Fix spacenet tutorial, allow for single bbox argument to SpatialExtent, and other fixes.

README.md

@@ -81,15 +81,13 @@ PySTAC uses [flake8](http://flake8.pycqa.org/en/latest/) and [yapf](https://gith
 To run the flake8 style checks:
 
 ```
-> flake8 pystac
-> flake8 tests
+> flake8 pystac tests
 ```
 
 To format code:
 
 ```
-> yapf -ipr pystac
-> yapf -ipr tests
+> yapf -ipr pystac tests
 ```
 
 You can also run the `./scripts/test` script to check flake8 and yapf.

docs/tutorials/pystac-spacenet-tutorial.ipynb

@@ -68,7 +68,7 @@
     "from botocore.errorfactory import ClientError\n",
     "import pystac\n",
     "from pystac.extensions import label\n",
-    "from shapely.geometry import GeometryCollection, Polygon, box, shape"
+    "from shapely.geometry import GeometryCollection, Polygon, box, shape, mapping"
    ]
   },
   {
@@ -217,7 +217,7 @@
     "    params['id'] = basename(uri).split('.')[0]\n",
     "    with rasterio.open(uri) as src:\n",
     "        params['bbox'] = list(src.bounds)\n",
-    "        params['geometry'] = box(*params['bbox']).__geo_interface__\n",
+    "        params['geometry'] = mapping(box(*params['bbox']))\n",
     "    params['datetime'] = capture_date\n",
     "    params['properties'] = {}\n",
     "    i = pystac.Item(**params)\n",
@@ -240,24 +240,53 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "bounds = GeometryCollection([shape(s.geometry) for s in spacenet.get_all_items()]).bounds\n",
+    "bounds = [list(GeometryCollection([shape(s.geometry) for s in spacenet.get_all_items()]).bounds)]\n",
     "vegas.extent.spatial = pystac.SpatialExtent(bounds)"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Currently, this STAC only exists in memory. We need to set all of the paths based on the root directory  we want to save off that catalog too, and then save a \"self contained\" catalog, which will have all links be relative and contain no 'self' links. We can do this all in one shot with the `normalize_and_save` method:"
+    "Currently, this STAC only exists in memory. We need to set all of the paths based on the root directory  we want to save off that catalog too, and then save a \"self contained\" catalog, which will have all links be relative and contain no 'self' links. We can do this by using the `normalize` method to set the HREFs of all of our STAC objects. We'll then validate the catalog, and then save:"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": 12,
    "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "<Catalog id=spacenet>"
+      ]
+     },
+     "execution_count": 12,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "spacenet.normalize_hrefs('spacenet-stac')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 13,
+   "metadata": {},
    "outputs": [],
    "source": [
-    "spacenet.normalize_and_save('spacenet-stac', catalog_type=pystac.CatalogType.SELF_CONTAINED)"
+    "spacenet.validate_all()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 14,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "spacenet.save(catalog_type=pystac.CatalogType.SELF_CONTAINED)"
    ]
   },
   {
@@ -285,7 +314,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 13,
+   "execution_count": 15,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -298,7 +327,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 14,
+   "execution_count": 16,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -314,7 +343,7 @@
     "        label_item = pystac.Item(\n",
     "            id='{}-labels'.format(item.id),\n",
     "            bbox=item.bbox,\n",
-    "            geometry=box(*item.bbox).__geo_interface__,\n",
+    "            geometry=mapping(box(*item.bbox)),\n",
     "            datetime=item.datetime,\n",
     "            properties={},\n",
     "            stac_extensions=[pystac.Extensions.LABEL]\n",
@@ -323,7 +352,12 @@
     "        label_item.ext.label.apply(\n",
     "            label_description='Building labels for scene {}'.format(item.id),\n",
     "            label_type=label.LabelType.VECTOR,\n",
-    "            label_properties=['partialBuilding']\n",
+    "            label_properties=['partialBuilding'],\n",
+    "            \n",
+    "            # Label classes is marked as required in 1.0.0-beta.2, so make it up.\n",
+    "            # Once this PR is released, this can be removed:\n",
+    "            # https://github.com/radiantearth/stac-spec/pull/905\n",
+    "            label_classes=[label.LabelClasses.create(classes=['building'], name='partialBuilding')]\n",
     "        )\n",
     "        \n",
     "        label_item.ext.label.add_geojson_labels(href=label_uri)\n",
@@ -347,7 +381,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 15,
+   "execution_count": 17,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -356,7 +390,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 16,
+   "execution_count": 18,
    "metadata": {},
    "outputs": [
     {
@@ -383,7 +417,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 17,
+   "execution_count": 19,
    "metadata": {},
    "outputs": [
     {
@@ -428,12 +462,40 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 18,
+   "execution_count": 20,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "<Catalog id=spacenet>"
+      ]
+     },
+     "execution_count": 20,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "spacenet_cog.normalize_hrefs('spacenet-cog-stac')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 21,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "spacenet_cog.validate_all()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 22,
    "metadata": {},
    "outputs": [],
    "source": [
-    "spacenet_cog.normalize_and_save('spacenet-cog-stac', \n",
-    "                                catalog_type=pystac.CatalogType.SELF_CONTAINED)"
+    "spacenet_cog.save(catalog_type=pystac.CatalogType.SELF_CONTAINED)"
    ]
   },
   {

pystac/collection.py

@@ -1,3 +1,4 @@
+import collections.abc
 from datetime import datetime
 import dateutil.parser
 from dateutil import tz
@@ -305,6 +306,12 @@ class SpatialExtent:
             2D Collection with only one bbox would be [[xmin, ymin, xmax, ymax]]
     """
     def __init__(self, bboxes):
+        # A common mistake is to pass in a single bbox instead of a list of bboxes.
+        # Account for this by transforming the input in that case.
+        if isinstance(bboxes, collections.abc.Sequence):
+            if not isinstance(bboxes[0], collections.abc.Sequence):
+                bboxes = [bboxes]
+
         self.bboxes = bboxes
 
     def to_dict(self):
@@ -388,6 +395,13 @@ class TemporalExtent:
         Datetimes are required to be in UTC.
     """
     def __init__(self, intervals):
+        # A common mistake is to pass in a single interval instead of a
+        # list of intervals. Account for this by transforming the input
+        # in that case.
+        if isinstance(intervals, collections.abc.Sequence):
+            if not isinstance(intervals[0], collections.abc.Sequence):
+                intervals = [intervals]
+
         for i in intervals:
             if i[0] is None and i[1] is None:
                 raise STACError('TemporalExtent interval must have either '

pystac/link.py

@@ -105,7 +105,7 @@ def get_href(self):
             else:
                 href = self.target
 
-            if is_absolute_href(href) and self.owner is not None:
+            if href and is_absolute_href(href) and self.owner is not None:
                 href = make_relative_href(href, self.owner.get_self_href())
         else:
             href = self.get_absolute_href()

pystac/validation/stac_validator.py

@@ -67,12 +67,17 @@ def validate(self, stac_dict, stac_object_type, stac_version, extensions, href=N
                STACValidator implementation.
         """
         results = []
-        core_result = self.validate_core(stac_dict, stac_object_type, stac_version, href)
+
+        # Pass the dict through JSON serialization and parsing, otherwise
+        # some valid properties can be marked as invalid (e.g. tuples in
+        # coordinate sequences for geometries).
+        json_dict = json.loads(json.dumps(stac_dict))
+        core_result = self.validate_core(json_dict, stac_object_type, stac_version, href)
         if core_result is not None:
             results.append(core_result)
 
         for extension_id in extensions:
-            ext_result = self.validate_extension(stac_dict, stac_object_type, stac_version,
+            ext_result = self.validate_extension(json_dict, stac_object_type, stac_version,
                                                  extension_id, href)
             if ext_result is not None:
                 results.append(ext_result)

requirements-dev.txt

@@ -1,3 +1,4 @@
+ipython==7.16.1
 jsonschema==3.2.0
 pylint==1.9.1
 Sphinx==1.8.0
@@ -6,5 +7,5 @@ sphinxcontrib-fulltoc==1.2.0
 sphinxcontrib-napoleon==0.7
 flake8==3.8.*
 yapf==0.28.*
-nbsphinx==0.4.3
+nbsphinx==0.7.1
 coverage==5.2.*

tests/test_collection.py

@@ -5,7 +5,7 @@
 from datetime import datetime
 
 import pystac
-from pystac.validation import (validate_dict, STACValidationError)
+from pystac.validation import validate_dict
 from pystac.serialization.identify import STACObjectType
 from pystac import (Collection, Item, Extent, SpatialExtent, TemporalExtent, CatalogType)
 from pystac.extensions.eo import Band
@@ -114,11 +114,6 @@ def test_multiple_extents(self):
         cloned_ext = ext.clone()
         self.assertDictEqual(cloned_ext.to_dict(), multi_ext_dict['extent'])
 
-        multi_ext_dict['extent']['spatial']['bbox'] = multi_ext_dict['extent']['spatial']['bbox'][0]
-        invalid_col = Collection.from_dict(multi_ext_dict)
-        with self.assertRaises(STACValidationError):
-            invalid_col.validate()
-
     def test_extra_fields(self):
         catalog = TestCases.test_case_2()
         collection = catalog.get_child('1a8c1632-fa91-4a62-b33e-3a87c2ebdf16')
@@ -179,3 +174,37 @@ def test_update_extents(self):
         self.assertEqual(
             [[item2.common_metadata.start_datetime, base_extent.temporal.intervals[0][1]]],
             collection.extent.temporal.intervals)
+
+
+class ExtentTest(unittest.TestCase):
+    def test_spatial_allows_single_bbox(self):
+        temporal_extent = TemporalExtent(intervals=[[datetime.utcnow(), None]])
+
+        # Pass in a single BBOX
+        spatial_extent = SpatialExtent(bboxes=RANDOM_BBOX)
+
+        collection_extent = Extent(spatial=spatial_extent, temporal=temporal_extent)
+
+        collection = Collection(id='test',
+                                description='test',
+                                extent=collection_extent,
+                                license='CC-BY-SA-4.0')
+        collection.set_self_href('/usr/collection.json')
+
+        collection.validate()
+
+    def test_temporal_allows_single_interval(self):
+        spatial_extent = SpatialExtent(bboxes=[RANDOM_BBOX])
+
+        # Pass in a single interval
+        temporal_extent = TemporalExtent(intervals=[datetime.utcnow(), None])
+
+        collection_extent = Extent(spatial=spatial_extent, temporal=temporal_extent)
+
+        collection = Collection(id='test',
+                                description='test',
+                                extent=collection_extent,
+                                license='CC-BY-SA-4.0')
+        collection.set_self_href('/usr/collection.json')
+
+        collection.validate()

tests/test_link.py

@@ -0,0 +1,24 @@
+from datetime import datetime
+import unittest
+
+import pystac
+from tests.utils import (RANDOM_BBOX, RANDOM_GEOM)
+
+
+class LinkTest(unittest.TestCase):
+    def test_link_doest_fail_if_href_is_none(self):
+        """Tests to cover a bug that was uncovered where a non-None HREF
+        was supposed"""
+        catalog = pystac.Catalog(id='test', description='test')
+        item = pystac.Item(id='test-item',
+                           geometry=RANDOM_GEOM,
+                           bbox=RANDOM_BBOX,
+                           datetime=datetime.utcnow(),
+                           properties={'key': 'one'})
+        catalog.add_item(item)
+        catalog.set_self_href('/some/href')
+        catalog.make_all_links_relative()
+
+        for link in catalog.links:
+            if link.rel == 'item':
+                self.assertIsNone(link.get_href())

tests/validation/test_validate.py

@@ -1,6 +1,7 @@
+from datetime import datetime
+import json
 import os
 import shutil
-import json
 import unittest
 from tempfile import TemporaryDirectory
 
@@ -108,3 +109,25 @@ def test_validate_all(self):
 
             with self.assertRaises(STACValidationError):
                 pystac.validation.validate_all(stac_dict, new_cat_href)
+
+    def test_validates_geojson_with_tuple_coordinates(self):
+        """This unit tests guards against a bug where if a geometry
+        dict has tuples instead of lists for the coordinate sequence,
+        which can be produced by shapely, then the geometry still passses
+        validation.
+        """
+        geom = {
+            'type':
+            'Polygon',
+            'coordinates': (((-115.3057626, 36.1265426997), (-115.3057626, 36.1282976997),
+                             (-115.3075176, 36.1282976997), (-115.3075176, 36.1265426997),
+                             (-115.3057626, 36.1265426997)), )
+        }
+
+        item = pystac.Item(id='test-item',
+                           geometry=geom,
+                           bbox=[-115.308, 36.126, -115.305, 36.129],
+                           datetime=datetime.utcnow(),
+                           properties={'key': 'one'})
+
+        self.assertIsNone(item.validate())