more consistent awareness of scenario reactions

better window management of strain design dialogs

cnapy/appdata.py

@@ -15,7 +15,7 @@
 import cobra
 from optlang.symbolics import Zero
 from optlang_enumerator.cobra_cnapy import CNApyModel
-from qtpy.QtCore import Qt, Signal, QObject
+from qtpy.QtCore import Qt, Signal, QObject, QStringListModel
 from qtpy.QtGui import QColor, QFont
 from qtpy.QtWidgets import QMessageBox
 
@@ -358,6 +358,39 @@ def clear(self):
         super().clear()
         self.__init__()
 
+class IDList(object):
+    """
+    provides a list of identifiers (id_list) and a corresponding QStringListModel (ids_model)
+    the identifiers can be set with the set_ids method
+    the implementation guarantees that id() of the properties id_list and ids_model
+    is constant so that they can be used like const references
+    """
+    def __init__(self):
+        self._id_list: list = []
+        self._ids_model: QStringListModel = QStringListModel()
+
+    def set_ids(self, *id_lists: List[str]):
+        self._id_list.clear()
+        for id_list in id_lists:
+            self._id_list[len(self._id_list):] = id_list
+        self._ids_model.setStringList(self._id_list)
+
+    @property # getter only
+    def id_list(self) -> List[str]:
+        return self._id_list
+
+    @property # getter only
+    def ids_model(self) -> QStringListModel:
+        return self._ids_model
+
+    def replace_entry(self, old: str, new: str):
+        idx = self._id_list.index(old)
+        self._id_list[idx] = new
+        self._ids_model.setData(self._ids_model.index(idx), new)
+
+    def __len__(self) -> int:
+        return len(self._id_list)
+
 class ProjectData:
     ''' The cnapy project data '''
 
@@ -389,6 +422,7 @@ def __init__(self):
             msgBox.exec()
 
         self.cobra_py_model = CNApyModel()
+        self.reaction_ids: IDList = IDList() # reaction IDs of the cobra_py_model and scenario reactions
 
         default_map = CnaMap("Map")
         self.maps = {"Map": default_map}
@@ -468,6 +502,9 @@ def collect_default_scenario_values(self) -> Tuple[List[str], List[Tuple[float,
                 values.append(parse_scenario(r.annotation['cnapy-default']))
         return reactions, values
 
+    def update_reaction_id_lists(self):
+        self.reaction_ids.set_ids(self.cobra_py_model.reactions.list_attr("id"), self.scen_values.reactions.keys())
+
     # currently unused
     # def scenario_hash_value(self):
     #     return hashlib.md5(pickle.dumps(sorted(self.scen_values.items()))).digest()

cnapy/gui_elements/central_widget.py

@@ -185,10 +185,12 @@ def handle_changed_reaction(self, previous_id: str, reaction: cobra.Reaction):
                 self.appdata.project.maps[mmap]["boxes"][reaction.id] = self.appdata.project.maps[mmap]["boxes"].pop(
                     previous_id)
                 reaction_has_box = True
-            if self.appdata.project.maps[mmap]["view"] == "escher":
+            if self.appdata.project.maps[mmap].get('view', '') == "escher":
                 escher_map_present = True
         if reaction_has_box or escher_map_present:
             self.update_reaction_on_maps(previous_id, reaction.id, reaction_has_box, escher_map_present)
+        if reaction.id != previous_id:
+            self.appdata.project.reaction_ids.replace_entry(previous_id, reaction.id)
         self.update_item_in_history(previous_id, reaction.id, reaction.name, ModelItemType.Reaction)
 
     def handle_deleted_reaction(self, reaction: cobra.Reaction):
@@ -203,6 +205,7 @@ def handle_deleted_reaction(self, reaction: cobra.Reaction):
             if reaction.id in self.appdata.project.maps[mmap]["boxes"].keys():
                 self.appdata.project.maps[mmap]["boxes"].pop(reaction.id)
         self.delete_reaction_on_maps(reaction.id)
+        self.appdata.project.update_reaction_id_lists()
 
         if self.appdata.auto_fba:
             self.parent.fba()

cnapy/gui_elements/flux_feasibility_dialog.py

@@ -83,7 +83,7 @@ def __init__(self, main_window: QMainWindow):
         hbox = QHBoxLayout()
         self.bm_label = QLabel("Biomass reaction: ")
         hbox.addWidget(self.bm_label)
-        self.bm_reac_id_select = QComplReceivLineEdit(self, self.appdata.project.cobra_py_model.reactions.list_attr("id"))
+        self.bm_reac_id_select = QComplReceivLineEdit(self, self.appdata.project.reaction_ids)
         self.bm_reac_id_select.setPlaceholderText("Choose a biomass reaction")
         self.bm_reac_id_select.textCorrect.connect(self.verify_biomass_reaction)
         hbox.addWidget(self.bm_reac_id_select)

cnapy/gui_elements/flux_optimization_dialog.py

@@ -1,14 +1,14 @@
 """The cnapy flux optimization dialog"""
 from random import randint
-from numpy import isnan, isinf
+from numpy import isinf
 import re
-from qtpy.QtCore import Qt, Signal, Slot
+from qtpy.QtCore import Qt, Slot
 from qtpy.QtWidgets import (QDialog, QHBoxLayout, QLabel, QComboBox,
-                            QMessageBox, QPushButton, QVBoxLayout, QFrame)
+                            QMessageBox, QPushButton, QVBoxLayout)
 
 from cnapy.appdata import AppData
 from cnapy.gui_elements.central_widget import CentralWidget
-from cnapy.utils import QComplReceivLineEdit, QHSeperationLine
+from cnapy.utils import QComplReceivLineEdit
 from straindesign import fba, linexpr2dict, linexprdict2str, avail_solvers
 from straindesign.names import *
 
@@ -23,7 +23,7 @@ def __init__(self, appdata: AppData, central_widget: CentralWidget):
         self.central_widget = central_widget
 
         numr = len(self.appdata.project.cobra_py_model.reactions)
-        self.reac_ids = self.appdata.project.cobra_py_model.reactions.list_attr("id")
+        self.reac_ids = self.appdata.project.reaction_ids.id_list
         if numr > 1:
             r1 = self.appdata.project.cobra_py_model.reactions[randint(0,numr-1)].id
         else:
@@ -45,7 +45,7 @@ def __init__(self, appdata: AppData, central_widget: CentralWidget):
         open_bracket.setFont(font)
         editor_layout.addWidget(open_bracket)
         flux_expr_layout = QVBoxLayout()
-        self.expr = QComplReceivLineEdit(self,self.reac_ids,check=True)
+        self.expr = QComplReceivLineEdit(self, self.appdata.project.reaction_ids, check=True)
         self.expr.setPlaceholderText('flux expression (e.g. 1.0 '+r1+')')
         flux_expr_layout.addWidget(self.expr)
         editor_layout.addItem(flux_expr_layout)

cnapy/gui_elements/main_window.py

@@ -688,12 +688,12 @@ def strain_design_with_setup(self, sd_setup):
     @Slot(str)
     def compute_strain_design(self,sd_setup):
         # launch progress viewer and computation thread
-        self.sd_viewer = SDComputationViewer(self.appdata, sd_setup)
+        self.sd_viewer = SDComputationViewer(self, self.appdata, sd_setup)
         self.sd_viewer.show_sd_signal.connect(self.show_strain_designs_with_setup, Qt.QueuedConnection)
         # connect signals to update progress
         self.sd_computation = SDComputationThread(self.appdata, sd_setup)
-        self.sd_computation.output_connector.connect(     self.sd_viewer.receive_progress_text,Qt.QueuedConnection)
-        self.sd_computation.finished_computation.connect( self.sd_viewer.conclude_computation, Qt.QueuedConnection)
+        self.sd_computation.output_connector.connect(self.sd_viewer.receive_progress_text, Qt.QueuedConnection)
+        self.sd_computation.finished_computation.connect(self.sd_viewer.conclude_computation, Qt.QueuedConnection)
         self.sd_viewer.cancel_computation.connect(self.terminate_strain_design_computation)
         # show dialog and launch process
         # self.sd_viewer.exec()
@@ -887,6 +887,7 @@ def load_scenario_file(self, filename, merge=False):
         self.appdata.project.comp_values.clear()
         self.appdata.project.fva_values.clear()
         self.central_widget.tabs.widget(ModelTabIndex.Scenario).recreate_scenario_items()
+        self.appdata.project.update_reaction_id_lists()
 
         if len(missing_reactions) > 0 :
             QMessageBox.warning(self, 'Unknown reactions in scenario',
@@ -1368,6 +1369,9 @@ def close_project_dialogs(self):
         if self.sd_dialog is not None:
             self.sd_dialog.close()
             self.sd_dialog = None
+        if self.sd_sols is not None:
+            self.sd_sols.close()
+            self.sd_sols = None
         if self.make_scenario_feasible_dialog is not None:
             self.make_scenario_feasible_dialog.close()
             self.make_scenario_feasible_dialog = None
@@ -1678,7 +1682,6 @@ def make_scenario_feasible(self):
             self.make_scenario_feasible_dialog = FluxFeasibilityDialog(self)
         else:
             self.make_scenario_feasible_dialog.modified_scenario = None
-            self.make_scenario_feasible_dialog.bm_reac_id_select.set_wordlist(self.appdata.project.cobra_py_model.reactions.list_attr("id"))
         self.make_scenario_feasible_dialog.show()
 
     def fba_optimize_reaction(self, reaction: str, mmin: bool):

cnapy/gui_elements/mode_navigator.py

@@ -375,8 +375,8 @@ def __init__(self, appdata: AppData, parent):
         self.appdata = appdata
         self.parent = parent
 
-        self.reac_ids = list(self.appdata.project.comp_values.keys()) #self.appdata.project.cobra_py_model.reactions.list_attr("id")
-        numr = len(self.reac_ids) # len(self.appdata.project.cobra_py_model.reactions)
+        self.reac_ids = list(self.appdata.project.comp_values.keys())
+        numr = len(self.reac_ids)
         if numr > 1:
             r1 = self.reac_ids[randint(0, numr-1)]
         else:

cnapy/gui_elements/plot_space_dialog.py

@@ -1,11 +1,11 @@
 """The flux space plot dialog"""
 
 from random import randint
-from qtpy.QtCore import Qt, Signal, Slot, QTimer
+from qtpy.QtCore import Qt
 from qtpy.QtWidgets import (QDialog, QHBoxLayout, QLabel, QMessageBox, QGroupBox, QComboBox, QLayout,
-                            QPushButton, QVBoxLayout, QFrame, QCheckBox,QLineEdit, QSizePolicy)
+                            QPushButton, QVBoxLayout, QFrame, QCheckBox,QLineEdit)
 from cnapy.utils import QComplReceivLineEdit, QHSeperationLine
-from straindesign import linexpr2dict, linexprdict2str, yopt, avail_solvers, plot_flux_space
+from straindesign import plot_flux_space
 from straindesign.names import *
 
 class PlotSpaceDialog(QDialog):
@@ -19,7 +19,6 @@ def __init__(self, appdata):
         self.appdata = appdata
 
         numr = len(self.appdata.project.cobra_py_model.reactions)
-        self.reac_ids = self.appdata.project.cobra_py_model.reactions.list_attr("id")
         self.r = ["" for _ in range(6)]
         if numr > 5:
             self.r = [self.appdata.project.cobra_py_model.reactions[randint(0,numr-1)].id for _ in self.r]
@@ -59,9 +58,9 @@ def __init__(self, appdata):
         self.x_combobox.insertItem(1,'yield')
         self.x_combobox.currentTextChanged.connect(self.x_combo_changed)
         x_num_den_layout.addWidget(self.x_combobox)
-        self.x_numerator = QComplReceivLineEdit(self,self.reac_ids,check=True)
+        self.x_numerator = QComplReceivLineEdit(self, self.appdata.project.reaction_ids, check=True)
         self.x_numerator.setPlaceholderText('flux rate or expression (e.g. 1.0 '+self.r[0]+')')
-        self.x_denominator = QComplReceivLineEdit(self,self.reac_ids,check=True)
+        self.x_denominator = QComplReceivLineEdit(self, self.appdata.project.reaction_ids, check=True)
         self.x_denominator.setPlaceholderText('denominator (e.g. 1.0 '+self.r[1]+')')
         x_num_den_layout.addWidget(self.x_numerator)
         self.x_denominator.setHidden(True)
@@ -83,9 +82,9 @@ def __init__(self, appdata):
         self.y_combobox.insertItem(1,'yield')
         self.y_combobox.currentTextChanged.connect(self.y_combo_changed)
         y_num_den_layout.addWidget(self.y_combobox)
-        self.y_numerator = QComplReceivLineEdit(self,self.reac_ids,check=True)
+        self.y_numerator = QComplReceivLineEdit(self, self.appdata.project.reaction_ids, check=True)
         self.y_numerator.setPlaceholderText('flux rate or expression (e.g. '+self.r[2]+')')
-        self.y_denominator = QComplReceivLineEdit(self,self.reac_ids,check=True)
+        self.y_denominator = QComplReceivLineEdit(self, self.appdata.project.reaction_ids, check=True)
         self.y_denominator.setPlaceholderText('denominator (e.g. '+self.r[3]+')')
         y_num_den_layout.addWidget(self.y_numerator)
         self.y_denominator.setHidden(True)
@@ -107,9 +106,9 @@ def __init__(self, appdata):
         self.z_combobox.insertItem(1,'yield')
         self.z_combobox.currentTextChanged.connect(self.z_combo_changed)
         z_num_den_layout.addWidget(self.z_combobox)
-        self.z_numerator = QComplReceivLineEdit(self,self.reac_ids,check=True)
+        self.z_numerator = QComplReceivLineEdit(self, self.appdata.project.reaction_ids, check=True)
         self.z_numerator.setPlaceholderText('flux rate or expression (e.g. '+self.r[4]+')')
-        self.z_denominator = QComplReceivLineEdit(self,self.reac_ids,check=True)
+        self.z_denominator = QComplReceivLineEdit(self, self.appdata.project.reaction_ids, check=True)
         self.z_denominator.setPlaceholderText('denominator (e.g. '+self.r[5]+')')
         z_num_den_layout.addWidget(self.z_numerator)
         self.z_denominator.setHidden(True)

cnapy/gui_elements/reactions_list.py

@@ -266,6 +266,7 @@ def add_new_reaction(self):
                 break
         reaction = cobra.Reaction(name)
         self.appdata.project.cobra_py_model.add_reactions([reaction])
+        self.appdata.project.update_reaction_id_lists()
         reaction.set_hash_value()
         self.appdata.project.cobra_py_model.set_stoichiometry_hash_object()
         self.reaction_list.blockSignals(True)