Added tests

tests/test_exporter.py

@@ -1,5 +1,6 @@
 import json
 import os
+from pathlib import Path
 
 import pytest
 from osgeo import ogr
@@ -50,9 +51,54 @@ def test_fragments_gpgk_export(ga_fragments, tmp_path):
     )  # minus dummy
 
 
-def test_fragments_gpkg_conversion_smoke(ga_fragment_path):
-    exporter = GeopackageExporter(ga_fragment_path, "fragment_export.gpkg")
+def test_fragments_to_gpgk_export(ga_fragments, tmp_path):
+    path = str(tmp_path / "only_fragment_export.gpkg")
+    ga_fragments.fragments.to_gpkg(path, "fragments")
+    s = ogr.Open(path)
+    layer = s.GetLayer("fragments")
+    assert layer.GetFeatureCount() == (
+        ga_fragments.fragments.id.size - 1
+    )  # minus dummy
+
+
+def test_fragments_to_geojson_export(ga_fragments, tmp_path):
+    path = str(tmp_path / "only_fragment_export.json")
+    ga_fragments.fragments.to_geojson(path, use_ogr=True)
+    s = ogr.Open(path)
+    layer = s.GetLayer(Path(path).name)
+    assert layer.GetFeatureCount() == (
+        ga_fragments.fragments.id.size - 1
+    )  # minus dummy
+    with open(path) as file:
+        data = json.load(file)
+        assert len(data["features"][0]["properties"]) == 2
+        assert "node_id" in data["features"][0]["properties"]
+
+    path = str(tmp_path / "only_fragment_export_2.json")
+    ga_fragments.fragments.to_geojson(path, use_ogr=False)
+    s = ogr.Open(path)
+    layer = s.GetLayer(Path(path).stem)
+    # We export more properties and use different layer name
+    assert layer.GetFeatureCount() == (
+        ga_fragments.fragments.id.size - 1
+    )  # minus dummy
+    with open(path) as file:
+        data = json.load(file)
+        assert len(data["features"][0]["properties"]) == 3
+        assert "node_id" in data["features"][0]["properties"]
+        assert "model_type" in data["features"][0]["properties"]
+
+
+def test_fragments_gpkg_conversion(ga_fragments, ga_fragment_path, tmp_path):
+    exporter = GeopackageExporter(
+        ga_fragment_path, str(tmp_path / "fragment_export.gpkg")
+    )
     exporter.export()
+    s = ogr.Open(str(tmp_path / "fragment_export.gpkg"))
+    layer = s.GetLayer("fragment")
+    assert layer.GetFeatureCount() == (
+        ga_fragments.fragments.id.size - 1
+    )  # minus dummy
 
 
 def test_meta_data_gpgk_export(ga, tmp_path):
@@ -157,6 +203,7 @@ def test_export_null(ga, tmp_path):
         ("grid", "grid_2D_open_water"),
         ("grid", "grid_2D_groundwater"),
         ("flowlines", "flowlines"),
+        ("fragments", "fragments"),
     ],
 )
 def test_export_method(ga_export, export_method, expected_filename):

tests/test_gridadmin.py

@@ -572,3 +572,29 @@ def test_lines_filter_id_in(self):
         )
         expected = self.parser.lines.data["line_coords"][:, trues]
         np.testing.assert_equal(filtered, expected)
+
+
+class FragmentFilterTests(unittest.TestCase):
+    def setUp(self):
+        grid_admin_h5_file = os.path.join(
+            test_file_dir, "fragments", "gridadmin_fragments.h5"
+        )
+        self.parser = GridH5Admin(grid_admin_h5_file)
+
+    def test_fragments_filter_id_eq(self):
+
+        filtered = self.parser.fragments.filter(id=3).data["node_id"]
+        (trues,) = np.where(self.parser.fragments.data["id"] == 3)
+        expected = self.parser.fragments.data["node_id"][trues]
+        np.testing.assert_equal(filtered, expected)
+
+    def test_fragments_filter_id_in(self):
+        filtered = self.parser.fragments.filter(id__in=list(range(3, 7))).data[
+            "node_id"
+        ]
+        (trues,) = np.where(
+            (self.parser.fragments.data["id"] >= 3)
+            & (self.parser.fragments.data["id"] < 7)
+        )
+        expected = self.parser.fragments.data["node_id"][trues]
+        np.testing.assert_equal(filtered, expected)

threedigrid/admin/exporter_constants.py

@@ -179,6 +179,8 @@
     "z_coordinate",
 ]
 
+FRAGMENTS_EXPORT_FIELDS = ["id", "node_id"]
+
 DEFAULT_EXPORT_FIELDS = {
     "Lines": "ALL",
     "Pipes": PIPES_EXPORT_FIELDS,
@@ -194,4 +196,5 @@
     "Breaches": BREACHES_EXPORT_FIELDS,
     "Levees": LEVEES_EXPORT_FIELDS,
     "Pumps": PUMPS_EXPORT_FIELDS,
+    "Fragments": FRAGMENTS_EXPORT_FIELDS,
 }

threedigrid/admin/prepare.py

@@ -508,6 +508,20 @@ def export_pumps(self):
             dest, indent=self._indent
         )
 
+    def export_fragments(self):
+        if not self.ga.fragments.id.size == 0:
+            logger.info(
+                "[*] Model {} does not have fragments, "
+                "skipping export fragments...".format(self.ga.model_name)
+            )
+            return
+
+        dest_ow = os.path.join(self._dest, "fragments" + self._extension)
+        getattr(
+            self.ga.fragments.reproject_to(self._epsg),
+            self._export_method,
+        )(dest_ow, indent=self._indent)
+
     def export_levees(self):
         """
         writes shapefile of levees

threedigrid/admin/serializers.py

@@ -5,7 +5,7 @@
 import numpy as np
 
 from threedigrid.admin import constants
-from threedigrid.geo_utils import raise_import_exception, transform_bbox
+from threedigrid.geo_utils import raise_import_exception, transform_bbox, transform_xys
 from threedigrid.orm.base.encoder import NumpyEncoder
 from threedigrid.orm.base.models import Model
 
@@ -127,6 +127,26 @@ def geos_iter(self):
                 )
                 properties = fill_properties(self.fields, data, i, model_type)
                 yield geojson.Feature(geometry=polygon, properties=properties)
+        elif content_type == "fragments":
+            for i in range(data["id"].shape[-1]):
+                coords = np.round(
+                    data["coords"][i].reshape(2, -1).astype("float64"),
+                    constants.LONLAT_DIGITS,
+                )
+                if (
+                    self._model.reproject_to_epsg is not None
+                    and self._model.reproject_to_epsg != self._model.epsg_code
+                ):
+                    # Pick reproject_to_epsg or original model epsg_code
+                    coords = transform_xys(
+                        np.array(coords[0]),
+                        np.array(coords[1]),
+                        self._model.epsg_code,
+                        self._model.reproject_to_epsg,
+                    )
+                polygon = geojson.Polygon(coords.T.tolist())
+                properties = fill_properties(self.fields, data, i, model_type)
+                yield geojson.Feature(geometry=polygon, properties=properties)
         elif content_type == "levees":
             for i in range(data["id"].shape[-1]):
                 coords = np.round(