Python SampleRunMetricsConnection.get_entry方法代码示例

# 需要导入模块: from scilifelab.db.statusdb import SampleRunMetricsConnection [as 别名]
# 或者: from scilifelab.db.statusdb.SampleRunMetricsConnection import get_entry [as 别名]
 def test_get_flowcell(self):
     """Test getting a flowcell for a given sample"""
     sample_con = SampleRunMetricsConnection(
         dbname="samples-test", username=self.user, password=self.pw, url=self.url
     )
     fc = sample_con.get_entry(self.examples["sample"], "flowcell")
     self.assertEqual(str(fc), self.examples["flowcell"])

# 需要导入模块: from scilifelab.db.statusdb import SampleRunMetricsConnection [as 别名]
# 或者: from scilifelab.db.statusdb.SampleRunMetricsConnection import get_entry [as 别名]
 def test_dbcon(self):
     """Test database connection and that we get expected values."""
     s_con = SampleRunMetricsConnection(dbname="samples-test", username="u", password="p")
     samples = [s_con.get_entry(x) for x in s_con.name_view]
     samples_d = {x["name"]: x for x in samples}
     self.assertEqual(samples_d["1_120924_AC003CCCXX_TGACCA"]["date"], "120924")
     self.assertEqual(samples_d["1_121015_BB002BBBXX_TGACCA"]["flowcell"], "BB002BBBXX")
     self.assertEqual(samples_d["2_120924_AC003CCCXX_ACAGTG"]["entity_type"], "sample_run_metrics")
     self.assertEqual(samples_d["3_120924_AC003CCCXX_ACAGTG"]["lane"], "3")
     self.assertEqual(samples_d["4_120924_AC003CCCXX_CGTTAA"]["sequence"], "CGTTAA")
     self.assertEqual(samples_d["2_121015_BB002BBBXX_TGACCA"]["project_id"], "P002")
     fc_con = FlowcellRunMetricsConnection(dbname="flowcells-test", username="u", password="p")
     flowcells = [fc_con.get_entry(x) for x in fc_con.name_view]
     flowcells_d = {x["name"]: x for x in flowcells}
     self.assertEqual(flowcells_d["120924_AC003CCCXX"]["name"], "120924_AC003CCCXX")
     self.assertEqual(flowcells_d["121015_BB002BBBXX"]["name"], "121015_BB002BBBXX")
     self.assertEqual(flowcells_d["120924_AC003CCCXX"]["entity_type"], "flowcell_run_metrics")
     p_con = ProjectSummaryConnection(dbname="projects-test", username="u", password="p")
     projects = [p_con.get_entry(x) for x in p_con.name_view]
     projects_d = {x["project_name"]: x for x in projects}
     self.assertEqual(projects_d["J.Doe_00_01"]["min_m_reads_per_sample_ordered"], 0.1)
     self.assertEqual(projects_d["J.Doe_00_01"]["no_of_samples"], 2)
     self.assertEqual(
         set(projects_d["J.Doe_00_01"]["samples"].keys()), set(["P001_101_index3", "P001_102", "P001_103"])
     )
     self.assertEqual(projects_d["J.Doe_00_01"]["customer_reference"], "GnuGenome")
     self.assertEqual(projects_d["J.Doe_00_02"]["min_m_reads_per_sample_ordered"], 0.2)
     self.assertEqual(projects_d["J.Doe_00_03"]["samples"].keys(), ["3_index6"])
     self.assertIn("A", projects_d["J.Doe_00_03"]["samples"]["3_index6"]["library_prep"])

# 需要导入模块: from scilifelab.db.statusdb import SampleRunMetricsConnection [as 别名]
# 或者: from scilifelab.db.statusdb.SampleRunMetricsConnection import get_entry [as 别名]
    def test_2_make_note(self):
        """Make a note subset by example flowcell and project"""
        s_con = SampleRunMetricsConnection(username=self.user, password=self.pw, url=self.url)
        fc_con = FlowcellRunMetricsConnection(username=self.user, password=self.pw, url=self.url)
        p_con = ProjectSummaryConnection(username=self.user, password=self.pw, url=self.url)
        paragraphs = sample_note_paragraphs()
        headers = sample_note_headers()
        samples = s_con.get_samples(self.examples["flowcell"], self.examples["project"])
        project = p_con.get_entry(self.examples["project"])
        samples = p_con.map_srm_to_name(self.examples["project"], fc_id=self.examples["flowcell"], use_bc_map=True)
        for k,v  in samples.items():
            s_param = parameters
            s = s_con.get_entry(k)
            s_param.update({key:s[srm_to_parameter[key]] for key in srm_to_parameter.keys()})
            fc = "{}_{}".format(s["date"], s["flowcell"])
            s_param["phix_error_rate"] = fc_con.get_phix_error_rate(str(fc), s["lane"])
            s_param['avg_quality_score'] = s_con.calc_avg_qv(s["name"])
            s_param['rounded_read_count'] = round(float(s_param['rounded_read_count'])/1e6,1) if s_param['rounded_read_count'] else None
            s_param['customer_name'] = project['samples'][v["sample"]].get('customer_name', None)

            if project:
                s_param['ordered_amount'] = p_con.get_ordered_amount(self.examples["project"])
                s_param['customer_reference'] = s_param.get('customer_reference', project['customer_reference'])
                s_param['uppnex_project_id'] = s_param.get('uppnex_project_id', project['uppnex_id'])
            s_param['success'] = sequencing_success(s_param, cutoffs)
            s_param.update({k:"N/A" for k in s_param.keys() if s_param[k] is None})
            make_note("{}.pdf".format(s["barcode_name"]), headers, paragraphs, **s_param)

# 需要导入模块: from scilifelab.db.statusdb import SampleRunMetricsConnection [as 别名]
# 或者: from scilifelab.db.statusdb.SampleRunMetricsConnection import get_entry [as 别名]
 def test_2_make_project_note(self):
     """Make a project note subset by flowcell and project"""
     s_con = SampleRunMetricsConnection(username=self.user, password=self.pw, url=self.url)
     fc_con = FlowcellRunMetricsConnection(username=self.user, password=self.pw, url=self.url)
     p_con = ProjectSummaryConnection(username=self.user, password=self.pw, url=self.url)
     paragraphs = project_note_paragraphs()
     headers = project_note_headers()
     param = parameters
     project = p_con.get_entry(self.examples["project"])
     if not project:
         print "No project named {}".format(self.examples["project"])
         return
     if project:
         ordered_amount = p_con.get_ordered_amount(self.examples["project"])
     else:
         return
         ordered_amount = self.pargs.ordered_million_reads
         
     ## Start collecting the data
     sample_table = []
     sample_list = project['samples']
     param.update({key:project.get(ps_to_parameter[key], None) for key in ps_to_parameter.keys()})
     samples = p_con.map_name_to_srm(self.examples["project"], check_consistency=True, use_bc_map=True)
     all_passed = True
     for k,v in samples.items():
         if k=="Unexpected":
             continue
         project_sample = sample_list[k]
         vals = {x:project_sample.get(prjs_to_table[x], None) for x in prjs_to_table.keys()}
         vals['MOrdered'] = ordered_amount
         vals['BarcodeSeq'] = s_con.get_entry(v.keys()[0], "sequence")
         
         ## Set status
         vals['Status'] = set_status(vals) if vals['Status'] is None else vals['Status']
         vals.update({k:"N/A" for k in vals.keys() if vals[k] is None})
         if vals['Status']=="N/A" or vals['Status']=="NP": all_passed = False
         sample_table.append([vals[k] for k in table_keys])
     if all_passed: param["finished"] = 'Project finished.'
     sample_table.sort()
     sample_table = list(sample_table for sample_table,_ in itertools.groupby(sample_table))
     sample_table.insert(0, ['ScilifeID', 'CustomerID', 'BarcodeSeq', 'MSequenced', 'MOrdered', 'Status'])
     paragraphs["Samples"]["tpl"] = make_sample_table(sample_table)
     make_note("{}.pdf".format(self.examples["project"]), headers, paragraphs, **param)

# 需要导入模块: from scilifelab.db.statusdb import SampleRunMetricsConnection [as 别名]
# 或者: from scilifelab.db.statusdb.SampleRunMetricsConnection import get_entry [as 别名]
def _project_status_note_table(project_name=None, username=None, password=None, url=None,
                               use_ps_map=True, use_bc_map=False, check_consistency=False,
                               ordered_million_reads=None, uppnex_id=None, customer_reference=None,
                               exclude_sample_ids={}, project_alias=None, sample_aliases={},
                               projectdb="projects", samplesdb="samples", flowcelldb="flowcells",
                               include_all_samples=False, param={}, **kw):

    # mapping project_summary to parameter keys
    ps_to_parameter = {"scilife_name":"scilife_name", "customer_name":"customer_name", "project_name":"project_name"}
    # mapping project sample to table
    table_keys = ['ScilifeID', 'SubmittedID', 'BarcodeSeq', 'MSequenced', 'MOrdered']

    output_data = {'stdout':StringIO(), 'stderr':StringIO(), 'debug':StringIO()}
    # Connect and run
    s_con = SampleRunMetricsConnection(dbname=samplesdb, username=username, password=password, url=url)
    fc_con = FlowcellRunMetricsConnection(dbname=flowcelldb, username=username, password=password, url=url)
    p_con = ProjectSummaryConnection(dbname=projectdb, username=username, password=password, url=url)

    #Get the information source for this project
    source = p_con.get_info_source(project_name)

    # Get project summary from project database
    sample_aliases = _literal_eval_option(sample_aliases, default={})
    prj_summary = p_con.get_entry(project_name)
    if not prj_summary:
        LOG.warn("No such project '{}'".format(project_name))
        return
    LOG.debug("Working on project '{}'.".format(project_name))

    # Determine if project is finished by getting all samples sequenced date
    try:
        all_samples_sequenced = prj_summary['project_summary']['all_samples_sequenced']
    except (TypeError,KeyError):
        all_samples_sequenced = False

    # Get sample run list and loop samples to make mapping sample -> {sampleruns}
    sample_run_list = _set_sample_run_list(project_name, flowcell=None, project_alias=project_alias, s_con=s_con)
    samples = {}
    for s in sample_run_list:
        prj_sample = p_con.get_project_sample(project_name, s.get("project_sample_name", None))
        if prj_sample:
            sample_name = prj_sample['project_sample'].get("scilife_name", None)
            s_d = {s["name"] : {'sample':sample_name, 'id':s["_id"]}}
            samples.update(s_d)
        else:
            if s["barcode_name"] in sample_aliases:
                s_d = {sample_aliases[s["barcode_name"]] : {'sample':sample_aliases[s["barcode_name"]], 'id':s["_id"]}}
                samples.update(s_d)
            else:
                s_d = {s["name"]:{'sample':s["name"], 'id':s["_id"], 'barcode_name':s["barcode_name"]}}
                LOG.warn("No mapping found for sample run:\n  '{}'".format(s_d))

    # Convert to mapping from desired sample name to list of aliases
    # Less important for the moment; one solution is to update the
    # Google docs summary table to use the P names
    sample_dict = prj_summary['samples']
    param.update({key:prj_summary.get(ps_to_parameter[key], None) for key in ps_to_parameter.keys()})
    param["ordered_amount"] = param.get("ordered_amount", p_con.get_ordered_amount(project_name, samples=sample_dict))

    if not param.get('customer_reference') :
        try:
            param['customer_reference'] = prj_summary['details']['customer_project_reference']
        except (TypeError,KeyError):
            param['customer_reference'] = prj_summary.get('customer_reference')
    param['uppnex_project_id'] = param.get('uppnex_project_id', prj_summary.get('uppnex_id'))

    # Override database values if options passed at command line
    if uppnex_id:
        param["uppnex_project_id"] = uppnex_id
    if customer_reference:
        param["customer_reference"] = customer_reference

    # Process options
    ordered_million_reads = _literal_eval_option(ordered_million_reads)
    exclude_sample_ids = _literal_eval_option(exclude_sample_ids, default={})

    ## Start collecting the data
    sample_table = []
    samples_excluded = []
    last_library_preps = p_con.get_latest_library_prep(project_name)
    last_library_preps_srm = [x for l in last_library_preps.values() for x in l]
    LOG.debug("Looping through sample map that maps project sample names to sample run metrics ids")
    for k,v in samples.items():
        LOG.debug("project sample '{}' maps to '{}'".format(k, v))
        if not include_all_samples:
            if v['sample'] not in last_library_preps.keys():
                LOG.info("No library prep information for sample {}; keeping in report".format(v['sample']))
            else:
                if k not in last_library_preps_srm:
                    LOG.info("Sample run {} ('{}') is not latest library prep ({}) for project sample {}: excluding from report".format(k, v["id"], ",".join(list(set(last_library_preps[v['sample']].values()))), v['sample']))
                    continue
        else:
            pass

        if re.search("Unexpected", k):
            continue
        barcode_seq = s_con.get_entry(k, "sequence")
        # Exclude sample id?
        if _exclude_sample_id(exclude_sample_ids, v['sample'], barcode_seq):
            samples_excluded.append(v['sample'])
#.........这里部分代码省略.........

# 需要导入模块: from scilifelab.db.statusdb import SampleRunMetricsConnection [as 别名]
# 或者: from scilifelab.db.statusdb.SampleRunMetricsConnection import get_entry [as 别名]
def project_status_note(project_name=None, username=None, password=None, url=None,
                        use_ps_map=True, use_bc_map=False, check_consistency=False,
                        ordered_million_reads=None, uppnex_id=None, customer_reference=None,
                        exclude_sample_ids={}, project_alias=None, sample_aliases={},
                        projectdb="projects", samplesdb="samples", flowcelldb="flowcells",
                        include_all_samples=False, **kw):
    """Make a project status note. Used keywords:

    :param project_name: project name
    :param user: db user name
    :param password: db password
    :param url: db url
    :param use_ps_map: use project summary mapping
    :param use_bc_map: use project to barcode name mapping
    :param check_consistency: check consistency between mappings
    :param ordered_million_reads: number of ordered reads in millions
    :param uppnex_id: the uppnex id
    :param customer_reference: customer project name
    :param exclude_sample_ids: exclude some sample ids from project note
    :param project_alias: project alias name
    :param sample_aliases: sample alias names
    :param projectdb: project db name
    :param samplesdb: samples db name
    :param flowcelldb: flowcells db name
    :param include_all_samples: include all samples in report
    """
    # parameters
    parameters = {
        "project_name" : project_name,
        "finished" : "Not finished, or cannot yet assess if finished.",
        }
    # mapping project_summary to parameter keys
    ps_to_parameter = {"scilife_name":"scilife_name", "customer_name":"customer_name", "project_name":"project_name"}
    # mapping project sample to table
    table_keys = ['ScilifeID', 'CustomerID', 'BarcodeSeq', 'MSequenced', 'MOrdered', 'Status']

    output_data = {'stdout':StringIO(), 'stderr':StringIO(), 'debug':StringIO()}
    # Connect and run
    s_con = SampleRunMetricsConnection(dbname=samplesdb, username=username, password=password, url=url)
    fc_con = FlowcellRunMetricsConnection(dbname=flowcelldb, username=username, password=password, url=url)
    p_con = ProjectSummaryConnection(dbname=projectdb, username=username, password=password, url=url)

    # Set report paragraphs
    paragraphs = project_note_paragraphs()
    headers = project_note_headers()
    # Set local param variable
    param = parameters
    
    # Get project summary from project database
    sample_aliases = _literal_eval_option(sample_aliases, default={})
    prj_summary = p_con.get_entry(project_name)
    if not prj_summary:
        LOG.warn("No such project '{}'".format(project_name))
        return
    LOG.debug("Working on project '{}'.".format(project_name))

    # Get sample run list and loop samples to make mapping sample -> {sampleruns}
    sample_run_list = _set_sample_run_list(project_name, flowcell=None, project_alias=project_alias, s_con=s_con)
    samples = {}
    for s in sample_run_list:
        prj_sample = p_con.get_project_sample(project_name, s.get("project_sample_name", None))
        if prj_sample:
            sample_name = prj_sample['project_sample'].get("scilife_name", None)
            s_d = {s["name"] : {'sample':sample_name, 'id':s["_id"]}}
            samples.update(s_d)
        else:
            if s["barcode_name"] in sample_aliases:
                s_d = {sample_aliases[s["barcode_name"]] : {'sample':sample_aliases[s["barcode_name"]], 'id':s["_id"]}}
                samples.update(s_d)
            else:
                s_d = {s["name"]:{'sample':s["name"], 'id':s["_id"], 'barcode_name':s["barcode_name"]}}
                LOG.warn("No mapping found for sample run:\n  '{}'".format(s_d))

    # Convert to mapping from desired sample name to list of aliases
    # Less important for the moment; one solution is to update the
    # Google docs summary table to use the P names
    sample_dict = prj_summary['samples']
    param.update({key:prj_summary.get(ps_to_parameter[key], None) for key in ps_to_parameter.keys()})
    param["ordered_amount"] = param.get("ordered_amount", p_con.get_ordered_amount(project_name))
    param['customer_reference'] = param.get('customer_reference', prj_summary.get('customer_reference'))
    param['uppnex_project_id'] = param.get('uppnex_project_id', prj_summary.get('uppnex_id'))

    # Override database values if options passed at command line
    if uppnex_id:
        param["uppnex_project_id"] = uppnex_id
    if customer_reference:
        param["customer_reference"] = customer_reference

    # Process options
    ordered_million_reads = _literal_eval_option(ordered_million_reads)
    exclude_sample_ids = _literal_eval_option(exclude_sample_ids, default={})

    ## Start collecting the data
    sample_table = []
    samples_excluded = []
    all_passed = True
    last_library_preps = p_con.get_latest_library_prep(project_name)
    last_library_preps_srm = [x for l in last_library_preps.values() for x in l] 
    LOG.debug("Looping through sample map that maps project sample names to sample run metrics ids")
    for k,v in samples.items():
#.........这里部分代码省略.........

# 需要导入模块: from scilifelab.db.statusdb import SampleRunMetricsConnection [as 别名]
# 或者: from scilifelab.db.statusdb.SampleRunMetricsConnection import get_entry [as 别名]
class TestQCUpload(PmFullTest):
    def setUp(self):
        self.app = self.make_app(
            argv=["qc", "upload-qc", flowcells[0], "--mtime", "10000"],
            extensions=["scilifelab.pm.ext.ext_qc", "scilifelab.pm.ext.ext_couchdb"],
        )
        self._run_app()
        self.s_con = SampleRunMetricsConnection(dbname="samples-test", username="u", password="p")
        self.p_con = ProjectSummaryConnection(dbname="projects-test", username="u", password="p")
        self.fc_con = FlowcellRunMetricsConnection(dbname="flowcells-test", username="u", password="p")

    def test_samplesheet(self):
        """Test samplesheet upload"""
        fc = self.fc_con.get_entry("120924_AC003CCCXX")
        self.assertEqual(fc["samplesheet_csv"][0]["Index"], "TGACCA")
        self.assertEqual(fc["samplesheet_csv"][0]["Description"], "J__Doe_00_01")
        self.assertEqual(fc["samplesheet_csv"][0]["FCID"], "C003CCCXX")
        self.assertEqual(fc["samplesheet_csv"][1]["SampleRef"], "hg19")
        self.assertEqual(fc["samplesheet_csv"][2]["SampleID"], "P001_101_index3")

    def test_qc_upload(self):
        """Test running qc upload to server"""
        self.app = self.make_app(
            argv=["qc", "upload-qc", flowcells[1], "--mtime", "100"],
            extensions=["scilifelab.pm.ext.ext_qc", "scilifelab.pm.ext.ext_couchdb"],
        )
        self._run_app()
        s = self.s_con.get_entry("4_120924_AC003CCCXX_CGTTAA")
        self.assertIsNone(s["project_sample_name"])
        self.assertEqual(s["project_id"], "P003")

    def test_qc_update(self):
        """Test running qc update of a project id"""
        s = self.s_con.get_entry("4_120924_AC003CCCXX_CGTTAA")
        s["project_id"] = None
        self.assertIsNone(s["project_id"])
        self.s_con.save(s)
        self.app = self.make_app(
            argv=["qc", "update", "--sample_prj", projects[2], "--project_id", "P003", "--debug", "--force"],
            extensions=["scilifelab.pm.ext.ext_qc", "scilifelab.pm.ext.ext_couchdb"],
        )
        self._run_app()
        s = self.s_con.get_entry("4_120924_AC003CCCXX_CGTTAA")
        self.assertEqual(s["project_id"], "P003")

    def test_qc_update_sample_names(self):
        """Test running qc update of project sample names"""
        s1 = self.s_con.get_entry("1_120924_AC003CCCXX_TGACCA")
        s2 = self.s_con.get_entry("2_120924_AC003CCCXX_ACAGTG")
        s1["project_sample_name"] = None
        s2["project_sample_name"] = None
        self.assertIsNone(s1["project_sample_name"])
        self.assertIsNone(s2["project_sample_name"])
        self.s_con.save(s1)
        self.s_con.save(s2)
        sample_map = {"P001_101_index3": "P001_101_index3", "P001_102_index6": "P001_102"}
        self.app = self.make_app(
            argv=[
                "qc",
                "update",
                "--sample_prj",
                projects[0],
                "--names",
                "{}".format(sample_map),
                "--debug",
                "--force",
            ],
            extensions=["scilifelab.pm.ext.ext_qc", "scilifelab.pm.ext.ext_couchdb"],
        )
        self._run_app()
        s1 = self.s_con.get_entry("1_120924_AC003CCCXX_TGACCA")
        s2 = self.s_con.get_entry("2_120924_AC003CCCXX_ACAGTG")
        self.assertEqual(s1["project_sample_name"], "P001_101_index3")
        self.assertEqual(s2["project_sample_name"], "P001_102")

# 需要导入模块: from scilifelab.db.statusdb import SampleRunMetricsConnection [as 别名]
# 或者: from scilifelab.db.statusdb.SampleRunMetricsConnection import get_entry [as 别名]
class TestQCUpload(PmFullTest):
    def setUp(self):
        """FIXME: All other tests depend on data being uploaded, so
        these are not real unit tests. The setup to TestQCUpload has to
        be run prior to other tests, else unexpected failures will
        occur."""
        self.app = self.make_app(argv = ['qc', 'upload-qc', flowcells[0], '--mtime',  '10000'], extensions=['scilifelab.pm.ext.ext_qc', 'scilifelab.pm.ext.ext_couchdb'])
        self._run_app()
        self.app = self.make_app(argv = ['qc', 'upload-qc', flowcells[1], '--mtime',  '10000'], extensions=['scilifelab.pm.ext.ext_qc', 'scilifelab.pm.ext.ext_couchdb'])
        self._run_app()
        self.s_con = SampleRunMetricsConnection(dbname="samples-test", username="u", password="p")
        self.p_con = ProjectSummaryConnection(dbname="projects-test", username="u", password="p")
        self.fc_con = FlowcellRunMetricsConnection(dbname="flowcells-test", username="u", password="p")

    def test_samplesheet(self):
        """Test samplesheet upload"""
        fc = self.fc_con.get_entry("120924_AC003CCCXX")
        self.assertEqual(fc["samplesheet_csv"][0]["Index"], "TGACCA")
        self.assertEqual(fc["samplesheet_csv"][0]["Description"], "J__Doe_00_01")
        self.assertEqual(fc["samplesheet_csv"][0]["FCID"], "C003CCCXX")
        self.assertEqual(fc["samplesheet_csv"][1]["SampleRef"], "hg19")
        self.assertEqual(fc["samplesheet_csv"][2]["SampleID"], "P002_101_index3")

    def test_qc_upload(self):
        """Test running qc upload to server. Slightly circular testing
        here - I setup the module with qc update so by definition the
        test must 'work'"""
        self.app = self.make_app(argv = ['qc', 'upload-qc', flowcells[1], '--mtime',  '100'], extensions=['scilifelab.pm.ext.ext_qc',  'scilifelab.pm.ext.ext_couchdb'])
        self._run_app()
        s = self.s_con.get_entry("4_120924_AC003CCCXX_CGTTAA")
        self.assertIsNone(s["project_sample_name"])
        self.assertEqual(s["project_id"], "P003")
        
    def test_qc_update(self):
        """Test running qc update of a project id"""
        s = self.s_con.get_entry("4_120924_AC003CCCXX_CGTTAA")
        s["project_id"]= None
        self.assertIsNone(s["project_id"])
        self.s_con.save(s)
        self.app = self.make_app(argv = ['qc', 'update', '--sample_prj', projects[2], '--project_id', 'P003', '--debug', '--force'], extensions=['scilifelab.pm.ext.ext_qc', 'scilifelab.pm.ext.ext_couchdb'])
        self._run_app()
        s = self.s_con.get_entry("4_120924_AC003CCCXX_CGTTAA")
        self.assertEqual(s["project_id"], "P003")

    def test_qc_update_sample_names(self):
        """Test running qc update of project sample names"""
        s1 = self.s_con.get_entry("1_120924_AC003CCCXX_TGACCA")
        s2 = self.s_con.get_entry("2_120924_AC003CCCXX_ACAGTG")
        s1["project_sample_name"] = None
        s2["project_sample_name"] = None
        self.assertIsNone(s1["project_sample_name"])
        self.assertIsNone(s2["project_sample_name"])
        self.s_con.save(s1)
        self.s_con.save(s2)
        sample_map = {'P001_101_index3': 'P001_101_index3', 'P001_102_index6':'P001_102'}
        self.app = self.make_app(argv = ['qc', 'update', '--sample_prj', projects[0], '--names', "{}".format(sample_map), '--debug', '--force'], extensions=['scilifelab.pm.ext.ext_qc',  'scilifelab.pm.ext.ext_couchdb'])
        self._run_app()
        s1 = self.s_con.get_entry("1_120924_AC003CCCXX_TGACCA")
        s2 = self.s_con.get_entry("2_120924_AC003CCCXX_ACAGTG")
        self.assertEqual(s1["project_sample_name"], "P001_101_index3")
        self.assertEqual(s2["project_sample_name"], "P001_102")