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, *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)
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)