added db_functions

olivierfriard · Jan 25, 2018 · a963da0 · a963da0
1 parent 6e7d9c0
commit a963da0
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diff --git a/README.TXT b/README.TXT
@@ -1,7 +1,7 @@
 BORIS
 Behavioral Observation Research Interactive Software
 
-Copyright 2012-2017 Olivier Friard
+Copyright 2012-2018 Olivier Friard
 
 BORIS is free software; you can redistribute it and/or modify
 it under the terms of the GNU General Public License as published by

diff --git a/boris.py b/boris.py
@@ -969,6 +969,7 @@ def irr_cohen_kappa(self):
             #paramPanelWindow.item.setCheckState(Qt.Unchecked)
             #paramPanelWindow.lwSubjects.addItem(paramPanelWindow.item)
 
+        paramPanelWindow.resize(500, 400)
         if paramPanelWindow.exec_():
             selected_subjects = paramPanelWindow.selectedSubjects
             include_modifiers = paramPanelWindow.cbIncludeModifiers.isChecked()
@@ -1000,6 +1001,11 @@ def irr_cohen_kappa(self):
                                  if "STATE" in self.pj[ETHOGRAM][x][TYPE].upper()
                                     and self.pj[ETHOGRAM][x]["code"] in observed_codes]
 
+        point_behaviors_codes = [self.pj[ETHOGRAM][x]["code"] for x in self.pj[ETHOGRAM]
+                                 if "POINT" in self.pj[ETHOGRAM][x][TYPE].upper()
+                                    and self.pj[ETHOGRAM][x]["code"] in observed_codes]
+
+
         if not state_behaviors_codes:
             QMessageBox.warning(self, programName, "No state event behaviors")
             return
@@ -1023,6 +1029,7 @@ def irr_cohen_kappa(self):
                               self.pj[OBSERVATIONS][obsid2][EVENTS],
                               interval,
                               state_behaviors_codes,
+                              point_behaviors_codes,
                               selected_subjects,
                               include_modifiers)
 
@@ -1962,7 +1969,18 @@ def edit_observation(self):
 
 
     def check_state_events_obs(self, obsId):
-
+        """
+        check state events
+        if no current observation check all observations
+        check if number is odd
+        
+        Args:
+            obsId (str): id of observation to check
+            
+        Returns:
+            set (bool, str): True/False, message
+        """
+
         # check if behaviors are defined as "state event"
         event_types = {self.pj[ETHOGRAM][idx]["type"] for idx in self.pj[ETHOGRAM]}
 
@@ -1981,15 +1999,17 @@ def check_state_events_obs(self, obsId):
 
             for behavior in sorted(set(behaviors)):
                 if behavior not in ethogram_behaviors:
-                    return (False, "The behaviour <b>{}</b> does not exist more in the ethogram.<br>".format(behavior))
+                    return (False, "The behaviour <b>{}</b> not found in the ethogram.<br>".format(behavior))
                 else:
-                    if "STATE" in self.eventType(behavior).upper():
+                    if STATE in self.eventType(behavior).upper():
                         flagStateEvent = True
                         lst, memTime = [], {}
                         for event in [event for event in self.pj[OBSERVATIONS][obsId][EVENTS]
                                       if event[EVENT_BEHAVIOR_FIELD_IDX] == behavior and
                                       event[EVENT_SUBJECT_FIELD_IDX] == subject]:
+
                             behav_modif = [event[EVENT_BEHAVIOR_FIELD_IDX], event[EVENT_MODIFIER_FIELD_IDX]]
+
                             if behav_modif in lst:
                                 lst.remove(behav_modif)
                                 del memTime[str(behav_modif)]
@@ -1998,7 +2018,7 @@ def check_state_events_obs(self, obsId):
                                 memTime[str(behav_modif)] = event[EVENT_TIME_FIELD_IDX]
 
                         for event in lst:
-                            out += ("""The behavior <b>{behavior}</b> {modifier}is not PAIRED for subject"""
+                            out += ("""The behavior <b>{behavior}</b> {modifier} is not PAIRED for subject"""
                                     """ "<b>{subject}</b>" at <b>{time}</b><br>""").format(
                                           behavior=behavior,
                                           modifier=("(modifier "+ event[1] + ") ") if event[1] else "",
@@ -2010,9 +2030,11 @@ def check_state_events_obs(self, obsId):
 
     def check_state_events(self, mode="all"):
         """
-        check state events for each subject in current observation
-        if no current observation check all observations
-        check if number is odd
+        check state events for each subject
+        use check_state_events_obs function
+        
+        Args:
+            mode (str): current: check current observation / all: ask user to select observations
         """
 
         tot_out = ""
@@ -4633,19 +4655,25 @@ def eventType(self, code):
 
     def loadEventsInDB(self, selectedSubjects, selectedObservations, selectedBehaviors):
         """
-        populate the db databse with events from selectedObservations, selectedSubjects and selectedBehaviors
-        selectedObservations: list
-        selectedSubjects: list
-        selectedBehaviors: list
+        populate an memory sqlite database with events from selectedObservations, selectedSubjects and selectedBehaviors
+        
+        Args:
+            selectedObservations (list):
+            selectedSubjects (list):
+            selectedBehaviors (list):
+            
+        Returns:
+            database cursor:
+
         """
         db = sqlite3.connect(":memory:")
-        
+
         '''
         if os.path.isfile("/tmp/boris_debug.sqlite"):
             os.system("rm /tmp/boris_debug.sqlite")
         db = sqlite3.connect("/tmp/boris_debug.sqlite")
         '''
-        
+
         db.row_factory = sqlite3.Row
         cursor = db.cursor()
         cursor.execute("""CREATE TABLE events (observation TEXT,
@@ -7546,12 +7574,10 @@ def export_aggregated_events(self):
                         if "media_info" in self.pj[OBSERVATIONS][obsId]:
                             duration1.append(self.pj[OBSERVATIONS][obsId]["media_info"]["length"][mediaFile])
                         else:
-                            #if "media_file_info" in
-                            print("no media_info tag")
+                            logging.info("no media_info tag for {} in observation {}" .format(mediaFile, obsId))
                 except:
-                    print("error")
-                    pass
-
+                    logging.critical(sys.exc_info()[1])
+                    QMessageBox.critical(None, programName, str(sys.exc_info()[1]), QMessageBox.Ok | QMessageBox.Default, QMessageBox.NoButton)
 
             total_length = "{0:.3f}".format(self.observationTotalMediaLength(obsId))
             logging.debug("media length for {0}: {1}".format(obsId, total_length))
@@ -8685,7 +8711,7 @@ def actionAbout_activated(self):
         about_dialog.setEscapeButton(QMessageBox.Ok)
 
         about_dialog.setInformativeText(("<b>{prog_name}</b> {ver} - {date}"
-        "<p>Copyright &copy; 2012-2017 Olivier Friard - Marco Gamba<br>"
+        "<p>Copyright &copy; 2012-2018 Olivier Friard - Marco Gamba<br>"
         "Department of Life Sciences and Systems Biology<br>"
         "University of Torino - Italy<br>"
         "<br>"
@@ -11050,6 +11076,7 @@ def changedFocusSlot(self, old, now):
             print(window.check_state_events_obs(observation_to_open)[1])
             sys.exit()
 
+
     if observation_to_open:
         r = window.load_observation(observation_to_open)
         if r:

diff --git a/db_functions.py b/db_functions.py
@@ -0,0 +1,119 @@
+
+def loadEventsInDB(self, selectedSubjects, selectedObservations, selectedBehaviors):
+
+    cursor = self.loadEventsInDB(plot_parameters["selected subjects"], selectedObservations, plot_parameters["selected behaviors"])
+
+    for subject in plot_parameters["selected subjects"]:
+
+        for behavior in plot_parameters["selected behaviors"]:
+
+            cursor.execute("SELECT occurence, modifiers, comment FROM events WHERE observation = ? AND subject = ? AND code = ? ORDER by occurence", (obsId, subject, behavior))
+            rows = list(cursor.fetchall())
+
+            if STATE in self.eventType(behavior).upper() and len(rows) % 2:  # unpaired events
+                flagUnpairedEventFound = True
+                continue
+
+            for idx, row in enumerate(rows):
+
+                if self.pj[OBSERVATIONS][obsId]["type"] in [MEDIA]:
+
+                    mediaFileIdx = [idx1 for idx1, x in enumerate(duration1) if row["occurence"] >= sum(duration1[0:idx1])][-1]
+                    mediaFileString = self.pj[OBSERVATIONS][obsId][FILE][PLAYER1][mediaFileIdx]
+                    fpsString = self.pj[OBSERVATIONS][obsId]["media_info"]["fps"][self.pj[OBSERVATIONS][obsId][FILE][PLAYER1][mediaFileIdx]]
+
+                if self.pj[OBSERVATIONS][obsId]["type"] in [LIVE]:
+                    mediaFileString = "LIVE"
+                    fpsString = "NA"
+
+                if POINT in self.eventType(behavior).upper():
+
+                    if outputFormat == "sql":
+                        out += template.format(observation=obsId,
+                                            date=self.pj[OBSERVATIONS][obsId]["date"].replace("T", " "),
+                                            media_file=mediaFileString,
+                                            total_length=total_length,
+                                            fps=fpsString,
+                                            subject=subject,
+                                            behavior=behavior,
+                                            modifiers=row["modifiers"].strip(),
+                                            event_type=POINT,
+                                            start="{0:.3f}".format(row["occurence"]),
+                                            stop=0,
+                                            comment_start=row["comment"],
+                                            comment_stop="")
+                    else:
+                        row_data = []
+                        row_data.extend([obsId,
+                                    self.pj[OBSERVATIONS][obsId]["date"].replace("T", " "),
+                                    mediaFileString,
+                                    total_length,
+                                    fpsString])
+
+                        # independent variables
+                        if "independent_variables" in self.pj:
+                            for idx_var in sorted_keys(self.pj["independent_variables"]):
+                                if self.pj["independent_variables"][idx_var]["label"] in self.pj[OBSERVATIONS][obsId]["independent_variables"]:
+                                   row_data.append(self.pj[OBSERVATIONS][obsId]["independent_variables"][self.pj["independent_variables"][idx_var]["label"]])
+                                else:
+                                    row_data.append("")
+
+                        row_data.extend([subject,
+                                    behavior,
+                                    row["modifiers"].strip(),
+                                    POINT,
+                                    "{0:.3f}".format(row["occurence"]), # start
+                                    "NA", # stop
+                                    "NA", # duration
+                                    row["comment"],
+                                    ""
+                                    ])
+                        data.append(row_data)
+
+
+                if STATE in self.eventType(behavior).upper():
+                    if idx % 2 == 0:
+                        if outputFormat == "sql":
+                            out += template.format(observation=obsId,
+                                                date=self.pj[OBSERVATIONS][obsId]["date"].replace("T", " "),
+                                                media_file=mediaFileString,
+                                                total_length=total_length,
+                                                fps=fpsString,
+                                                subject=subject,
+                                                behavior=behavior,
+                                                modifiers=row["modifiers"].strip(),
+                                                event_type=STATE,
+                                                start="{0:.3f}".format(row["occurence"]),
+                                                stop="{0:.3f}".format(rows[idx + 1]["occurence"]),
+                                                comment_start=row["comment"],
+                                                comment_stop=rows[idx + 1]["comment"])
+
+                        else:
+                            row_data = []
+
+                            row_data.extend([obsId,
+                                    self.pj[OBSERVATIONS][obsId]["date"].replace("T", " "),
+                                    mediaFileString,
+                                    total_length,
+                                    fpsString])
+
+                            # independent variables
+                            if "independent_variables" in self.pj:
+                                for idx_var in sorted_keys(self.pj["independent_variables"]):
+                                    if self.pj["independent_variables"][idx_var]["label"] in self.pj[OBSERVATIONS][obsId]["independent_variables"]:
+                                       row_data.append(self.pj[OBSERVATIONS][obsId]["independent_variables"][self.pj["independent_variables"][idx_var]["label"]])
+                                    else:
+                                        row_data.append("")
+
+                            row_data.extend([subject,
+                                    behavior,
+                                    row["modifiers"].strip(),
+                                    STATE,
+                                    "{0:.3f}".format(row["occurence"]),
+                                    "{0:.3f}".format(rows[idx + 1]["occurence"]),
+                                    "{0:.3f}".format(rows[idx + 1]["occurence"] - row["occurence"]),
+                                    row["comment"],
+                                    rows[idx + 1]["comment"]
+                                    ])
+
+                            data.append(row_data)
diff --git a/dialog.py b/dialog.py
@@ -3,7 +3,7 @@
 """
 BORIS
 Behavioral Observation Research Interactive Software
-Copyright 2012-2017 Olivier Friard
+Copyright 2012-2018 Olivier Friard
 
 This file is part of BORIS.
 

diff --git a/edit_event.py b/edit_event.py
@@ -3,7 +3,7 @@
 """
 BORIS
 Behavioral Observation Research Interactive Software
-Copyright 2012-2017 Olivier Friard
+Copyright 2012-2018 Olivier Friard
 
 This file is part of BORIS.
 
@@ -35,16 +35,18 @@
 
 from config import *
 
+
 if QT_VERSION_STR[0] == "4":
     from edit_event_ui import Ui_Form
-else:
+if QT_VERSION_STR[0] == "5":
     from edit_event_ui5 import Ui_Form
 
+
 class DlgEditEvent(QDialog, Ui_Form):
 
     def __init__(self, log_level, parent=None):
 
-        super(DlgEditEvent, self).__init__(parent)
+        super().__init__(parent)
         logging.basicConfig(level=log_level)
         self.setupUi(self)
 

diff --git a/edit_event.ui b/edit_event.ui
@@ -139,6 +139,9 @@
          <property name="text">
           <string>OK</string>
          </property>
+         <property name="default">
+          <bool>true</bool>
+         </property>
         </widget>
        </item>
       </layout>

diff --git a/edit_event_ui.py b/edit_event_ui.py
@@ -2,8 +2,7 @@
 
 # Form implementation generated from reading ui file 'edit_event.ui'
 #
-# Created: Tue Dec 15 12:51:27 2015
-#      by: PyQt4 UI code generator 4.11.2
+# Created by: PyQt4 UI code generator 4.11.4
 #
 # WARNING! All changes made in this file will be lost!
 
@@ -84,6 +83,7 @@ def setupUi(self, Form):
         self.pbCancel.setObjectName(_fromUtf8("pbCancel"))
         self.horizontalLayout.addWidget(self.pbCancel)
         self.pbOK = QtGui.QPushButton(Form)
+        self.pbOK.setDefault(True)
         self.pbOK.setObjectName(_fromUtf8("pbOK"))
         self.horizontalLayout.addWidget(self.pbOK)
         self.verticalLayout.addLayout(self.horizontalLayout)

diff --git a/edit_event_ui5.py b/edit_event_ui5.py
@@ -2,7 +2,7 @@
 
 # Form implementation generated from reading ui file 'edit_event.ui'
 #
-# Created by: PyQt5 UI code generator 5.6
+# Created by: PyQt5 UI code generator 5.9
 #
 # WARNING! All changes made in this file will be lost!
 
@@ -69,6 +69,7 @@ def setupUi(self, Form):
         self.pbCancel.setObjectName("pbCancel")
         self.horizontalLayout.addWidget(self.pbCancel)
         self.pbOK = QtWidgets.QPushButton(Form)
+        self.pbOK.setDefault(True)
         self.pbOK.setObjectName("pbOK")
         self.horizontalLayout.addWidget(self.pbOK)
         self.verticalLayout.addLayout(self.horizontalLayout)