diff --git a/src/aliby/pipeline.py b/src/aliby/pipeline.py index a9ed692ef5bc1a85817ed0bf437089bb767378c0..5336d427272cc78b26edd8cba96d882baf133474 100644 --- a/src/aliby/pipeline.py +++ b/src/aliby/pipeline.py @@ -84,7 +84,9 @@ class PipelineParameters(ParametersABC): directory = Path(general.get("directory", "../data")) - with dispatch_dataset(expt_id) as conn: + with dispatch_dataset( + expt_id, **general.get("server_info", {}) + ) as conn: directory = directory / conn.unique_name if not directory.exists(): directory.mkdir(parents=True) @@ -685,39 +687,39 @@ class Pipeline(ProcessABC): # Delete datasets to overwrite and update pipeline data # Use existing parameters - with h5py.File(filename, "a") as f: - pparams = PipelineParameters.from_yaml( - f.attrs["parameters"] - ).to_dict() - - for k, v in ow.items(): - if v: - for gname in self.writer_groups[k]: - if gname in f: - del f[gname] - - pparams[k] = config[k] - meta.add_fields( - { - "parameters": PipelineParameters.from_dict( - pparams - ).to_yaml() - }, - overwrite=True, - ) - - meta.run() - meta.add_fields( # Add non-logfile metadata - { - "aliby_version": version("aliby"), - "baby_version": version("aliby-baby"), - "omero_id": config["general"]["id"], - "image_id": image_id, - "parameters": PipelineParameters.from_dict( - pparams - ).to_yaml(), - } - ) + # with h5py.File(filename, "a") as f: + # pparams = PipelineParameters.from_yaml( + # f.attrs["parameters"] + # ).to_dict() + + # for k, v in ow.items(): + # if v: + # for gname in self.writer_groups[k]: + # if gname in f: + # del f[gname] + + # pparams[k] = config[k] + # meta.add_fields( + # { + # "parameters": PipelineParameters.from_dict( + # pparams + # ).to_yaml() + # }, + # overwrite=True, + # ) + + meta.run() + meta.add_fields( # Add non-logfile metadata + { + "aliby_version": version("aliby"), + "baby_version": version("aliby-baby"), + "omero_id": config["general"]["id"], + "image_id": image_id, + "parameters": PipelineParameters.from_dict( + pparams + ).to_yaml(), + } + ) tps = min(general_config["tps"], image.data.shape[0])