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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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