def binpid2zip(pid, outfile, log_callback=None):
def log(msg):
if log_callback is not None:
log_callback(msg)
"""Generate a zip file given a canonical pid"""
parsed = parse_pid(pid)
bin_pid = ''.join([parsed[NAMESPACE], parsed[BIN_LID]])
timestamp = iso8601(strptime(parsed[TIMESTAMP], parsed[TIMESTAMP_FORMAT]))
log('copying raw data for %s to temp files ...' % bin_pid)
with tempfile.NamedTemporaryFile() as hdr_tmp:
hdr_path = hdr_tmp.name
drain(UrlSource(bin_pid+'.hdr'), LocalFileSink(hdr_path))
hdr = parse_hdr_file(hdr_path)
with tempfile.NamedTemporaryFile() as adc_tmp:
adc_path = adc_tmp.name
drain(UrlSource(bin_pid+'.adc'), LocalFileSink(adc_path))
adc = Adc(adc_path, parsed[SCHEMA_VERSION])
unstitched_targets = add_pids(adc.get_targets(), bin_pid)
stitched_targets = list_stitched_targets(unstitched_targets)
with tempfile.NamedTemporaryFile() as roi_tmp:
roi_path = roi_tmp.name
drain(UrlSource(bin_pid+'.roi'), LocalFileSink(roi_path))
canonical_pid = bin_pid
log('copied raw data for %s' % canonical_pid)
"""*parsed_pid - result of parsing pid
*canonical_pid - canonicalized with URL prefix
*targets - list of (stitched) targets
*hdr - result of parsing header file
*timestamp - timestamp (FIXME in what format?)
*roi_path - path to ROI file
outfile - where to write resulting zip file"""
log('creating zip file for %s' % bin_pid)
with open(outfile,'wb') as fout:
return bin2zip(parsed,bin_pid,stitched_targets,hdr,timestamp,roi_path,fout)
def serve_pid(pid):
req = DashboardRequest(pid, request)
try:
paths = get_fileset(req.parsed)
except NotFound:
abort(404)
hdr_path = paths['hdr_path']
adc_path = paths['adc_path']
roi_path = paths['roi_path']
adc = Adc(adc_path, req.schema_version)
heft = 'full' # heft is either short, medium, or full
if 'extension' in req.parsed:
extension = req.parsed['extension']
if 'target' in req.parsed:
canonical_bin_pid = canonicalize(req.url_root, req.time_series, req.bin_lid)
target_no = int(req.parsed['target'])
# pull three targets, then find any stitched pair
targets = adc.get_some_targets(target_no-1, 3)
targets = list_stitched_targets(targets)
for t in targets:
if t[TARGET_NUMBER] == target_no:
target = t
add_pid(target, canonical_bin_pid)
# check for image
mimetype = mimetypes.types_map['.' + extension]
if mimetype.startswith('image/'):
if req.product=='raw':
img = get_target_image(req.parsed, target, roi_path)
return Response(as_bytes(img,mimetype),mimetype=mimetype)
if req.product=='blob':
return serve_blob_image(req.parsed, mimetype)
if req.product=='blob_outline':
img = get_target_image(req.parsed, target, roi_path)
return serve_blob_image(req.parsed, mimetype, outline=True, target_img=img)
# not an image, so get more metadata
targets = get_targets(adc, canonical_bin_pid)
# not an image, check for JSON
if extension == 'json':
return Response(json.dumps(target),mimetype=MIME_JSON)
target = get_target_metadata(target,targets)
# more metadata representations. we'll need the header
hdr = parse_hdr_file(hdr_path)
if extension == 'xml':
return Response(target2xml(req.canonical_pid, target, req.timestamp, canonical_bin_pid), mimetype='text/xml')
if extension == 'rdf':
return Response(target2rdf(req.canonical_pid, target, req.timestamp, canonical_bin_pid), mimetype='text/xml')
if extension in ['html', 'htm']:
template = {
'static': STATIC,
'target_pid': req.canonical_pid,
'bin_pid': canonical_bin_pid,
'properties': target,
'target': target.items(), # FIXME use order_keys
'date': req.timestamp
}
return template_response('target.html',**template)
else: # bin
if req.extension in ['hdr', 'adc', 'roi']:
path = dict(hdr=hdr_path, adc=adc_path, roi=roi_path)[req.extension]
mimetype = dict(hdr='text/plain', adc='text/csv', roi='application/octet-stream')[req.extension]
return Response(file(path,'rb'), direct_passthrough=True, mimetype=mimetype)
try:
if req.product in ['blobs','blob']: # accept old url pattern
return serve_blob_bin(req.parsed)
if req.product=='features':
return serve_features_bin(req.parsed)
if req.product=='class_scores':
return serve_class_scores_bin(req.parsed)
except NotFound:
abort(404)
# gonna need targets unless heft is medium or below
targets = []
if req.product != 'short':
targets = get_targets(adc, req.canonical_pid)
# end of views
# not a special view, handle representations of targets
if req.extension=='csv':
adc_cols = req.parsed[ADC_COLS].split(' ')
lines = targets2csv(targets,adc_cols)
return Response('\n'.join(lines)+'\n',mimetype='text/csv')
# we'll need the header for the other representations
hdr = parse_hdr_file(hdr_path)
if req.extension in ['html', 'htm']:
targets = list(targets)
context, props = split_hdr(hdr)
template = {
'static': STATIC,
'bin_pid': req.canonical_pid,
'time_series': req.time_series,
'context': context,
'properties': props,
'targets': targets,
'target_pids': [t['pid'] for t in targets],
'date': req.timestamp,
'files': get_files(req.parsed,check=True) # note: ORM call!
}
print get_files(req.parsed)
return template_response('bin.html', **template)
if req.extension=='json':
if req.product=='short':
return Response(bin2json_short(req.canonical_pid,hdr,req.timestamp),mimetype=MIME_JSON)
if req.product=='medium':
return Response(bin2json_medium(req.canonical_pid,hdr,targets,req.timestamp),mimetype=MIME_JSON)
return Response(bin2json(req.canonical_pid,hdr,targets,req.timestamp),mimetype=MIME_JSON)
if req.extension=='xml':
return Response(bin2xml(req.canonical_pid,hdr,targets,req.timestamp),mimetype='text/xml')
if req.extension=='rdf':
return Response(bin2rdf(req.canonical_pid,hdr,targets,req.timestamp),mimetype='text/xml')
if req.extension=='zip':
# look to see if the zipfile is resolvable
try:
zip_path = get_product_file(req.parsed, 'binzip')
if os.path.exists(zip_path):
return Response(file(zip_path), direct_passthrough=True, mimetype='application/zip')
except NotFound:
pass
except:
raise
buffer = BytesIO()
bin2zip(req.parsed,req.canonical_pid,targets,hdr,req.timestamp,roi_path,buffer)
return Response(buffer.getvalue(), mimetype='application/zip')
return 'unimplemented'
def get_targets(adc, bin_pid, stitched=True):
us_targets = list(get_unstitched_targets(adc, bin_pid))
if stitched:
return list_stitched_targets(us_targets)
else:
return us_targets