Python CharonSession.project_create方法代码示例

# 需要导入模块: from ngi_pipeline.database.classes import CharonSession [as 别名]
# 或者: from ngi_pipeline.database.classes.CharonSession import project_create [as 别名]
    def test_workflows(self):
        config_file_path = locate_ngi_config()
        config = load_yaml_config(config_file_path)

        for workflow_name, workflow_dict in config.get("test_data", {}).get("workflows", {}).iteritems():
            # Load and rewrite config file as needed
            customize_config_dict = workflow_dict.get("customize_config")
            if customize_config_dict:
                config = update_dict(config, customize_config_dict)

            #self._install_test_files(workflow_dict)
            LOG.info('Starting test analysis pipeline for workflow "{}"'.format(workflow_name))
            try:
                local_files = workflow_dict["local_files"]
            except KeyError:
                raise ValueError("Required paths to input files for testing do not"
                                 "exist in config file (test_data.workflows."
                                 "{}.local_files); cannot proceed.".format(workflow_name))
            try:
                flowcell_path = local_files["flowcell"]
            except KeyError:
                raise ValueError("Path to flowcell is required and not specified "
                                 "in configuration file (test_data.workflows."
                                 "{}.local_files.flowcell); cannot proceed.".format(workflow_name))
            try:
                test_project = workflow_dict["test_project"]
                test_proj_id = test_project["project_id"]
                test_proj_name = test_project["project_name"]
                test_proj_bpa = test_project["bpa"]
            except KeyError as e:
                raise ValueError("Test project information is missing from config "
                                 "file (under test_data.workflows.{}.test_project "
                                 "({}); cannot proceed.".format(workflow_name, e.msg))
            charon_session = CharonSession(config=config)
            try:
                charon_session.project_delete(projectid=test_proj_id)
            except CharonError:
                pass
            charon_session.project_create(projectid=test_proj_id, name=test_proj_name,
                                          status="OPEN", best_practice_analysis=test_proj_bpa)

            process_demultiplexed_flowcells([flowcell_path], fallback_libprep="A",
                                            config=config)

# 需要导入模块: from ngi_pipeline.database.classes import CharonSession [as 别名]
# 或者: from ngi_pipeline.database.classes.CharonSession import project_create [as 别名]
def create_charon_entries_from_project(project, best_practice_analysis="whole_genome_reseq",
                                       sequencing_facility="NGI-S",
                                       force_overwrite=False, delete_existing=False,
                                       retry_on_fail=True):
    """Given a project object, creates the relevant entries in Charon.
    This code is remarkably shoddy as I created it in a hurry and then later
    it became a part of the pipeline. Use at your own risk! Ha ha.

    :param NGIProject project: The NGIProject object
    :param str best_practice_analysis: The workflow to assign for this project (default "variant_calling")
    :param str sequencing_facility: The facility that did the sequencing
    :param bool force_overwrite: If this is set to true, overwrite existing entries in Charon (default false)
    :param bool delete_existing: Don't just update existing entries, delete them and create new ones (default false)
    """
    charon_session = CharonSession()
    update_failed=False
    try:
        status = "OPEN"
        LOG.info('Creating project "{}" with status "{}", best practice analysis "{}", '
                 'and sequencing_facility {}'.format(project, status,
                                                     best_practice_analysis,
                                                     sequencing_facility))
        charon_session.project_create(projectid=project.project_id,
                                      name=project.name,
                                      status=status,
                                      best_practice_analysis=best_practice_analysis,
                                      sequencing_facility=sequencing_facility)
        LOG.info('Project "{}" created in Charon.'.format(project))
    except CharonError as e:
        if e.status_code == 400:
            if force_overwrite:
                LOG.warn('Overwriting data for project "{}"'.format(project))
                charon_session.project_update(projectid=project.project_id,
                                              name=project.name,
                                              status=status,
                                              best_practice_analysis=best_practice_analysis,
                                              sequencing_facility=sequencing_facility)
                LOG.info('Project "{}" updated in Charon.'.format(project))
            else:
                LOG.info('Project "{}" already exists; moving to samples...'.format(project))
        else:
            raise
    for sample in project:
        if delete_existing:
            LOG.warn('Deleting existing sample "{}"'.format(sample))
            try:
                charon_session.sample_delete(projectid=project.project_id,
                                             sampleid=sample.name)
            except CharonError as e:
                update_failed=True
                LOG.error('Could not delete sample "{}": {}'.format(sample, e))
        try:
            analysis_status = "TO_ANALYZE"
            LOG.info('Creating sample "{}" with analysis_status "{}"'.format(sample, analysis_status))
            charon_session.sample_create(projectid=project.project_id,
                                         sampleid=sample.name,
                                         analysis_status=analysis_status)
            LOG.info('Project/sample "{}/{}" created in Charon.'.format(project, sample))
        except CharonError as e:
            if e.status_code == 400:
                if force_overwrite:
                    LOG.warn('Overwriting data for project "{}" / '
                             'sample "{}"'.format(project, sample))
                    charon_session.sample_update(projectid=project.project_id,
                                                 sampleid=sample.name,
                                                 analysis_status=analysis_status)
                    LOG.info('Project/sample "{}/{}" updated in Charon.'.format(project, sample))
                else:
                    LOG.info('Project "{}" / sample "{}" already exists; moving '
                             'to libpreps'.format(project, sample))
            else:
                update_failed=True
                LOG.error(e)
                continue
        for libprep in sample:
            if delete_existing:
                LOG.warn('Deleting existing libprep "{}"'.format(libprep))
                try:
                    charon_session.libprep_delete(projectid=project.project_id,
                                                  sampleid=sample.name,
                                                  libprepid=libprep.name)
                except CharonError as e:
                    LOG.warn('Could not delete libprep "{}": {}'.format(libprep, e))
            try:
                qc = "PASSED"
                LOG.info('Creating libprep "{}" with qc status "{}"'.format(libprep, qc))
                charon_session.libprep_create(projectid=project.project_id,
                                              sampleid=sample.name,
                                              libprepid=libprep.name,
                                              qc=qc)
                LOG.info(('Project/sample/libprep "{}/{}/{}" created in '
                          'Charon').format(project, sample, libprep))
            except CharonError as e:
                if e.status_code == 400:
                    if force_overwrite:
                        LOG.warn('Overwriting data for project "{}" / '
                                 'sample "{}" / libprep "{}"'.format(project, sample,
                                                                     libprep))
                        charon_session.libprep_update(projectid=project.project_id,
                                                      sampleid=sample.name,
#.........这里部分代码省略.........

# 需要导入模块: from ngi_pipeline.database.classes import CharonSession [as 别名]
# 或者: from ngi_pipeline.database.classes.CharonSession import project_create [as 别名]
def create_charon_entries_from_project(project, workflow="NGI", force_overwrite=False):
    """Given a project object, creates the relevant entries
    in Charon.

    :param NGIProject project: The NGIProject object
    :param str workflow: The workflow to assign for this project (default NGI)
    :param bool force_overwrite: If this is set to true, overwrite existing entries in Charon (default false)
    """
    charon_session = CharonSession()
    try:
        status="SEQUENCED"
        LOG.info('Creating project "{}" with status "{}" and workflow "{}"'.format(project, status, workflow))
        charon_session.project_create(projectid=project.project_id,
                                      name=project.name,
                                      status=status,
                                      pipeline=workflow)
    except CharonError:
        if force_overwrite:
            LOG.warn('Overwriting data for project "{}"'.format(project))
            charon_session.project_update(projectid=project.project_id,
                                          name=project.name,
                                          status=status,
                                          pipeline=workflow)
        else:
            LOG.info('Project "{}" already exists; moving to samples...'.format(project))

    for sample in project:
        try:
            LOG.info('Creating sample "{}"'.format(sample))
            charon_session.sample_create(projectid=project.project_id,
                                         sampleid=sample.name,
                                         status="NEW")
        except CharonError:
            if force_overwrite:
                LOG.warn('Overwriting data for project "{}" / '
                         'sample "{}"'.format(project, sample))
                charon_session.sample_update(projectid=project.project_id,
                                             sampleid=sample.name,
                                             status="NEW")
            else:
                LOG.info('Project "{}" / sample "{}" already exists; moving '
                         'to libpreps'.format(project, sample))

        for libprep in sample:
            try:
                LOG.info('Creating libprep "{}"'.format(libprep))
                charon_session.libprep_create(projectid=project.project_id,
                                              sampleid=sample.name,
                                              libprepid=libprep.name,
                                              status="NEW")
            except CharonError:
                if force_overwrite:
                    LOG.warn('Overwriting data for project "{}" / '
                             'sample "{}" / libprep "{}"'.format(project, sample,
                                                                 libprep))
                    charon_session.libprep_update(projectid=project.project_id,
                                                  sampleid=sample.name,
                                                  libprepid=libprep.name,
                                                  status="NEW")
                else:
                    LOG.info('Project "{}" / sample "{}" / libprep "{}" already '
                             'exists; moving to libpreps'.format(project, sample, libprep))

            for seqrun in libprep:
                try:
                    LOG.info('Creating seqrun "{}"'.format(seqrun))
                    charon_session.seqrun_create(projectid=project.project_id,
                                                 sampleid=sample.name,
                                                 libprepid=libprep.name,
                                                 seqrunid=seqrun.name,
                                                 total_reads=0,
                                                 mean_autosomal_coverage=0,
                                                 sequencing_status="DONE",
                                                 alignment_status="NEW")
                except CharonError as e:
                    if force_overwrite:
                        LOG.warn('Overwriting data for project "{}" / '
                                 'sample "{}" / libprep "{}" / '
                                 'seqrun "{}"'.format(project, sample,
                                                      libprep, seqrun))
                        charon_session.seqrun_update(projectid=project.project_id,
                                                     sampleid=sample.name,
                                                     libprepid=libprep.name,
                                                     seqrunid=seqrun.name,
                                                     status="NEW")
                    else:
                        LOG.info('Project "{}" / sample "{}" / libprep "{}" / '
                                 'seqrun "{}" already exists; next...'.format(project, sample,
                                                                              libprep, seqrun))