def manage_fu_from_HTS(existing_fu, meas, filename, sha1, url_path, hts_path):
#fixing bug str "true", str "false" for meas.type
if isinstance(meas.type, basestring):
bool_type = str2bool(meas.type)
meas.type = bool_type
if existing_fu:
print "-------- EXISTING FILE FROM HTS--------"
meas.fus.append(existing_fu)
DBSession.add(meas)
DBSession.flush()
return existing_fu
###########################################################################################
else:
#new files_up building
fu = Files_up()
fu.path = hts_path
#save the filename and the extension to the database
fu.filename = filename
if '.' in filename:
extension = filename.split('.')[-1]
fu.extension = extension
else:
fu.extension = "not specified"
fu.sha1 = sha1
fu.url_path = url_path
#add to the crossing table (measurement <-> file uploaded)
meas.fus.append(fu)
#adding new measurement and new files_up to the db
DBSession.add(meas)
DBSession.add(fu)
DBSession.flush()
return fu
def manage_fu_from_HTS(existing_fu, meas, filename, sha1, url_path, hts_path):
#fixing bug str "true", str "false" for meas.type
if isinstance(meas.type, basestring):
bool_type = str2bool(meas.type)
meas.type = bool_type
if existing_fu:
print "-------- EXISTING FILE FROM HTS--------"
meas.fus.append(existing_fu)
DBSession.add(meas)
DBSession.flush()
return existing_fu
###########################################################################################
else:
#new files_up building
fu = Files_up()
fu.path = hts_path
#save the filename and the extension to the database
fu.filename = filename
if '.' in filename:
extension = filename.split('.')[-1]
fu.extension = extension
else:
fu.extension = "not specified"
fu.sha1 = sha1
fu.url_path = url_path
#add to the crossing table (measurement <-> file uploaded)
meas.fus.append(fu)
#adding new measurement and new files_up to the db
DBSession.add(meas)
DBSession.add(fu)
DBSession.flush()
return fu
def manage_fu(existing_fu, meas, public_dirname, filename, sha1, up_data, url_path, url_up, dest_raw, dest_processed, tmp_path, lab):
tmpdir_to_delete = os.path.abspath(os.path.join(tmp_path, os.path.pardir))
#fixing bug str "true", str "false" for meas.type
if isinstance(meas.type, basestring):
bool_type = str2bool(meas.type)
meas.type = bool_type
if existing_fu:
print "-------- EXISTING FILE --------"
#create symbolic link
source = existing_fu.path + "/" + sha1
if meas.type:
dest = dest_raw + sha1
#test symlin existance
if os.path.islink(dest):
symlink_e = "This file was already in your personal folder"
else:
symlink_e = "This file was added to your personal folder"
os.symlink(source, dest)
else:
dest = dest_processed + sha1
#test symlink existance
if os.path.islink(dest):
symlink_e = "This file was already in your personal folder"
else:
symlink_e = "This file was added to your personal folder"
os.symlink(source, dest)
meas.fus.append(existing_fu)
DBSession.add(meas)
DBSession.flush()
flash(symlink_e + ", measurement created")
#remove the tmp file if it didn't come from HTSStation
if not tmpdir_to_delete.startswith('/data'):
shutil.rmtree(tmpdir_to_delete)
#raise redirect("./")
return existing_fu
###########################################################################################
else:
#new files_up building
fu = Files_up()
#raw test for path orientation
if meas.type:
fu.path = path_raw(lab)
data_dirname = os.path.join(public_dirname, fu.path)
else:
fu.path = path_processed(lab)
data_dirname = os.path.join(public_dirname, fu.path)
#save the filename and the extension to the database
fu.filename = filename
if '.' in filename:
extension = filename.split('.')[-1]
fu.extension = extension
# root, ext = os.path.splitext(filename)
# DOUBLE_EXTENSIONS = ['tar.gz','tar.bz2','bedGraph.gz','bed.gz']
# if any([filename.endswith(x) for x in DOUBLE_EXTENSIONS]):
# root, first_ext = os.path.splitext(root)
# ext = first_ext + ext
# fu.extension = ext
# else:
# fu.extension = ext
else:
fu.extension = "not specified"
data_path = os.path.join(data_dirname, str(sha1))
fu.sha1 = sha1
fu.url_path = url_path
#writing the file into the server HD
#version browser
try:
with open(data_path, "w") as d:
if up_data is not None:
d.write(up_data.value)
elif url_path is not None and url_up:
u = urllib2.urlopen(url_path)
while True:
buffer = u.read(8192)
if not buffer:
break
d.write(buffer)
else:
print "ERROR"
#version commandline
except:
shutil.move(tmp_path, data_path)
#symlink
source = data_path
if meas.type:
dest = dest_raw + sha1
if os.path.islink(dest):
symlink_e = "This file was already in your personal folder"
else:
symlink_e = "This file was added to your personal folder"
os.symlink(source, dest)
else:
dest = dest_processed + sha1
if os.path.islink(dest):
symlink_e = "This file was already in your personal folder"
else:
symlink_e = "This file was added to your personal folder"
os.symlink(source, dest)
#add to the crossing table (measurement <-> file uploaded)
meas.fus.append(fu)
#adding new measurement and new files_up to the db
DBSession.add(meas)
DBSession.add(fu)
DBSession.flush()
if meas.type:
flash(symlink_e + ", raw data was successfully created")
else:
flash(symlink_e + ", processed data was successfully created")
#remove the tmp file if it didn't come from HTSStation
if not tmpdir_to_delete.startswith('/data'):
shutil.rmtree(tmpdir_to_delete)
return fu
def manage_fu(existing_fu, meas, public_dirname, filename, sha1, up_data,
url_path, url_up, dest_raw, dest_processed, tmp_path, lab):
tmpdir_to_delete = os.path.abspath(os.path.join(tmp_path, os.path.pardir))
#fixing bug str "true", str "false" for meas.type
if isinstance(meas.type, basestring):
bool_type = str2bool(meas.type)
meas.type = bool_type
if existing_fu:
print "-------- EXISTING FILE --------"
#create symbolic link
source = existing_fu.path + "/" + sha1
if meas.type:
dest = dest_raw + sha1
#test symlin existance
if os.path.islink(dest):
symlink_e = "This file was already in your personal folder"
else:
symlink_e = "This file was added to your personal folder"
os.symlink(source, dest)
else:
dest = dest_processed + sha1
#test symlink existance
if os.path.islink(dest):
symlink_e = "This file was already in your personal folder"
else:
symlink_e = "This file was added to your personal folder"
os.symlink(source, dest)
meas.fus.append(existing_fu)
DBSession.add(meas)
DBSession.flush()
flash(symlink_e + ", measurement created")
#remove the tmp file if it didn't come from HTSStation
if not tmpdir_to_delete.startswith('/data'):
shutil.rmtree(tmpdir_to_delete)
#raise redirect("./")
return existing_fu
###########################################################################################
else:
#new files_up building
fu = Files_up()
#raw test for path orientation
if meas.type:
fu.path = path_raw(lab)
data_dirname = os.path.join(public_dirname, fu.path)
else:
fu.path = path_processed(lab)
data_dirname = os.path.join(public_dirname, fu.path)
#save the filename and the extension to the database
fu.filename = filename
if '.' in filename:
extension = filename.split('.')[-1]
fu.extension = extension
# root, ext = os.path.splitext(filename)
# DOUBLE_EXTENSIONS = ['tar.gz','tar.bz2','bedGraph.gz','bed.gz']
# if any([filename.endswith(x) for x in DOUBLE_EXTENSIONS]):
# root, first_ext = os.path.splitext(root)
# ext = first_ext + ext
# fu.extension = ext
# else:
# fu.extension = ext
else:
fu.extension = "not specified"
data_path = os.path.join(data_dirname, str(sha1))
fu.sha1 = sha1
fu.url_path = url_path
#writing the file into the server HD
#version browser
try:
with open(data_path, "w") as d:
if up_data is not None:
d.write(up_data.value)
elif url_path is not None and url_up:
u = urllib2.urlopen(url_path)
while True:
buffer = u.read(8192)
if not buffer:
break
d.write(buffer)
else:
print "ERROR"
#version commandline
except:
shutil.move(tmp_path, data_path)
#symlink
source = data_path
if meas.type:
dest = dest_raw + sha1
if os.path.islink(dest):
symlink_e = "This file was already in your personal folder"
else:
symlink_e = "This file was added to your personal folder"
os.symlink(source, dest)
else:
dest = dest_processed + sha1
if os.path.islink(dest):
symlink_e = "This file was already in your personal folder"
else:
symlink_e = "This file was added to your personal folder"
os.symlink(source, dest)
#add to the crossing table (measurement <-> file uploaded)
meas.fus.append(fu)
#adding new measurement and new files_up to the db
DBSession.add(meas)
DBSession.add(fu)
DBSession.flush()
if meas.type:
flash(symlink_e + ", raw data was successfully created")
else:
flash(symlink_e + ", processed data was successfully created")
#remove the tmp file if it didn't come from HTSStation
if not tmpdir_to_delete.startswith('/data'):
shutil.rmtree(tmpdir_to_delete)
return fu
