def register(experiment_id, acquisition_id):
"""
.. http:post:: /api/experiments/(string:experiment_id)/acquisitions/(string:acquisition_id)/register
Register a single directory (passed as parameter `path` in the
JSON request) as the directory containing all the files for
the given acquisition.
Calling this method twice with different `path` parameters
will result in an error (so you cannot combine the contents of
two directories by 'registering' them). On the other hand,
the *same* directory can be registered over and over again
without adverse side-effects; the method is idempotent in this
sense.
**Example request**:
.. sourcecode:: http
Content-Type: application/json
{
"path": "/fullpath/to/serversidedata"
}
**Example response**:
.. sourcecode:: http
HTTP/1.1 200 OK
Content-Type: application/json
{
"data": "/fullpath/to/serversidedata"
}
:reqheader Authorization: JWT token issued by the server
:statuscode 200: no error
:statuscode 500: server error
"""
data = request.get_json()
path = data['path']
logger.info('Registering microscope files from path `%s` ...', path)
try:
filenames = [
f for f in os.listdir(path)
if (not f.startswith('.')
and not os.path.isdir(os.path.join(path, f)))
]
except OSError as err:
logger.error("Cannot list directory `%s`: %s", path, err)
raise
with tm.utils.ExperimentSession(experiment_id) as session:
experiment = session.query(tm.Experiment).one()
microscope_type = experiment.microscope_type
img_regex, metadata_regex = get_microscope_type_regex(microscope_type)
acquisition = session.query(tm.Acquisition).get(acquisition_id)
plate = session.query(tm.Plate).get(acquisition.plate_id)
# check for image files already registered
img_filenames = [f.name for f in acquisition.microscope_image_files]
img_files = [
tm.MicroscopeImageFile(
name=f, acquisition_id=acquisition.id
)
for f in filenames
if img_regex.search(f) and
f not in img_filenames
]
# check for metadata already registered
meta_filenames = [f.name for f in acquisition.microscope_metadata_files]
meta_files = [
tm.MicroscopeMetadataFile(
name=secure_filename(f), acquisition_id=acquisition.id
)
for f in filenames
if metadata_regex.search(f) and
f not in meta_filenames
]
session.bulk_save_objects(img_files + meta_files)
# trigger creation of directories
acquisition.location
acquisition.microscope_metadata_location
# link root directory
path_to_link = os.path.join(
LibraryConfig().storage_home,
('experiment_{}'
'/plates/plate_{}'
'/acquisitions/acquisition_{}'
'/microscope_images'
.format(experiment.id, plate.id, acquisition.id)))
if not os.path.exists(path_to_link):
try:
os.symlink(path, path_to_link)
except Exception as err:
logger.debug(
"Error linking source directory `%s` to TM directory `%s`: %s",
path, path_to_link, err)
raise
else:
# path exists, check if it is correct
p1 = os.path.realpath(path)
p2 = os.path.realpath(path_to_link)
if p1 != p2:
raise ValueError(
"Acquisition {a} of plate {p} of experiment {e}"
" is already linked to directory `{d}`"
.format(
a=acquisition.id,
p=plate.id,
e=epxeriment.id,
d=p1))
microscope_files = session.query(tm.MicroscopeImageFile).filter_by(acquisition_id=acquisition.id).all()
for microscope_file in microscope_files:
microscope_file.location
microscope_file.status = 'COMPLETE'
return jsonify(message='ok')
def register_upload(experiment_id, acquisition_id):
"""
.. http:post:: /api/experiments/(string:experiment_id)/acquisitions/(string:acquisition_id)/upload/register
Notify the server that an upload for this acquisition is imminent.
The client has to wait for this response before uploading files.
**Example request**:
.. sourcecode:: http
Content-Type: application/json
{
"files": ["file1.png", "file2.png", ...]
}
**Example response**:
.. sourcecode:: http
HTTP/1.1 200 OK
Content-Type: application/json
{
"data": ["file1.png", "file2.png", ...]
}
:reqheader Authorization: JWT token issued by the server
:statuscode 200: no error
:statuscode 500: server error
"""
logger.info('register microscope files for upload')
data = request.get_json()
files = data['files']
if len(files) == 0:
raise MalformedRequestError(
'No files supplied. Cannot register upload.'
)
with tm.utils.ExperimentSession(experiment_id) as session:
experiment = session.query(tm.Experiment).one()
microscope_type = experiment.microscope_type
img_regex, metadata_regex = get_microscope_type_regex(microscope_type)
acquisition = session.query(tm.Acquisition).get(acquisition_id)
img_filenames = [f.name for f in acquisition.microscope_image_files]
img_files = [
tm.MicroscopeImageFile(
name=secure_filename(f), acquisition_id=acquisition.id
)
for f in files
if img_regex.search(f) and
secure_filename(f) not in img_filenames
]
meta_filenames = [f.name for f in acquisition.microscope_metadata_files]
meta_files = [
tm.MicroscopeMetadataFile(
name=secure_filename(f), acquisition_id=acquisition.id
)
for f in files
if metadata_regex.search(f) and
secure_filename(f) not in meta_filenames
]
session.bulk_save_objects(img_files + meta_files)
# Trigger creation of directories
acquisition.location
acquisition.microscope_images_location
acquisition.microscope_metadata_location
with tm.utils.ExperimentSession(experiment_id) as session:
image_filenames = session.query(tm.MicroscopeImageFile.name).\
filter(tm.MicroscopeImageFile.status != FileUploadStatus.COMPLETE).\
all()
metadata_filenames = session.query(tm.MicroscopeMetadataFile.name).\
filter(tm.MicroscopeMetadataFile.status != FileUploadStatus.COMPLETE).\
all()
all_filenames = image_filenames + metadata_filenames
logger.info('registered %d files', len(all_filenames))
return jsonify(data=[f.name for f in all_filenames])
def register(experiment_id, acquisition_id):
"""
.. http:post:: /api/experiments/(string:experiment_id)/acquisitions/(string:acquisition_id)/register
Pass the NFS path to the data to the server.
The client has to wait for this response before uploading files.
**Example request**:
.. sourcecode:: http
Content-Type: application/json
{
"path": "/fullpath/to/serversidedata"
}
**Example response**:
.. sourcecode:: http
HTTP/1.1 200 OK
Content-Type: application/json
{
"data": "/fullpath/to/serversidedata"
}
:reqheader Authorization: JWT token issued by the server
:statuscode 200: no error
:statuscode 500: server error
"""
logger.info('register microscope files')
data = request.get_json()
path = data['path']
logger.info('path given by the client: %s', path)
# Parse storage_home variable from tissuemaps.cfg file
parser = SafeConfigParser()
parser.read('/home/tissuemaps/.tmaps/tissuemaps.cfg')
storage_home_path = parser.get('tmlib', 'storage_home')
path_to_link = os.path.join(
storage_home_path,
'experiment_{}/plates/plate_{}/acquisitions/acquisition_{}/microscope_images'
)
filenames = [
f for f in os.listdir(path)
if (not f.startswith('.') and not os.path.isdir(os.path.join(path, f)))
]
with tm.utils.ExperimentSession(experiment_id) as session:
experiment = session.query(tm.Experiment).one()
microscope_type = experiment.microscope_type
img_regex, metadata_regex = get_microscope_type_regex(microscope_type)
acquisition = session.query(tm.Acquisition).get(acquisition_id)
# single plate only
plate = session.query(tm.Plate).one()
logger.info(
'path to link: %s',
path_to_link.format(experiment.id, plate.id, acquisition.id))
logger.info('experiment %s', experiment.id)
logger.info('acquisition %s', acquisition)
logger.info('plate %s', plate)
# check for image files already registered
img_filenames = [f.name for f in acquisition.microscope_image_files]
logger.debug('img_filenames %s', img_filenames)
img_files = [
tm.MicroscopeImageFile(name=f, acquisition_id=acquisition.id)
for f in filenames
if img_regex.search(f) and f not in img_filenames
]
# check for metadata already registered
meta_filenames = [
f.name for f in acquisition.microscope_metadata_files
]
meta_files = [
tm.MicroscopeMetadataFile(name=secure_filename(f),
acquisition_id=acquisition.id)
for f in filenames
if metadata_regex.search(f) and f not in meta_filenames
]
session.bulk_save_objects(img_files + meta_files)
# Trigger creation of directories
acquisition.location
#acquisition.microscope_images_location
acquisition.microscope_metadata_location
os.symlink(
path, path_to_link.format(experiment.id, plate.id, acquisition.id))
microscope_files = session.query(tm.MicroscopeImageFile).filter_by(
acquisition_id=acquisition.id).all()
for microscope_file in microscope_files:
microscope_file.location
microscope_file.status = 'COMPLETE'
return jsonify(message='ok')