Merge branch 'master' into 517-clean-up-requirements

bindings/python/dlite-entity-python.i

@@ -384,7 +384,29 @@ def get_instance(id: str, metaid: str = None, check_storages: bool = True) -> "I
 
     @classmethod
     def from_dict(cls, d, id=None, single=None, check_storages=True):
-        """Load the instance from dictionary."""
+        """Load the instance from dictionary.
+
+        Arguments:
+            d: Dict to parse.  It should be of the same form as returned
+                by the Instance.asdict() method.
+            id: Identity of the returned instance.
+
+                If `d` is in single-entity form with no explicit 'uuid' or
+                'uri', its identity will be assigned by `id`.  Otherwise
+                `id` must be consistent with the 'uuid' and/or 'uri'
+                fields of `d`.
+
+                If `d` is in multi-entity form, `id` is used to select the
+                instance to return.
+            single: A boolean, None or "auto".  Determines whether to
+                assume that the dict is in single-entity form.
+                If `single` is None or "auto", the form is inferred.
+            check_storages: Whether to check if the instance already exists
+                in storages specified in `dlite.storage_path`.
+
+        Returns:
+            New instance.
+        """
         from dlite.utils import instance_from_dict
         return instance_from_dict(
             d, id=id, single=single, check_storages=check_storages,

bindings/python/utils.py

@@ -80,7 +80,8 @@ def instance_from_dict(d, id=None, single=None, check_storages=True):
         Whether the dict is assumed to be in single-entity form
         If `single` is None or "auto", the form is inferred.
     check_storages: bool
-        Whether to check if the instance already exists in storages.
+        Whether to check if the instance already exists in storages
+        specified in `dlite.storage_path`.
     """
     if single is None or single == 'auto':
         single = True if 'properties' in d else False

cmake/patch-activate.sh

@@ -1,13 +1,61 @@
-#!/bin/sh
-#
-# Patch virtualenv activate script to support LD_LIBRARY_PATH
-#
+#!/bin/bash
+
+help() {
+cat <<EOF
+Usage: patch-activate.sh [--package PACKAGE]
+
+Patch virtualenv activate script to support LD_LIBRARY_PATH
+
+Options:
+  -h, --help   Show this help and exit.
+  -p PACKAGE, --package PACKAGE
+               Insert root directory of this Python package to
+               LD_LIBRARY_PATH.
+
+How to use this script:
+  1. Make sure that environment variable VIRTUAL_ENV is set to the
+     root directory of your virtual environments.
+  2. Activate your virtual environment.
+  3. Run `patch-activate.sh`
+  4. Deactivate and reactivate your virtual environment to ensure that
+     LD_LIBRARY_PATH is properly set.
+EOF
+}
+
+# Usage: app_package PACKAGE
+# Append path to root of Python package to `libdirs`
+add_package() {
+    pkgdir=$(dirname $(python -c "import $1; print($1.__file__)"))
+    relpath=$(realpath --relative-to="$VIRTUAL_ENV" "$pkgdir")
+    if [ "${relpath#..}" = "$relpath" ]; then
+        libdirs="$libdirs:\$VIRTUAL_ENV/$relpath"
+    else
+        echo ""; exit 1
+    fi
+}
+
+
+set -e
 
 if [ -z "$VIRTUAL_ENV" ]; then
    echo "Not in a virtual environment" >&2
    exit 1
 fi
 
+libdirs="\$VIRTUAL_ENV/lib"
+
+# Parse options
+while true; do
+    case "$1" in
+        '')            break;;
+        -h|--help)     help; exit 0;;
+        -p|--package)  add_package $2; shift;;
+        *)             echo "Invalid argument: '$1'"; exit 1;;
+    esac
+    shift
+done
+
+
 cd $VIRTUAL_ENV/bin
 
 patch -u -f -F 1 <<EOF
@@ -30,7 +78,7 @@ patch -u -f -F 1 <<EOF
  export PATH
 
 +_OLD_VIRTUAL_LD_LIBRARY_PATH="\$LD_LIBRARY_PATH"
-+LD_LIBRARY_PATH="\$VIRTUAL_ENV/lib:\$LD_LIBRARY_PATH"
++LD_LIBRARY_PATH="$libdirs:\$LD_LIBRARY_PATH"
 +export LD_LIBRARY_PATH
 +
  # unset PYTHONHOME if set

requirements_full.txt

@@ -11,4 +11,4 @@ tripper>=0.2.5,<0.3
 pydantic>=1.10.0,<3
 typing_extensions>=4.1,<5
 requests>=2.10,<3
-jsonschema>=4.0,<4.18
+#jsonschema>=4.0,<4.18

storages/python/python-storage-plugins/http.py

@@ -1,19 +1,37 @@
+"""DLite storage plugin for fetching instances with HTTP GET requests.
+
+This simple plugin was initially added to support the entity service (see
+https://github.com/SINTEF/dlite-entities-service), but may have other uses.
+"""
 import json
 import requests
 
 import dlite
+from dlite.options import Options
 
 
 class http(dlite.DLiteStorageBase):
-    """DLite storage plugin that fetches entities with http GET."""
-
-    def open(self, uri, options=None):
-        """Opens `uri`."""
-
-    def load(self, id):
-        """Returns instance retrieved from HTTP GET on `id`."""
-        r = requests.get(id)
-        content = json.loads(r.content)
-        if "detail" in content:
-            raise dlite.DLiteError(content["detail"])
-        return dlite.Instance.from_json(content)
+    """DLite storage plugin that fetches instances with HTTP GET."""
+
+    def open(self, location, options=None):
+        """Opens `location`.
+
+        Arguments:
+            location: web address to access
+            options: Supported options:
+                - `single`: Whether the input is assumed to be in single-
+                      entity form.  The default (`"auto"`) will try to infer
+                      it automatically.
+        """
+        self.options = Options("single=auto")
+
+        r = requests.get(location)
+        self.content = json.loads(r.content)
+        if "detail" in self.content:
+            raise dlite.DLiteStorageOpenError(content["detail"])
+
+    def load(self, id=None):
+        """Returns instance retrieved from HTTP GET."""
+        s = self.options.single
+        single = s if s == "auto" else dlite.asbool(s)
+        return dlite.Instance.from_dict(self.content, id=id, single=single)

storages/python/tests-python/CMakeLists.txt

@@ -11,6 +11,7 @@ set(python-tests
   test_minio
   test_template
   test_template-jinja
+  test_http
   )
 
 include(FindPythonModule)

storages/python/tests-python/test_http.py

@@ -0,0 +1,51 @@
+try:
+    import requests
+except ModuleNotFoundError:
+    print("requests not installed, skipping test")
+    raise SystemExit(44)  # skip test
+
+import dlite
+
+
+url = "https://raw.githubusercontent.com/SINTEF/dlite/master/storages/python/tests-python/input/test_meta.json"
+
+meta = dlite.Instance.from_location("http", url)
+
+assert str(meta) == """
+{
+  "uri": "http://onto-ns.com/meta/0.1/TestEntity",
+  "description": "test entity with explicit meta",
+  "dimensions": {
+    "L": "first dim",
+    "M": "second dim",
+    "N": "third dim"
+  },
+  "properties": {
+    "myblob": {
+      "type": "blob3"
+    },
+    "mydouble": {
+      "type": "float64",
+      "unit": "m",
+      "description": "A double following a single character..."
+    },
+    "myfixstring": {
+      "type": "string3",
+      "description": "A fix string."
+    },
+    "mystring": {
+      "type": "string",
+      "description": "A string pointer."
+    },
+    "myshort": {
+      "type": "uint16",
+      "description": "An unsigned short integer."
+    },
+    "myarray": {
+      "type": "int32",
+      "shape": ["L", "M", "N"],
+      "description": "An array string pointer."
+    }
+  }
+}
+""".strip()