Move test entities and input and output files to sub-directories (#731)

# Description
Moved entities, input and output files to respectively sub-directories
in the Python tests.

Closes #689 
Addresses also issue #609 

While updating the tests to use the new sub-directories, a few other
path-related issues were discovered and fixed:
* two potential segfaults in dlite-storage.i and dlite.rdf.c if an
invalid path is provided were fixed
* raise DLiteParseError instead of DLiteOtherError for invalid json
input
* allow to hide DLiteOtherError by using DLiteUnknownError.


## Type of change
- [x] Bug fix & code cleanup
- [ ] New feature
- [ ] Documentation update
- [ ] Test update

## Checklist for the reviewer
This checklist should be used as a help for the reviewer.

- [ ] Is the change limited to one issue?
- [ ] Does this PR close the issue?
- [ ] Is the code easy to read and understand?
- [ ] Do all new feature have an accompanying new test?
- [ ] Has the documentation been updated as necessary?

bindings/python/dlite-storage.i

@@ -52,7 +52,7 @@ Returns next instance or None if exhausted.") next;
  if (dlite_storage_iter_next($self->s, $self->state, uuid) == 0) {
  DLiteInstance *inst = dlite_instance_load($self->s, uuid);
  // Why isn't the refcount already increased?
- dlite_instance_incref(inst);
+ if (inst) dlite_instance_incref(inst);
  return inst;
  }
  return NULL;

bindings/python/scripts/CMakeLists.txt

@@ -32,26 +32,30 @@ install(
 # Tests
 test_success(
  dlite-validate-Person
- dlite-validate ../tests/Person.json
+ dlite-validate ../tests/entities/Person.json
 )
 test_success(
  dlite-validate-persons
- dlite-validate -p ../tests/Person.json -i a1d8d35f-723c-5ea1-abaf-8fc8f1d0982f
- ../tests/persons.json
+ dlite-validate
+ -p ../tests/entities/Person.json
+ -i a1d8d35f-723c-5ea1-abaf-8fc8f1d0982f
+ ../tests/input/persons.json
 )
 test_success(
  dlite-validate-persons2
  dlite-validate
- --storage-path=../tests
+ --storage-path=../tests/entities
  --id=Ada
  --show
- ../tests/persons.json
+ ../tests/input/persons.json
  )
 
 # No --id for storage with multiple instances
 test_failure(
  dlite-validate-persons-fail2
- dlite-validate --storage-path ../tests/Person.json --show ../tests/persons.json
+ dlite-validate
+ --storage-path ../tests/entities/Person.json
+ --show ../tests/input/persons.json
 )
 
 # The "dimensions" keyword is required

bindings/python/tests/.gitignore

@@ -1,16 +1,2 @@
 .gdb_history
 __pycache__
-
-inst.ttl
-inst.yaml
-test.json
-test.yaml
-
-xxx.json
-xxx2.json
-yyy.json
-
-myentity.json
-persons2.json
-
-db.xml

bindings/python/tests/CMakeLists.txt

@@ -23,6 +23,7 @@ set(tests
  test_postgresql2_read
  test_ref_type
  test_pydantic
+ test_iri
 )
 
 foreach(test ${tests})

bindings/python/tests/entities/Invalid1.json

@@ -1,7 +1,19 @@
 {
- "name": "Missing version",
- "namespace": "http://onto-ns.com/meta",
- "meta": "http://onto-ns.com/meta/0.3/EntitySchema",
- "dimensions": {}
- "properties": {}
+ "uri": "http://onto-ns.com/meta/0.1/Invalid1",
+ "description": "An datamodel for an item with float type and invalid shape name.",
+ "dimensions": {
+ "nf": "Number of eigen-frequencies."
+ },
+ "properties": {
+ "name": {
+ "type": "str",
+ "description": "Name of the item."
+ },
+ "f": {
+ "type": "float64",
+ "shape": ["nf_MISPELLED"],
+ "unit": "Hz",
+ "description": "The magic eigen-frequencies of the item."
+ }
+ }
 }

bindings/python/tests/entities/Invalid2.json

@@ -1,7 +1,15 @@
 {
- "name": "Missing namespace",
- "version": "0.0.1",
- "meta": "http://onto-ns.com/meta/0.3/EntitySchema",
- "dimensions": {}
- "properties": {}
+ "uri": "http://onto-ns.com/meta/0.1/Invalid2",
+ "description": "A datamodel with ref-types with invalid shape name...",
+ "dimensions": {
+ "nrefs": "Number of references to Ref datamodels."
+ },
+ "properties": {
+ "items": {
+ "type": "ref",
+ "$ref": "http://onto-ns.com/meta/0.1/Item",
+ "shape": ["INVALID_nrefs"],
+ "description": "List of Item datamodels."
+ }
+ }
 }

bindings/python/tests/entities/Invalid3.json

@@ -1,5 +1,19 @@
 {
- "url": "http://onto-ns.com/meta/0.1/Invalid3",
- "description": "Missing properties",
- "dimensions": {}
+ "uri": "http://onto-ns.com/meta/0.1/Invalid3",
+ "description": "Invalid JSON (square bracket for dimensions instead of braces).",
+ "dimensions": [
+ "nfrequencies": "Number of eigen-frequencies."
+ ],
+ "properties": {
+ "name": {
+ "type": "str",
+ "description": "Name of the item."
+ },
+ "f": {
+ "type": "float64",
+ "shape": ["nf"],
+ "unit": "Hz",
+ "description": "The magic eigen-frequencies of the item."
+ }
+ }
 }

bindings/python/tests/entities/Invalid5.json

@@ -0,0 +1,7 @@
+{
+ "name": "Missing version",
+ "namespace": "http://onto-ns.com/meta",
+ "meta": "http://onto-ns.com/meta/0.3/EntitySchema",
+ "dimensions": {}
+ "properties": {}
+}

bindings/python/tests/entities/Invalid6.json

@@ -0,0 +1,7 @@
+{
+ "name": "Missing namespace",
+ "version": "0.0.1",
+ "meta": "http://onto-ns.com/meta/0.3/EntitySchema",
+ "dimensions": {}
+ "properties": {}
+}

bindings/python/tests/entities/Invalid7.json

@@ -0,0 +1,5 @@
+{
+ "url": "http://onto-ns.com/meta/0.1/Invalid7",
+ "description": "Missing properties",
+ "dimensions": {}
+}

bindings/python/tests/entities/Person.json

@@ -1,34 +1,23 @@
 {
- "name": "Person",
- "version": "0.1",
- "namespace": "http://onto-ns.com/meta",
- "meta": "http://onto-ns.com/meta/0.3/EntitySchema",
+ "uri": "http://onto-ns.com/meta/0.1/Person",
  "description": "A person.",
- "dimensions": [
- {
- "name": "N",
- "description": "Number of skills."
- }
- ],
- "properties": [
- {
- "name": "name",
+ "dimensions": {
+ "N": "Number of skills."
+ },
+ "properties": {
+ "name": {
  "type": "string",
  "description": "Full name."
  },
- {
- "name": "age",
+ "age": {
  "type": "float",
  "unit": "years",
  "description": "Age of person."
  },
- {
- "name": "skills",
+ "skills": {
  "type": "string",
- "dims": [
- "N"
- ],
+ "shape": ["N"],
  "description": "List of skills."
  }
- ]
+ }
 }

bindings/python/tests/global_dlite_state_mod2.py

@@ -1,15 +1,16 @@
 #!/usr/bin/env python
-# -*- coding: utf-8 -*-
-import os
+from pathlib import Path
 
 import dlite
 from dlite import Instance, Dimension, Property, Relation
 
 assert len(dlite.istore_get_uuids()) == 3 + 3
 
-thisdir = os.path.abspath(os.path.dirname(__file__))
 
-url = "json://" + thisdir + "/MyEntity.json"
+thisdir = Path(__file__).absolute().parent
+entitydir = thisdir / "entities"
+
+url = f"json://{entitydir}/MyEntity.json"
 
 # myentity is already defined via test_global_dlite_state, no new instance is added to istore
 myentity = Instance.from_url(url)

bindings/python/tests/output/.gitignore

@@ -1,2 +1,4 @@
 *.json
 *.yaml
+*.ttl
+db.xml

bindings/python/tests/test_collection.py

@@ -6,6 +6,8 @@
 
 thisdir = Path(__file__).resolve().parent
 outdir = thisdir / "output"
+indir = thisdir / "input"
+entitydir = thisdir / "entities"
 
 
 # Create collection
@@ -23,7 +25,7 @@
 assert rel is None
 
 # Create instances
-url = f"json://{thisdir}/MyEntity.json?mode=r"
+url = f"json://{entitydir}/MyEntity.json?mode=r"
 e = dlite.Instance.from_url(url)
 inst1 = dlite.Instance.from_metaid(e.uri, [3, 2])
 inst2 = dlite.Instance.from_metaid(e.uri, (3, 4), "myinst")