Merge 57d20ec into d6e5a45

HISTORY.rst

@@ -2,6 +2,20 @@
 History
 =======
 
+Unreleased / master
+-------------------
+
+* Object model for Screening tables
+* set_role
+* New module for crystal imaging: xtalimaging
+
+5.5.0 (2020-01-07)
+------------------
+
+New methods:
+ * upsert_program_message
+ * upsert_sample_image_auto_score
+
 5.4.1 (2019-11-12)
 ------------------
 

ispyb/interface/factory.py

@@ -42,6 +42,11 @@ def mx_screening(self):
         """MX screening tables"""
         return self._get_data_area("mxscreening", "MXScreening")
 
+    @property
+    def xtal_imaging(self):
+        """Crystal imaging tables"""
+        return self._get_data_area("xtalimaging", "XtalImaging")
+
     @property
     def shipping(self):
         """Shipping tables"""

ispyb/sp/xtalimaging.py

@@ -0,0 +1,69 @@
+from __future__ import absolute_import, division, print_function
+
+from ispyb.interface.dataarea import DataArea
+
+
+class XtalImaging(DataArea):
+    """provides methods for accessing crystal imaging tables."""
+
+    def upsert_sample_image(
+        self,
+        id=None,
+        sample_id=None,
+        inspection_id=None,
+        microns_per_pixel_x=None,
+        microns_per_pixel_y=None,
+        image_full_path=None,
+        comments=None,
+    ):
+        """Store new or update existing sample image.
+
+        :param image_full_path: The full path to the sample image
+        :return: The sample_image_id.
+        """
+        return self.get_connection().call_sp_write(
+            procname="upsert_sample_image",
+            args=[
+                id,
+                sample_id,
+                inspection_id,
+                microns_per_pixel_x,
+                microns_per_pixel_y,
+                image_full_path,
+                comments,
+            ],
+        )
+
+    def upsert_sample_image_auto_score(
+        self, image_full_path, schema_name, score_class, probability
+    ):
+        """Store new or update existing automatic score for a sample image.
+
+        :param image_full_path: The full path to the sample image
+        :param schema_name: The name of the scoring schema, e.g. MARCO
+        :param score_class: A string that describes the thing we're scoring, e.g. crystal, clear, precipitant, other
+        :param probability: A float indicating the probability that the image contains the score_class
+        """
+        self.get_connection().call_sp_write(
+            procname="upsert_sample_image_auto_score",
+            args=[image_full_path, schema_name, score_class, probability],
+        )
+
+    def retrieve_container_for_barcode(self, barcode):
+        """Retrieve info about the container indetified by the give barcode."""
+        return self.get_connection().call_sp_retrieve(
+            procname="retrieve_container_for_barcode", args=[barcode]
+        )
+
+    def retrieve_container_for_inspection_id(self, inspection_id):
+        """Retrieve info about the container identified by container inspection ID"""
+        return self.get_connection().call_sp_retrieve(
+            procname="retrieve_container_for_inspection_id", args=[inspection_id]
+        )
+
+    def retrieve_sample_for_container_id_and_location(self, container_id, location):
+        """Retrieve info about the sample identified by the given container ID and its location."""
+        return self.get_connection().call_sp_retrieve(
+            procname="retrieve_sample_for_container_id_and_location",
+            args=[container_id, location],
+        )

tests/test_xtalimaging.py

@@ -0,0 +1,39 @@
+from __future__ import absolute_import, division, print_function
+
+
+def test_xtal_imaging(testdb):
+    testdb.set_role("ispyb_import")
+    xtalimaging = testdb.xtal_imaging
+
+    container = xtalimaging.retrieve_container_for_barcode("test_plate2")
+    cid = container[0]["containerId"]
+
+    assert cid is not None
+    assert cid > 0
+
+    sample = xtalimaging.retrieve_sample_for_container_id_and_location(
+        container_id=cid, location=1
+    )
+    sid = sample[0]["sampleId"]
+
+    assert sid is not None
+    assert sid > 0
+
+    si_full_path = "/dls/i03/data/2018/cm14451-99/something_new.jpg"
+    siid = xtalimaging.upsert_sample_image(
+        sample_id=sid,
+        microns_per_pixel_x=12.03,
+        microns_per_pixel_y=12.04,
+        image_full_path=si_full_path,
+    )
+
+    assert siid is not None
+    assert siid > 0
+
+    xtalimaging.upsert_sample_image_auto_score(si_full_path, "MARCO", "crystal", 0.65)
+
+    container = xtalimaging.retrieve_container_for_inspection_id(4)
+    cid2 = container[0]["containerId"]
+
+    assert cid2 is not None
+    assert cid2 == 34874