Add Post runs examples

.gitignore

@@ -226,3 +226,4 @@ cython_debug/
 
 .gitkeep
 run/
+tests/resources/outputs/

tests/post_runs_examples/access_remote_files.py

@@ -0,0 +1,54 @@
+#!/usr/bin/env python3
+# coding: utf-8
+import json
+from pathlib import Path
+from typing import BinaryIO, Dict, Tuple
+
+import requests
+from requests import Response
+
+from genpei.type import RunRequest
+
+URL: str = "localhost:8080"
+SCRIPT_DIR: Path = \
+    Path(__file__).parent.resolve()
+RES_D: Path = \
+    SCRIPT_DIR.parent.joinpath("resources").resolve()
+
+
+def main() -> None:
+    data: RunRequest = {
+        "workflow_params": json.dumps({
+            "fastq_1": {
+                "class": "File",
+                "location": "https://raw.githubusercontent.com/suecharo/" +
+                            "genpei/master/tests/resources/" +
+                            "ERR034597_1.small.fq.gz"
+            },
+            "fastq_2": {
+                "class": "File",
+                "location": "https://raw.githubusercontent.com/suecharo/" +
+                            "genpei/master/tests/resources/" +
+                            "ERR034597_2.small.fq.gz"
+            }
+        }),
+        "workflow_type": "CWL",
+        "workflow_type_version": "v1.0",
+        "tags": json.dumps({
+            "workflow_name": "trimming_and_qc_remote"
+        }),
+        "workflow_engine_parameters": json.dumps({}),
+        "workflow_url": "https://raw.githubusercontent.com/suecharo/" +
+                        "genpei/master/tests/resources/" +
+                        "trimming_and_qc_remote.cwl"
+    }
+    files: Dict[str, Tuple[str, BinaryIO]] = {}
+    response: Response = \
+        requests.post(f"http://{URL}/runs", data=data, files=files)
+
+    print(response.status_code)
+    print(json.dumps(json.loads(response.text), indent=2))
+
+
+if __name__ == "__main__":
+    main()

tests/post_runs_examples/attach_all_files.py

@@ -0,0 +1,59 @@
+#!/usr/bin/env python3
+# coding: utf-8
+import json
+from pathlib import Path
+from typing import BinaryIO, Dict, Tuple
+
+import requests
+from requests import Response
+
+from genpei.type import RunRequest
+
+URL: str = "localhost:8080"
+SCRIPT_DIR: Path = \
+    Path(__file__).parent.resolve()
+RES_D: Path = \
+    SCRIPT_DIR.parent.joinpath("resources").resolve()
+
+
+def main() -> None:
+    data: RunRequest = {
+        "workflow_params": json.dumps({
+            "fastq_1": {
+                "class": "File",
+                "path": "./ERR034597_1.small.fq.gz"
+            },
+            "fastq_2": {
+                "class": "File",
+                "path": "./ERR034597_1.small.fq.gz"
+            }
+        }),
+        "workflow_type": "CWL",
+        "workflow_type_version": "v1.0",
+        "tags": json.dumps({
+            "workflow_name": "trimming_and_qc_remote"
+        }),
+        "workflow_engine_parameters": json.dumps({}),
+        "workflow_url": "./trimming_and_qc.cwl"
+    }
+    files: Dict[str, Tuple[str, BinaryIO]] = {
+        "fastq_1": ("ERR034597_1.small.fq.gz",
+                    RES_D.joinpath("ERR034597_1.small.fq.gz").open(mode="rb")),
+        "fastq_2": ("ERR034597_2.small.fq.gz",
+                    RES_D.joinpath("ERR034597_2.small.fq.gz").open(mode="rb")),
+        "workflow": ("trimming_and_qc.cwl",
+                     RES_D.joinpath("trimming_and_qc.cwl").open(mode="rb")),
+        "tool_1": ("fastqc.cwl",
+                   RES_D.joinpath("fastqc.cwl").open(mode="rb")),
+        "tool_2": ("trimmomatic_pe.cwl",
+                   RES_D.joinpath("trimmomatic_pe.cwl").open(mode="rb"))
+    }
+    response: Response = \
+        requests.post(f"http://{URL}/runs", data=data, files=files)
+
+    print(response.status_code)
+    print(json.dumps(json.loads(response.text), indent=2))
+
+
+if __name__ == "__main__":
+    main()

tests/post_runs_examples/get_inputs_from_mount.py

@@ -0,0 +1,48 @@
+#!/usr/bin/env python3
+# coding: utf-8
+import json
+from pathlib import Path
+from typing import BinaryIO, Dict, Tuple
+
+import requests
+from requests import Response
+
+from genpei.type import RunRequest
+
+URL: str = "localhost:8080"
+SCRIPT_DIR: Path = \
+    Path(__file__).parent.resolve()
+RES_D: Path = \
+    SCRIPT_DIR.parent.joinpath("resources").resolve()
+
+
+def main() -> None:
+    data: RunRequest = {
+        "workflow_params": json.dumps({
+            "fastq_1": {
+                "class": "File",
+                "location": str(RES_D.joinpath("ERR034597_1.small.fq.gz"))
+            },
+            "fastq_2": {
+                "class": "File",
+                "location": str(RES_D.joinpath("ERR034597_2.small.fq.gz"))
+            }
+        }),
+        "workflow_type": "CWL",
+        "workflow_type_version": "v1.0",
+        "tags": json.dumps({
+            "workflow_name": "trimming_and_qc"
+        }),
+        "workflow_engine_parameters": json.dumps({}),
+        "workflow_url": str(RES_D.joinpath("trimming_and_qc.cwl"))
+    }
+    files: Dict[str, Tuple[str, BinaryIO]] = {}
+    response: Response = requests.post(
+        f"http://{URL}/runs", data=data, files=files)
+
+    print(response.status_code)
+    print(json.dumps(json.loads(response.text), indent=2))
+
+
+if __name__ == "__main__":
+    main()

tests/post_runs_examples/put_outputs_on_mount.py

@@ -0,0 +1,56 @@
+#!/usr/bin/env python3
+# coding: utf-8
+import json
+from pathlib import Path
+from typing import BinaryIO, Dict, Tuple
+
+import requests
+from requests import Response
+
+from genpei.type import RunRequest
+
+URL: str = "localhost:8080"
+SCRIPT_DIR: Path = \
+    Path(__file__).parent.resolve()
+RES_D: Path = \
+    SCRIPT_DIR.parent.joinpath("resources").resolve()
+
+
+def main() -> None:
+    data: RunRequest = {
+        "workflow_params": json.dumps({
+            "fastq_1": {
+                "class": "File",
+                "location": "https://raw.githubusercontent.com/suecharo/" +
+                            "genpei/master/tests/resources/" +
+                            "ERR034597_1.small.fq.gz"
+            },
+            "fastq_2": {
+                "class": "File",
+                "location": "https://raw.githubusercontent.com/suecharo/" +
+                            "genpei/master/tests/resources/" +
+                            "ERR034597_2.small.fq.gz"
+            }
+        }),
+        "workflow_type": "CWL",
+        "workflow_type_version": "v1.0",
+        "tags": json.dumps({
+            "workflow_name": "trimming_and_qc_remote"
+        }),
+        "workflow_engine_parameters": json.dumps({
+            "--outdir": str(RES_D.joinpath("outputs"))
+        }),
+        "workflow_url": "https://raw.githubusercontent.com/suecharo/" +
+                        "genpei/master/tests/resources/" +
+                        "trimming_and_qc_remote.cwl"
+    }
+    files: Dict[str, Tuple[str, BinaryIO]] = {}
+    response: Response = \
+        requests.post(f"http://{URL}/runs", data=data, files=files)
+
+    print(response.status_code)
+    print(json.dumps(json.loads(response.text), indent=2))
+
+
+if __name__ == "__main__":
+    main()

tests/test_get_run_id.py

@@ -23,7 +23,7 @@ def test_get_run_id(tmpdir: LocalPath) -> None:
     app: Flask = create_app(Path(tmpdir))
     app.testing = True
     client: FlaskClient[Response] = app.test_client()
-    from .post_runs.test_access_remote_files import access_remote_files
+    from .post_runs_tests.test_access_remote_files import access_remote_files
     posts_res: Response = access_remote_files(client)
     posts_res_data: RunId = posts_res.get_json()
 

tests/test_get_run_id_status.py

@@ -23,7 +23,7 @@ def test_get_runs(tmpdir: LocalPath) -> None:
     app: Flask = create_app(Path(tmpdir))
     app.testing = True
     client: FlaskClient[Response] = app.test_client()
-    from .post_runs.test_access_remote_files import access_remote_files
+    from .post_runs_tests.test_access_remote_files import access_remote_files
     posts_res: Response = access_remote_files(client)
     posts_res_data: RunId = posts_res.get_json()
 

tests/test_get_runs.py

@@ -22,7 +22,7 @@ def test_get_runs(tmpdir: LocalPath) -> None:
     app: Flask = create_app(Path(tmpdir))
     app.testing = True
     client: FlaskClient[Response] = app.test_client()
-    from .post_runs.test_access_remote_files import access_remote_files
+    from .post_runs_tests.test_access_remote_files import access_remote_files
     posts_res: Response = access_remote_files(client)
     posts_res_data: RunId = posts_res.get_json()
 

tests/test_post_run_id_cancel.py

@@ -23,7 +23,7 @@ def test_post_run_id_cancel(tmpdir: LocalPath) -> None:
     app: Flask = create_app(Path(tmpdir))
     app.testing = True
     client: FlaskClient[Response] = app.test_client()
-    from .post_runs.test_access_remote_files import access_remote_files
+    from .post_runs_tests.test_access_remote_files import access_remote_files
     posts_res: Response = access_remote_files(client)
     posts_res_data: RunId = posts_res.get_json()