Filters are working!

common_widgets/page_selector.py

@@ -57,16 +57,16 @@ def setup_layout(self):
         self.setLayout(layout)
 
     def goto_first_page(self):
-        self.query.first_page()
+        self.query.first_page().commit()
 
     def goto_previous_page(self):
-        self.query.previous_page()
+        self.query.previous_page().commit()
 
     def goto_next_page(self):
-        self.query.next_page()
+        self.query.next_page().commit()
 
     def goto_last_page(self):
-        self.query.last_page()
+        self.query.last_page().commit()
 
     def update_page_selector(self):
         # Block signals to avoid infinite loops
@@ -85,7 +85,7 @@ def update_page_selector(self):
         self.rows_lineedit.blockSignals(False)
 
     def set_page(self, page):
-        self.query.set_page(int(page) if page else 1)
+        self.query.set_page(int(page) if page else 1).commit()
 
     def set_rows_per_page(self, rows_per_page):
-        self.query.set_limit(int(rows_per_page or 10))
+        self.query.set_limit(int(rows_per_page or 10)).commit()

config_folder/validation_methods/validation_immuno.yaml

@@ -14,6 +14,8 @@ steps:
     query:
       select:
         fields:
+          - '"Chrom"'
+          - '"Position"'
           - '"Project.recurrence"'
           - '"Recurrence.cosmic"'
           - '"Phastcons"'
@@ -39,7 +41,6 @@ steps:
           - '"Variant.effect"'
           - '"Clinvar.clinical.significance"'
           - '"Glims"'
-          - '"Position"'
           - '"PROVEAN"'
           - '"NbrReadAlt"'
           - '"MUTATIONTASTER"'
@@ -55,7 +56,6 @@ steps:
           - '"CADD.phred"'
           - '"dbscsnv.Rf.score"'
           - '"Histo_majoritaire.cosmic"'
-          - '"Chrom"'
           - '''#''||"Background color" AS ''.backgroundcolor'''
           - '"Background color"'
         tables:
@@ -69,6 +69,8 @@ steps:
         order_by:
           - field: main_table.Chrom
             order: ASC
+          - field: main_table.Position
+            order: ASC
   - title: VAF en rouge + SUIVI uniquement
     description: Trié par chromosome et par position
     query:

filters_model.py

@@ -58,8 +58,8 @@ def add_child(self, parent: QModelIndex, item: FilterItem):
 
     def add_filter(self, expression: str):
         """Add a filter to the root element of the model"""
-        index = self.index(0, 0, self.index(0, 0, self.index(0, 0)))
-        self.add_child(index, FilterItem(FilterType.LEAF, expression=expression))
+        root_filter = self.index(0, 0, QModelIndex())
+        self.add_child(root_filter, FilterItem(FilterType.LEAF, expression=expression))
 
     def remove_child(self, index: QModelIndex):
         """Remove a child from the parent index"""
@@ -281,22 +281,15 @@ def add_child(self):
         index = self.view.currentIndex()
         if not index.isValid():
             return
-        print("Before", self.model.to_dict())
         self.model.add_child(index, FilterItem(FilterType.LEAF, "a=3"))
-        print("After", self.model.to_dict())
 
     def remove_child(self):
-        print("Before")
-        print(self.model.to_dict())
         index = self.view.currentIndex()
         if not index.isValid():
             return
 
         self.model.remove_child(index)
 
-        print("After")
-        print(self.model.to_dict())
-
     def context_menu_requested(self, p: QPoint):
         menu = QMenu()
         add_child_action = menu.addAction("Add Child")

filters_widget.py

@@ -35,8 +35,23 @@ def add_filter_leaf(self):
         index = self.filters_view.currentIndex()
         if not index.isValid():
             return
-        expression = qw.QInputDialog.getText(self, "Expression", "Enter expression")
-        item = FilterItem(FilterType.LEAF, expression, None)
+        print("Adding LEAF expression to index ", index)
+        expression, _ = qw.QInputDialog.getText(self, "Expression", "Enter expression")
+        item = FilterItem(FilterType.LEAF, expression, alias=None, parent=None)
+        self.model.add_child(index, item)
+
+    def add_filter_and(self):
+        index = self.filters_view.currentIndex()
+        if not index.isValid():
+            return
+        item = FilterItem(FilterType.AND, None, alias=None, parent=None)
+        self.model.add_child(index, item)
+
+    def add_filter_or(self):
+        index = self.filters_view.currentIndex()
+        if not index.isValid():
+            return
+        item = FilterItem(FilterType.OR, None, alias=None, parent=None)
         self.model.add_child(index, item)
 
     def remove_filter(self):
@@ -51,6 +66,12 @@ def context_menu_requested(self, pos):
         add_filter_action = menu.addAction("Add filter")
         add_filter_action.triggered.connect(self.add_filter_leaf)
 
+        add_filter_and_action = menu.addAction("Add AND filter")
+        add_filter_and_action.triggered.connect(self.add_filter_and)
+
+        add_filter_or_action = menu.addAction("Add OR filter")
+        add_filter_or_action.triggered.connect(self.add_filter_or)
+
         remove_filter_action = menu.addAction("Remove filter")
         remove_filter_action.triggered.connect(self.remove_filter)
 

query.py

@@ -86,9 +86,6 @@ class Query(qc.QObject):
     # Signal for external use (tell the UI to update)
     query_changed = qc.Signal()
 
-    # Signal for internal use (tell the model to update)
-    internal_changed = qc.Signal()
-
     def __init__(self, datalake: "dl.DataLake", parent=None):
         super().__init__(parent)
         self.datalake = datalake
@@ -103,8 +100,6 @@ def __init__(self, datalake: "dl.DataLake", parent=None):
         )
         self.filter_model.model_changed.connect(self.update_data)
 
-        self.internal_changed.connect(self.update_data)
-
     def init_state(self):
         # When we create a new Query, we want to reset everything, except for the datalake path...
         self.query_template = None
@@ -127,15 +122,12 @@ def init_state(self):
 
         self.variables = dict()
 
-        self.internal_changed.emit()
-
         return self
 
     def add_variable(self, key: str, value: str):
         if key in Query.RESERVED_VARIABLES:
             raise ValueError(f"Variable name {key} is reserved")
         self.variables[key] = value
-        self.internal_changed.emit()
         return self
 
     def get_variable(self, key: str) -> str:
@@ -149,7 +141,6 @@ def get_limit(self) -> int:
 
     def set_limit(self, limit: int):
         self.limit = limit
-        self.internal_changed.emit()
         return self
 
     def get_offset(self) -> int:
@@ -165,7 +156,6 @@ def get_page(self) -> int:
     def set_page(self, page: int):
         self.current_page = page
         self.set_offset((page - 1) * self.limit)
-        self.internal_changed.emit()
         return self
 
     def previous_page(self):
@@ -228,20 +218,17 @@ def get_editable_table_name(self) -> str:
 
     def set_editable_table_name(self, name: str):
         self.editable_table_name = name
-        self.internal_changed.emit()
         return self
 
     def set_selected_samples(self, samples: List[str]):
         self.selected_samples = samples
-        self.internal_changed.emit()
         return self
 
     def get_selected_samples(self) -> List[str]:
         return self.selected_samples
 
     def set_selected_genes(self, genes: List[str]):
         self.selected_genes = genes
-        self.internal_changed.emit()
         return self
 
     def get_selected_genes(self) -> List[str]:
@@ -255,7 +242,6 @@ def generate_query_template_from_json(self, data: dict) -> "Query":
             data (dict): The json object to build the query template from
         """
         self.query_template = build_query_template(data)
-        self.internal_changed.emit()
         return self
 
     def select_query(self, paginated=True):
@@ -342,13 +328,8 @@ def update_data(self):
             self.offset = 0
         self.query_changed.emit()
 
-    def mute(self):
-        self.blockSignals(True)
-        return self
-
-    def unmute(self):
-        self.blockSignals(False)
-        return self
+    def commit(self):
+        self.update_data()
 
     def to_json(self):
         return {

query_table_widget.py

@@ -98,7 +98,9 @@ def show_table_context_menu(self, pos):
     def show_row_userdata(self, index: qc.QModelIndex):
         row_data = index.data(qc.Qt.ItemDataRole.UserRole)
         dialog = qw.QMessageBox(self)
-        dialog.setText(str(row_data))
+        dialog.setText(
+            "".join(f"<br><b>{k}</b>: {v}</br>" for k, v in row_data.items())
+        )
         dialog.setWindowTitle(qc.QCoreApplication.tr("Données sous-jacentes"))
         dialog.exec()
 

validation_widget.py

@@ -320,15 +320,15 @@ def setup_step(self, step_definition: dict):
         ):
             return
 
-        self.query.mute().set_readonly_table(
+        self.query.set_readonly_table(
             self.validation_parquet_files
         ).set_editable_table_name(self.validation_table_uuid).set_selected_genes(
             self.validation_gene_names
         ).set_selected_samples(
             self.validation_sample_names
-        ).unmute().generate_query_template_from_json(
+        ).generate_query_template_from_json(
             step_definition
-        )
+        ).commit()
 
     def start_validation(self, selected_validation: dict):
         if not self.datalake: