Species suggestion Backend (#467)

* modify grts_cell to sample_frame_id, the real name

* add species range model, management loading command, admin interface

* GET species support for recordingId, GRTSCell and Sample_frame_Id for listing

* mark geojson file as generated to remove line count

* mark geojson file as vendored to remove line count

* add category label back to Species results

* Update .gitattributes

Co-authored-by: Brian Helba <brian.helba@kitware.com>

* Update bats_ai/core/management/commands/load_species_geojson.py

Co-authored-by: Brian Helba <brian.helba@kitware.com>

* swap to tuples to lists for admin

* prevent nullable for SpeciesRange.source_feature_id field

* update GEOJSON location, add loading to migration

* default to CONUS_SAMPLE_FRAME_ID=14 for unknown sample_frame_ids

* cleanup species view

* pathlib for DEFAULT_GEOJSON

* rename species.geojson to species-ranges.geojson

* Update bats_ai/core/management/commands/load_species_geojson.py

Co-authored-by: Brian Helba <brian.helba@kitware.com>

* allow more failing errors in load species range

* remove unecessary pk, and default to false if geom exists and overlap is false

* in_range output comments, species-range ingestion description

---------

Co-authored-by: Brian Helba <brian.helba@kitware.com>

Author: BryonLewis

.gitattributes

@@ -1,4 +1,5 @@
 client/package-lock.json linguist-generated=true
+bats_ai/core/data/species-ranges.geojson linguist-vendored=true
 uv.lock linguist-generated=true
 assets/example.wav filter=lfs diff=lfs merge=lfs -text
 assets/model.mobilenet.onnx filter=lfs diff=lfs merge=lfs -text

README.md

@@ -190,10 +190,18 @@ on all pipelines for new MRs.  The automated checks in GitLab are optional, but
 it is highly recommended to perform these checks locally prior to pushing new
 commits.
 
-
-
 ### Spectrogram contours
 
-Spectrogram processing tasks honor `DJANGO_BATAI_SAVE_SPECTROGRAM_CONTOURS` environment variable. 
+Spectrogram processing tasks honor `DJANGO_BATAI_SAVE_SPECTROGRAM_CONTOURS` environment variable.
 Set to `False` by default so workers skip contour extraction (less DB storage space); set to `True` if you need
 contours in the UI (UI for contours currently disabled due to performance)
+
+### Species Suggestions by Range
+
+The suggested species for a given location are determined by spatial data stored in `/bats_ai/core/data/species-range.geojson`.
+As part of the default migrations this data is ingested into the SpeciesRange database and used for determining suggested
+species based on  a Recording (internal GRTS_Cell_ID and sample_frame_id).
+The if the same species is found multiple times in the geojson the last geometry will be used.
+In the future if species-ranges change the managment command of `./manage.py load_species_geojson [optional Geojson Path]`
+can be used to reload the default species-range.geojson
+if no path is provided or a new one and will update/replace any previous data.

bats_ai/core/admin/__init__.py

@@ -18,6 +18,7 @@
 from .recording_tag import RecordingTagAdmin
 from .sequence_annotations import SequenceAnnotationsAdmin
 from .species import SpeciesAdmin
+from .species_range import SpeciesRangeAdmin
 from .spectrogram import SpectrogramAdmin
 from .spectrogram_image import SpectrogramImageAdmin
 from .user import UserAdmin
@@ -41,6 +42,7 @@
     "RecordingTagAdmin",
     "SequenceAnnotationsAdmin",
     "SpeciesAdmin",
+    "SpeciesRangeAdmin",
     "SpectrogramAdmin",
     "SpectrogramImageAdmin",
     "UserAdmin",

bats_ai/core/admin/recording.py

@@ -30,7 +30,7 @@ class RecordingAdmin(admin.ModelAdmin):
         "comments",
         "recording_location",
         "grts_cell_id",
-        "grts_cell",
+        "sample_frame_id",
         "site_name",
         "detector",
         "software",

bats_ai/core/admin/species_range.py

@@ -0,0 +1,23 @@
+from __future__ import annotations
+
+from django.contrib import admin
+from django.contrib.gis.admin import GISModelAdmin
+
+from bats_ai.core.models import SpeciesRange
+
+
+@admin.register(SpeciesRange)
+class SpeciesRangeAdmin(GISModelAdmin):
+    list_display = [
+        "id",
+        "species",
+        "source_feature_id",
+    ]
+    list_select_related = ["species"]
+    search_fields = [
+        "species__species_code",
+        "species__common_name",
+        "source_feature_id",
+    ]
+    autocomplete_fields = ["species"]
+    ordering = ["species__species_code"]