Merge branch 'master' into roles

.travis.yml

@@ -28,6 +28,7 @@ before_install:
 - mysql -u root -D ispybtest < grants/ispyb_processing.sql
 - mysql -u root -D ispybtest < grants/ispyb_import.sql
 - mysql -u root -e "CREATE USER ispyb_api@'localhost' IDENTIFIED BY 'password_1234'; GRANT ispyb_processing to ispyb_api@'localhost'; GRANT ispyb_import to ispyb_api@'localhost'; SET DEFAULT ROLE ispyb_processing FOR ispyb_api@'localhost';"
+- mysql -u root -e "CREATE USER ispyb_api_future@'localhost' IDENTIFIED BY 'password_4321'; GRANT SELECT ON ispybtest.* to ispyb_api_future@'localhost';"
 
 before_script:
 - cp conf/config.example.cfg conf/config.cfg

conf/config.example.cfg

@@ -7,3 +7,12 @@ port = 3306
 db = ispybtest
 reconn_attempts = 6
 reconn_delay = 1
+
+[ispyb]
+username = ispyb_api_future
+password = password_4321
+host = localhost
+port = 3306
+database = ispybtest
+reconn_attempts = 6
+reconn_delay = 1

ispyb/model/__future__.py

@@ -105,11 +105,41 @@ def __exit__(cm, *args):
     ispyb.model.datacollection.DataCollection.integrations = (
         _get_linked_autoprocintegration_for_dc
     )
+    ispyb.model.datacollection.DataCollection.screenings = _get_linked_screenings_for_dc
     ispyb.model.datacollection.DataCollection.pdb = _get_linked_pdb_for_dc
     import ispyb.model.processingprogram
 
     ispyb.model.processingprogram.ProcessingProgram.reload = _get_autoprocprogram
 
+    import ispyb.model.screening
+
+    ispyb.model.screening.Screening.outputs = _get_linked_outputs_for_screening
+    ispyb.model.screening.Screening.reload = _get_screening
+
+    ispyb.model.screening.ScreeningOutput.lattices = (
+        _get_linked_lattices_for_screening_output
+    )
+    ispyb.model.screening.ScreeningOutput.strategies = (
+        _get_linked_strategies_for_screening_output
+    )
+    ispyb.model.screening.ScreeningOutput.reload = _get_screening_output
+
+    ispyb.model.screening.ScreeningOutputLattice.reload = _get_screening_output_lattice
+
+    ispyb.model.screening.ScreeningStrategy.wedges = (
+        _get_linked_wedges_for_screening_strategy
+    )
+    ispyb.model.screening.ScreeningStrategy.reload = _get_screening_strategy
+
+    ispyb.model.screening.ScreeningStrategyWedge.sub_wedges = (
+        _get_linked_sub_wedges_for_screening_strategy_wedge
+    )
+    ispyb.model.screening.ScreeningStrategyWedge.reload = _get_screening_strategy_wedge
+
+    ispyb.model.screening.ScreeningStrategySubWedge.reload = (
+        _get_screening_strategy_sub_wedge
+    )
+
 
 def _get_autoprocprogram(self):
     # https://jira.diamond.ac.uk/browse/SCI-7414
@@ -173,6 +203,201 @@ def _get_linked_pdb_for_dc(self):
         ]
 
 
+@property
+def _get_linked_screenings_for_dc(self):
+    import ispyb.model.screening
+
+    with _db_cc() as cursor:
+        cursor.run(
+            "SELECT screeningId, comments, shortComments, programVersion "
+            "FROM Screening "
+            "WHERE dataCollectionId = %s "
+            "ORDER BY screeningId",
+            self.dcid,
+        )
+        return [
+            ispyb.model.screening.Screening(ir["screeningId"], self._db, preload=ir)
+            for ir in cursor.fetchall()
+        ]
+
+
+@property
+def _get_linked_outputs_for_screening(self):
+    import ispyb.model.screening
+
+    with _db_cc() as cursor:
+        cursor.run(
+            "SELECT screeningOutputId, alignmentSuccess, indexingSuccess, strategySuccess, program "
+            "FROM ScreeningOutput "
+            "WHERE screeningid = %s "
+            "ORDER BY screeningOutputId",
+            self._screening_id,
+        )
+        return [
+            ispyb.model.screening.ScreeningOutput(
+                ir["screeningOutputId"], self._db, preload=ir
+            )
+            for ir in cursor.fetchall()
+        ]
+
+
+@property
+def _get_linked_lattices_for_screening_output(self):
+    import ispyb.model.screening
+
+    with _db_cc() as cursor:
+        cursor.run(
+            "SELECT screeningOutputLatticeId, spaceGroup, "
+            "unitCell_a, unitCell_b, unitCell_c, "
+            "unitCell_alpha, unitCell_beta, unitCell_gamma "
+            "FROM ScreeningOutputLattice "
+            "WHERE screeningoutputid = %s "
+            "ORDER BY screeningOutputLatticeId",
+            self._output_id,
+        )
+        return [
+            ispyb.model.screening.ScreeningOutputLattice(
+                ir["screeningOutputLatticeId"], self._db, preload=ir
+            )
+            for ir in cursor.fetchall()
+        ]
+
+
+@property
+def _get_linked_strategies_for_screening_output(self):
+    import ispyb.model.screening
+
+    with _db_cc() as cursor:
+        cursor.run(
+            "SELECT screeningStrategyId, anomalous, program, "
+            "exposureTime, rankingResolution "
+            "FROM ScreeningStrategy "
+            "WHERE screeningoutputid = %s "
+            "ORDER BY screeningStrategyId",
+            self._output_id,
+        )
+        return [
+            ispyb.model.screening.ScreeningStrategy(
+                ir["screeningStrategyId"], self._db, preload=ir
+            )
+            for ir in cursor.fetchall()
+        ]
+
+
+@property
+def _get_linked_wedges_for_screening_strategy(self):
+    import ispyb.model.screening
+
+    with _db_cc() as cursor:
+        cursor.run(
+            "SELECT screeningStrategyWedgeId, chi, completeness, kappa, "
+            "multiplicity, numberOfImages, phi, resolution, wedgeNumber "
+            "FROM ScreeningStrategyWedge "
+            "WHERE screeningStrategyId = %s "
+            "ORDER BY screeningStrategyWedgeId",
+            self._strategy_id,
+        )
+        return [
+            ispyb.model.screening.ScreeningStrategyWedge(
+                ir["screeningStrategyWedgeId"], self._db, preload=ir
+            )
+            for ir in cursor.fetchall()
+        ]
+
+
+@property
+def _get_linked_sub_wedges_for_screening_strategy_wedge(self):
+    import ispyb.model.screening
+
+    with _db_cc() as cursor:
+        cursor.run(
+            "SELECT axisEnd, axisStart, completeness, exposureTime, "
+            "multiplicity, numberOfImages, oscillationRange, resolution, "
+            "rotationAxis, subWedgeNumber, transmission, "
+            "screeningStrategySubWedgeId "
+            "FROM ScreeningStrategySubWedge "
+            "WHERE screeningStrategyWedgeId = %s "
+            "ORDER BY screeningStrategySubWedgeId",
+            self._wedge_id,
+        )
+        return [
+            ispyb.model.screening.ScreeningStrategySubWedge(
+                ir["screeningStrategySubWedgeId"], self._db, preload=ir
+            )
+            for ir in cursor.fetchall()
+        ]
+
+
+def _get_screening(self):
+    with _db_cc() as cursor:
+        cursor.run(
+            "SELECT comments, shortComments, programVersion "
+            "FROM Screening "
+            "WHERE screeningId = %s",
+            self._screening_id,
+        )
+        self._data = cursor.fetchone()
+
+
+def _get_screening_output(self):
+    with _db_cc() as cursor:
+        cursor.run(
+            "SELECT alignmentSuccess, indexingSuccess, strategySuccess, program "
+            "FROM ScreeningOutput "
+            "WHERE screeningOutputId = %s",
+            self._output_id,
+        )
+        self._data = cursor.fetchone()
+
+
+def _get_screening_output_lattice(self):
+    with _db_cc() as cursor:
+        cursor.run(
+            "SELECT spaceGroup, unitCell_a, unitCell_b, unitCell_c, "
+            "unitCell_alpha, unitCell_beta, unitCell_gamma "
+            "FROM ScreeningOutputLattice "
+            "WHERE screeningOutputLatticeId = %s",
+            self._lattice_id,
+        )
+        self._data = cursor.fetchone()
+
+
+def _get_screening_strategy(self):
+    with _db_cc() as cursor:
+        cursor.run(
+            "SELECT anomalous, program, exposureTime, rankingResolution "
+            "FROM ScreeningStrategy "
+            "WHERE screeningStrategyId = %s",
+            self._strategy_id,
+        )
+        self._data = cursor.fetchone()
+
+
+def _get_screening_strategy_wedge(self):
+    with _db_cc() as cursor:
+        cursor.run(
+            "SELECT chi, completeness, kappa, multiplicity, numberOfImages, "
+            "phi, resolution, wedgeNumber "
+            "FROM ScreeningStrategyWedge "
+            "WHERE screeningStrategyWedgeId = %s",
+            self._wedge_id,
+        )
+        self._data = cursor.fetchone()
+
+
+def _get_screening_strategy_sub_wedge(self):
+    with _db_cc() as cursor:
+        cursor.run(
+            "SELECT axisEnd, axisStart, completeness, exposureTime, "
+            "multiplicity, numberOfImages, oscillationRange, resolution, "
+            "rotationAxis, subWedgeNumber, transmission "
+            "FROM ScreeningStrategySubWedge "
+            "WHERE screeningStrategySubWedgeId = %s",
+            self._sub_wedge_id,
+        )
+        self._data = cursor.fetchone()
+
+
 def test_connection():
     """A test function to verify that the database connection is alive."""
     with _db_cc() as cursor:

ispyb/model/datacollection.py

@@ -49,6 +49,11 @@ def integrations(self):
         """Returns the list of IntegrationResult objects associated with this DC."""
         raise NotImplementedError("TODO: Not implemented yet")
 
+    @property
+    def screenings(self):
+        """Returns the list of Screening objects associated with this DC."""
+        raise NotImplementedError("TODO: Not implemented yet")
+
     @property
     def file_template_full(self):
         """Template for file names with full directory path. As with file_template
@@ -193,7 +198,9 @@ def __init__(self, dcgid, db_conn, preload=None):
 
     def reload(self):
         """Load/update information from the database."""
-        self._data = self._db.mx_acquisition.retrieve_data_collection_group(self._dcgid)[0]
+        self._data = self._db.mx_acquisition.retrieve_data_collection_group(
+            self._dcgid
+        )[0]
 
     @property
     def dcgid(self):

ispyb/model/interface.py

@@ -3,6 +3,7 @@
 import ispyb.model.datacollection
 import ispyb.model.processingprogram
 import ispyb.model.processingjob
+import ispyb.model.screening
 
 
 class ObjectModelMixIn:
@@ -24,6 +25,42 @@ def get_processing_job(self, jobid):
         return ispyb.model.processingjob.ProcessingJob(jobid, self.mx_processing)
 
     def get_processing_program(self, appid):
-        """Return an ProcessingProgram object representing the information
+        """Return a ProcessingProgram object representing the information
         about a processing program invocation."""
         return ispyb.model.processingprogram.ProcessingProgram(appid, self)
+
+    def get_screening(self, screening_id):
+        """Return a Screening object representing the information
+        about a Screening result."""
+        return ispyb.model.screening.Screening(screening_id, self)
+
+    def get_screening_output(self, screening_output_id):
+        """Return a ScreeningOutput object representing the information
+        about a ScreeningOutput result."""
+        return ispyb.model.screening.ScreeningOutput(screening_output_id, self)
+
+    def get_screening_output_lattice(self, screening_output_lattice_id):
+        """Return a ScreeningOutputLattice object representing the information
+        about a ScreeningOutputLattice result."""
+        return ispyb.model.screening.ScreeningOutputLattice(
+            screening_output_lattice_id, self
+        )
+
+    def get_screening_strategy(self, screening_strategy_id):
+        """Return a ScreeningStrategy object representing the information
+        about a ScreeningStrategy result."""
+        return ispyb.model.screening.ScreeningStrategy(screening_strategy_id, self)
+
+    def get_screening_strategy_wedge(self, screening_strategy_wedge_id):
+        """Return a ScreeningStrategyWedge object representing the information
+        about a ScreeningStrategyWedge result."""
+        return ispyb.model.screening.ScreeningStrategyWedge(
+            screening_strategy_wedge_id, self
+        )
+
+    def get_screening_strategy_sub_wedge(self, screening_strategy_sub_wedge_id):
+        """Return a ScreeningStrategySubWedge object representing the
+        information about a ScreeningStrategySubWedge result."""
+        return ispyb.model.screening.ScreeningStrategySubWedge(
+            screening_strategy_sub_wedge_id, self
+        )