Merge pull request #24 from Australian-Imaging-Service/no-direct-access

Adds `--no-direct-archive` option

Author: tclose

xnat4tests/cli.py

@@ -85,8 +85,17 @@ def cli(ctx, config):
     default="info",
     help="Set the level of logging detail",
 )
+@click.option(
+    "--direct-archive/--no-direct-archive",
+    type=bool,
+    default=True,
+    help=(
+        "Whether to use direct-to-archive uploads when adding sample data. This is "
+        "faster but requires XNAT 1.8.2 or later"
+    ),
+)
 @click.pass_context
-def start_cli(ctx, loglevel, keep_mounts, rebuild, relaunch, with_data):
+def start_cli(ctx, loglevel, keep_mounts, rebuild, relaunch, with_data, direct_archive):
 
     set_loggers(loglevel)
 
@@ -95,7 +104,7 @@ def start_cli(ctx, loglevel, keep_mounts, rebuild, relaunch, with_data):
     )
 
     for dataset in with_data:
-        add_data(dataset, config_name=ctx.obj)
+        add_data(dataset, config_name=ctx.obj, direct_archive=direct_archive)
 
 
 @cli.command(
@@ -151,11 +160,20 @@ def restart_cli(ctx, loglevel):
     default="info",
     help="Set the level of logging detail",
 )
+@click.option(
+    "--direct-archive/--no-direct-archive",
+    type=bool,
+    default=True,
+    help=(
+        "Whether to use direct-to-archive uploads when adding sample data. This is "
+        "faster but requires XNAT 1.8.2 or later"
+    ),
+)
 @click.pass_context
-def add_data_cli(ctx, loglevel, dataset):
+def add_data_cli(ctx, loglevel, dataset, direct_archive):
 
     set_loggers(loglevel)
-    add_data(dataset, config_name=ctx.obj)
+    add_data(dataset, config_name=ctx.obj, direct_archive=direct_archive)
 
 
 @cli.group(

xnat4tests/config.py

@@ -14,7 +14,7 @@
 class BuildArgs:
     xnat_version: str = "1.9.2.1"
     xnat_cs_plugin_version: str = "3.7.2"
-    xnat_batch_launch_plugin_version: str = "0.8.0"
+    xnat_batch_launch_plugin_version: str = "0.8.0-xpl"
     java_ms: str = "256m"
     java_mx: str = "2g"
 

xnat4tests/data.py

@@ -32,7 +32,11 @@ def set_cwd(path):
         os.chdir(pwd)
 
 
-def add_data(dataset: str, config_name: str or dict = "default"):
+def add_data(
+    dataset: str,
+    config_name: ty.Union[str, dict] = "default",
+    direct_archive: bool = True,
+):
     """Uploads sample test data into the XNAT repository for use in test regimes
 
     Parameters
@@ -70,6 +74,7 @@ def add_data(dataset: str, config_name: str or dict = "default"):
             project_id="dummydicomproject",
             subject_id="dummydicomsubject",
             session_id="dummydicomsession",
+            direct_archive=direct_archive,
         )
 
     elif dataset == "openneuro-t1w":
@@ -129,6 +134,7 @@ def add_data(dataset: str, config_name: str or dict = "default"):
             project_id="TRAINING",
             subject_id="CONT01",
             session_id="CONT01_MR01",
+            direct_archive=direct_archive,
         )
 
         _upload_dicom_data(
@@ -137,6 +143,7 @@ def add_data(dataset: str, config_name: str or dict = "default"):
             project_id="TRAINING",
             subject_id="CONT02",
             session_id="CONT02_MR01",
+            direct_archive=direct_archive,
         )
 
         _upload_dicom_data(
@@ -145,6 +152,7 @@ def add_data(dataset: str, config_name: str or dict = "default"):
             project_id="TRAINING",
             subject_id="CONT01",
             session_id="CONT01_MR02",
+            direct_archive=direct_archive,
         )
 
         _upload_dicom_data(
@@ -153,6 +161,7 @@ def add_data(dataset: str, config_name: str or dict = "default"):
             project_id="TRAINING",
             subject_id="CONT02",
             session_id="CONT02_MR02",
+            direct_archive=direct_archive,
         )
 
         _upload_dicom_data(
@@ -161,6 +170,7 @@ def add_data(dataset: str, config_name: str or dict = "default"):
             project_id="TRAINING",
             subject_id="TEST01",
             session_id="TEST01_MR01",
+            direct_archive=direct_archive,
         )
 
         _upload_dicom_data(
@@ -169,6 +179,7 @@ def add_data(dataset: str, config_name: str or dict = "default"):
             project_id="TRAINING",
             subject_id="TEST01",
             session_id="TEST01_MR02",
+            direct_archive=direct_archive,
         )
 
         _upload_dicom_data(
@@ -177,6 +188,7 @@ def add_data(dataset: str, config_name: str or dict = "default"):
             project_id="TRAINING",
             subject_id="TEST02",
             session_id="TEST02_MR01",
+            direct_archive=direct_archive,
         )
 
         _upload_dicom_data(
@@ -185,6 +197,7 @@ def add_data(dataset: str, config_name: str or dict = "default"):
             project_id="TRAINING",
             subject_id="TEST02",
             session_id="TEST02_MR02",
+            direct_archive=direct_archive,
         )
 
     else:
@@ -199,6 +212,7 @@ def _upload_dicom_data(
     project_id: str,
     subject_id: str,
     session_id: str,
+    direct_archive: bool = True,
 ):
 
     if isinstance(to_upload, str):
@@ -269,10 +283,10 @@ def _upload_dicom_data(
                         f"/archive/projects/{project_id}/subjects"
                         f"/{subject_id}/experiments/{session_id}"
                     ),
-                    "Direct-Archive": True,
+                    "Direct-Archive": direct_archive,
                     "overwrite": True,
                 },
-                file_=f,
+                stream=f,
                 content_type="application/zip",
                 method="post",
             )