From f982c0e16636a6a5f87870f868014ab47188b871 Mon Sep 17 00:00:00 2001 From: domna Date: Wed, 21 Feb 2024 10:59:09 +0100 Subject: [PATCH] Remove remaining `--input-file` arguments --- examples/json_map/README.md | 6 +++--- examples/mpes/README.md | 4 ++-- pynxtools/dataconverter/readers/json_map/reader.py | 8 +++++--- tests/dataconverter/test_convert.py | 1 - 4 files changed, 10 insertions(+), 9 deletions(-) diff --git a/examples/json_map/README.md b/examples/json_map/README.md index 788cb6890..14990b65f 100644 --- a/examples/json_map/README.md +++ b/examples/json_map/README.md @@ -19,17 +19,17 @@ user@box:~$ dataconverter --nxdl NXmynxdl --generate-template > mynxdl.mapping.j ### Automatically merge partial NeXus files ```console -user@box:~$ dataconverter --nxdl NXiv_temp --input-file voltage_and_temperature.nxs --input-file current.nxs --output auto_merged.nxs +user@box:~$ dataconverter --nxdl NXiv_temp voltage_and_temperature.nxs current.nxs --output auto_merged.nxs ``` ### Map and copy over data to new NeXus file ```console -user@box:~$ dataconverter --nxdl NXiv_temp --mapping merge_copied.mapping.json --input-file voltage_and_temperature.nxs --input-file current.nxs --output merged_copied.nxs +user@box:~$ dataconverter --nxdl NXiv_temp --mapping merge_copied.mapping.json voltage_and_temperature.nxs current.nxs --output merged_copied.nxs ``` ### Map and link over data to new NeXus file ```console -user@box:~$ dataconverter --nxdl NXiv_temp --mapping merge_linked.mapping.json --input-file voltage_and_temperature.nxs --input-file current.nxs --output merged_linked.nxs +user@box:~$ dataconverter --nxdl NXiv_temp --mapping merge_linked.mapping.json voltage_and_temperature.nxs current.nxs --output merged_linked.nxs ``` ## Contact person in FAIRmat for this reader diff --git a/examples/mpes/README.md b/examples/mpes/README.md index d5f682fb3..3947c172f 100644 --- a/examples/mpes/README.md +++ b/examples/mpes/README.md @@ -23,8 +23,8 @@ For XPS data you may use the data in [`tests/data/dataconverter/readers/xps`](ht ```shell dataconverter --reader xps \\ --nxdl NXmpes \\ - --input-file eln_data.yaml \\ - --input-file In-situ_PBTTT_XPS_SPECS.xml \\ + eln_data.yaml \\ + In-situ_PBTTT_XPS_SPECS.xml \\ --output xps_example.nxs ``` diff --git a/pynxtools/dataconverter/readers/json_map/reader.py b/pynxtools/dataconverter/readers/json_map/reader.py index 80d97fad3..a6c5d8883 100644 --- a/pynxtools/dataconverter/readers/json_map/reader.py +++ b/pynxtools/dataconverter/readers/json_map/reader.py @@ -16,16 +16,17 @@ # limitations under the License. # """An example reader implementation for the DataConverter.""" -from typing import Tuple, Any import json import pickle +from typing import Any, Tuple + import numpy as np import xarray from mergedeep import merge +from pynxtools.dataconverter import hdfdict from pynxtools.dataconverter.readers.base.reader import BaseReader from pynxtools.dataconverter.template import Template -from pynxtools.dataconverter import hdfdict def parse_slice(slice_string): @@ -211,7 +212,7 @@ def read( {x: "/hierarchical/path/in/your/datafile" for x in template} ) raise IOError( - "Please supply a JSON mapping file: --input-file" + "Please supply a JSON mapping file: " " my_nxdl_map.mapping.json\n\n You can use this " "template for the required fields: \n" + str(template) ) @@ -228,3 +229,4 @@ def read( # This has to be set to allow the convert script to use this reader. Set it to "MyDataReader". READER = JsonMapReader +READER = JsonMapReader diff --git a/tests/dataconverter/test_convert.py b/tests/dataconverter/test_convert.py index a631e463a..3d316d7e4 100644 --- a/tests/dataconverter/test_convert.py +++ b/tests/dataconverter/test_convert.py @@ -146,7 +146,6 @@ def test_links_and_virtual_datasets(tmp_path): "NXtest", "--reader", "example", - "--input-file", os.path.join(dirpath, "testdata.json"), "--output", os.path.join(tmp_path, "test_output.h5"),