fusion.json: Fix metadata parsing (#199)

* Fix metadata parsing & add test.

* docs

docs/source/version.5_2.rst

@@ -15,13 +15,14 @@ Developed in the `ConCat Lab <https://tu.berlin/en/concat>`_ at Technische Unive
 
 New features in ``yadg-5.2`` are:
 
-  - Implemented support for merged/appended files in :mod:`~yadg.extractors.eclab.mpr`. Test files taken from the data available at https://zenodo.org/doi/10.5281/zenodo.12165685. Thanks to Arnd Koeppe from KIT for bringing the issue up.
-  - Implemented support for the Modular Potentio technique in :mod:`~yadg.extractors.eclab.mpr`. Thanks to Graham Kimbell and Clea Burgel from Empa for providing test data.
-  - Implemented support for the Constant Current and Constant Voltage techniques in :mod:`~yadg.extractors.eclab.mpr`. Thanks to Carla Terboven from HZB for providing test data.
+  - Implemented support for merged/appended files in :mod:`yadg.extractors.eclab.mpr`. Test files taken from the data available at https://zenodo.org/doi/10.5281/zenodo.12165685. Thanks to Arnd Koeppe from KIT for bringing the issue up.
+  - Implemented support for the Modular Potentio technique in :mod:`yadg.extractors.eclab.mpr`. Thanks to Graham Kimbell and Clea Burgel from Empa for providing test data.
+  - Implemented support for the Constant Current and Constant Voltage techniques in :mod:`yadg.extractors.eclab.mpr`. Thanks to Carla Terboven from HZB for providing test data.
 
 Other changes in ``yadg-5.2`` are:
 
 Bug fixes in ``yadg-5.2`` include:
 
-  - Increased supported I-range values in :mod:`~yadg.extractors.eclab` up to 193.
-  - Implemented support for a 33-parameter GCPL file in :mod:`~yadg.extractors.eclab.mpr`.
+  - Increased supported I-range values in :mod:`yadg.extractors.eclab` up to 193.
+  - Implemented support for a 33-parameter GCPL file in :mod:`yadg.extractors.eclab.mpr`.
+  - Fixed parsing of optional metadata in :mod:`yadg.extractors.fusion.json`. Thanks to Emiliano Dal Molin for finding the bug and providing test data.

src/yadg/extractors/fusion/json.py

@@ -53,15 +53,13 @@
 
 
 def chromdata(jsdata: dict, uts: float) -> Dataset:
-    metadata = {
-        "method": jsdata.get("methodName", "n/a"),
-        "version": jsdata.get("softwareVersion", {}).get("version", None),
-        "datafile": jsdata.get("sequence", {}).get("location", None),
-    }
-
-    sampleid = jsdata.get("annotations", {}).get("name", None)
-    if sampleid is not None:
-        metadata["sampleid"] = sampleid
+    metadata = {}
+    metadata["method"] = jsdata["methodName"]
+    metadata["version"] = jsdata["softwareVersion"]["version"]
+    if jsdata.get("sequence") is not None:
+        metadata["datafile"] = jsdata["sequence"].get("location")
+    if jsdata.get("annotations") is not None:
+        metadata["sampleid"] = jsdata["annotations"].get("name", None)
 
     units = {
         "height": None,
@@ -138,13 +136,6 @@ def chromdata(jsdata: dict, uts: float) -> Dataset:
 
 
 def chromtrace(jsdata: dict, uts: float) -> DataTree:
-    metadata = {
-        "method": jsdata.get("methodName", "n/a"),
-        "sampleid": jsdata.get("annotations", {}).get("name", None),
-        "version": jsdata.get("softwareVersion", {}).get("version", None),
-        "datafile": jsdata.get("sequence", {}).get("location", None),
-    }
-
     # sort detector keys to ensure alphabetic order for ID matching
     traces = sorted(jsdata["detectors"].keys())
     vals = {}
@@ -184,7 +175,6 @@ def chromtrace(jsdata: dict, uts: float) -> DataTree:
         vals[detname] = fvals
 
     dt = DataTree.from_dict(vals)
-    dt.attrs = dict(original_metadata=metadata)
     return dt
 
 

tests/test_x_fusion_json.py

@@ -12,6 +12,7 @@
         "15p-Cu-10mA-01 - Jun 08 2022, 16;23.fusion-data",
         "AgPTFE28_100mA_NaS_01 - Aug 13 2021, 17;56.fusion-data",
         "AgPTFE28_100mA_NaS_01 - Aug 13 2021, 18;18.fusion-data",
+        "issue_198.fusion-data",
     ],
 )
 def test_fusion_json(infile, datadir):