Merge pull request #130 from cmu-delphi/development

Development

Author: dmytrotsko

src/fixtures/available_geography.json

@@ -4,7 +4,7 @@
       "pk": 1,
       "fields": {
         "name": "county",
-        "display_name": "ADM2 (e.g. U.S. counties)",
+        "display_name": "County/ADM 2",
         "display_order_number": 3,
         "used_in": "signals",
         "created": "2023-08-09T19:23:22.597131",
@@ -28,7 +28,7 @@
       "pk": 3,
       "fields": {
         "name": "hrr",
-        "display_name": "Hospital Referral Regions (HRRs)",
+        "display_name": "Hospital Referral Region (HRR)",
         "display_order_number": 6,
         "used_in": "signals",
         "created": "2023-08-09T19:23:22.597131",
@@ -40,7 +40,7 @@
       "pk": 4,
       "fields": {
         "name": "msa",
-        "display_name": "Metropolitan Statistical Areas (MSAs)",
+        "display_name": "Metropolitan Statistical Area (MSA)",
         "display_order_number": 5,
         "used_in": "signals",
         "created": "2023-08-09T19:23:22.597131",
@@ -64,7 +64,7 @@
       "pk": 6,
       "fields": {
         "name": "state",
-        "display_name": "ADM1 (e.g. U.S. states)",
+        "display_name": "State/ADM 1",
         "display_order_number": 2,
         "used_in": "signals",
         "created": "2023-08-09T19:23:22.597131",

src/signal_sets/resources.py

@@ -26,20 +26,20 @@ def process_geographic_scope(row) -> None:
     """
     Processes geographic scope.
     """
-    if row["Geo Scope with index"]:
-        geographic_scope = row["Geo Scope with index"]
+    if row["Geographic Coverage"]:
+        geographic_scope = row["Geographic Coverage"]
         geographic_scope_obj, _ = GeographicScope.objects.get_or_create(
             name=geographic_scope, used_in="signal_sets"
         )
-        row["Geo Scope with index"] = geographic_scope_obj.id
+        row["Geographic Coverage"] = geographic_scope_obj.id
 
 
 def process_severity_pyramid_rungs(row) -> None:
     """
     Processes pathogen.
     """
-    if row["Severity Pyramid Rung(s)"]:
-        severity_pyramid_rungs = row["Severity Pyramid Rung(s)"].split(",")
+    if row["Surveillance Categories"]:
+        severity_pyramid_rungs = row["Surveillance Categories"].split(",")
         for severity_pyramid_rung in severity_pyramid_rungs:
             severity_pyramid_rung = severity_pyramid_rung.strip()
             severity_pyramid_rung_obj, _ = SeverityPyramidRung.objects.get_or_create(
@@ -65,18 +65,18 @@ def process_datasources(row) -> None:
     """
     Processes data source.
     """
-    if row["Data Source"]:
-        data_source = row["Data Source"]
+    if row["Original Data Provider"]:
+        data_source = row["Original Data Provider"]
         data_source_obj, _ = DataSource.objects.get_or_create(name=data_source)
-        row["Data Source"] = data_source_obj
+        row["Original Data Provider"] = data_source_obj
 
 
 def fix_boolean_fields(row) -> Any:
     """
     Fixes boolean fields.
     """
     fields = [
-        "Include in signal app",
+        "Include in indicator app",
     ]
     for k in fields:
         if row[k] == "TRUE":
@@ -88,9 +88,9 @@ def fix_boolean_fields(row) -> Any:
 
 class SignalSetResource(resources.ModelResource):
 
-    name = Field(attribute="name", column_name="Signal Set name* ")
-    short_name = Field(attribute="short_name", column_name="Signal Set Short Name")
-    description = Field(attribute="description", column_name="Signal Set Description*")
+    name = Field(attribute="name", column_name="Indicator Set name* ")
+    short_name = Field(attribute="short_name", column_name="Indicator Set Short Name")
+    description = Field(attribute="description", column_name="Indicator Set Description*")
     maintainer_name = Field(
         attribute="maintainer_name", column_name="Maintainer/\nKey Contact *"
     )
@@ -100,7 +100,7 @@ class SignalSetResource(resources.ModelResource):
     organization = Field(attribute="organization", column_name="Organization")
     data_source = Field(
         attribute="data_source",
-        column_name="Data Source",
+        column_name="Original Data Provider",
         widget=widgets.ForeignKeyWidget(DataSource, field="name"),
     )
     endpoint = Field(attribute="endpoint", column_name="Endpoint")
@@ -115,12 +115,12 @@ class SignalSetResource(resources.ModelResource):
     data_type = Field(attribute="data_type", column_name="Type(s) of Data*")
     geographic_scope = Field(
         attribute="geographic_scope",
-        column_name="Geo Scope with index",
+        column_name="Geographic Coverage",
         widget=widgets.ForeignKeyWidget(GeographicScope),
     )
     geographic_granularity = Field(
         attribute="geographic_granularity",
-        column_name="Geographic Granularity*",
+        column_name="Geographic Levels",
     )
     preprocessing_description = Field(
         attribute="preprocessing_description",
@@ -142,21 +142,18 @@ class SignalSetResource(resources.ModelResource):
         attribute="reporting_lag", column_name="Reporting Lag (nominal)"
     )
     demographic_scope = Field(
-        attribute="demographic_scope", column_name="Demographic Scope"
+        attribute="demographic_scope", column_name="Population"
     )
     revision_cadence = Field(
         attribute="revision_cadence", column_name="Revision Cadence"
     )
-    demographic_scope = Field(
-        attribute="demographic_scope", column_name="Demographic Scope*"
-    )
     demographic_granularity = Field(
-        attribute="demographic_granularity", column_name="Demographic Granularity*"
+        attribute="demographic_granularity", column_name="Population Stratifiers"
     )
     censoring = Field(attribute="censoring", column_name="Censoring")
     missingness = Field(attribute="missingness", column_name="Missingness")
     dua_required = Field(attribute="dua_required", column_name="DUA required?")
-    license = Field(attribute="license", column_name="License ")
+    license = Field(attribute="license", column_name="Data Use Terms")
     dataset_location = Field(
         attribute="dataset_location", column_name="Dataset Location"
     )
@@ -218,7 +215,7 @@ def save_instance(self, instance, is_create, row, **kwargs):
             pass
 
     def skip_row(self, instance, original, row, import_validation_errors=None):
-        if not row["Include in signal app"]:
+        if not row["Include in indicator app"]:
             return True
 
     def after_import_row(self, row, row_result, **kwargs):
@@ -227,7 +224,7 @@ def after_import_row(self, row, row_result, **kwargs):
             for pathogen in row["Pathogen(s)/Syndrome(s)"].split(","):
                 pathogen = Pathogen.objects.get(name=pathogen, used_in="signal_sets")
                 signal_set_obj.pathogens.add(pathogen)
-            for severity_pyramid_rung in row["Severity Pyramid Rung(s)"].split(","):
+            for severity_pyramid_rung in row["Surveillance Categories"].split(","):
                 severity_pyramid_rung = SeverityPyramidRung.objects.filter(
                     name=severity_pyramid_rung,
                     used_in="signal_sets"

src/signals/resources.py

@@ -33,7 +33,7 @@ def fix_boolean_fields(row) -> Any:
         "Is Cumulative",
         "Has StdErr",
         "Has Sample Size",
-        "Include in signal app",
+        "Include in indicator app",
     ]
     for k in fields:
         if row[k] == "TRUE":
@@ -60,18 +60,18 @@ def process_signal_type(row) -> None:
     """
     Processes signal type.
     """
-    if row["Signal Type"]:
-        signal_type = row["Signal Type"]
+    if row["Indicator Type"]:
+        signal_type = row["Indicator Type"]
         signal_type_obj, _ = SignalType.objects.get_or_create(name=signal_type)
-        row["Signal Type"] = signal_type_obj
+        row["Indicator Type"] = signal_type_obj
 
 
 def process_format_type(row) -> None:
     """
     Processes format type.
     """
     if row["Format"]:
-        format_type = row["Format"]
+        format_type = row["Format"].strip()
         format_type_obj, _ = FormatType.objects.get_or_create(name=format_type)
         row["Format"] = format_type_obj
     else:
@@ -82,24 +82,24 @@ def process_severity_pyramid_rungs(row) -> None:
     """
     Processes severity pyramid rungs.
     """
-    if row["Severity Pyramid Rungs"]:
-        severity_pyramid_rung = row["Severity Pyramid Rungs"].strip()
+    if row["Surveillance Categories"]:
+        severity_pyramid_rung = row["Surveillance Categories"].strip()
         if severity_pyramid_rung.startswith("None"):
-            row["Severity Pyramid Rungs"] = None
+            row["Surveillance Categories"] = None
         else:
             severity_pyramid_rung_obj, _ = SeverityPyramidRung.objects.get_or_create(
                 name=severity_pyramid_rung,
                 used_in="signals",
                 defaults={"used_in": "signals", "display_name": severity_pyramid_rung},
             )
-        row["Severity Pyramid Rungs"] = severity_pyramid_rung_obj.id
+        row["Surveillance Categories"] = severity_pyramid_rung_obj.id
     else:
         none_severity_pyramid_rung_obj, _ = SeverityPyramidRung.objects.get_or_create(
             name="N/A",
             used_in="signals",
             defaults={"used_in": "signals", "display_name": "N/A"},
         )
-        row["Severity Pyramid Rungs"] = none_severity_pyramid_rung_obj.id
+        row["Surveillance Categories"] = none_severity_pyramid_rung_obj.id
 
 
 def process_category(row) -> None:
@@ -116,12 +116,12 @@ def process_geographic_scope(row) -> None:
     """
     Processes geographic scope.
     """
-    if row["Geographic Scope"]:
-        geographic_scope = row["Geographic Scope"]
+    if row["Geographic Coverage"]:
+        geographic_scope = row["Geographic Coverage"]
         geographic_scope_obj, _ = GeographicScope.objects.get_or_create(
             name=geographic_scope, used_in="signals", defaults={"used_in": "signals"}
         )
-        row["Geographic Scope"] = geographic_scope_obj.id
+        row["Geographic Coverage"] = geographic_scope_obj.id
 
 
 def process_source(row) -> None:
@@ -138,8 +138,8 @@ def process_available_geographies(row) -> None:
     """
     Processes available geographies.
     """
-    if row["Available Geography"]:
-        geographies: str = row["Available Geography"].split(",")
+    if row["Geographic Levels"]:
+        geographies: str = row["Geographic Levels"].split(",")
         delphi_aggregated_geographies: str = row["Delphi-Aggregated Geography"].split(
             ","
         )
@@ -156,7 +156,7 @@ def process_available_geographies(row) -> None:
                 },
             )
             signal = Signal.objects.get(
-                name=row["Signal"], source=row["Source Subdivision"]
+                name=row["Indicator"], source=row["Source Subdivision"]
             )
             signal_geography, _ = SignalGeography.objects.get_or_create(
                 geography=geography_instance, signal=signal
@@ -167,12 +167,12 @@ def process_available_geographies(row) -> None:
 
 
 def process_base(row) -> None:
-    if row["Signal BaseName"]:
+    if row["Indicator BaseName"]:
         source: SourceSubdivision = SourceSubdivision.objects.get(
             name=row["Source Subdivision"]
         )
         base_signal: Signal = Signal.objects.get(
-            name=row["Signal BaseName"], source=source
+            name=row["Indicator BaseName"], source=source
         )
         row["base"] = base_signal.id
 
@@ -213,7 +213,7 @@ class SignalBaseResource(ModelResource):
     Resource class for importing Signals base.
     """
 
-    name = Field(attribute="name", column_name="Signal")
+    name = Field(attribute="name", column_name="Indicator")
     display_name = Field(attribute="display_name", column_name="Name")
     base = Field(
         attribute="base",
@@ -241,9 +241,9 @@ class SignalResource(ModelResource):
     Resource class for importing and exporting Signal models
     """
 
-    name = Field(attribute="name", column_name="Signal")
+    name = Field(attribute="name", column_name="Indicator")
     display_name = Field(attribute="display_name", column_name="Name")
-    member_name = Field(attribute="member_name", column_name="Member Name")
+    member_name = Field(attribute="member_name", column_name="Member API Name")
     member_short_name = Field(
         attribute="member_short_name", column_name="Member Short Name"
     )
@@ -257,7 +257,7 @@ class SignalResource(ModelResource):
     )
     signal_type = Field(
         attribute="signal_type",
-        column_name="Signal Type",
+        column_name="Indicator Type",
         widget=widgets.ForeignKeyWidget(SignalType, field="name"),
     )
     active = Field(attribute="active", column_name="Active")
@@ -282,11 +282,11 @@ class SignalResource(ModelResource):
         attribute="typical_revision_cadence", column_name="Typical Revision Cadence"
     )
     demographic_scope = Field(
-        attribute="demographic_scope", column_name="Demographic Scope"
+        attribute="demographic_scope", column_name="Population"
     )
     severity_pyramid_rung = Field(
         attribute="severity_pyramid_rung",
-        column_name="Severity Pyramid Rungs",
+        column_name="Surveillance Categories",
         widget=widgets.ForeignKeyWidget(SeverityPyramidRung),
     )
     category = Field(
@@ -296,12 +296,12 @@ class SignalResource(ModelResource):
     )
     geographic_scope = Field(
         attribute="geographic_scope",
-        column_name="Geographic Scope",
+        column_name="Geographic Coverage",
         widget=widgets.ForeignKeyWidget(GeographicScope),
     )
     available_geographies = Field(
-        attribute="available_geographies",
-        column_name="Available Geographies",
+        attribute="available_geography",
+        column_name="Geographic Levels",
         widget=widgets.ManyToManyWidget(Geography, field="name", separator=","),
     )
     temporal_scope_start = Field(
@@ -330,17 +330,17 @@ class SignalResource(ModelResource):
     data_censoring = Field(attribute="data_censoring", column_name="Data Censoring")
     missingness = Field(attribute="missingness", column_name="Missingness")
     organization_access_list = Field(
-        attribute="organization_access_list", column_name="Who may access this signal?"
+        attribute="organization_access_list", column_name="Who may access this indicator?"
     )
     organization_sharing_list = Field(
         attribute="organization_sharing_list",
-        column_name="Who may be told about this signal?",
+        column_name="Who may be told about this indicator?",
     )
-    license = Field(attribute="license", column_name="License")
+    license = Field(attribute="license", column_name="Data Use Terms")
     restrictions = Field(attribute="restrictions", column_name="Use Restrictions")
     signal_set = Field(
         attribute="signal_set",
-        column_name="Signal Set",
+        column_name="Indicator Set",
         widget=widgets.ForeignKeyWidget(SignalSet, field="name"),
     )
 
@@ -401,16 +401,16 @@ def before_import_row(self, row, **kwargs) -> None:
         process_geographic_scope(row)
         process_source(row)
         process_links(row, dua_column_name="Link to DUA", link_column_name="Link")
-        if not row.get("Signal Set"):
-            row["Signal Set"] = None
+        if not row.get("Indicator Set"):
+            row["Indicator Set"] = None
         if not row.get("Source Subdivision"):
             row["Source Subdivision"] = None
 
     def skip_row(self, instance, original, row, import_validation_errors=None):
-        if not row["Include in signal app"]:
+        if not row["Include in indicator app"]:
             try:
                 signal = Signal.objects.get(
-                    name=row["Signal"], source=row["Source Subdivision"]
+                    name=row["Indicator"], source=row["Source Subdivision"]
                 )
                 signal.delete()
             except Signal.DoesNotExist:
@@ -423,7 +423,7 @@ def after_import_row(self, row, row_result, **kwargs):
             for link in row["Links"]:
                 signal_obj.related_links.add(link)
             process_available_geographies(row)
-            signal_obj.severity_pyramid_rung = SeverityPyramidRung.objects.get(id=row["Severity Pyramid Rungs"])
+            signal_obj.severity_pyramid_rung = SeverityPyramidRung.objects.get(id=row["Surveillance Categories"])
             signal_obj.format_type = row["Format"]
             signal_obj.save()
         except Signal.DoesNotExist as e:

src/templates/index.html

@@ -83,7 +83,7 @@
                                 data-mdb-placement="right"
                                 data-mdb-content="Discover, display and download real-time infectious disease indicators (time series) that track a variety of pathogens, diseases and syndromes in a variety of locations (primarily within the USA).
                                                 Browse the list, or filter it first by locations and pathogens of interest, by surveillance categories, and more.
-                                                Expand any row to expose and select from a set of related indicators, then hit ""Show Selected Indicators"" at bottom to plot or export your selected indicators, or to generate code snippets to retrieve them from the Delphi Epidata API.
+                                                Expand any row to expose and select from a set of related indicators, then hit 'Show Selected Indicators' at bottom to plot or export your selected indicators, or to generate code snippets to retrieve them from the Delphi Epidata API.
                                                 Most indicators are served from the Delphi Epidata real-time repository, but some may be available only from third parties or may require prior approval."
                                 >
                                 <i class="far fa-circle-question"></i>