Add files as argument in CLI

examples/apm/Write.NXapm.Example.1.ipynb

@@ -248,8 +248,8 @@
     "    INPUT_RANGE = input_range_file_name[case_id]\n",
     "    OUTPUT = output_file_name[case_id]\n",
     "\n",
-    "    ! dataconverter --reader apm --nxdl NXapm --input-file $ELN --input-file $OASIS \\\n",
-    "    --input-file $INPUT_RECON --input-file $INPUT_RANGE --output $OUTPUT"
+    "    ! dataconverter --reader apm --nxdl NXapm $ELN $OASIS \\\n",
+    "    $INPUT_RECON $INPUT_RANGE --output $OUTPUT"
    ]
   },
   {
@@ -369,7 +369,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "# use matplotlib and numpy to plot histogram data \n",
+    "# use matplotlib and numpy to plot histogram data\n",
     "xy = np.zeros([nbins, 2], np.float64)\n",
     "xy[:,0] = np.linspace(mqmin + mqincr, mqmax + mqincr, nbins, endpoint=True)\n",
     "xy[:,1] = 0.5  # * np.ones([nbins], np.float64)  # 0.5 to be able to plot logarithm you can not measure half an atom\n",
@@ -417,7 +417,7 @@
    "source": [
     "# save the figure\n",
     "figfn = nxs_file_name + \".MassToChargeStateRatio.png\"\n",
-    "fig.savefig(figfn, dpi=300, facecolor=\"w\", edgecolor=\"w\", orientation=\"landscape\", format=\"png\", \n",
+    "fig.savefig(figfn, dpi=300, facecolor=\"w\", edgecolor=\"w\", orientation=\"landscape\", format=\"png\",\n",
     "            transparent=False, bbox_inches=\"tight\", pad_inches=0.1, metadata=None)\n",
     "# plt.close(\"all\")\n",
     "print(f\"{figfn} stored to disk.\")"
@@ -484,7 +484,7 @@
    },
    "outputs": [],
    "source": [
-    "! dataconverter --reader apm --nxdl NXapm --input-file synthesize1 --output apm.case0.nxs"
+    "! dataconverter --reader apm --nxdl NXapm synthesize1 --output apm.case0.nxs"
    ]
   },
   {

examples/ellipsometry/README.md

@@ -9,7 +9,7 @@ This is an example to use the dataconvert with the `ellips` reader and the `NXel
 Just execute
 
 ```shell
-dataconverter --reader ellips --nxdl NXellipsometry --input-file eln_data.yaml --output SiO2onSi.nxs
+dataconverter --reader ellips --nxdl NXellipsometry eln_data.yaml --output SiO2onSi.nxs
 ```
 
 in this directory.

examples/em_nion/Write.NXem_nion.Example.1.ipynb

@@ -207,7 +207,7 @@
     "    SWIFT = swift_proj_file_name[case_id]\n",
     "    OUTPUT = output_file_name[case_id]\n",
     "\n",
-    "    ! dataconverter --reader em_nion --nxdl NXem --input-file $ELN --input-file $SWIFT --output $OUTPUT"
+    "    ! dataconverter --reader em_nion --nxdl NXem $ELN $SWIFT --output $OUTPUT"
    ]
   },
   {

examples/em_om/Write.NXem_ebsd.Example.1.ipynb

@@ -244,7 +244,7 @@
     "! dataconverter \\\n",
     "--reader em_om \\\n",
     "--nxdl NXem_ebsd \\\n",
-    "--input-file eln_data_em_om.yaml \\\n",
+    "eln_data_em_om.yaml \\\n",
     "--output \"em_om.case0.nxs\""
    ]
   },
@@ -280,7 +280,7 @@
     "    INPUT = input_data_file_name[case_id]\n",
     "    OUTPUT = output_file_name[case_id]\n",
     "\n",
-    "    ! dataconverter --reader em_om --nxdl NXem_ebsd --input-file $ELN --input-file $INPUT --output $OUTPUT"
+    "    ! dataconverter --reader em_om --nxdl NXem_ebsd $ELN $INPUT --output $OUTPUT"
    ]
   },
   {

examples/em_spctrscpy/Write.NXem.Example.1.ipynb

@@ -213,7 +213,7 @@
     "    INPUT = input_data_file_name[case_id]\n",
     "    OUTPUT = output_file_name[case_id]\n",
     "\n",
-    "    ! dataconverter --reader em_spctrscpy --nxdl NXem --input-file $ELN --input-file $INPUT --output $OUTPUT"
+    "    ! dataconverter --reader em_spctrscpy --nxdl NXem $ELN $INPUT --output $OUTPUT"
    ]
   },
   {
@@ -266,7 +266,7 @@
    },
    "outputs": [],
    "source": [
-    "! dataconverter --reader em_spctrscpy --nxdl NXem --input-file synthesize1 --output em_sp.case0.nxs"
+    "! dataconverter --reader em_spctrscpy --nxdl NXem synthesize1 --output em_sp.case0.nxs"
    ]
   },
   {

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

examples/mpes/README.md

@@ -10,9 +10,9 @@ If you want to use some example data you can find small example files in [`tests
 ```shell
 dataconverter --reader mpes \\
     --nxdl NXmpes \\
-    --input-file xarray_saved_small_calibration \\
-    --input-file config_file.json \\
-    --input-file eln_data.yaml \\
+    xarray_saved_small_calibration \\
+    config_file.json \\
+    eln_data.yaml \\
     --output mpes_example.nxs
 ```
 
@@ -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
 ```
 

pynxtools/dataconverter/README.md

@@ -16,17 +16,20 @@ Converts experimental data to NeXus/HDF5 files based on any provided NXDL.
 
 ```console
 user@box:~$ dataconverter --help
-Usage: dataconverter [OPTIONS]
+Usage: dataconverter [OPTIONS] [FILES]...
 
   The CLI entrypoint for the convert function
 
 Options:
-  --input-file TEXT               The path to the input data file to read.
-                                  (Repeat for more than one file.)
-  --reader [apm|ellips|em_nion|em_om|em_spctrscpy|example|hall|json_map|json_yml|mpes|rii_database|sts|transmission|xps]
+  --input-file TEXT               Deprecated: Please use the positional file
+                                  arguments instead. The path to the input
+                                  data file to read. (Repeat for more than one
+                                  file.)
+  --reader [apm|ellips|em_nion|em_om|em_spctrscpy|example|hall|json_map|json_yml|rii_database|transmission|xps|xrd|mpes]
                                   The reader to use. default="example"
   --nxdl TEXT                     The name of the NXDL file to use without
-                                  extension.
+                                  extension.This option is required if no '--
+                                  params-file' is supplied.
   --output TEXT                   The path to the output NeXus file to be
                                   generated.
   --generate-template             Just print out the template generated from
@@ -45,13 +48,13 @@ Options:
 #### Merge partial NeXus files into one
 
 ```console
-user@box:~$ dataconverter --nxdl nxdl --input-file partial1.nxs --input-file partial2.nxs
+user@box:~$ dataconverter --nxdl nxdl partial1.nxs partial2.nxs
 ```
 
 #### Map an HDF5/JSON/(Python Dict pickled in a pickle file)
 
 ```console
-user@box:~$ dataconverter --nxdl nxdl --input-file any_data.hdf5 --mapping my_custom_map.mapping.json
+user@box:~$ dataconverter --nxdl nxdl any_data.hdf5 --mapping my_custom_map.mapping.json
 ```
 
 #### You can find actual examples with data files at [`examples/json_map`](../../examples/json_map/).
@@ -60,7 +63,7 @@ user@box:~$ dataconverter --nxdl nxdl --input-file any_data.hdf5 --mapping my_cu
 #### Use with multiple input files
 
 ```console
-user@box:~$ dataconverter --nxdl nxdl --input_file metadata --input_file data.raw --input_file otherfile
+user@box:~$ dataconverter --nxdl nxdl metadata data.raw otherfile
 ```
 
 ## Writing a Reader

pynxtools/dataconverter/convert.py

@@ -22,16 +22,17 @@
 import logging
 import os
 import sys
-from typing import List, Tuple, Optional
 import xml.etree.ElementTree as ET
+from pathlib import Path
+from typing import List, Optional, Tuple
 
 import click
 import yaml
 
-from pynxtools.dataconverter.readers.base.reader import BaseReader
 from pynxtools.dataconverter import helpers
-from pynxtools.dataconverter.writer import Writer
+from pynxtools.dataconverter.readers.base.reader import BaseReader
 from pynxtools.dataconverter.template import Template
+from pynxtools.dataconverter.writer import Writer
 from pynxtools.nexus import nexus
 
 logger = logging.getLogger(__name__)
@@ -280,11 +281,15 @@ def parse_params_file(params_file):
 
 
 @click.command()
+@click.argument("files", nargs=-1, type=click.Path(exists=True))
 @click.option(
     "--input-file",
     default=[],
     multiple=True,
-    help="The path to the input data file to read. (Repeat for more than one file.)",
+    help=(
+        "Deprecated: Please use the positional file arguments instead. "
+        "The path to the input data file to read. (Repeat for more than one file.)"
+    ),
 )
 @click.option(
     "--reader",
@@ -295,8 +300,10 @@ def parse_params_file(params_file):
 @click.option(
     "--nxdl",
     default=None,
-    required=False,
-    help="The name of the NXDL file to use without extension.",
+    help=(
+        "The name of the NXDL file to use without extension."
+        "This option is required if no '--params-file' is supplied."
+    ),
 )
 @click.option(
     "--output",
@@ -333,6 +340,7 @@ def parse_params_file(params_file):
 )
 # pylint: disable=too-many-arguments
 def convert_cli(
+    files: Tuple[str, ...],
     input_file: Tuple[str, ...],
     reader: str,
     nxdl: str,
@@ -348,29 +356,44 @@ def convert_cli(
     if params_file:
         try:
             convert(**parse_params_file(params_file))
+            return
         except TypeError as exc:
             sys.tracebacklimit = 0
-            raise TypeError(
+            raise click.UsageError(
                 (
                     "Please make sure you have the following entries in your "
                     "parameter file:\n\n# NeXusParser Parameter File - v0.0.1"
                     "\n\ndataconverter:\n\treader: value\n\tnxdl: value\n\tin"
                     "put-file: value"
                 )
             ) from exc
-    else:
-        if nxdl is None:
-            sys.tracebacklimit = 0
-            raise IOError(
-                "\nError: Please supply an NXDL file with the option:"
-                " --nxdl <path to NXDL>"
-            )
-        if mapping:
-            reader = "json_map"
-            if mapping:
-                input_file = input_file + tuple([mapping])
-        convert(input_file, reader, nxdl, output, generate_template, fair, undocumented)
+    if nxdl is None:
+        raise click.UsageError("Missing option '--nxdl'")
+    if mapping:
+        reader = "json_map"
+        input_file = input_file + tuple([mapping])
 
+    file_list = []
+    for file in files:
+        if os.path.isdir(file):
+            p = Path(file)
+            for f in p.rglob("*"):
+                if f.is_file():
+                    file_list.append(str(f))
+            continue
+        file_list.append(file)
+
+    if input_file:
+        logger.warning(
+            "The --input-file option is deprecated. Please use the positional arguments instead."
+        )
 
-if __name__ == "__main__":
-    convert_cli()  # pylint: disable=no-value-for-parameter
+    convert(
+        tuple(file_list) + input_file,
+        reader,
+        nxdl,
+        output,
+        generate_template,
+        fair,
+        undocumented,
+    )

pynxtools/dataconverter/readers/json_map/README.md

@@ -21,7 +21,7 @@ There are some example files you can use:
 [data.json](/tests/data/dataconverter/readers/json_map/data.json)
 
 ```console
-user@box:~$ dataconverter --nxdl NXtest --input-file data.json --mapping data.mapping.json
+user@box:~$ dataconverter --nxdl NXtest data.json --mapping data.mapping.json
 ```
 
 ##### [Example](/examples/json_map/) with HDF5 files.
@@ -34,23 +34,23 @@ The mapping files will always be based on the Template the dataconverter generat
 The right hand side values of the Template keys are what you can modify.
 
 Here are the three different ways you can fill the right hand side of the Template keys:
-* Write the nested path in your datafile. This is indicated by a leading `/` before the word `entry` to make `/entry/data/current_295C` below. 
+* Write the nested path in your datafile. This is indicated by a leading `/` before the word `entry` to make `/entry/data/current_295C` below.
 Example:
 
 ```json
   "/ENTRY[entry]/DATA[data]/current_295C": "/entry/data/current_295C",
   "/ENTRY[entry]/NXODD_name/posint_value": "/a_level_down/another_level_down/posint_value",
 ```
 
-* Write the values directly in the mapping file for missing data from your data file. 
+* Write the values directly in the mapping file for missing data from your data file.
 
 ```json
 
   "/ENTRY[entry]/PROCESS[process]/program": "Bluesky",
   "/ENTRY[entry]/PROCESS[process]/program/@version": "1.6.7"
 ```
 
-* Write JSON objects with a link key. This follows the same link mechanism that the dataconverter implements. In the context of this reader, you can only use external links to your data files. In the example below, `current.nxs` is an already existing HDF5 file that we link to in our new NeXus file without copying over the data. The format is as follows: 
+* Write JSON objects with a link key. This follows the same link mechanism that the dataconverter implements. In the context of this reader, you can only use external links to your data files. In the example below, `current.nxs` is an already existing HDF5 file that we link to in our new NeXus file without copying over the data. The format is as follows:
 `"link": "<filename>:<path_in_file>"`
 Note: This only works for HDF5 files currently.
 

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)
                 )

pynxtools/dataconverter/readers/xps/README.md

@@ -23,8 +23,8 @@ An example script to run the XPS reader:
  ! dataconverter \
 --reader xps \
 --nxdl NXmpes \
---input-file $<xps-file path> \
---input-file $<eln-file path> \
+$<xps-file path> \
+$<eln-file path> \
 --output <output-file path>.test.nxs
 ```
 Note that none of the supported file format have data/values for all required and recommended fields and attributes in NXmpes. In order for the validation step of the **XPS** reader to pass,

pynxtools/dataconverter/readers/xrd/README.md

@@ -32,8 +32,8 @@ The reader can be run from Jupyter-notebook or Jupyter-lab with the following co
  ! dataconverter \
 --reader xrd \
 --nxdl NXxrd_pan \
---input-file $<xps-file location> \
---input-file $<eln-file location> \
+$<xps-file location> \
+$<eln-file location> \
 --output <output-file location>.nxs
 ```