def test_parse_panel_info_lines():
    ## GIVEN a panel with some info
    panel_lines = [
        '##panel_id=panel1',
        '##institute=cust000',
        '##version=1.0',
        '##date=2016-12-09',
        '##display_name=Test panel',
        '#hgnc_id\thgnc_symbol',
        '7481\tMT-TF'
    ]
    ## WHEN parsing the information
    panel_info = get_panel_info(panel_lines)
    ## THEN assert that no information except a date is returned
    for key in panel_info:
        if key == 'panel_id':
            assert panel_info[key] == 'panel1'
        elif key == 'institute':
            assert panel_info[key] == 'cust000'
        elif key == 'version':
            assert panel_info[key] == '1.0'
        elif key == 'display_name':
            assert panel_info[key] == 'Test panel'
        elif key == 'date':
            assert type(panel_info[key]) is type(datetime.datetime.now())
Beispiel #2
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def test_parse_panel_info_lines():
    ## GIVEN a panel with some info
    panel_lines = [
        "##panel_id=panel1",
        "##institute=cust000",
        "##version=1.0",
        "##date=2016-12-09",
        "##display_name=Test panel",
        "#hgnc_id\thgnc_symbol",
        "7481\tMT-TF",
    ]
    ## WHEN parsing the information
    panel_info = get_panel_info(panel_lines)
    ## THEN assert that no information except a date is returned
    for key in panel_info:
        if key == "panel_id":
            assert panel_info[key] == "panel1"
        elif key == "institute":
            assert panel_info[key] == "cust000"
        elif key == "version":
            assert panel_info[key] == "1.0"
        elif key == "display_name":
            assert panel_info[key] == "Test panel"
        elif key == "date":
            assert type(panel_info[key]) is type(datetime.datetime.now())
Beispiel #3
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def test_parse_panel_info_no_info():
    ## GIVEN no information at all
    panel_lines = []
    ## WHEN parsing the information
    panel_info = get_panel_info(panel_lines)
    ## THEN assert that no information except a date is returned
    for key in panel_info:
        if key != "date":
            assert panel_info[key] is None
        else:
            assert type(panel_info[key]) is type(datetime.datetime.now())
def test_parse_panel_info_no_info():
    ## GIVEN no information at all
    panel_lines = []
    ## WHEN parsing the information
    panel_info = get_panel_info(panel_lines)
    ## THEN assert that no information except a date is returned
    for key in panel_info:
        if key != 'date':
            assert panel_info[key] == None
        else:
            assert type(panel_info[key]) is type(datetime.datetime.now())
Beispiel #5
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def test_parse_panel_file(panel_handle):
    ## GIVEN a panel with some info
    panel_lines = panel_handle
    ## WHEN parsing the information
    panel_info = get_panel_info(panel_lines)
    ## THEN assert that no information except a date is returned
    for key in panel_info:
        if key == "panel_id":
            assert panel_info[key] == "panel1"
        elif key == "institute":
            assert panel_info[key] == "cust000"
        elif key == "version":
            assert panel_info[key] == "1.0"
        elif key == "display_name":
            assert panel_info[key] == "Test panel"
        elif key == "date":
            assert type(panel_info[key]) is type(datetime.datetime.now())
def test_parse_panel_file(panel_handle):
    ## GIVEN a panel with some info
    panel_lines = panel_handle
    ## WHEN parsing the information
    panel_info = get_panel_info(panel_lines)
    ## THEN assert that no information except a date is returned
    for key in panel_info:
        if key == 'panel_id':
            assert panel_info[key] == 'panel1'
        elif key == 'institute':
            assert panel_info[key] == 'cust000'
        elif key == 'version':
            assert panel_info[key] == '1.0'
        elif key == 'display_name':
            assert panel_info[key] == 'Test panel'
        elif key == 'date':
            assert type(panel_info[key]) is type(datetime.datetime.now())
def test_parse_panel_file(panel_handle):
    ## GIVEN a panel with some info
    panel_lines = panel_handle
    ## WHEN parsing the information
    panel_info = get_panel_info(panel_lines)
    ## THEN assert that no information except a date is returned
    for key in panel_info:
        if key == 'panel_id':
            assert panel_info[key] == 'panel1'
        elif key == 'institute':
            assert panel_info[key] == 'cust000'
        elif key == 'version':
            assert panel_info[key] == '1.0'
        elif key == 'display_name':
            assert panel_info[key] == 'Test panel'
        elif key == 'date':
            assert type(panel_info[key]) is type(datetime.datetime.now())
def test_parse_panel_info_lines():
    ## GIVEN a panel with some info
    panel_lines = [
        '##panel_id=panel1', '##institute=cust000', '##version=1.0',
        '##date=2016-12-09', '##display_name=Test panel',
        '#hgnc_id\thgnc_symbol', '7481\tMT-TF'
    ]
    ## WHEN parsing the information
    panel_info = get_panel_info(panel_lines)
    ## THEN assert that no information except a date is returned
    for key in panel_info:
        if key == 'panel_id':
            assert panel_info[key] == 'panel1'
        elif key == 'institute':
            assert panel_info[key] == 'cust000'
        elif key == 'version':
            assert panel_info[key] == '1.0'
        elif key == 'display_name':
            assert panel_info[key] == 'Test panel'
        elif key == 'date':
            assert type(panel_info[key]) is type(datetime.datetime.now())
Beispiel #9
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def panel(context, date, display_name, version, panel_type, panel_id, path, institute, omim, api_key):
    """Add a gene panel to the database."""

    adapter = context.obj['adapter']
    if not path:
        if not omim:
            LOG.warning("Please provide a gene panel file or specify omim")
            context.abort()

    if omim:
        api_key = api_key or context.obj.get('omim_api_key')
        if not api_key:
            LOG.warning("Please provide a omim api key to load the omim gene panel")
            context.abort()
        #Check if OMIM-AUTO exists
        if adapter.gene_panel(panel_id='OMIM-AUTO'):
            LOG.warning("OMIM-AUTO already exists in database")
            LOG.info("To create a new version use scout update omim")
            return

        try:
            adapter.load_omim_panel(api_key, version=1.0)
        except Exception as err:
            LOG.error(err)
            context.abort()

        return

    panel_lines = get_file_handle(path)

    try:
        panel_info = get_panel_info(
            panel_lines=panel_lines,
            panel_id=panel_id,
            institute=institute,
            version=version,
            date=date,
            display_name=display_name
            )
    except Exception as err:
        LOG.warning(err)
        context.abort()

    version = None
    if panel_info.get('version'):
        version = float(panel_info['version'])

    panel_id = panel_info['panel_id']
    display_name = panel_info['display_name'] or panel_id
    institute = panel_info['institute']
    date = panel_info['date']

    if not institute:
        LOG.warning("A Panel has to belong to a institute")
        context.abort()

    #Check if institute exists in database
    if not adapter.institute(institute):
        LOG.warning("Institute {0} does not exist in database".format(institute))
        context.abort()

    if not panel_id:
        LOG.warning("A Panel has to have a panel id")
        context.abort()
    
    if version:
        existing_panel = adapter.gene_panel(panel_id, version)
    else:
        existing_panel = adapter.gene_panel(panel_id)
        ## Assuming version 1.0
        version = 1.0

    if existing_panel:
        LOG.info("found existing panel")
        if version == existing_panel['version']:
            LOG.warning("Panel with same version exists in database")
            LOG.info("Reload with updated version")
            context.abort()
        display_name = display_name or existing_panel['display_name']
        institute = institute or existing_panel['institute']

    try:
        adapter.load_panel(
            path=path, 
            institute=institute, 
            panel_id=panel_id, 
            date=date, 
            panel_type=panel_type, 
            version=version, 
            display_name=display_name
        )
    except Exception as err:
        LOG.warning(err)
        context.abort()
Beispiel #10
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def load_panel(
    panel_path,
    adapter,
    date=None,
    display_name=None,
    version=None,
    panel_type=None,
    panel_id=None,
    institute=None,
):
    """Load a manually curated gene panel into scout

    Args:
        panel_path(str): path to gene panel file
        adapter(scout.adapter.MongoAdapter)
        date(str): date of gene panel on format 2017-12-24
        display_name(str)
        version(float)
        panel_type(str)
        panel_id(str)
        institute(str)

    """
    panel_lines = get_file_handle(panel_path)

    try:
        # This will parse panel metadata if includeed in panel file
        panel_info = get_panel_info(
            panel_lines=panel_lines,
            panel_id=panel_id,
            institute=institute,
            version=version,
            date=date,
            display_name=display_name,
        )
    except Exception as err:
        raise err

    version = None
    if panel_info.get("version"):
        version = float(panel_info["version"])

    panel_id = panel_info["panel_id"]
    display_name = panel_info["display_name"] or panel_id
    institute = panel_info["institute"]
    date = panel_info["date"]

    if not institute:
        raise SyntaxError("A Panel has to belong to a institute")

    # Check if institute exists in database
    if not adapter.institute(institute):
        raise SyntaxError("Institute {0} does not exist in database".format(institute))

    if not panel_id:
        raise SyntaxError("A Panel has to have a panel id")

    if version:
        existing_panel = adapter.gene_panel(panel_id, version)
    else:
        ## Assuming version 1.0
        existing_panel = adapter.gene_panel(panel_id)
        version = 1.0
        LOG.info("Set version to %s", version)

    if existing_panel:
        LOG.info("found existing panel")
        if version == existing_panel["version"]:
            LOG.warning("Panel with same version exists in database")
            LOG.info("Reload with updated version")
            raise SyntaxError()
        display_name = display_name or existing_panel["display_name"]
        institute = institute or existing_panel["institute"]

    parsed_panel = parse_gene_panel(
        path=panel_path,
        institute=institute,
        panel_type=panel_type,
        date=date,
        version=version,
        panel_id=panel_id,
        display_name=display_name,
    )

    try:
        adapter.load_panel(parsed_panel=parsed_panel)
    except Exception as err:
        raise err
Beispiel #11
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def panel(context, date, display_name, version, panel_type, panel_id, path,
          institute):
    """Add a gene panel to the database."""
    adapter = context.obj['adapter']
    panel_lines = get_file_handle(path)

    try:
        panel_info = get_panel_info(panel_lines=panel_lines,
                                    panel_id=panel_id,
                                    institute=institute,
                                    version=version,
                                    date=date,
                                    display_name=display_name)
    except Exception as err:
        LOG.warning(err)
        context.abort()

    version = None
    if panel_info.get('version'):
        version = float(panel_info['version'])

    panel_id = panel_info['panel_id']
    display_name = panel_info['display_name'] or panel_id
    institute = panel_info['institute']
    date = panel_info['date']

    if not institute:
        LOG.warning("A Panel has to belong to a institute")
        context.abort()

    if not panel_id:
        LOG.warning("A Panel has to have a panel id")
        context.abort()

    if version:
        existing_panel = adapter.gene_panel(panel_id, version)
    else:
        existing_panel = adapter.gene_panel(panel_id)
        ## Assuming version 1.0
        version = 1.0

    if existing_panel:
        LOG.info("found existing panel")
        if version == existing_panel['version']:
            LOG.warning("Panel with same version exists in database")
            LOG.info("Reload with updated version")
            context.abort()
        display_name = display_name or existing_panel['display_name']
        institute = institute or existing_panel['institute']

    try:
        adapter.load_panel(path=path,
                           institute=institute,
                           panel_id=panel_id,
                           date=date,
                           panel_type=panel_type,
                           version=version,
                           display_name=display_name)
    except Exception as err:
        LOG.warning(err)
        context.abort()