diff --git a/data/_SLURM_Image_Transfer.py b/data/_SLURM_Image_Transfer.py index c7f1f7b..bc45d1a 100644 --- a/data/_SLURM_Image_Transfer.py +++ b/data/_SLURM_Image_Transfer.py @@ -193,7 +193,7 @@ def save_as_ome_tiff(conn, image, folder_name=None): f.write(piece) -def save_as_zarr(suuid, image, folder_name=None): +def save_as_zarr(conn, suuid, image, folder_name=None): extension = "zarr" name = os.path.basename(image.getName()) img_name = "%s.%s" % (name, extension) @@ -216,8 +216,7 @@ def save_as_zarr(suuid, image, folder_name=None): # command = f'omero zarr -s "$CONFIG_omero_master_host" -k "{suuid}" export --bf Image:{image.getId()}' cmd1 = 'export JAVA_HOME=$(readlink -f /usr/bin/java | sed "s:/bin/java::")' - # TODO: replace "omeroserver" with a lookup, very likely the client/gateway knows the server - command = f'omero zarr -s "omeroserver" -k "{suuid}" --output {exp_dir} export Image:{image.getId()}' + command = f'omero zarr -s "{conn.host}" -k "{suuid}" --output {exp_dir} export Image:{image.getId()}' cmd = cmd1 + " && " + command print(cmd) process = subprocess.Popen( @@ -457,7 +456,7 @@ def get_t_range(size_t, script_params): else: save_as_ome_tiff(conn, img, folder_name) elif format == 'ZARR': - save_as_zarr(suuid, img, folder_name) + save_as_zarr(conn, suuid, img, folder_name) else: size_x = pixels.getSizeX() size_y = pixels.getSizeY() diff --git a/workflows/SLURM_CellPose_Segmentation.py b/workflows/SLURM_CellPose_Segmentation.py index 38e3f0c..82bba8b 100644 --- a/workflows/SLURM_CellPose_Segmentation.py +++ b/workflows/SLURM_CellPose_Segmentation.py @@ -113,7 +113,7 @@ def runScript(): client = omscripts.client(params) # Unpack script input values - cellpose_version = unwrap(client.getInput("Version")) + cellpose_version = unwrap(client.getInput("CellPose_Version")) zipfile = unwrap(client.getInput("Folder_Name")) email = unwrap(client.getInput("E-mail")) if email == _DEFAULT_MAIL: