Update pytests

CHANGELOG.md

@@ -3,8 +3,13 @@
 Observes [Semantic Versioning](https://semver.org/spec/v2.0.0.html) standard and
 [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) convention.
 
+## [0.1.1] - 2023-08-31
+
++ Update - Incorporate suggestions from previous PR to improve pytests
+
 ## [0.1.0] - Unreleased
 
 + Add - Workflow pipeline, pytests, CICD
 
+[0.1.1]: https://github.com/datajoint/workflow-zstack/releases/tag/0.1.1
 [0.1.0]: https://github.com/datajoint/workflow-zstack/releases/tag/0.1.0

README.md

@@ -53,7 +53,7 @@ a tutorial environment and notebook to learn the pipeline.
    to ensure you have `resource-manager` permissions for your account. 
 2. Follow the instructions below to set up the
    [intern](https://github.com/jhuapl-boss/intern) REST API locally. 
-   + Create a new folder `.intern` in your root directory.
+   + Create a new folder `.intern` in your user directory.
    + Create a configuration file `intern.cfg` within the `.intern` folder. The
      path to this file should be `~/.intern/intern.cfg`. 
    + The `intern.cfg` file should contain the following exactly as shown below:

tests/conftest.py

@@ -16,7 +16,7 @@
 
 
 sessions_dirs = [
-    "subject1",
+    "subject2",
 ]
 
 # ---------------------- FIXTURES ----------------------
@@ -57,15 +57,15 @@ def insert_upstream(pipeline):
 
     subject.Subject.insert1(
         dict(
-            subject="subject1",
+            subject="subject2",
             sex="M",
             subject_birth_date="2023-01-01",
             subject_description="Cellpose segmentation of volumetric data."),
         skip_duplicates=True,
     )
 
     session_key = dict(
-        subject="subject1",
+        subject="subject2",
         session_id=0,
     )
     session.Session.insert1(
@@ -77,7 +77,7 @@ def insert_upstream(pipeline):
     )
 
     session.SessionDirectory.insert1(
-        dict(session_key, session_dir="subject1/session1"),
+        dict(session_key, session_dir="subject2"),
         skip_duplicates=True,
     )
     scan.Scan.insert1(
@@ -102,21 +102,20 @@ def volume_volume(pipeline):
 
 
 @pytest.fixture(scope="session")
-def volume_segmentation_task(pipeline):
+def volume_segmentation_param_set(pipeline):
     volume = pipeline["volume"]
-    key = (volume.Volume & "subject='subject1'").fetch1("KEY")
+    key = (volume.Volume & "subject='subject2'").fetch1("KEY")
     volume.SegmentationParamSet.insert_new_params(
         segmentation_method="cellpose",
         paramset_idx=1,
         params=dict(
-            diameter=8,
+            diameter=None,
             min_size=2,
             do_3d=False,
             anisotropy=0.5,
             model_type="nuclei",
             channels=[[0, 0]],
             z_axis=0,
-            skip_duplicates=True,
         ),
     )
     yield
@@ -125,6 +124,7 @@ def volume_segmentation_task(pipeline):
 @pytest.fixture(scope="session")
 def volume_segmentation_task(pipeline):
     volume = pipeline["volume"]
+    key = (volume.Volume & "subject='subject2'").fetch1("KEY")
     volume.SegmentationTask.insert1(dict(
         key,
         paramset_idx=1,
@@ -135,15 +135,15 @@ def volume_segmentation_task(pipeline):
 @pytest.fixture(scope="session")
 def volume_segmentation(pipeline):
     volume = pipeline["volume"]
-    key = (volume.Volume & "subject='subject1'").fetch1("KEY")
+    key = (volume.Volume & "subject='subject2'").fetch1("KEY")
     volume.Segmentation.populate(key)
     yield
 
 
 @pytest.fixture(scope="session")
 def volume_voxel_size(pipeline):
     volume = pipeline["volume"]
-    key = (volume.Volume & "subject='subject1'").fetch1("KEY")
+    key = (volume.Volume & "subject='subject2'").fetch1("KEY")
     volume.VoxelSize.insert1(
         dict(
             key,
@@ -158,10 +158,10 @@ def volume_voxel_size(pipeline):
 def bossdb_volume_upload_task(pipeline):
     bossdb = pipeline["bossdb"]
     volume = pipeline["volume"]
-    key = (volume.Segmentation & "subject='subject1'").fetch1("KEY")
+    key = (volume.Segmentation & "subject='subject2'").fetch1("KEY")
     col_name = "dataJointTestUpload"
     exp_name = "CaImagingFinal"
-    chn_name = "test1"
+    chn_name = "test2"
 
     bossdb.VolumeUploadTask.insert1(
         dict(

tests/test_export.py

@@ -15,15 +15,15 @@ def test_export(pipeline):
 
     subject.Subject.insert1(
         dict(
-            subject="subject1",
+            subject="subject2",
             sex="M",
             subject_birth_date="2023-01-01",
             subject_description="Cellpose segmentation of volumetric data."),
         skip_duplicates=True,
     )
 
     session_key = dict(
-        subject="subject1",
+        subject="subject2",
         session_id=0,
     )
     session.Session.insert1(
@@ -35,7 +35,7 @@ def test_export(pipeline):
     )
 
     session.SessionDirectory.insert1(
-        dict(session_key, session_dir="subject1/session1"),
+        dict(session_key, session_dir="subject2"),
         skip_duplicates=True,
     )
     scan.Scan.insert1(
@@ -46,11 +46,11 @@ def test_export(pipeline):
         ),
         skip_duplicates=True,
     )
-    volume.Volume.populate()
-    key = (volume.Volume & "subject='subject1'").fetch1("KEY")
+    volume.Volume.populate(session_key)
+    key = (volume.Volume & "subject='subject2'").fetch1("KEY")
     volume.SegmentationParamSet.insert_new_params(
         segmentation_method="cellpose",
-        paramset_idx=2,
+        paramset_idx=1,
         params=dict(
             diameter=None,
             min_size=2,
@@ -59,29 +59,29 @@ def test_export(pipeline):
             model_type="nuclei",
             channels=[[0, 0]],
             z_axis=0,
-            skip_duplicates=True,
         ),
     )
     volume.SegmentationTask.insert1(dict(
         key,
-        paramset_idx=2,
+        paramset_idx=1,
         task_mode="trigger",
         ),
     skip_duplicates=True,
     )
-    segmentation_key = (volume.SegmentationTask & "subject='subject1'").fetch1("KEY")
+    segmentation_key = (volume.SegmentationTask & "subject='subject2'").fetch1("KEY")
     volume.Segmentation.populate(segmentation_key)
     volume.VoxelSize.insert1(
         dict(
-            segmentation_key,
+            **session_key,
+            scan_id=0,
             width=0.001,
             height=0.001,
             depth=0.001,
             )
         )
     col_name = "dataJointTestUpload"
     exp_name = "CaImagingFinal"
-    chn_name = "test1"
+    chn_name = "test2"
 
     bossdb.VolumeUploadTask.insert1(
         dict(

workflow_zstack/__init__.py

@@ -14,4 +14,4 @@
     "VOLUME_ROOT_DATA_DIR", dj.config["custom"].get("volume_root_data_dir", "")
 )
 
-db_prefix = dj.config["custom"].get("database.prefix", "")
+db_prefix = dj.config["custom"].get("database.prefix", "")

workflow_zstack/paths.py

@@ -33,16 +33,18 @@ def get_volume_tif_file(scan_key):
     Raises:
         FileNotFoundError: If the tiff file(s) are not found.
     """
-    # Folder structure: root / subject / session / .tif (raw)    
+    # Folder structure: root / subject / session / .tif (raw)
     sess_dir = find_full_path(
         get_volume_root_data_dir(),
         pathlib.Path((session.SessionDirectory & scan_key).fetch1("session_dir")),
     )
-    
+
     tiff_filepaths = [fp.as_posix() for fp in sess_dir.rglob("*.tif")]
 
     if tiff_filepaths:
-        assert len(tiff_filepaths) == 1, "More than 1 `.tif` file in file path. Please ensure the session directory contains only 1 image file."
+        assert (
+            len(tiff_filepaths) == 1
+        ), "More than 1 `.tif` file in file path. Please ensure the session directory contains only 1 image file."
         return tiff_filepaths[0]
     else:
         raise FileNotFoundError(f"No tiff file found in {sess_dir}")

workflow_zstack/reference.py

@@ -7,20 +7,9 @@
 
 @schema
 class Device(dj.Lookup):
-    """Table for managing lab equipment.
-
-    Attributes:
-        device ( varchar(32) ): Device short name.
-        modality ( varchar(64) ): Modality for which this device is used.
-        description ( varchar(256) ): Optional. Description of device.
-    """
-
     definition = """
-    device             : varchar(32)
+    device_id           : smallint
     ---
-    modality           : varchar(64)
-    description=null   : varchar(256)
+    device_name         : varchar(32)  # user-friendly name of the device
+    device_description  : varchar(256)
     """
-    contents = [
-        ["scanner1", "fluorescence microscope", ""],
-    ]

workflow_zstack/version.py

@@ -1,2 +1,2 @@
 """Package metadata."""
-__version__ = "0.1.0"
+__version__ = "0.1.1"