Merge pull request #654 from czbiohub-sf/update-study-form-csv

Update study form csv

Author: i-jey

ulc_mm_package/QtGUI/oracle.py

@@ -646,6 +646,7 @@ def _maybe_start_study_form(self):
 
     def get_study_metadata(self):
         self.study_metadata = self.study_form_dialog.get_form_input()
+        self.study_form_dialog.close()
         self.save_form()
 
     def save_form(self):

ulc_mm_package/QtGUI/study_metadata_form.py

@@ -1,5 +1,5 @@
 from pathlib import Path
-from typing import Dict, List, Optional
+from typing import Dict, List, Optional, Tuple
 
 from PyQt5.QtCore import QDate
 from PyQt5.QtGui import QIntValidator
@@ -84,7 +84,6 @@ def create_widget_for_field(field_def):
 
         default = field_def.get("default")
         if default is not None:
-            print("default is")
             idx = w.findText(default)
             if idx >= 0:
                 w.setCurrentIndex(idx)
@@ -139,7 +138,7 @@ def __init__(self, cfg: dict, parent=None):
                 self.btn_start.setEnabled(False)
             layout.addRow(label, widget)
 
-        self.btn_start.clicked.connect(self.accept)
+        self.btn_start.clicked.connect(self.validate)
         btn_cancel.clicked.connect(self.close)
 
         layout.addRow(btn_cancel, self.btn_start)
@@ -162,34 +161,76 @@ def __init__(self, cfg: dict, parent=None):
         # run an initial check to set OK button state
         self.check_required()
 
+    def _get_widget_text(self, w: QWidget) -> Optional[str]:
+        if isinstance(w, QTextEdit):
+            return w.toPlainText()
+        elif isinstance(w, QLineEdit):
+            return w.text()
+        elif isinstance(w, QComboBox):
+            return "" if w.currentIndex() < 0 else w.currentText()
+        elif isinstance(w, QListWidget):
+            return "\n".join(i.text() for i in w.selectedItems())
+
+        if hasattr(w, "text"):
+            return w.text()
+        return None
+
+    def _is_empty(self, w) -> bool:
+        text = self._get_widget_text(w)
+        return (text is not None) and (not text.strip())
+
+    def _has_value_and_valid(self, w: QWidget) -> bool:
+        if self._is_empty(w):
+            return True
+
+        if isinstance(w, QTextEdit):
+            return bool(w.toPlainText().strip())
+        elif isinstance(w, QLineEdit):
+            text = w.text().strip()
+            return bool(text) and w.hasAcceptableInput()
+        elif isinstance(w, QComboBox):
+            return w.currentIndex() >= 0
+        elif isinstance(w, QListWidget):
+            return len(w.selectedItems()) >= 0
+
+        if hasattr(w, "text"):
+            return bool(w.text().strip())
+
+        return False
+
+    def _check_widget(self, w: QWidget, field: dict) -> Tuple[bool, str]:
+        required = field.get("required")
+        if self._is_empty(w) and required:
+            return False, "Required"
+
+        if not self._has_value_and_valid(w):
+            return False, "Invalid"
+
+        return True, ""
+
     def check_required(self):
         """Ensure that all required widgets have a value."""
-        all_filled = True
-        for w in self._required_widgets:
-            if hasattr(w, "toPlainText"):
-                if not w.toPlainText().strip():
-                    all_filled = False
-                    break
-            elif hasattr(w, "text"):
-                if not w.text().strip():
-                    all_filled = False
-                    break
-            elif hasattr(w, "currentIndex"):
-                # -1 index means no selection made
-                if w.currentIndex() < 0:
-                    all_filled = False
-                    break
-        if all_filled:
-            self.btn_start.setEnabled(True)
-        else:
-            self.btn_start.setEnabled(False)
+        self.btn_start.setEnabled(
+            all([self._has_value_and_valid(x) for x in self._required_widgets])
+        )
+
+    def validate(self):
+        for lbl, (w, field) in self._widgets.items():
+            valid, error_msg = self._check_widget(w, field)
+            if not valid:
+                print(lbl, field, error_msg)
+                w.setFocus()
+                return
+        self.accept()
 
     def get_form_input(self):
         result = {"study_id": self.config_data["study_description"]["key"]}
         errors = []
-        for name, (widget, field) in self._widgets.items():
+        possible_choices = []
+        subkeys = []
+        for _, (widget, field) in self._widgets.items():
             t = field["datatype"]
-
+            key = field.get("key")
             if t == "string":
                 value = (
                     widget.toPlainText() if field.get("multiline") else widget.text()
@@ -209,10 +250,20 @@ def get_form_input(self):
                 value = widget.currentData()
             elif t == "multiselect":
                 value = [x.text() for x in widget.selectedItems()]
+                possible_choices = [
+                    widget.item(i).text() for i in range(widget.count())
+                ]
+                subkeys = field["subkeys"]
             else:
                 value = None
 
-            result[name] = value
+            # Accommodate the multiselect case separately (i.e. save each choice as its own col)
+            if isinstance(value, list):
+                selected_set = set(value)
+                for choice, choice_key in zip(possible_choices, subkeys):
+                    result[choice_key] = choice in selected_set
+            else:
+                result[key] = value
 
         if errors:
             raise ValueError("\n".join(errors))

ulc_mm_package/study_configurations/_example-config.toml

@@ -4,13 +4,13 @@ name = "Example Study"
 
 # Metadata fields
 [[metadata]]
-key = "key1_blah"
+key = "key1"
 label = "numbers galore"
 datatype = "int"
 required = true
 
 [[metadata]]
-key = "key2_blah"
+key = "key2"
 label = "string stuff"
 datatype = "string"
 required = true
@@ -21,12 +21,15 @@ label = "choices"
 datatype = "enum"
 choices = ["control", "low_dose", "high_dose"]
 default = "control"
+required = true
 
 [[metadata]]
 key = "key4"
 label = "Multiselect"
 datatype = "multiselect"
 choices = ["pickme", "orme", "orwho", "or", "allofus"]
+subkeys = ["choice1", "choice2", "choice3", "choice4", "choice5"]
+required = false
 
 
 [[metadata]]