_get_consensus_peaks.py
Source:ccbr_get_consensus_peaks.py
1import os2import argparse3import uuid4import pandas5parser = argparse.ArgumentParser(description="""6Get consensus peaks from multiple narrowPeak files7This is similar to the consensus MAX peaks from https://dx.doi.org/10.5936%2Fcsbj.2014010028On Biowulf the following modules need to be pre-loaded9module load bedops10module load bedtools11module load ucsc12""",formatter_class=argparse.RawTextHelpFormatter)13parser.add_argument('--peakfiles', required = True, nargs = '+', help = 'space separated list of peakfiles')14parser.add_argument('--outbed', required = True, dest = 'outbed', help = 'consensus output bed file')15parser.add_argument('--nofilter', action = 'store_true', default = 'store_false',required = False,dest = 'nofilter',help = ' do not filter keep all peaks with score')16deleteFiles=[]17args = parser.parse_args()18print(args)19out=open(args.outbed,'w')20filter=0.521rand_name=str(uuid.uuid4())22# concat23cmd="cat"24for p in args.peakfiles:25 cmd+=" "+p26cmd+=" | cut -f1-3 > "+rand_name+".concat.bed"27deleteFiles.append(rand_name+".concat.bed")28print(cmd)29os.system(cmd)30# sort and merge31cmd="bedSort "+rand_name+".concat.bed "+rand_name+".concat.bed && bedtools merge -i "+rand_name+".concat.bed > "+rand_name+".merged.bed"32deleteFiles.append(rand_name+".merged.bed")33print(cmd)34os.system(cmd)35# check merged count36npeaks=len(open(rand_name+".merged.bed").readlines())37if (npeaks==0):38 out.close()39 exit("Number of merged peaks = 0")40count=041for p in args.peakfiles:42 count+=143 sortedfile=p + ".sorted." + rand_name44 countfile=p + ".counts." + rand_name45 cmd = "cut -f1-3 " + p + " > " + sortedfile + " && bedSort " + sortedfile + " " + sortedfile46 print(cmd)47 os.system(cmd)48 cmd = "bedmap --delim '\t' --echo-ref-name --count " + rand_name + ".merged.bed " + sortedfile + "|awk -F'\t\' -v OFS='\t' '{if ($2>1){$2=1}{print}}' > " + countfile49 print(cmd)50 os.system(cmd)51 deleteFiles.append(countfile)52 deleteFiles.append(sortedfile)53 if count==1:54 df=pandas.read_csv(countfile,delimiter="\t")55 df.columns=["peakid",countfile]56 else:57 dfx=pandas.read_csv(countfile,delimiter="\t")58 dfx.columns=["peakid",countfile]59 df=df.merge(dfx,on="peakid")60df=df.set_index("peakid")61df=df.sum(axis=1)/len(df.columns)62df=pandas.DataFrame({'peakid':df.index,'score':df.values})63for index, row in df.iterrows():64 chrom,coords=row["peakid"].split(":")65 start,end=coords.split("-")66 if args.nofilter==True:67 out.write("%s\t%s\t%s\t%s\t%.3f\t.\n"%(chrom,start,end,row["peakid"],float(row["score"])))68 elif float(row["score"])>filter:69 out.write("%s\t%s\t%s\t%s\t%.3f\t.\n"%(chrom,start,end,row["peakid"],float(row["score"])))70out.close()71for f in deleteFiles:72 os.remove(f)...
utils.py
Source:utils.py
1import os2import uuid3from functools import wraps4from django.conf import settings5from django.contrib.sites.models import Site6from django.core.urlresolvers import reverse7def absolute_url_reverse(url_name=None, **kwargs):8 domain = Site.objects.get_current().domain9 path = '/'10 if url_name:11 path = reverse(url_name, **kwargs)12 full_url = "{}://{}{}".format(settings.DEFAULT_HTTP_PROTOCOL,13 domain, path)14 return full_url15def generate_upload_path(instance, filename, dirname=None):16 """17 Generate path with random file name for FileField.18 """19 ext = os.path.splitext(filename)[1].lstrip('.')20 rand_name = "{}.{}".format(uuid.uuid4().hex, ext)21 if dirname:22 rand_name = "{}/{}".format(dirname, rand_name)23 return rand_name24def disable_for_loaddata(signal_handler):25 """26 Decorator that turns off signal handlers when loading fixture data.27 """28 @wraps(signal_handler)29 def wrapper(*args, **kwargs):30 if kwargs.get('raw'):31 return32 signal_handler(*args, **kwargs)...
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