def test_upload_ln_s_no_access(self):
txt = 'hello\n'
omero_data_dir = '/tmp'
f = create_path(suffix=".txt")
f.write_text(txt)
with pytest.raises(omero.ApiUsageException):
upload_ln_s(self.client, f, omero_data_dir, 'text/plain')
def main(conn, filepath):
path = Path(filepath)
filename = path.name
if path.suffix != '.zip':
sys.exit("Not a zip file")
img_name = path.stem
tmp = list(conn.getObjects("Image", attributes={"name": img_name}))
if len(tmp) == 0:
sys.exit("No Image found")
if len(tmp) > 1:
sys.exit("More than one Image found")
tgt = tmp[0]
existingfas = set(
a.getFile().name for a in tgt.listAnnotations()
if isinstance(a, omero.gateway.FileAnnotationWrapper))
if filename in existingfas:
sys.exit("File already attached.")
print("Attaching {} to Image {} [{}]".format(path.resolve(), tgt.getName(), tgt.getId()))
if not DRY_RUN:
fo = upload_ln_s(conn.c, path.resolve(), OMERO_DATA_DIR, MIMETYPE)
fa = omero.model.FileAnnotationI()
fa.setFile(fo._obj)
fa.setNs(omero.rtypes.rstring(NAMESPACE))
fa = conn.getUpdateService().saveAndReturnObject(fa)
fa = omero.gateway.FileAnnotationWrapper(conn, fa)
tgt.linkAnnotation(fa)
def main(conn, args):
path = Path(args.file)
filename = path.name
target_type = args.target.split(":")[0]
target_id = args.target.split(":")[1]
tmp = list(conn.getObjects(target_type, attributes={"id": target_id}))
if len(tmp) == 0:
sys.exit("Target found")
if len(tmp) > 1:
sys.exit("More than one Target found")
tgt = tmp[0]
existingfas = set(a.getFile().name for a in tgt.listAnnotations()
if isinstance(a, omero.gateway.FileAnnotationWrapper))
if filename in existingfas:
sys.exit("File already attached.")
print("Attaching {} to {} {} [{}]".format(path.resolve(), target_type,
tgt.getName(), tgt.getId()))
fo = upload_ln_s(conn.c, path.resolve(), OMERO_DATA_DIR, args.mimetype)
fa = omero.model.FileAnnotationI()
fa.setFile(fo._obj)
fa.setNs(omero.rtypes.rstring(args.namespace))
fa = conn.getUpdateService().saveAndReturnObject(fa)
fa = omero.gateway.FileAnnotationWrapper(conn, fa)
tgt.linkAnnotation(fa)
def upload_and_link(conn, attachment, project):
fo = upload_ln_s(conn.c, attachment, OMERO_DATA_DIR, MIMETYPE)
fa = FileAnnotationI()
fa.setFile(fo._obj)
fa.setNs(omero.rtypes.rstring(NAMESPACE))
fa = conn.getUpdateService().saveAndReturnObject(fa)
fa = omero.gateway.FileAnnotationWrapper(conn, fa)
project.linkAnnotation(fa)
def upload_and_link(conn, target, attachment):
print("upload_and_link", attachment)
attachment = os.path.join(FILESETS_DIR, attachment)
fo = upload_ln_s(conn.c, attachment, OMERO_DATA_DIR, MIMETYPE)
fa = FileAnnotationI()
fa.setFile(fo._obj)
fa.setNs(omero.rtypes.rstring(NAMESPACE))
fa = conn.getUpdateService().saveAndReturnObject(fa)
fa = omero.gateway.FileAnnotationWrapper(conn, fa)
target.linkAnnotation(fa)
def upload_and_link(conn, attachment, image):
fa = image.getAnnotation(ns=NAMESPACE)
if fa is not None:
log.warning("Found file annotation. Skipping upload")
return
log.info("Uploading and linking %s to %s" % (attachment, image.getName()))
fo = upload_ln_s(conn.c, attachment, OMERO_DATA_DIR, MIMETYPE)
fa = FileAnnotationI()
fa.setFile(fo._obj)
fa.setNs(omero.rtypes.rstring(NAMESPACE))
fa = conn.getUpdateService().saveAndReturnObject(fa)
fa = omero.gateway.FileAnnotationWrapper(conn, fa)
image.linkAnnotation(fa)
def link(conn, target, attachment, is_image):
fo = upload_ln_s(conn.c, attachment, OMERO_DATA_DIR, MIMETYPE)
fa = omero.model.FileAnnotationI()
fa.setFile(fo._obj)
fa.setNs(omero.rtypes.rstring(NAMESPACE))
fa = conn.getUpdateService().saveAndReturnObject(fa)
fa = omero.gateway.FileAnnotationWrapper(conn, fa)
if is_image:
tg = conn.getObject("Image", target.getId().getValue())
tg.linkAnnotation(fa)
else:
for d in target:
tg = conn.getObject("Dataset", d.getId().getValue())
tg.linkAnnotation(fa)
def test_upload_ln_s(self):
txt = 'hello\n'
omero_data_dir = self.root.sf.getConfigService().getConfigValue(
'omero.data.dir')
assert omero_data_dir
f = create_path(suffix=".txt")
f.write_text(txt)
ofile = upload_ln_s(self.client, f, omero_data_dir, 'text/plain')
assert ofile.getHash() == 'f572d396fae9206628714fb2ce00f72e94f2258f'
assert ofile.getSize() == 6
with ofile.asFileObj() as fo:
assert fo.read().decode('utf-8') == txt
omero_path = os.path.join(omero_data_dir, 'Files',
long_to_path(ofile.id))
assert os.path.islink(omero_path)
assert os.readlink(omero_path) == str(f)
def main(conn):
for im in get_images(conn):
print('Image: %d' % im.id)
mask_files, filenames = get_mask_files(im)
attached = set(get_label_files_in_t_order(im, filenames, check=False))
for mf in mask_files:
if mf in attached:
continue
print('Uploading: %s' % mf)
if not DRYRUN:
fo = upload_ln_s(conn.c, mf, OMERO_DATA_DIR, 'image/tiff')
fa = omero.model.FileAnnotationI()
fa.setFile(fo._obj)
fa.setNs(omero.rtypes.rstring(NAMESPACE))
fa = conn.getUpdateService().saveAndReturnObject(fa)
fa = omero.gateway.FileAnnotationWrapper(conn, fa)
im.linkAnnotation(fa)
for im in get_images(conn):
print('Image: %d' % im.id)
rois = create_rois(im)
if not DRYRUN:
save_rois(conn, im, rois)
def main(conn):
image_attachment_map, dataset_attachment_map = get_feature_files()
errors = []
for im in get_images(conn):
print('Image: %d' % im.id)
existing = existing_file_attachments(im)
try:
seg = image_attachment_map[im.name]
except KeyError:
errors.append('No segmentation found for {}'.format(im.name))
continue
if os.path.basename(seg) in existing:
print('Skipping {} ➔ {}'.format(seg, im.name))
continue
print('Uploading (in-place) {} ➔ {}'.format(seg, im.name))
if not DRYRUN:
fo = upload_ln_s(conn.c, seg, OMERO_DATA_DIR, 'image/tiff')
fa = omero.model.FileAnnotationI()
fa.setFile(fo._obj)
fa.setNs(omero.rtypes.rstring(NAMESPACE))
fa = conn.getUpdateService().saveAndReturnObject(fa)
fa = omero.gateway.FileAnnotationWrapper(conn, fa)
im.linkAnnotation(fa)
if errors:
print('{} errors:'.format(len(errors)))
for err in errors:
print(err)
for ds in get_datasets(conn):
print('Dataset:{} {}'.format(ds.id, ds.name))
existing = existing_file_attachments(ds)
features = dataset_attachment_map[ds.name]
if features in existing:
print('Skipping {} ➔ {}'.format(features, ds.name))
continue
print('Uploading {} ➔ {}'.format(features, ds.name))
if not DRYRUN:
fo = conn.c.upload(features, type='text/tab-separated-values')
fa = omero.model.FileAnnotationI()
fa.setFile(omero.model.OriginalFileI(fo.id, False))
fa.setNs(rstring(NAMESPACE))
link = omero.model.DatasetAnnotationLinkI()
link.setParent(ds._obj)
link.setChild(fa)
link = conn.getUpdateService().saveAndReturnObject(link)
roisvc = conn.getRoiService()
for im in get_images(conn):
if SKIP_IF_EXISTING_ROIS and roisvc.findByImage(im.id, None).rois:
print('Image:{} {} has ROIs, skipping'.format(im.id, im.name))
continue
print('Image:{} {}'.format(im.id, im.name))
try:
labels = get_labels(im, image_attachment_map)
rois = create_rois(im, labels)
if not DRYRUN:
save_rois(conn, im, rois)
except KeyError:
print('No segmentation found for {}'.format(im.name))
except ValueError as e:
print('ERROR in {}: {}'.format(im.name, e))