added test cases

tests/schemapack_/fixtures/data.py

@@ -30,5 +30,6 @@ def _get_example_data(name: str) -> DataPack:
     return load_datapack(EXAMPLE_DATA_DIR / f"{name}.datapack.yaml")
 
 
-VALID_MINIMAL_DATA = _get_example_data("valid_minimal")
+MINIMAL_DATA = _get_example_data("minimal")
+ADVANCED_DATA = _get_example_data("advanced")
 INVALID_MINIMAL_DATA = _get_example_data("invalid_minimal")

tests/schemapack_/fixtures/example_content_schemas/Dataset.schema.json

@@ -0,0 +1,17 @@
+{
+  "$schema": "http://json-schema.org/draft-07/schema#",
+  "additionalProperties": false,
+  "description": "A dataset that is a collection of files.",
+  "properties": {
+    "alias": {
+      "type": "string"
+    },
+    "dac_contact": {
+      "type": "string"
+    }
+  },
+  "required": [
+    "alias"
+  ],
+  "type": "object"
+}

tests/schemapack_/fixtures/example_content_schemas/Experiment.schema.json

@@ -0,0 +1,17 @@
+{
+  "$schema": "http://json-schema.org/draft-07/schema#",
+  "additionalProperties": false,
+  "description": "An experiment containing one or multiple samples.",
+  "properties": {
+    "alias": {
+      "type": "string"
+    },
+    "description": {
+      "type": "string"
+    }
+  },
+  "required": [
+    "alias"
+  ],
+  "type": "object"
+}

tests/schemapack_/fixtures/example_content_schemas/File.schema.json

@@ -0,0 +1,30 @@
+{
+  "$schema": "http://json-schema.org/draft-07/schema#",
+  "additionalProperties": false,
+  "description": "A file is an object that contains information generated from a process, either an Experiment or an Analysis.",
+  "properties": {
+    "alias": {
+      "type": "string"
+    },
+    "checksum": {
+      "type": "string"
+    },
+    "filename": {
+      "type": "string"
+    },
+    "format": {
+      "type": "string"
+    },
+    "size": {
+      "type": "integer"
+    }
+  },
+  "required": [
+    "alias",
+    "filename",
+    "format",
+    "checksum",
+    "size"
+  ],
+  "type": "object"
+}

tests/schemapack_/fixtures/example_content_schemas/Sample.schema.json

@@ -0,0 +1,17 @@
+{
+  "$schema": "http://json-schema.org/draft-07/schema#",
+  "additionalProperties": false,
+  "description": "A sample used to generate files in the context of an experiment.",
+  "properties": {
+    "alias": {
+      "type": "string"
+    },
+    "description": {
+      "type": "string"
+    }
+  },
+  "required": [
+    "alias"
+  ],
+  "type": "object"
+}

tests/schemapack_/fixtures/example_data/advanced.datapack.yaml

@@ -0,0 +1,56 @@
+datapack: 0.1.0
+resources:
+  File:
+    file_a:
+      content:
+        alias: file_a
+        filename: file_a.fastq
+        format: FASTQ
+        checksum: 1a5ac10ab42911dc0224172c118a326d9a4c03969112a2f3eb1ad971e96e92b8
+        size: 12321
+    file_b:
+      content:
+        alias: file_b
+        filename: file_b.fastq
+        format: FASTQ
+        checksum: 2b5ac10ab42911dc0224172c118a326d9a4c03969112a2f3eb1ad971e96e92c9
+        size: 12314
+    file_c:
+      content:
+        alias: file_c
+        filename: file_c.fastq
+        format: FASTQ
+        checksum: a9c24870071da03f78515e6197048f3a2172e90e597e9250cd01a0cb8f0986ed
+        size: 12123
+  Dataset:
+    dataset_1:
+      content:
+        alias: dataset_1
+        dac_contact: dac@example.org
+      relations:
+        files:
+          - file_a
+          - file_b
+          - file_c
+  Sample:
+    sample_x:
+      content:
+        alias: sample_x
+      relations:
+        files:
+          - file_a
+          - file_b
+    sample_y:
+      content:
+        alias: sample_y
+      relations:
+        files:
+          - file_c
+  Experiment:
+    experiment_i:
+      content:
+        alias: experiment_i
+      relations:
+        samples:
+          - sample_x
+          - sample_y

tests/schemapack_/fixtures/example_models/advanced.schemapack.yaml

@@ -0,0 +1,31 @@
+# a simple schemapack with the content schemas being embedded
+schemapack: 0.1.0
+classes:
+  File:
+    id:
+      from_content: alias
+    content: ../example_content_schemas/File.schema.json
+  Dataset:
+    id:
+      from_content: alias
+    content: ../example_content_schemas/Dataset.schema.json
+    relations:
+      files:
+        to: File
+        cardinality: many_to_many
+  Sample:
+    id:
+      from_content: alias
+    content: ../example_content_schemas/Sample.schema.json
+    relations:
+      files:
+        to: File
+        cardinality: one_to_many
+  Experiment:
+    id:
+      from_content: alias
+    content: ../example_content_schemas/Experiment.schema.json
+    relations:
+      samples:
+        to: Sample
+        cardinality: one_to_many

tests/schemapack_/fixtures/example_models/minimal.schemapack.yaml

@@ -4,45 +4,11 @@ classes:
   File:
     id:
       from_content: alias
-    content:
-      "$schema": "http://json-schema.org/draft-07/schema#"
-      additionalProperties: false
-      description: A file is an object that contains information generated from a process,
-        either an Experiment or an Analysis.
-      properties:
-        alias:
-          type: string
-        checksum:
-          type: string
-        filename:
-          type: string
-        format:
-          type: string
-        size:
-          type: integer
-      required:
-        - alias
-        - filename
-        - format
-        - checksum
-        - size
-      type: object
+    content: ../example_content_schemas/File.schema.json
   Dataset:
     id:
       from_content: alias
-    content:
-      "$schema": "http://json-schema.org/draft-07/schema#"
-      additionalProperties: false
-      description: A dataset that is a collection of files.
-      properties:
-        alias:
-          type: string
-        dac_contact:
-          type: string
-      required:
-        - alias
-      type: object
-
+    content: ../example_content_schemas/Dataset.schema.json
     relations:
       files:
         to: File

tests/schemapack_/fixtures/example_transformations/Readme.md

@@ -0,0 +1,33 @@
+<!--
+ Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+ for the German Human Genome-Phenome Archive (GHGA)
+
+ Licensed under the Apache License, Version 2.0 (the "License");
+ you may not use this file except in compliance with the License.
+ You may obtain a copy of the License at
+
+     http://www.apache.org/licenses/LICENSE-2.0
+
+ Unless required by applicable law or agreed to in writing, software
+ distributed under the License is distributed on an "AS IS" BASIS,
+ WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ See the License for the specific language governing permissions and
+ limitations under the License.
+
+-->
+
+This directory contains test cases for testing builtin transformation.
+
+Names of sub-directories correspond to the transformation names.
+Each sub-sub-directory represents a test case.
+A test case is defined by following four files:
+- `config.yaml` - the transformation config
+- `input.datapack.yaml` - the input data for this transformation, if not present,
+  the [../example_data/advanced.datapack.yaml](../example_data/advanced.datapack.yaml)
+  is used
+- `input.schemapack.yaml` - the model for the input data, if not present,
+  the
+  [../example_models/advanced.schemapack.yaml](../example_models/advanced.schemapack.yaml)
+  is used
+- `transformed.datapack.yaml` - the expected data output of the transformation
+- `transformed.schemapack.yaml` - the expected model output of the transformation

tests/schemapack_/fixtures/example_transformations/infer_references/active_reference/config.yaml

@@ -0,0 +1,5 @@
+inferred_relations:
+  Experiment:
+    files:
+      path: "Experiment(samples)>Sample(files)>File"
+      expect_multiple: true

tests/schemapack_/fixtures/example_transformations/infer_references/active_reference/transformed.datapack.yaml

@@ -0,0 +1,60 @@
+datapack: 0.1.0
+resources:
+  File:
+    file_a:
+      content:
+        alias: file_a
+        filename: file_a.fastq
+        format: FASTQ
+        checksum: 1a5ac10ab42911dc0224172c118a326d9a4c03969112a2f3eb1ad971e96e92b8
+        size: 12321
+    file_b:
+      content:
+        alias: file_b
+        filename: file_b.fastq
+        format: FASTQ
+        checksum: 2b5ac10ab42911dc0224172c118a326d9a4c03969112a2f3eb1ad971e96e92c9
+        size: 12314
+    file_c:
+      content:
+        alias: file_c
+        filename: file_c.fastq
+        format: FASTQ
+        checksum: a9c24870071da03f78515e6197048f3a2172e90e597e9250cd01a0cb8f0986ed
+        size: 12123
+  Dataset:
+    dataset_1:
+      content:
+        alias: dataset_1
+        dac_contact: dac@example.org
+      relations:
+        files:
+          - file_a
+          - file_b
+          - file_c
+  Sample:
+    sample_x:
+      content:
+        alias: sample_x
+      relations:
+        files:
+          - file_a
+          - file_b
+    sample_y:
+      content:
+        alias: sample_y
+      relations:
+        files:
+          - file_c
+  Experiment:
+    experiment_i:
+      content:
+        alias: experiment_i
+      relations:
+        samples:
+          - sample_x
+          - sample_y
+        files: # <-
+          - file_a
+          - file_b
+          - file_c

tests/schemapack_/fixtures/example_transformations/infer_references/active_reference/transformed.schemapack.yaml

@@ -0,0 +1,33 @@
+schemapack: 0.1.0
+classes:
+  File:
+    id:
+      from_content: alias
+    content: ../example_content_schemas/File.schema.json
+  Dataset:
+    id:
+      from_content: alias
+    content: ../example_content_schemas/Dataset.schema.json
+    relations:
+      files:
+        to: File
+        cardinality: many_to_many
+  Sample:
+    id:
+      from_content: alias
+    content: ../example_content_schemas/Sample.schema.json
+    relations:
+      files:
+        to: File
+        cardinality: one_to_many
+  Experiment:
+    id:
+      from_content: alias
+    content: ../example_content_schemas/Experiment.schema.json
+    relations:
+      samples:
+        to: Sample
+        cardinality: one_to_many
+      files: # <-
+        to: File
+        cardinality: many_to_many

tests/schemapack_/fixtures/example_transformations/infer_references/complex_reference/config.yaml

@@ -0,0 +1,5 @@
+inferred_relations:
+  Dataset:
+    samples:
+      path: "Dataset(files)>File<(files)Sample"
+      expected_multiple: true