Merge up-to-date with main

smaht-dac · Dec 17, 2024 · 836850f · 836850f
2 parents a545dd2 + fd354a2
commit 836850f
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diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -7,13 +7,27 @@ smaht-portal
 Change Log
 ----------
 
-0.119.0
+0.121.0
 =======
 `PR 300 SN Remove basecalling <https://github.com/smaht-dac/smaht-portal/pull/300>`
 
 * Remove Basecalling item and transfer properties to Software item
 
 
+0.120.0
+=======
+`PR 306 SN Add cell_sorting_method <https://github.com/smaht-dac/smaht-portal/pull/306>`
+
+* Add property `cell_sorting_method` to AnalytePreparation
+
+
+0.119.0
+=======
+`PR 304 SN remove recovery_datetime from tissue <https://github.com/smaht-dac/smaht-portal/pull/304>`_
+
+* Remove `recovery_datetime` from Tissue after having moved the property to TissueCollection, as it is protected information
+
+
 0.118.0
 =======
 `PR 303 SN Rnaseq filenames <https://github.com/smaht-dac/smaht-portal/pull/303>`

diff --git a/pyproject.toml b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "encoded"
-version = "0.119.0"
+version = "0.121.0"
 description = "SMaHT Data Analysis Portal"
 authors = ["4DN-DCIC Team <[email protected]>"]
 license = "MIT"

diff --git a/src/encoded/schemas/analyte_preparation.json b/src/encoded/schemas/analyte_preparation.json
@@ -75,6 +75,28 @@
                 ]
             }
         },
+        "cell_sorting_method": {
+            "title": "Cell Sorting Method",
+            "description": "Cell sorting method for analyte extraction, if applicable. Relevant for extraction for single-cell assays",
+            "type": "array",
+            "minItems": 1,
+            "uniqueItems": true,
+            "items": {
+                "type": "string",
+                "enum": [
+                    "Fluoresence-activated",
+                    "Magnetic-activated",
+                    "Selective Media",
+                    "Laser Capture Microdissection",
+                    "Micromanipulation",
+                    "Isopycnic Sedimentation",
+                    "Velocity Sedimentation",
+                    "Centrifugation",
+                    "Filtering",
+                    "Microfluidics"
+                ]
+            }
+        },
         "extraction_method": {
             "title": "Extraction Method",
             "description": "Method of analyte extraction",

diff --git a/src/encoded/schemas/tissue.json b/src/encoded/schemas/tissue.json
@@ -80,7 +80,7 @@
             ]
         },
         "schema_version": {
-            "default": "3"
+            "default": "4"
         },
         "submitted_id": {
             "pattern": "^[A-Z0-9]{3,}_TISSUE_[A-Z0-9-_.]{4,}$"
@@ -113,19 +113,6 @@
             "description": "Notes from prosector report on the tissue recovery",
             "type": "string"
         },
-        "recovery_datetime": {
-            "title": "Recovery Datetime",
-            "description": "Date and time of tissue recovery",
-            "type": "string",
-            "anyOf": [
-                {
-                    "format": "date-time"
-                },
-                {
-                    "format": "date"
-                }
-            ]
-        },
         "sample_count": {
             "title": "Sample Count",
             "description": "Number of samples produced from the tissue",

diff --git a/src/encoded/tests/data/workbook-inserts/analyte.json b/src/encoded/tests/data/workbook-inserts/analyte.json
@@ -16,7 +16,8 @@
         "concentration_unit": "ng/uL",
         "samples": [
             "TEST_TISSUE-SAMPLE_LIVER"
-        ]
+        ],
+        "analyte_preparation": "TEST_ANALYTE-PREPARATION_LIVER"
     },
     {
         "uuid": "ecff361b-a0ce-4805-9201-301e42c868bf",
@@ -121,5 +122,22 @@
             "TEST_TISSUE-SAMPLE_LIVER",
             "TEST_TISSUE-SAMPLE_LIVER_2"
         ]
+    },
+    {
+        "uuid": "fa2191da-52d8-40a0-95a4-ae116b9ea518",
+        "submission_centers": [
+            "smaht"
+        ],
+        "submitted_id": "TEST_ANALYTE_LIVER-CELL",
+        "molecule": [
+            "DNA"
+        ],
+        "molecule_detail": [
+            "Total DNA"
+        ],
+        "samples": [
+            "TEST_CELL-SAMPLE_LIVER-CELL"
+        ],
+        "analyte_preparation": "TEST_ANALYTE-PREPARATION_LIVER-CELL"
     }
 ]
diff --git a/src/encoded/tests/data/workbook-inserts/analyte_preparation.json b/src/encoded/tests/data/workbook-inserts/analyte_preparation.json
@@ -5,11 +5,22 @@
             "smaht"
         ],
         "submitted_id": "TEST_ANALYTE-PREPARATION_LIVER",
-        "cell_lysis_method": [
-            "Chemical"
-        ],
         "extraction_method": [
             "Magnetic Beads"
         ]
+    },
+    {
+        "uuid": "6ba66ffb-d509-4b75-9c91-00f317138383",
+        "submission_centers": [
+            "smaht"
+        ],
+        "submitted_id": "TEST_ANALYTE-PREPARATION_LIVER-CELL",
+        "cell_sorting_method": [
+            "Magnetic-activated"
+        ],
+        "cell_lysis_method": [
+            "Chemical"
+        ],
+        "suspension_type": "Whole Cell"
     }
 ]
diff --git a/src/encoded/tests/data/workbook-inserts/library.json b/src/encoded/tests/data/workbook-inserts/library.json
@@ -14,7 +14,8 @@
         "fragment_mean_length": 150.7,
         "insert_mean_length": 150.2,
         "preparation_date": "2023-05-11",
-        "assay": "bulk_wgs"
+        "assay": "bulk_wgs",
+        "library_preparation": "TEST_LIBRARY-PREPARATION_LIVER"
     },
     {
         "uuid": "f14533e1-de91-4390-9c16-28e420029d41",

diff --git a/src/encoded/tests/test_upgrade_tissue.py b/src/encoded/tests/test_upgrade_tissue.py
@@ -22,4 +22,24 @@ def test_upgrade_tissue_2_3(
             "tissue", tissue, current_version="2", target_version="3"
         )
         == expected
+    )
+
+
+@pytest.mark.parametrize(
+    "tissue,expected",
+    [
+        ({}, {"schema_version": "4"}),
+        ({"recovery_datetime": "2024-12-01"}, {"schema_version": "4"}),
+    ],
+)
+def test_upgrade_tissue_3_4(
+    app: Router, tissue: Dict[str, Any], expected: Dict[str, Any]
+) -> None:
+    """Test tissue upgrader from version 3 to 4."""
+    upgrader = get_upgrader(app)
+    assert (
+        upgrader.upgrade(
+            "tissue", tissue, current_version="3", target_version="4"
+        )
+        == expected
     )
diff --git a/src/encoded/upgrade/tissue.py b/src/encoded/upgrade/tissue.py
@@ -16,3 +16,10 @@ def upgrade_tissue_2_3(value: Dict[str, Any], system: Dict[str, Any]) -> Dict[st
     existing_recovery_interval = value.get("recovery_interval")
     if existing_recovery_interval:
         del value["recovery_interval"]
+
+
+@upgrade_step("tissue", "3", "4")
+def upgrade_tissue_3_4(value: Dict[str, Any], system: Dict[str, Any]) -> Dict[str, Any]:
+    existing_recovery_datetime = value.get("recovery_datetime")
+    if existing_recovery_datetime:
+        del value["recovery_datetime"]