add --set-global-attr key value option

to facilitate dynamic replacement of `{{key}}` in the given file

NRS11/globalAttributes_NRS11.yaml

@@ -31,7 +31,7 @@ time_coverage_end: AUTOPOPULATE
 time_coverage_duration: P1D
 time_coverage_resolution: P60S
 platform: NOAA NRS11 mooring
-instrument: AUH model ITC-1032, SN ####
+instrument: "AUH model ITC-1032, SN {{serial_number}}"
 cdm_data_type: TimeSeries
 references: >-
   Computation of single-sided mean-square sound pressure spectral density with 1 Hz resolution

justfile

@@ -114,6 +114,7 @@ main-nrs11 date='20200101' *more_args='':
                  --gs \
                  --json-base-dir=$WS/noaa-passive-bioacoustic_nrs_11_2019-2021 \
                  --global-attrs="$WS/globalAttributes_NRS11.yaml" \
+                 --set-global-attr serial_number "000000" \
                  --variable-attrs="$WS/variableAttributes_NRS11.yaml" \
                  --voltage-multiplier=2.5 \
                  --sensitivity-uri="$WS/NRS11_H5R6_sensitivity_hms5kHz.nc" \
@@ -139,6 +140,7 @@ main-nrs11-multiple-days year month *days="":
              --gs \
              --json-base-dir=$WS/noaa-passive-bioacoustic_nrs_11_2019-2021 \
              --global-attrs="$WS/globalAttributes_NRS11.yaml" \
+             --set-global-attr serial_number "000000" \
              --variable-attrs="$WS/variableAttributes_NRS11.yaml" \
              --voltage-multiplier=2.5 \
              --sensitivity-uri="$WS/NRS11_H5R6_sensitivity_hms5kHz.nc" \

src/main.py

@@ -62,6 +62,7 @@ def main(opts):
         output_prefix=opts.output_prefix,
         gen_csv=opts.gen_csv,
         global_attrs_uri=opts.global_attrs,
+        set_global_attrs=opts.set_global_attrs,
         variable_attrs_uri=opts.variable_attrs,
         voltage_multiplier=opts.voltage_multiplier,
         sensitivity_uri=opts.sensitivity_uri,

src/main_args.py

@@ -39,6 +39,18 @@ def parse_arguments():
         help="URI of JSON file with global attributes to be added to the NetCDF file.",
     )
 
+    parser.add_argument(
+        "--set-global-attr",
+        type=str,
+        nargs=2,
+        default=None,
+        metavar=("key", "value"),
+        dest="set_global_attrs",
+        action="append",
+        help="Replace {{key}} with the given value for every occurrence of {{key}}"
+             " in the global attrs file.",
+    )
+
     parser.add_argument(
         "--variable-attrs",
         type=str,

src/process_helper.py

@@ -40,6 +40,7 @@ def __init__(
         gen_netcdf: bool = True,
         gen_csv: bool = False,
         global_attrs_uri: Optional[str] = None,
+        set_global_attrs: Optional[list[list[str]]] = None,
         variable_attrs_uri: Optional[str] = None,
         voltage_multiplier: Optional[float] = None,
         sensitivity_uri: Optional[str] = None,
@@ -61,6 +62,8 @@ def __init__(
             True to also generate CSV version of the result.
         :param global_attrs_uri:
             URI of JSON file with global attributes to be added to the NetCDF file.
+        :param set_global_attrs:
+            List of [key, value] pairs to be considered for the global attributes.
         :param variable_attrs_uri:
             URI of JSON file with variable attributes to be added to the NetCDF file.
         :param voltage_multiplier:
@@ -86,6 +89,7 @@ def __init__(
             + f"\n    gen_netcdf:             {gen_netcdf}"
             + f"\n    gen_csv:                {gen_csv}"
             + f"\n    global_attrs_uri:       {global_attrs_uri}"
+            + f"\n    set_global_attrs:       {set_global_attrs}"
             + f"\n    variable_attrs_uri:     {variable_attrs_uri}"
             + f"\n    voltage_multiplier:     {voltage_multiplier}"
             + f"\n    sensitivity_uri:        {sensitivity_uri}"
@@ -106,7 +110,7 @@ def __init__(
 
         self.metadata_helper = MetadataHelper(
             self.logger,
-            self._load_attributes("global", global_attrs_uri),
+            self._load_attributes("global", global_attrs_uri, set_global_attrs),
             self._load_attributes("variable", variable_attrs_uri),
         )
 
@@ -140,14 +144,20 @@ def __init__(
         pathlib.Path(output_dir).mkdir(exist_ok=True)
 
     def _load_attributes(
-        self, what: str, attrs_uri: Optional[str]
+        self,
+        what: str,
+        attrs_uri: Optional[str],
+        set_attrs: Optional[list[list[str]]] = None,
     ) -> Optional[OrderedDict[str, Any]]:
         if attrs_uri:
             self.logger.info(f"Loading {what} attributes from {attrs_uri=}")
             filename = self.file_helper.get_local_filename(attrs_uri)
             if filename is not None:
                 with open(filename, "r", encoding="UTF-8") as f:
-                    return parse_attributes(f.read(), pathlib.Path(filename).suffix)
+                    res = parse_attributes(f.read(), pathlib.Path(filename).suffix)
+                    for k, v in set_attrs or []:
+                        res[k] = v
+                    return res
             else:
                 self.logger.error(f"Unable to resolve '{attrs_uri=}'. Ignoring it.")
         else:
@@ -287,15 +297,18 @@ def process_segment_at_hour_minute(self, at_hour: int, at_minute: int):
 
     def _get_global_attributes(self, year: int, month: int, day: int):
         coverage_date = f"{year:04}-{month:02}-{day:02}"
+        global_attrs = {
+            "time_coverage_start": f"{coverage_date} 00:00:00Z",
+            "time_coverage_end": f"{coverage_date} 23:59:00Z",
+            "date_created": datetime.utcnow().strftime("%Y-%m-%d"),
+        }
         md_helper = self.metadata_helper
-        md_helper.set_some_global_attributes(
-            {
-                "time_coverage_start": f"{coverage_date} 00:00:00Z",
-                "time_coverage_end": f"{coverage_date} 23:59:00Z",
-                "date_created": datetime.utcnow().strftime("%Y-%m-%d"),
-            }
-        )
+        md_helper.set_some_global_attributes(global_attrs)
         # TODO get PyPAM version from somewhere
-        snippets = {"{{PyPAM_version}}": "0.2.0"}
+        snippets = {"{{PyPAM_version}}": "0.3.0"}
         global_attrs = md_helper.get_global_attributes()
+        # for each, key, have the {{key}} snippet for replacement
+        # in case it is used in any values:
+        for k, v in global_attrs.items():
+            snippets["{{" + k + "}}"] = v
         return replace_snippets(global_attrs, snippets)