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 test_integrity(self,b):
parsed = parse_pid(b.lid)
schema_version = parsed[SCHEMA_VERSION]
fs = {}
for f in b.files:
fs[f.filetype] = f.local_path
try:
check_fileset(fs, schema_version)
return True
except:
return False
def accepts_product(product_pid):
parsed = parse_pid(product_pid)
namespace = parsed[NAMESPACE]
product = parsed[PRODUCT]
ep = '%sapi/accepts_products/%s' % (namespace, product)
try:
return requests.get(ep).json()[product]
except:
return False
def do_webcache(pid,job):
parsed = parse_pid(pid)
bin_pid = ''.join([parsed[NAMESPACE], parsed[BIN_LID]])
mosaic_base_url = '%sapi/mosaic/size/800x600/scale/0.33/page/1' % parsed[NAMESPACE]
mosaic_json = '%s/%s.json' % (mosaic_base_url, bin_pid)
mosaic_jpg = '%s/%s.jpg' % (mosaic_base_url, bin_pid)
logging.warn('WEBCACHE hitting %s' % mosaic_json)
r1 = requests.get(mosaic_json)
json = r1.json() # read it, and throw it away
logging.warn('WEBCACHE hitting %s' % mosaic_jpg)
r2 = requests.get(mosaic_jpg)
img_data = StringIO(r2.content) # read it, and throw it away
logging.warn('WEBCACHE done for %s' % pid)
def get_product_destination(session, pid, product_type=None):
parsed = parse_pid(pid)
if product_type is None:
product_type = parsed[PRODUCT]
ts_label = parsed[TS_LABEL]
if product_type=='multiblob': # sidecar files for features
product_type='features'
roots = get_data_roots(session, ts_label, product_type=product_type)
if not roots:
raise NotFound('no product destination found')
root = roots[0]
S = next(get_resolver().ifcb.files.product_path(root=root,**parsed))
return S[FILE_PATH]
def extract_features(pid,job):
def log_callback(msg):
logging.warn('FEATURES %s' % msg)
client.heartbeat(pid,message=msg)
parsed_pid = parse_pid(pid)
bin_lid = parsed_pid[LID]
bin_pid = ''.join([parsed_pid[NAMESPACE], parsed_pid[LID]])
binzip_url = ''.join([bin_pid,'_binzip.zip'])
blob_url = ''.join([bin_pid,'_blob.zip'])
features_url = ''.join([bin_pid,'_features.csv'])
multiblob_url = ''.join([bin_pid,'_multiblob.csv'])
if exists(features_url):
log_callback('skipping %s - features exist' % pid)
return
log_callback('computing features for %s' % pid)
with safe_tempdir() as binzip_dir:
# download bin zip
binzip_path = os.path.join(binzip_dir, '%s.zip' % bin_lid)
log_callback('downloading %s to %s' % (binzip_url, binzip_path))
download(binzip_url, binzip_path)
# download blob zip
blob_path = os.path.join(binzip_dir, '%s_blob.zip' % bin_lid)
log_callback('downloading %s to %s' % (blob_url, blob_path))
download(blob_url, blob_path)
# compute features
with safe_tempdir() as job_dir:
# output of matlab job
feature_csv = os.path.join(job_dir, csvname(bin_pid))
multiblob_csv = os.path.join(job_dir, 'multiblob', multiblobname(bin_pid))
# params for matlab job
namespace = os.path.dirname(binzip_path) + '/'
lid = os.path.basename(binzip_path)
matlab = Matlab(MATLAB_EXEC_PATH, MATLAB_PATH, output_callback=log_callback)
cmd = 'bin_features(\'%s\',\'%s\',\'%s\',\'chatty\')' % (namespace, lid, job_dir + '/')
log_callback('running %s' % cmd)
matlab.run(cmd)
log_callback('matlab exited')
if os.path.exists(feature_csv):
log_callback('features found at %s' % feature_csv)
else:
raise Exception('no features found')
log_callback('uploading %s' % features_url)
upload(feature_csv, features_url)
if os.path.exists(multiblob_csv):
log_callback('multiblob found at %s' % multiblob_csv)
log_callback('uploading %s' % multiblob_url)
upload(multiblob_csv, multiblob_url)
log_callback('complete')
client.wakeup()
def do_binzip(pid, job):
def log_callback(msg):
logging.warn('BINZIP %s' % msg)
client.heartbeat(pid,message=msg)
parsed = parse_pid(pid)
binzip_url = '%s%s_binzip.zip' % (parsed[NAMESPACE], parsed[BIN_LID])
log_callback('creating zipfile for %s' % pid)
with tempfile.NamedTemporaryFile() as zip_tmp:
zip_path = zip_tmp.name
binpid2zip(pid, zip_path)
# construct binzip URL
log_callback('depositing %s' % binzip_url)
upload(zip_path, binzip_url)
log_callback('deposited %s' % binzip_url)
client.wakeup()
def do_acc(pid, job):
parsed = parse_pid(pid)
lid = parsed[LID]
ts_label = parsed[TS_LABEL]
roots = get_data_roots(session, ts_label) # get raw data roots
fileset = parsed_pid2fileset(parsed, roots)
fileset[LID] = lid
session.expire_all() # don't be stale!
acc = Accession(session,ts_label)#,fast=True)
# FIXME fast=True disables checksumming
client.update(pid,ttl=3600) # allow 1hr for accession
ret = acc.add_fileset(fileset)
if ret=='ADDED':
schedule_products(pid, client)
session.commit()
client.wakeup()
elif ret=='FAILED':
raise Exception('accession failed')
def extract_blobs(pid,job):
def log_callback(msg):
logging.warn('BLOBS %s' % msg)
client.heartbeat(pid,message=msg)
parsed_pid = parse_pid(pid)
bin_lid = parsed_pid[LID]
bin_pid = ''.join([parsed_pid[NAMESPACE], parsed_pid[LID]])
binzip_url = ''.join([bin_pid,'_binzip.zip'])
binzip_file = os.path.basename(binzip_url)
deposit_url = '%s_blobs.zip' % bin_pid
if exists(deposit_url):
log_callback('skipping %s - blobs exist' % pid)
return
log_callback('computing blobs for %s' % pid)
with safe_tempdir() as binzip_dir:
# first, copy the zipfile to a temp dir
binzip_path = os.path.join(binzip_dir, '%s.zip' % bin_lid)
log_callback('downloading %s to %s' % (binzip_url, binzip_path))
download(binzip_url, binzip_path)
# now run bin_blobs
with safe_tempdir() as job_dir:
# configure matlab
matlab = Matlab(MATLAB_EXEC_PATH, MATLAB_PATH, output_callback=log_callback)
# run command
blobs_file = os.path.join(job_dir, blob_zip_name(bin_pid))
cmd = 'bin_blobs(\'%s\',\'%s\',\'%s\')' % (bin_pid, binzip_path, job_dir)
log_callback('running %s' % cmd)
matlab.run(cmd)
log_callback('MATLAB done, checking for %s' % blobs_file)
if not os.path.exists(blobs_file):
raise Exception('missing output file')
log_callback('depositing %s' % blobs_file)
upload(blobs_file, deposit_url)
log_callback('deposited %s' % blobs_file)
log_callback('completed %s' % bin_pid)
client.wakeup()
def accession_demo(session,ts_label,root):
# now accede
for fs in get_resolver().ifcb.files.list_raw_filesets(root):
lid = fs['lid']
try:
parsed = parse_pid(lid)
except:
print 'barf %s' % lid
raise
ts = text2utcdatetime(parsed['timestamp'], parsed['timestamp_format'])
b = Bin(ts_label=ts_label, lid=lid, sample_time=ts)
session.add(b)
# now make mostly bogus fixity entries
now = datetime.now()
paths = [fs['hdr_path'], fs['adc_path'], fs['roi_path']]
filetypes = ['hdr','adc','roi']
for path,filetype in zip(paths,filetypes):
length = os.stat(path).st_size
name = os.path.basename(path)
#checksum = sha1_file(path)
checksum = 'placeholder'
f = File(local_path=path, filename=name, length=length, filetype=filetype, sha1=checksum, fix_time=now)
b.files.append(f)
session.commit()
def new_bin(self,lid):
parsed = parse_pid(lid)
sample_time = get_timestamp(parsed)
return Bin(ts_label=self.ts_label, lid=lid, sample_time=sample_time)
def pid2fileset(pid,roots):
parsed_pid = parse_pid(pid)
return parsed_pid2fileset(parsed_pid,roots)
