Modifications required to include processing config from context

Author: clemgoyens

hypernets_processor/__init__.py

@@ -1,4 +1,3 @@
-from hypernets_processor.data_io.hypernets_reader import read_hypernets_data
 from hypernets_processor.data_io.hypernets_ds_builder import HypernetsDSBuilder
 from hypernets_processor.data_io.hypernets_writer import HypernetsWriter
 from hypernets_processor.main_processor import HypernetsProcessor

hypernets_processor/calibration/calibrate.py

@@ -23,5 +23,5 @@ def __init__(self):
     def get_names(self):
         return self.measurement_functions.keys()
 
-    def get_measurement_function(self,name):
+    def get_measurement_function(self,name) -> object:
         return self.measurement_functions[name]

hypernets_processor/calibration/measurement_functions/measurement_function_factory.py

@@ -4,7 +4,7 @@
 from hypernets_processor.version import __version__
 from hypernets_processor.utils.config import get_config_value
 import dataset
-
+import configparser
 
 """___Authorship___"""
 __author__ = "Sam Hunt"
@@ -36,6 +36,7 @@ def __init__(self, processor_config=None, job_config=None, logger=None):
         self.metadata_db = None
         self.anomoly_db = None
 
+
         # Unpack processor_config to set relevant attributes
         if processor_config is not None:
             self.unpack_config(processor_config)
@@ -52,7 +53,7 @@ def __init__(self, processor_config=None, job_config=None, logger=None):
 
         # Connect to anomoly database
         if "anomoly_db_url" in self.get_config_names():
-            self.anomoly_db = dataset.connect(self.get_config_value("anomoly_db_url")
+            self.anomoly_db = dataset.connect(self.get_config_value("anomoly_db_url"))
 
     def unpack_config(self, config, protected_values=None):
         """
@@ -61,14 +62,15 @@ def unpack_config(self, config, protected_values=None):
         :type config: configparser.RawConfigParser
         :param config: config data
         """
+        cp = configparser.ConfigParser()
+        cp.read(config)
 
         protected_values = [] if protected_values is None else protected_values
-
-        for section in config.sections():
-            for name in config[section].keys():
+        for section in cp.sections():
+            for name in cp[section].keys():
 
                 if name not in protected_values:
-                    value = get_config_value(config, section, name)
+                    value = get_config_value(cp, section, name)
                     self.set_config_value(name, value)
 
     def set_config_value(self, name, value):

hypernets_processor/context.py

@@ -1,3 +1,4 @@
+
 """
 Variable definitions for Hypernets land a water network data products
 """
@@ -42,7 +43,6 @@
                                                          "units": "nm",
                                                          "preferred_symbol": "wv"},
                                           "encoding": {'dtype': np.uint16, "scale_factor": 1.0, "offset": 0.0}},
-
                            "bandwidth": {"dim": [WL_DIM],
                                          "dtype": np.float32,
                                          "attributes": {},

hypernets_processor/data_io/format/variables.py

@@ -89,6 +89,7 @@ def create_ds_template(self, dim_sizes_dict, ds_format, propagate_ds=None):
         if self.context is not None:
 
             metadata_db = self.context.metadata_db
+            print(metadata_db)
 
             # Evaluate queries for metadata_db to populate product metadata
             metadata_db_query = None