Example #1
0
    def post(self, request, *args, **kwargs):

        from_old_template = False

        if 'isa_tab_url' in request.POST:
            # TODO: I think isa_tab_url is already a full url,
            # making this redundant.
            full_isa_tab_url = get_full_url(request.POST['isa_tab_url'])
            from_old_template = True
        else:
            request_body = request.body
            if not request_body:
                err_msg = "Neither form data nor a request body has been sent."
                logger.error(err_msg)
                return HttpResponseBadRequest(err_msg)

            try:
                body = json.loads(request_body)
            except Exception as e:
                err_msg = "Request body is no valid JSON"
                logger.error("%s: %s" % (err_msg, e))
                return HttpResponseBadRequest("%s." % err_msg)

            if "data_set_uuid" in body:
                data_set_uuid = body["data_set_uuid"]
            else:
                err_msg = "Request body doesn't contain data_set_uuid."
                logger.error(err_msg)
                return HttpResponseBadRequest(err_msg)

            try:
                full_isa_tab_url = DataSet.objects.get(
                    uuid=data_set_uuid).get_isa_archive().get_datafile_url()
            except (DataSet.DoesNotExist, DataSet.MultipleObjectsReturned,
                    Exception) as e:
                err_msg = "Something went wrong"
                logger.error("%s: %s" % (err_msg, e))
                return HttpResponseBadRequest("%s." % err_msg)

        if from_old_template:
            # Redirect to process_isa_tab view
            response = HttpResponseRedirect(
                get_full_url(reverse('process_isa_tab')))
        else:
            # Redirect to process_isa_tab view with arg 'ajax' if request is
            #  not coming from old Django Template
            response = HttpResponseRedirect(
                get_full_url(reverse('process_isa_tab', args=['ajax'])))

        # set cookie
        response.set_cookie('isa_tab_url', full_isa_tab_url)

        return response
Example #2
0
    def post(self, request, *args, **kwargs):

        from_old_template = False

        if 'isa_tab_url' in request.POST:
            full_isa_tab_url = get_full_url(request.POST['isa_tab_url'])
            from_old_template = True
        else:
            request_body = request.body
            if not request_body:
                err_msg = "Neither form data nor a request body has been sent."
                logger.error(err_msg)
                return HttpResponseBadRequest(err_msg)

            try:
                body = json.loads(request_body)
            except Exception as e:
                err_msg = "Request body is no valid JSON"
                logger.error("%s: %s" % (err_msg, e))
                return HttpResponseBadRequest("%s." % err_msg)

            if "data_set_uuid" in body:
                data_set_uuid = body["data_set_uuid"]
            else:
                err_msg = "Request body doesn't contain data_set_uuid."
                logger.error(err_msg)
                return HttpResponseBadRequest(err_msg)

            try:
                full_isa_tab_url = get_full_url(DataSet.objects.get(
                    uuid=data_set_uuid).get_isa_archive().get_datafile_url())
            except (DataSet.DoesNotExist, DataSet.MultipleObjectsReturned,
                    Exception) as e:
                err_msg = "Something went wrong"
                logger.error("%s: %s" % (err_msg, e))
                return HttpResponseBadRequest("%s." % err_msg)

        if from_old_template:
            # Redirect to process_isa_tab view
            response = HttpResponseRedirect(
                reverse('process_isa_tab')
            )
        else:
            # Redirect to process_isa_tab view with arg 'ajax' if request is
            #  not coming from old Django Template
            response = HttpResponseRedirect(
                reverse('process_isa_tab', args=['ajax'])
            )

        # set cookie
        response.set_cookie('isa_tab_url', full_isa_tab_url)

        return response
Example #3
0
def get_file_name(nodeuuid, sampFile=None, is_file_uuid=False):
    """Helper function for getting a file_name from a filestore uuid
    :param fileuuid: Filestore uuid
    :type fileuuid: String
    """
    # if uuid is a file_store uuid (associated w/ analysis results)
    if is_file_uuid:
        temp_fs = FileStoreItem.objects.get(uuid=nodeuuid)
    else:
        # getting the current file_uuid from the given node_uuid
        curr_file_uuid = Node.objects.get(uuid=nodeuuid).file_uuid
        # checking to see if it has a file_server item
        temp_fs = get_aux_file_item(curr_file_uuid)

    # If no associated file_server auxiliary file then use main data file for
    # IGV
    if temp_fs is None:
        # getting file information based on file_uuids
        temp_fs = FileStoreItem.objects.get(uuid=curr_file_uuid)

    temp_name = temp_fs.datafile.name.split('/')
    temp_name = temp_name[len(temp_name) - 1]

    # full path to selected UUID File
    temp_url = get_full_url(temp_fs.get_datafile_url())

    # IGV SEG FILE HACK
    if sampFile:
        if temp_name.startswith("metaData"):
            new_name = temp_name.split("_")
            if len(new_name) > 1:
                temp_name = new_name[0]

    return temp_name, temp_url
Example #4
0
def addIGVSamples(fields, results_samp, annot_samples=None):
    """creates phenotype file for IGV
    :param samples: Solr results for samples to be included
    :type samples: Array.
    :param annot_samples: includes annotation files included with solr results
    :type annot_samples: Array
    """
    # creates human readable indexes of fields to iterate over
    fields_dict = {}
    for i in fields:
        find_index = i.find("_Characteristics_")
        if find_index > -1:
            new_key = i.split("_Characteristics_")[0]
            fields_dict[i] = new_key

    # Creating temp file to enter into file_store
    tempsampname = tempfile.NamedTemporaryFile(delete=False)

    # writing header to sample file
    tempsampname.write("#sampleTable" + "\n")

    # writing column names to sample file
    col_names = "Linking_id"
    for k, v in fields_dict.iteritems():
        col_names = col_names + '\t' + v
    tempsampname.write(col_names + "\n")

    # iterating over sample files
    pheno_results = get_sample_lines(fields_dict, results_samp)
    tempsampname.write(pheno_results)

    # if annotations are not null
    if annot_samples:
        pheno_annot = get_sample_lines(fields_dict, annot_samples)
        tempsampname.write(pheno_annot)

    # closing temp file
    tempsampname.close()

    # getting file_store_uuid
    filestore_uuid = create(tempsampname.name, permanent=True, filetype="txt")
    filestore_item = import_file(filestore_uuid, permanent=True, refresh=True)

    # file to rename
    temp_file = filestore_item.datafile.name.split('/')
    temp_file = temp_file[len(temp_file) - 1] + '.txt'

    # rename file by way of file_store
    filestore_item = rename(filestore_uuid, temp_file)

    # getting file information based on file_uuids
    curr_fs = FileStoreItem.objects.get(uuid=filestore_uuid)

    # full path to selected UUID File
    curr_url = get_full_url(curr_fs.get_datafile_url())

    # delete temp file
    os.unlink(tempsampname.name)

    return curr_url
Example #5
0
 def test_get_full_url_remote_file(self):
     """Check if the source URL is returned for files that have not been
     imported
     """
     # create FileStoreItem instances without any disk operations
     item_from_url = FileStoreItem.objects.create(source=self.url_source,
                                                  sharename=self.sharename)
     self.assertEqual(get_full_url(item_from_url.get_datafile_url()),
                      item_from_url.source)
Example #6
0
 def test_get_full_url_remote_file(self):
     """Check if the source URL is returned for files that have not been
     imported
     """
     # create FileStoreItem instances without any disk operations
     item_from_url = FileStoreItem.objects.create(source=self.url_source,
                                                  sharename=self.sharename)
     self.assertEqual(get_full_url(item_from_url.get_datafile_url()),
                      item_from_url.source)
def logout(request):
    token = request.session.get('webinar_access_token')
    if token is not None:
        requests.post(get_full_url(request, 'revoke-token'),
                      data={
                          'token': token,
                      })
        request.session.pop('webinar_access_token', None)
    return redirect('index')
Example #8
0
    def test_get_full_url_local_file(self):
        """Check if the full URL is properly returned for files that exist
        in Refinery
        """
        # create FileStoreItem instances without any disk operations
        local_file = FileStoreItem.objects.create(datafile=SimpleUploadedFile(
            self.filename, 'Coffee is delicious!'),
                                                  source=self.path_source,
                                                  sharename=self.sharename)

        self.assertEqual(
            get_full_url(local_file.get_datafile_url()),
            '{}://{}{}'.format(settings.REFINERY_URL_SCHEME,
                               Site.objects.get_current().domain,
                               local_file.datafile.url))
Example #9
0
    def post(self, request, *args, **kwargs):
        serializer_class = self.get_serializer_class()
        serializer = serializer_class(data=request.data,
                                      context={'request': request})
        serializer.is_valid(raise_exception=True)
        shortcut = serializer.validated_data['shortcut']
        full_url = get_full_url(shortcut)

        if full_url:
            return JsonResponse({
                'status': 'ok',
                'full_url': full_url
            },
                                status=status.HTTP_200_OK)
        return HttpResponseBadRequest()
def index(request):
    # create callback url
    callback_url = get_full_url(request, 'callback')
    # get access token from session
    token = request.session.get('webinar_access_token')
    context = {
        'registered':
        bool(token is not None),
        'auth_url':
        (f'{settings.OAUTH_SERVER_URL}/o/authorize?response_type=code'
         f'&client_id={settings.CLIENT_ID}&redirect_uri={callback_url}'),
        'form':
        ResourceForm()
    }
    return render(request, 'front/index.html', context)
def token(request):
    """
    Gets token with auth code. Input should be in the format:
    {"code": "code"}
    """
    redir_url = get_full_url(request, 'callback')
    resp = requests.post(
        f'{OAUTH_SERVER_URL}/o/token/',
        data={
            'grant_type': 'authorization_code',
            'redirect_uri': redir_url,
            'code': request.data['code'],
            'client_id': CLIENT_ID,
            'client_secret': CLIENT_SECRET,
        },
    )
    return Response(resp.json())
def callback(request):
    # clear stored auth code
    request.session.pop('webinar_auth_code', None)
    # get auth code sent from Authorization server
    code = request.GET.get('code')
    if code is not None:
        # save it in the session
        request.session['webinar_auth_code'] = code
        resp = requests.post(get_full_url(request, 'get-token'),
                             data={
                                 'code': code,
                             })
        resp_data = resp.json()
        if 'access_token' in resp_data:
            # delete auth code, as it is no longer needed
            request.session.pop('webinar_auth_code', None)
            request.session['webinar_access_token'] = resp_data['access_token']
    return redirect('index')
Example #13
0
def _import_analysis_in_galaxy(ret_list, library_id, connection):
    """Take workflow configuration and import files into galaxy
    assign galaxy_ids to ret_list

    """
    logger.debug("Uploading analysis input files to Galaxy")
    for fileset in ret_list:
        for k, v in fileset.iteritems():

            cur_item = fileset[k]

            # getting the current file_uuid from the given node_uuid
            try:
                curr_file_uuid = Node.objects.get(
                    uuid=cur_item['node_uuid']).file_uuid
            except Node.DoesNotExist:
                logger.error("Couldn't fetch Node")
                return None

            try:
                current_filestore_item = FileStoreItem.objects.get_item(
                    uuid=curr_file_uuid)
            except FileStoreItem.DoesNotExist:
                logger.error("Couldn't fetch FileStoreItem")
                return None

            # Create url based on filestore_item's location (local file or
            # external file)
            file_url = get_full_url(current_filestore_item.get_datafile_url())

            try:
                file_id = connection.libraries.upload_file_from_url(
                    library_id, file_url)[0]['id']
            except (galaxy.client.ConnectionError, IOError) as exc:
                logger.error(
                    "Failed adding file '%s' to Galaxy "
                    "library '%s': %s", curr_file_uuid, library_id, exc)
                raise

            cur_item["id"] = file_id

    return ret_list
Example #14
0
def import_analysis_in_galaxy(ret_list, library_id, connection):
    """Take workflow configuration and import files into galaxy
    assign galaxy_ids to ret_list

    """
    logger.debug("Uploading analysis input files to Galaxy")
    for fileset in ret_list:
        for k, v in fileset.iteritems():

            cur_item = fileset[k]

            # getting the current file_uuid from the given node_uuid
            try:
                curr_file_uuid = Node.objects.get(
                    uuid=cur_item['node_uuid']).file_uuid
            except Node.DoesNotExist:
                logger.error("Couldn't fetch Node!")
                return None

            try:
                current_filestore_item = FileStoreItem.objects.get_item(
                    uuid=curr_file_uuid)
            except FileStoreItem.DoesNotExist:
                logger.error("Couldn't fetch FileStoreItem!")
                return None

            # Create url based on filestore_item's location (local file or
            # external file)
            file_url = get_full_url(current_filestore_item.get_datafile_url())

            try:
                file_id = connection.libraries.upload_file_from_url(
                        library_id, file_url)[0]['id']
            except (galaxy.client.ConnectionError, IOError) as exc:
                logger.error("Failed adding file '%s' to Galaxy "
                             "library '%s': %s",
                             curr_file_uuid, library_id, exc)
                raise

            cur_item["id"] = file_id

    return ret_list
Example #15
0
    def test_get_full_url_local_file(self):
        """Check if the full URL is properly returned for files that exist
        in Refinery
        """
        # create FileStoreItem instances without any disk operations
        local_file = FileStoreItem.objects.create(source=self.path_source,
                                                  sharename=self.sharename)

        local_file.datafile = self.test_file

        local_file.save()

        self.assertEqual(
            get_full_url(local_file.get_datafile_url()),
            '{}://{}{}'.format(
                            settings.REFINERY_URL_SCHEME,
                            Site.objects.get_current().domain,
                            local_file.datafile.url
                         )
        )
Example #16
0
def create_temp_filename_and_url(temp_fs, samp_file):
    """Helper function for creating a temporary filename and file url from a
    given FileStore Item and sample file
    :param temp_fs: Filestore uuid
    :type temp_fs: FileStoreItem
    :param samp_file: T/F value for # IGV SEG FILE HACK
    :type samp_file: Bool
    :returns: temp_name, temp_url
    """
    temp_name = temp_fs.datafile.name.split('/')
    temp_name = temp_name[len(temp_name) - 1]

    # full path to selected UUID File
    temp_url = get_full_url(temp_fs.get_datafile_url())

    # IGV SEG FILE HACK
    if samp_file:
        if temp_name.startswith("metaData"):
            new_name = temp_name.split("_")
            if len(new_name) > 1:
                temp_name = new_name[0]

    return temp_name, temp_url
Example #17
0
def create_temp_filename_and_url(temp_fs, samp_file):
    """Helper function for creating a temporary filename and file url from a
    given FileStore Item and sample file
    :param temp_fs: Filestore uuid
    :type temp_fs: FileStoreItem
    :param samp_file: T/F value for # IGV SEG FILE HACK
    :type samp_file: Bool
    :returns: temp_name, temp_url
    """
    temp_name = temp_fs.datafile.name.split("/")
    temp_name = temp_name[len(temp_name) - 1]

    # full path to selected UUID File
    temp_url = get_full_url(temp_fs.get_datafile_url())

    # IGV SEG FILE HACK
    if samp_file:
        if temp_name.startswith("metaData"):
            new_name = temp_name.split("_")
            if len(new_name) > 1:
                temp_name = new_name[0]

    return temp_name, temp_url
Example #18
0
 def get(self, request, shortcut):
     full_url = get_full_url(shortcut)
     if full_url:
         return HttpResponseRedirect(full_url)
     return HttpResponseBadRequest()
Example #19
0
def create_igv_session(genome, uuids, is_file_uuid=False):
    """ Creates session file for selected file uuids, returns newly created
    filestore uuid
    :param is_file_uuid:
    :param genome: Genome to be used in session file i.e. hg18, dm3
    :type genome: string.
    :param uuids: Array of UUIDs to be used
    :type uuids: array.
    :param uuids: Host URL i.e. 127.0.0.1:8000
    :type uuids: string
    """
    # Create IGV Session file and put into Filestore
    """
    http://www.postneo.com/projects/pyxml/

    <?xml version="1.0" encoding="UTF-8"?>
        <Global genome="hg18" locus="EGFR" version="3">
        <Resources>
            <Resource name="RNA Genes"
            path="http://www.broadinstitute.org/igvdata/tcga/gbm/GBM_batch1-8_level3_exp.txt.recentered.080820.gct.tdf"/>
            <Resource name="RNA Genes"
            path="http://www.broadinstitute.org/igvdata/annotations/hg18/rna_genes.bed"/>
            <Resource name="sno/miRNA"
            path="http://www.broadinstitute.org/igvdata/tcga/gbm/Sample_info.txt"/>
        </Resources>
    </Global>
    """
    logger.debug("visualization_manager.create_igv_session called")

    # Create the minidom document
    doc = Document()
    # Create the <wml> base element
    xml = doc.createElement("Global")
    xml.setAttribute("genome", genome)
    xml.setAttribute("locus", "All")
    xml.setAttribute("version", "4")
    doc.appendChild(xml)
    # Add Resources
    xml_resources = doc.createElement("Resources")
    xml.appendChild(xml_resources)
    # get paths to url
    for samp in uuids:
        # gets filestore item
        curr_name, curr_url = get_file_name(samp, is_file_uuid=is_file_uuid)

        logger.debug('New resource: ' + curr_name + ' - ' + curr_url)

        # What to do if fs does not exist?
        if curr_name:
            # creates Resource element
            res = doc.createElement("Resource")
            res.setAttribute("name", curr_name)
            res.setAttribute("path", curr_url)
            xml_resources.appendChild(res)
    # Creating temp file to enter into file_store
    tempfilename = tempfile.NamedTemporaryFile(delete=False)
    tempfilename.write(doc.toprettyxml(indent="  "))
    tempfilename.close()
    # getting file_store_uuid
    filestore_uuid = create(tempfilename.name, filetype="xml")
    filestore_item = import_file(filestore_uuid, refresh=True)
    # file to rename
    temp_name = filestore_item.datafile.name.split('/')
    temp_name = temp_name[len(temp_name) - 1] + '.xml'
    # rename file by way of file_store
    filestore_item = rename(filestore_uuid, temp_name)
    # delete temp file
    os.unlink(tempfilename.name)
    # Url for session file
    fs_url = get_full_url(filestore_item.get_datafile_url())
    # IGV url for automatic launch of Java Webstart
    igv_url = "http://www.broadinstitute.org/igv/projects/current/igv.php" \
              "?sessionURL=" + fs_url
    return igv_url
Example #20
0
def add_igv_samples(fields, results_samp, annot_samples=None):
    """creates phenotype file for IGV
    :param samples: Solr results for samples to be included
    :type samples: Array.
    :param annot_samples: includes annotation files included with solr results
    :type annot_samples: Array
    """
    # creates human readable indexes of fields to iterate over
    fields_dict = {}
    for i in fields:
        find_index = i.find("_Characteristics_")
        if find_index > -1:
            new_key = i.split("_Characteristics_")[0]
            fields_dict[i] = new_key

    # Creating temp file to enter into file_store
    temp_sample_name = tempfile.NamedTemporaryFile(delete=False)

    # writing header to sample file
    temp_sample_name.write("#sampleTable" + "\n")

    # writing column names to sample file
    col_names = "Linking_id"
    for k, v in fields_dict.iteritems():
        col_names = col_names + '\t' + v
    temp_sample_name.write(col_names + "\n")

    # iterating over sample files
    pheno_results = get_sample_lines(fields_dict, results_samp)
    try:
        temp_sample_name.write(pheno_results)
    except UnicodeEncodeError as e:
        logger.error("Could not write results to file: %s. "
                     "Trying again with the content to write encoded "
                     "properly." % e)
        temp_sample_name.write(pheno_results.encode("utf-8"))

    # if annotations are not null
    if annot_samples:
        pheno_annot = get_sample_lines(fields_dict, annot_samples)
        temp_sample_name.write(pheno_annot)

    # closing temp file
    temp_sample_name.close()

    # getting file_store_uuid
    filestore_uuid = create(temp_sample_name.name, filetype="txt")
    filestore_item = import_file(filestore_uuid, refresh=True)

    # file to rename
    temp_file = filestore_item.datafile.name.split('/')
    temp_file = temp_file[len(temp_file) - 1] + '.txt'

    # rename file by way of file_store
    filestore_item = rename(filestore_uuid, temp_file)

    # getting file information based on file_uuids
    curr_fs = FileStoreItem.objects.get(uuid=filestore_uuid)

    # full path to selected UUID File
    curr_url = get_full_url(curr_fs.get_datafile_url())

    # delete temp file
    os.unlink(temp_sample_name.name)

    return curr_url
Example #21
0
def createIGVsessionAnnot(genome, uuids, annot_uuids=None, samp_file=None):
    """Creates session file for selected file uuids, returns newly created
    filestore uuid
    :param genome: Genome to be used in session file i.e. hg18, dm3
    :type genome: string.
    :param uuids: Array of UUIDs to be used
    :type uuids: array.
    :param uuids: Host URL i.e. 127.0.0.1:8000
    :type uuids: string
    """
    # Create IGV Session file and put into Filestore
    """
    http://www.postneo.com/projects/pyxml/

    <?xml version="1.0" encoding="UTF-8"?>
        <Global genome="hg18" locus="EGFR" version="3">
        <Resources>
            <Resource name="RNA Genes"
            path="http://www.broadinstitute.org/igvdata/tcga/gbm/GBM_batch1-8_level3_exp.txt.recentered.080820.gct.tdf"/>
            <Resource name="RNA Genes"
            path="http://www.broadinstitute.org/igvdata/annotations/hg18/rna_genes.bed"/>
            <Resource name="sno/miRNA"
            path="http://www.broadinstitute.org/igvdata/tcga/gbm/Sample_info.txt"/>
        </Resources>
    </Global>
    """
    # Create the minidom document
    doc = Document()
    # Create the <wml> base element
    xml = doc.createElement("Global")
    xml.setAttribute("genome", genome)
    xml.setAttribute("locus", "All")
    xml.setAttribute("version", "4")
    doc.appendChild(xml)
    # Add Resources
    xml_resources = doc.createElement("Resources")
    xml.appendChild(xml_resources)
    # adding selected samples to xml file
    addIGVResource(uuids["node_uuid"], xml_resources, doc)
    if annot_uuids:
        # adding selected samples to xml file
        addIGVResource(annot_uuids["node_uuid"], xml_resources, doc)
    # adds sample information file to IGV session file
    if samp_file:
        # <Resource name="Sample Information"
        # path="http://igv.broadinstitute.org/data/hg18/tcga/gbm/gbmsubtypes/sampleTable.txt.gz"/>
        # creates Resource element
        res = doc.createElement("Resource")
        res.setAttribute("name", "Sample Information")
        res.setAttribute("path", samp_file)
        xml_resources.appendChild(res)
    # <HiddenAttributes>
    #    <Attribute name="DATA FILE"/>
    #    <Attribute name="Linking_id"/>
    #    <Attribute name="DATA TYPE"/>
    # </HiddenAttributes>
    # Adding parameters to hide basic unnecessary sample info
    hidden_attr = doc.createElement("HiddenAttributes")
    xml.appendChild(hidden_attr)

    attr = doc.createElement("Attribute")
    attr.setAttribute("name", "DATA FILE")
    hidden_attr.appendChild(attr)

    attr = doc.createElement("Attribute")
    attr.setAttribute("name", "Linking_id")
    hidden_attr.appendChild(attr)

    attr = doc.createElement("Attribute")
    attr.setAttribute("name", "DATA TYPE")
    hidden_attr.appendChild(attr)

    # Creating temp file to enter into file_store
    tempfilename = tempfile.NamedTemporaryFile(delete=False)
    tempfilename.write(doc.toprettyxml(indent="  "))
    tempfilename.close()

    # getting file_store_uuid
    filestore_uuid = create(tempfilename.name, permanent=True, filetype="xml")
    filestore_item = import_file(filestore_uuid, permanent=True, refresh=True)

    # file to rename
    temp_name = filestore_item.datafile.name.split('/')
    temp_name = temp_name[len(temp_name) - 1] + '.xml'

    # rename file by way of file_store
    filestore_item = rename(filestore_uuid, temp_name)

    # delete temp file
    os.unlink(tempfilename.name)

    # Url for session file
    sessionfile_url = get_full_url(filestore_item.get_datafile_url())

    # IGV url for automatic launch of Java Webstart
    igv_url = "http://www.broadinstitute.org/igv/projects/current/igv.php" \
              "?sessionURL=" + sessionfile_url

    return igv_url
Example #22
0
def createIGVsession(genome, uuids, is_file_uuid=False):
    """ Creates session file for selected file uuids, returns newly created
    filestore uuid
    :param genome: Genome to be used in session file i.e. hg18, dm3
    :type genome: string.
    :param uuids: Array of UUIDs to be used
    :type uuids: array.
    :param uuids: Host URL i.e. 127.0.0.1:8000
    :type uuids: string
    """
    # Create IGV Session file and put into Filestore
    """
    http://www.postneo.com/projects/pyxml/

    <?xml version="1.0" encoding="UTF-8"?>
        <Global genome="hg18" locus="EGFR" version="3">
        <Resources>
            <Resource name="RNA Genes"
            path="http://www.broadinstitute.org/igvdata/tcga/gbm/GBM_batch1-8_level3_exp.txt.recentered.080820.gct.tdf"/>
            <Resource name="RNA Genes"
            path="http://www.broadinstitute.org/igvdata/annotations/hg18/rna_genes.bed"/>
            <Resource name="sno/miRNA"
            path="http://www.broadinstitute.org/igvdata/tcga/gbm/Sample_info.txt"/>
        </Resources>
    </Global>
    """
    logger.debug("visualization_manager.createIGVsession called")

    # Create the minidom document
    doc = Document()
    # Create the <wml> base element
    xml = doc.createElement("Global")
    xml.setAttribute("genome", genome)
    xml.setAttribute("locus", "All")
    xml.setAttribute("version", "4")
    doc.appendChild(xml)
    # Add Resources
    xml_resources = doc.createElement("Resources")
    xml.appendChild(xml_resources)
    # get paths to url
    for samp in uuids:
        # gets filestore item
        curr_name, curr_url = get_file_name(samp, is_file_uuid=is_file_uuid)

        logger.debug('New resource: ' + curr_name + ' - ' + curr_url)

        # What to do if fs does not exist?
        if (curr_name):
            # creates Resource element
            res = doc.createElement("Resource")
            res.setAttribute("name", curr_name)
            res.setAttribute("path", curr_url)
            xml_resources.appendChild(res)
    # Creating temp file to enter into file_store
    tempfilename = tempfile.NamedTemporaryFile(delete=False)
    tempfilename.write(doc.toprettyxml(indent="  "))
    tempfilename.close()
    # getting file_store_uuid
    filestore_uuid = create(tempfilename.name, permanent=True, filetype="xml")
    filestore_item = import_file(filestore_uuid, permanent=True, refresh=True)
    # file to rename
    temp_name = filestore_item.datafile.name.split('/')
    temp_name = temp_name[len(temp_name) - 1] + '.xml'
    # rename file by way of file_store
    filestore_item = rename(filestore_uuid, temp_name)
    # delete temp file
    os.unlink(tempfilename.name)
    # Url for session file
    fs_url = get_full_url(filestore_item.get_datafile_url())
    # IGV url for automatic launch of Java Webstart
    igv_url = "http://www.broadinstitute.org/igv/projects/current/igv.php" \
              "?sessionURL=" + fs_url
    return igv_url
Example #23
0
def create_igv_session_annot(genome, uuids, annot_uuids=None, samp_file=None):
    """Creates session file for selected file uuids, returns newly created
    filestore uuid
    :param genome: Genome to be used in session file i.e. hg18, dm3
    :type genome: string.
    :param uuids: Array of UUIDs to be used
    :type uuids: array.
    :param uuids: Host URL i.e. 127.0.0.1:8000
    :type uuids: string
    """
    # Create IGV Session file and put into Filestore
    """
    http://www.postneo.com/projects/pyxml/

    <?xml version="1.0" encoding="UTF-8"?>
        <Global genome="hg18" locus="EGFR" version="3">
        <Resources>
            <Resource name="RNA Genes"
            path="http://www.broadinstitute.org/igvdata/tcga/gbm/GBM_batch1-8_level3_exp.txt.recentered.080820.gct.tdf"/>
            <Resource name="RNA Genes"
            path="http://www.broadinstitute.org/igvdata/annotations/hg18/rna_genes.bed"/>
            <Resource name="sno/miRNA"
            path="http://www.broadinstitute.org/igvdata/tcga/gbm/Sample_info.txt"/>
        </Resources>
    </Global>
    """
    # Create the minidom document
    doc = Document()
    # Create the <wml> base element
    xml = doc.createElement("Global")
    xml.setAttribute("genome", genome)
    xml.setAttribute("locus", "All")
    xml.setAttribute("version", "4")
    doc.appendChild(xml)
    # Add Resources
    xml_resources = doc.createElement("Resources")
    xml.appendChild(xml_resources)
    # adding selected samples to xml file
    add_igv_resource(uuids["node_uuid"], xml_resources, doc)
    if annot_uuids:
        # adding selected samples to xml file
        add_igv_resource(annot_uuids["node_uuid"], xml_resources, doc)
    # adds sample information file to IGV session file
    if samp_file:
        # <Resource name="Sample Information"
        # path="http://igv.broadinstitute.org/data/hg18/tcga/gbm/gbmsubtypes/sampleTable.txt.gz"/>
        # creates Resource element
        res = doc.createElement("Resource")
        res.setAttribute("name", "Sample Information")
        res.setAttribute("path", samp_file)
        xml_resources.appendChild(res)
    # <HiddenAttributes>
    #    <Attribute name="DATA FILE"/>
    #    <Attribute name="Linking_id"/>
    #    <Attribute name="DATA TYPE"/>
    # </HiddenAttributes>
    # Adding parameters to hide basic unnecessary sample info
    hidden_attr = doc.createElement("HiddenAttributes")
    xml.appendChild(hidden_attr)

    attr = doc.createElement("Attribute")
    attr.setAttribute("name", "DATA FILE")
    hidden_attr.appendChild(attr)

    attr = doc.createElement("Attribute")
    attr.setAttribute("name", "Linking_id")
    hidden_attr.appendChild(attr)

    attr = doc.createElement("Attribute")
    attr.setAttribute("name", "DATA TYPE")
    hidden_attr.appendChild(attr)

    # Creating temp file to enter into file_store
    tempfilename = tempfile.NamedTemporaryFile(delete=False)
    tempfilename.write(doc.toprettyxml(indent="  "))
    tempfilename.close()

    # getting file_store_uuid
    filestore_uuid = create(tempfilename.name, filetype="xml")
    filestore_item = import_file(filestore_uuid, refresh=True)

    # file to rename
    temp_name = filestore_item.datafile.name.split('/')
    temp_name = temp_name[len(temp_name) - 1] + '.xml'

    # rename file by way of file_store
    filestore_item = rename(filestore_uuid, temp_name)

    # delete temp file
    os.unlink(tempfilename.name)

    # Url for session file
    sessionfile_url = get_full_url(filestore_item.get_datafile_url())

    # IGV url for automatic launch of Java Webstart
    igv_url = "http://www.broadinstitute.org/igv/projects/current/igv.php" \
              "?sessionURL=" + sessionfile_url

    return igv_url
Example #24
0
def add_igv_samples(fields, results_samp, annot_samples=None):
    """creates phenotype file for IGV
    :param samples: Solr results for samples to be included
    :type samples: Array.
    :param annot_samples: includes annotation files included with solr results
    :type annot_samples: Array
    """
    # creates human readable indexes of fields to iterate over
    fields_dict = {}
    for i in fields:
        find_index = i.find("_Characteristics_")
        if find_index > -1:
            new_key = i.split("_Characteristics_")[0]
            fields_dict[i] = new_key

    # Creating temp file to enter into file_store
    temp_sample_name = tempfile.NamedTemporaryFile(delete=False)

    # writing header to sample file
    temp_sample_name.write("#sampleTable" + "\n")

    # writing column names to sample file
    col_names = "Linking_id"
    for k, v in fields_dict.iteritems():
        col_names = col_names + "\t" + v
    temp_sample_name.write(col_names + "\n")

    # iterating over sample files
    pheno_results = get_sample_lines(fields_dict, results_samp)
    try:
        temp_sample_name.write(pheno_results)
    except UnicodeEncodeError as e:
        logger.error(
            "Could not write results to file: %s. " "Trying again with the content to write encoded " "properly.", e
        )
        temp_sample_name.write(pheno_results.encode("utf-8"))

    # if annotations are not null
    if annot_samples:
        pheno_annot = get_sample_lines(fields_dict, annot_samples)
        temp_sample_name.write(pheno_annot)

    # closing temp file
    temp_sample_name.close()

    # getting file_store_uuid
    filestore_uuid = create(temp_sample_name.name, filetype="txt")
    filestore_item = import_file(filestore_uuid, refresh=True)

    # file to rename
    temp_file = filestore_item.datafile.name.split("/")
    temp_file = temp_file[len(temp_file) - 1] + ".txt"

    # rename file by way of file_store
    filestore_item = rename(filestore_uuid, temp_file)

    # getting file information based on file_uuids
    curr_fs = FileStoreItem.objects.get(uuid=filestore_uuid)

    # full path to selected UUID File
    curr_url = get_full_url(curr_fs.get_datafile_url())

    # delete temp file
    os.unlink(temp_sample_name.name)

    return curr_url