Python Lims.get_processes方法代码示例

# 需要导入模块: from genologics.lims import Lims [as 别名]
# 或者: from genologics.lims.Lims import get_processes [as 别名]
def generate_output(project_id, dest_plate_list, best_sample_struct,total_lanes, req_lanes, lane_maps, rounded_ratios, 
                    target_clusters, clusters_per_lane, extra_lanes, lane_volume, pool_excess, final_pool_sizes, volume_ratios, desired_ratios):
    """"Gathers the container id and well name for all samples in project"""
    timestamp = datetime.fromtimestamp(time()).strftime('%Y-%m-%d_%H:%M')
    
    #Cred to Denis for providing a base epp
    location = dict()
    lims = Lims(BASEURI, USERNAME, PASSWORD)
    allProjects = lims.get_projects()
    for proj in allProjects:
        if proj.id == project_id:
            projName = proj.name 
            break
    
    #Sets up source id    
    #All normalization processes for project
    norms=['Library Normalization (MiSeq) 4.0', 'Library Normalization (Illumina SBS) 4.0','Library Normalization (HiSeq X) 1.0']
    pros=lims.get_processes(type=norms, projectname=projName)
    #For all processes
    for p in pros:
        #For all artifacts in process
        for o in p.all_outputs():
            #If artifact is analyte type and has project name in sample
            if o.type=="Analyte" and project_id in o.name:
                location[o.name.split()[0]] = list()
                location[o.name.split()[0]].append(o.location[0].id)
                location[o.name.split()[0]].append(o.location[1])
    
    #Continue coding from here
    generate_summary(projName, best_sample_struct, timestamp, project_id, dest_plate_list, total_lanes, req_lanes, 
                     lane_maps, rounded_ratios, target_clusters, clusters_per_lane, extra_lanes, volume_ratios, desired_ratios, lane_volume, pool_excess)
    generate_csv(projName, timestamp, location, dest_plate_list, total_lanes, best_sample_struct, rounded_ratios, lane_volume, pool_excess, final_pool_sizes)
    generate_dumpfile(projName, timestamp, location, dest_plate_list, total_lanes, best_sample_struct, rounded_ratios, lane_volume, pool_excess, final_pool_sizes)

# 需要导入模块: from genologics.lims import Lims [as 别名]
# 或者: from genologics.lims.Lims import get_processes [as 别名]
def main(args):
    log = []
    lims = Lims(BASEURI,USERNAME,PASSWORD)
    process = Process(lims, id=args.pid)
    for swp_iomap in process.input_output_maps:
        if swp_iomap[1]['output-generation-type'] !=  'PerInput':
            continue
        inp_artifact = swp_iomap[0]['uri']
        amount_check_pros = lims.get_processes(type='Amount confirmation QC', inputartifactlimsid=inp_artifact.id)
        amount_check_pros.sort(reverse=True, key=lambda x:x.date_run)
        try:
            correct_amount_check_pro = amount_check_pros[0]
        except KeyError:
            sys.exit("Cannot find an Amount Confirmation QC step for artifact {}".format(inp_artifact.id))
        else:
            for iomap in correct_amount_check_pro.input_output_maps:
                if iomap[1]['output-generation-type'] !=  'PerInput':
                    continue
                if iomap[0]['limsid'] == inp_artifact.id:
                    for udf_name in ['Concentration', 'Conc. Units', 'Total Volume (uL)']:
                        try:
                            swp_iomap[1]['uri'].udf[udf_name] = iomap[1]['uri'].udf[udf_name]
                        except:
                            import pdb;pdb.set_trace()
                    swp_iomap[1]['uri'].udf['Amount taken (ng)'] = iomap[1]['uri'].udf['Amount to take (ng)']
                    swp_iomap[1]['uri'].put()

# 需要导入模块: from genologics.lims import Lims [as 别名]
# 或者: from genologics.lims.Lims import get_processes [as 别名]
def main(args):
    log = []
    lims = Lims(BASEURI,USERNAME,PASSWORD)
    process = Process(lims, id=args.pid)
    for io in process.input_output_maps:
        if io[1]['output-generation-type'] != 'PerInput':
            continue
        try:
            starting_amount = obtain_amount(io[0]['uri'])
        except Exception as e:
            log.append(str(e))
            starting_amount = 0

        log.append("Starting amount of {} : {} ng".format(io[0]['uri'].samples[0].name, starting_amount))
        current_amount = starting_amount
        #preps
        preps = lims.get_processes(inputartifactlimsid=io[0]['uri'].id, type=["Setup Workset/Plate", "Amount confirmation QC"])
        for pro in preps:
            if pro.id == args.pid:
                continue # skip the current step
            for prepio in pro.input_output_maps:
                if prepio[1]['output-generation-type'] == 'PerInput' and prepio[0]['uri'].id == io[0]['uri'].id:
                    if "Amount taken (ng)" in prepio[1]['uri'].udf: #should always be true
                        prep_amount = prepio[1]['uri'].udf["Amount taken (ng)"]
                        log.append("Removing {} ng for prep {} for sample {}".format(prep_amount, pro.id, io[0]['uri'].samples[0].name))
                        current_amount = current_amount - prep_amount
                    else:
                        log.append("No Amount Taken found for prep {} of sample {}".format(pro.id, io[0]['uri'].samples[0].name))

        if current_amount < 0:
            log.append("Estimated amount for sample {} is {}, correcting to zero".format(io[0]['uri'].samples[0].name, current_amount))
            current_amount = 0

        update_output_values(io[0]['uri'], io[1]['uri'], current_amount)

        with open("amount_check_log.txt", "w") as f:
            f.write("\n".join(log))

        for out in process.all_outputs():
            if out.name == "QC Assignment Log File" :
                for f in out.files:
                    lims.request_session.delete(f.uri)
                lims.upload_new_file(out, "amount_check_log.txt") 

# 需要导入模块: from genologics.lims import Lims [as 别名]
# 或者: from genologics.lims.Lims import get_processes [as 别名]
NOTE: You need to set the BASEURI, USERNAME AND PASSWORD.

Per Kraulis, Science for Life Laboratory, Stockholm, Sweden.
"""

from genologics.lims import Lims

# Login parameters for connecting to a LIMS instance.
# NOTE: Modify according to your setup.
from genologics.site_cloud import BASEURI, USERNAME, PASSWORD

# Create the LIMS interface instance, and check the connection and version.
lims = Lims(BASEURI, USERNAME, PASSWORD)
lims.check_version()

# Get the list of all processes.
processes = lims.get_processes()
print len(processes), 'processes in total'

process = processes[0]

print process, process.type, process.type.name
for process in lims.get_processes(type=process.type.name):
    print process

name = '1a. Fragment DNA (TruSeq DNA) 3.0'
print name
for process in lims.get_processes(type=name):
    print process

# 需要导入模块: from genologics.lims import Lims [as 别名]
# 或者: from genologics.lims.Lims import get_processes [as 别名]
def generate_output(project, destid, total_lanes, req_lanes, lane_maps, acc_ratios):
    #Gathers the container id and well name for all samples in project
    #Cred to Denis for providing a base epp
    location = dict()
    lims = Lims(BASEURI, USERNAME, PASSWORD)
    allProjects = lims.get_projects()
    for proj in allProjects:
        if proj.id == project:
            projName = proj.name 
            break

    #All normalization processes for project
    norms=['Library Normalization (MiSeq) 4.0', 'Library Normalization (Illumina SBS) 4.0','Library Normalization (HiSeq X) 1.0']
    pros=lims.get_processes(type=norms, projectname=projName)
    #For all processes
    for p in pros:
        #For all artifacts in process
        for o in p.all_outputs():
            #If artifact is analyte type and has project name in sample
            if o.type=="Analyte" and project in o.name:
                location[o.name.split()[0]] = list()
                location[o.name.split()[0]].append(o.location[0].id)
                location[o.name.split()[0]].append(o.location[1])
                
    #PRINT section
    #Print stats including duplicates
    timestamp = datetime.fromtimestamp(time()).strftime('%Y-%m-%d_%H:%M')
    sumName = projName,  "_summary_", timestamp,".txt"
    sumName = ''.join(sumName)
    with open(sumName, "w") as summary:
        if sum(req_lanes.values()) != 0:
            OPT = sum(total_lanes)/sum(req_lanes.values())
        else: 
            OPT = 0
        output = "Ideal lanes (same schema): ", str(sum(req_lanes.values())) , ", Total lanes: ", str(sum(total_lanes)), ", OPT: ", str(round(OPT,3)),'\n'
        output = ''.join(output)
        summary.write( output )
        output = "Unique pools: ", str(len(total_lanes)), ", Average pool duplication: ", str(sum(total_lanes)/float(len(total_lanes))) ,'\n'
        output = ''.join(output)
        summary.write( output )
        
        bin = 0
        for index in xrange(1, len(lane_maps)+1):
            bin  += 1
            summary.write('\n')
            output = "Wells ", str(bin) , '-' , str(bin+int(total_lanes[index-1])-1),':','\n'
            output = ''.join(output)
            summary.write( output )
            bin += int(total_lanes[index-1]-1)
            for counter in xrange(1, len(lane_maps[index])):
                output = str(lane_maps[index][counter]),' ', str(acc_ratios[index][counter]), "%",'\n'
                output = ''.join(output)
                summary.write( output )

    
    #Creates csv   
    name = projName,"_repool_",timestamp,".csv"
    name = ''.join(name)
    wells = ['Empty','A','B','C','D','E','F','G','H']
    #Index 0 is number, index 1 is Letter
    wellIndex = [1, 1]
    destNo = 0
    
    with open(name, 'w') as csvfile:
        writer = csv.writer(csvfile)
        for index in xrange(1, len(lane_maps)+1):
            for dupes in xrange(1, int(total_lanes[index-1])+1):
                if lane_maps[index] == 0:
                    raise Exception('Error: Project not logged in x_flowcells database!')
                
                for counter in xrange(1, len(lane_maps[index])):
                    #<source plate ID>,<source well>,<volume>,<destination plate ID>,<destination well>
                    #Destination well 200 microL, minimum pipette 2 microL; acc_ratios multiplied by 2.
                    sample = lane_maps[index][counter]
                    position = wells[wellIndex[1]],':',str(wellIndex[0])
                    position = ''.join(position)
                    try:
                        output = location[sample][0],location[sample][1],str(int(acc_ratios[index][counter]*2)),str(destid[destNo]),position
                    except KeyError:
                        print "Error: Samples incorrectly parsed into database, thus causing sample name conflicts!"
                    if not acc_ratios[index][counter] == 0:
                        writer.writerow(output)
                #Increment wellsindex
                if not acc_ratios[index][counter] == 0:
                    if not wellIndex[1] >= 8:
                        wellIndex[1] += 1
                    else:
                        wellIndex[1] = 1
                        if not wellIndex[0] >= 8:
                            wellIndex[0] += 1
                        else:
                            wellIndex[0] = 1
                            destNo += 1
                            try:
                                destid[destNo]
                            except IndexError:
                                print "Critical error; not enough destination plates provided"

# 需要导入模块: from genologics.lims import Lims [as 别名]
# 或者: from genologics.lims.Lims import get_processes [as 别名]
def namesetter(PID):

    lims = Lims(BASEURI, USERNAME, PASSWORD)
    lims.check_version()
    #Find LIMS entry with same PID
    allProjects = lims.get_projects()
    for proj in allProjects:
        if proj.id == PID:
            limsproject = proj.name
            break
    #Error handling
    if not 'limsproject' in locals():
        print "{} not available in LIMS.".format(PID)
        return None
    
    #Enter project summary process
    stepname=['Project Summary 1.3']
    process=lims.get_processes(type=stepname, projectname=limsproject)
    #Error handling
    if process == []:
        print "{} for {} is not available in LIMS.".format(stepname, limsproject)
        return None

    loop = True
    while loop:
        if "Bioinfo responsible" in process[0].udf:
            response = process[0].udf["Bioinfo responsible"]
        else:
            response = "Unassigned"
        print "Existing Bioinfo responsible for project {} aka {} is: {}".format(limsproject, PID, response.encode('utf-8'))
        
        #Checks for valid name
        in_responsibles = False
        config_responsibles =Udfconfig(lims, id="1128")
        while not in_responsibles:
            newname = raw_input("Enter name of new Bioinfo responsible: ")
            for names in config_responsibles.presets:
                if newname in names:
                    in_responsibles = True
                    newname = names
            if not in_responsibles:
                print "Subset {} not found in accepted Bioinfo responsible list.".format(newname)
            else:
                print "Suggested name is {}".format(newname)
        
        confirmation = raw_input("Project {} aka {} will have {} as new Bioinfo responsible, is this correct (Y/N)? ".format(limsproject, PID, newname))
        if confirmation == 'Y' or confirmation == 'y':
            try:
                newname.decode('ascii')
                process[0].udf["Bioinfo responsible"] = unicode(newname)
                process[0].put()
                print "Project {} aka {} assigned to {}".format(limsproject, PID, newname)
                return None
            except UnicodeDecodeError:
                #Weird solution due to put function
                process[0].udf["Bioinfo responsible"] = response
                print "ERROR: You tried to use a special character, didn't you? Don't do that. New standards and stuff..."
        elif confirmation == 'N' or confirmation == 'n':
            loop = False
        else:
            print "Invalid answer."