def get(self, *args, **kwargs):
        barcode = self.get_argument('barcode', None)
        filetype = self.get_argument('filetype', None)

        if barcode is None or filetype is None:
            raise HTTPError(400, "Incorrectly formed GET request")

        # Check access to file
        has_access = ag_data.check_access(self.current_user, barcode)

        if not has_access:
            self.set_status(403)
            self.render("403.html", skid=self.current_user)
            return

        if filetype not in FILETYPES:
            raise HTTPError(400, "Unrecognized filetype")

        filetype_path, filetype_suffix = FILETYPES[filetype]
        fname = barcode + filetype_suffix
        fullpath = join(filetype_path, fname)

        if not exists(join(AMGUT_CONFIG.base_data_dir, fullpath)):
            raise HTTPError(400, "File %s is not available" % fullpath)

        self.set_header('Content-Description', 'File Transfer')
        self.set_header('Content-Type', 'application/octet-stream')
        self.set_header('Content-Transfer-Encoding', 'binary')
        self.set_header('Expires', '0')
        self.set_header('Cache-Control', 'no-cache')
        self.set_header('X-Accel-Redirect', '/protected/' + fullpath)
        self.set_header('Content-Disposition',
                        'attachment; filename=%s' % fname)

        self.finish()
Exemple #2
0
    def get(self, *args, **kwargs):
        barcode = self.get_argument('barcode', None)
        filetype = self.get_argument('filetype', None)

        if barcode is None or filetype is None:
            raise HTTPError(400, "Incorrectly formed GET request")

        # Check access to file
        has_access = ag_data.check_access(self.current_user, barcode)

        if not has_access:
            self.set_status(403)
            self.render("403.html", skid=self.current_user)
            return

        if filetype not in FILETYPES:
            raise HTTPError(400, "Unrecognized filetype")

        filetype_path, filetype_suffix = FILETYPES[filetype]
        fname = barcode + filetype_suffix
        fullpath = join(filetype_path, fname)

        if not exists(join(AMGUT_CONFIG.base_data_dir, fullpath)):
            raise HTTPError(400, "File %s is not available" % fullpath)

        self.set_header('Content-Description', 'File Transfer')
        self.set_header('Content-Type', 'application/octet-stream')
        self.set_header('Content-Transfer-Encoding', 'binary')
        self.set_header('Expires', '0')
        self.set_header('Cache-Control', 'no-cache')
        self.set_header('X-Accel-Redirect', '/protected/' + fullpath)
        self.set_header('Content-Disposition',
                        'attachment; filename=%s' % fname)

        self.finish()
    def get(self, barcode):
        # nothing else to do
        barcode = barcode.strip("/")  # for nginx rewrites

        if barcode is None:
            tl = text_locale["handlers"]
            self.render("taxa_summary.html", skid=self.current_user, loginerror=tl["BARCODE_ERROR"])
            return

        has_access = ag_data.check_access(self.current_user, barcode)
        if not has_access:
            self.set_status(403)
            self.render("403.html", skid=self.current_user)
            return

        # we need this path to access the filesystem
        taxa_summary_fp = join(AMGUT_CONFIG.base_data_dir, "taxa-summaries", barcode + ".txt")

        # and we need this path for users to access the file
        taxa_summary_url = join(media_locale["SITEBASE"], "results", "taxa-summaries", barcode + ".txt")

        # read lines from taxa summary table, omit comment lines
        with open(taxa_summary_fp, "U") as fp:
            lines = [x.replace(";", "\t").strip() for x in fp if not x.startswith("#")]

        # remove the greengenes prefixes. If hierarchy is delimitd by
        # semicolon- space, the GG prefix may be preceded by a space
        lines = [sub(" *?[kpcofg]__", "", x) for x in lines]

        # we must operate on the genus and percent abundance columns
        # individually, so it must be split into individual cells
        lines = [x.split("\t") for x in lines]

        for i in range(len(lines)):
            for j in range(len(lines[i])):
                if lines[i][j] == "":
                    lines[i][j] = "---"

            # format the last column to be a 2.2 number, and center it
            relative_abundance = float(lines[i][-1])
            relative_abundance *= 100
            lines[i][-1] = "%2.2f" % relative_abundance

        # generate headers
        headers = ["Kingdom", "Phylum", "Class", "Order", "Family", "Genus", "Relative Abundance (%)"]

        self.render(
            "taxa_summary.html",
            headers=headers,
            data=lines,
            barcode=barcode,
            file_path=taxa_summary_url,
            loginerror="",
            skid=self.current_user,
        )
    def get(self, barcode):
        # nothing else to do
        barcode = barcode.strip('/')  # for nginx rewrites

        if barcode is None:
            tl = text_locale['handlers']
            self.render('taxa_summary.html', skid=self.current_user,
                        loginerror=tl["BARCODE_ERROR"])
            return

        has_access = ag_data.check_access(self.current_user, barcode)
        if not has_access:
            self.set_status(403)
            self.render("403.html", skid=self.current_user)
            return

        # we need this path to access the filesystem
        taxa_summary_fp = join(AMGUT_CONFIG.base_data_dir, 'taxa-summaries',
                               barcode+'.txt')

        # and we need this path for users to access the file
        taxa_summary_url = join(media_locale['SITEBASE'], 'results',
                                'taxa-summaries', barcode+'.txt')

        # read lines from taxa summary table, omit comment lines
        lines = [x.replace(';', '\t').strip() for x in
            open(taxa_summary_fp, 'U').readlines() if not x.startswith('#')]

        # remove the greengenes prefixes. If hierarchy is delimitd by
        # semicolon- space, the GG prefix may be preceded by a space
        lines = [sub(' *?[kpcofg]__', '', x) for x in lines]

        # we must operate on the genus and percent abundance columns
        # individually, so it must be split into individual cells
        lines = [x.split('\t') for x in lines]

        for i in range(len(lines)):
            for j in range(len(lines[i])):
                if lines[i][j] == '':
                    lines[i][j] = '---'

            # format the last column to be a 2.2 number, and center it
            relative_abundance = float(lines[i][-1])
            relative_abundance *= 100
            lines[i][-1] = '%2.2f' % relative_abundance

        # generate headers
        headers = ['Kingdom', 'Phylum', 'Class', 'Order', 'Family',
            'Genus', 'Relative Abundance (%)']

        self.render('taxa_summary.html', headers=headers, data=lines,
                    barcode=barcode, file_path=taxa_summary_url, loginerror="",
                    skid=self.current_user)
    def get(self, barcode):
        if barcode is None:
            self.redirect(media_locale['SITEBASE'] + '/authed/portal/')
            return

        has_access = ag_data.check_access(self.current_user, barcode)
        if not has_access:
            self.set_status(403)
            self.render("403.html", skid=self.current_user)
            return

        self.render('interactive_report.html', skid=self.current_user,
                    barcode=barcode)
Exemple #6
0
    def get(self, barcode):
        if barcode is None:
            self.redirect(media_locale['SITEBASE'] + '/authed/portal/')
            return

        has_access = ag_data.check_access(self.current_user, barcode)
        if not has_access:
            self.set_status(403)
            self.render("403.html", skid=self.current_user)
            return

        self.render('interactive_report.html',
                    skid=self.current_user,
                    barcode=barcode)
    def _sample_overview_renderer(self):
        barcode = self.get_argument('barcode', None)
        if barcode is None:
            self.redirect(media_locale['SITEBASE'] + '/authed/portal/')
            return

        has_access = ag_data.check_access(self.current_user, barcode)
        if not has_access:
            self.set_status(403)
            self.render("403.html", skid=self.current_user)
            return

        sample_data = ag_data.getAGBarcodeDetails(barcode)

        if not sample_data:
            self.set_status(404)
            self.render("404.html", skid=self.current_user)
            return

        web_barcode_pdf, web_barcode_txt = _get_data_path(barcode)
        unidentified_results = _get_per_sample_results(barcode)
        per_sample_data = _get_per_sample_data(barcode)

        sample_time = sample_data['sample_time']
        sample_date = sample_data['sample_date']

        status = sample_data['status']
        if status is None:
            bgcolor = '#FFF'
            status = 'Submitted'
        elif status == 'Received':
            bgcolor = '#AFA'
        else:
            bgcolor = '#FFF'

        sample_origin = sample_data['site_sampled']
        if sample_origin is None:
            sample_origin = sample_data['environment_sampled']

        notes = sample_data['notes']
        if notes is None:
            notes = ''

        self.render('sample_overview.html', skid=self.current_user,
                    barcode_pdf=web_barcode_pdf, barcode_txt=web_barcode_txt,
                    bgcolor=bgcolor, status=status, barcode=barcode,
                    sample_origin=sample_origin, sample_date=sample_date,
                    sample_time=sample_time, notes=notes,
                    unidentified_results=unidentified_results,
                    per_sample_data=per_sample_data)
    def _sample_overview_renderer(self):
        barcode = self.get_argument('barcode', None)
        if barcode is None:
            self.redirect(media_locale['SITEBASE'] + '/authed/portal/')
            return

        has_access = ag_data.check_access(self.current_user, barcode)
        if not has_access:
            self.set_status(403)
            self.render("403.html", skid=self.current_user)
            return

        sample_data = ag_data.getAGBarcodeDetails(barcode)

        if not sample_data:
            self.set_status(404)
            self.render("404.html", skid=self.current_user)
            return

        web_barcode_pdf, web_barcode_txt = _get_data_path(barcode)

        sequence_url = None
        biomv1_url = None
        classic_url = None
        sequence_url = None

        api_base = 'http://api.microbio.me/americangut/1/'
        req = requests.get(api_base + 'sample/%s' % barcode)
        if req.status_code == 200 and req.content != "(null)":
            bc_with_suf = json.loads(req.content)[0]
            biomv1_url = api_base + 'otu/%s/json' % bc_with_suf
            classic_url = api_base + 'otu/%s/txt' % bc_with_suf

            seq_req = requests.get(api_base + 'sequence/%s' % bc_with_suf)
            if seq_req.status_code == 200:
                sequence_url = json.loads(seq_req.content)[0]['fastq_url']

        sample_time = sample_data['sample_time']
        sample_date = sample_data['sample_date']

        status = sample_data['status']
        if status is None:
            bgcolor = '#FFF'
            status = 'Submitted'
        elif status == 'Received':
            bgcolor = '#AFA'
        else:
            bgcolor = '#FFF'

        sample_origin = sample_data['site_sampled']
        if sample_origin is None:
            sample_origin = sample_data['environment_sampled']

        notes = sample_data['notes']
        if notes is None:
            notes = ''

        self.render('sample_overview.html', skid=self.current_user,
                    barcode_pdf=web_barcode_pdf, barcode_txt=web_barcode_txt,
                    bgcolor=bgcolor, status=status, barcode=barcode,
                    sample_origin=sample_origin, sample_date=sample_date,
                    sample_time=sample_time, notes=notes,
                    sequence_url=sequence_url, biomv1_url=biomv1_url,
                    classic_url=classic_url)
    def get(self, barcode):
        # nothing else to do
        barcode = barcode.strip('/')  # for nginx rewrites

        if barcode is None:
            tl = text_locale['handlers']
            self.render('taxa_summary.html',
                        skid=self.current_user,
                        loginerror=tl["BARCODE_ERROR"])
            return

        has_access = ag_data.check_access(self.current_user, barcode)
        if not has_access:
            self.set_status(403)
            self.render("403.html", skid=self.current_user)
            return

        # we need this path to access the filesystem
        taxa_summary_fp = join(AMGUT_CONFIG.base_data_dir, 'taxa-summaries',
                               barcode + '.txt')

        # and we need this path for users to access the file
        taxa_summary_url = join(media_locale['SITEBASE'], 'results',
                                'taxa-summaries', barcode + '.txt')

        # read lines from taxa summary table, omit comment lines
        with open(taxa_summary_fp, 'U') as fp:
            lines = [
                x.replace(';', '\t').strip() for x in fp
                if not x.startswith('#')
            ]

        # remove the greengenes prefixes. If hierarchy is delimitd by
        # semicolon- space, the GG prefix may be preceded by a space
        lines = [sub(' *?[kpcofg]__', '', x) for x in lines]

        # we must operate on the genus and percent abundance columns
        # individually, so it must be split into individual cells
        lines = [x.split('\t') for x in lines]

        for i in range(len(lines)):
            for j in range(len(lines[i])):
                if lines[i][j] == '':
                    lines[i][j] = '---'

            # format the last column to be a 2.2 number, and center it
            relative_abundance = float(lines[i][-1])
            relative_abundance *= 100
            lines[i][-1] = '%2.2f' % relative_abundance

        # generate headers
        headers = [
            'Kingdom', 'Phylum', 'Class', 'Order', 'Family', 'Genus',
            'Relative Abundance (%)'
        ]

        self.render('taxa_summary.html',
                    headers=headers,
                    data=lines,
                    barcode=barcode,
                    file_path=taxa_summary_url,
                    loginerror="",
                    skid=self.current_user)