add folder level selection

docs/trial_folder_structure/LARK.json

@@ -12,7 +12,7 @@
     "rt_dose_pres": {
       "path": "/{clinical_trial}/{test_centre}/Patient Plans/Patient {centre_patient_no}/Dose/",
       "display_name": "RT Dose (prescription level)",
-      "field_type": "file",
+      "field_type": "folder",
       "level": "prescription",
       "allowed": [
         "application/dicom"
@@ -31,15 +31,15 @@
     "rt_plan_pres": {
       "path": "/{clinical_trial}/{test_centre}/Patient Plans/Patient {centre_patient_no}/Plan/",
       "display_name": "RT Plan (prescription level)",
-      "field_type": "file",
+      "field_type": "folder",
       "level": "prescription",
       "allowed": [
         "application/dicom"
       ],
       "file_name": []
     },
     "rt_structure_pres": {
-      "path": "/{clinical_trial}/{test_centre}/Patient Structure Sets/Patient {centre_patient_no}/{fraction_name}/",
+      "path": "/{clinical_trial}/{test_centre}/Patient Structure Sets/Patient {centre_patient_no}/",
       "display_name": "RT Structure (prescription level)",
       "field_type": "folder",
       "level": "fraction",
@@ -50,7 +50,7 @@
     "planned_dvh_pres": {
       "path": "/{clinical_trial}/{test_centre}/Dose Reconstruction/DVH/Patient {centre_patient_no}/",
       "display_name": "Planned DVH (prescription level)",
-      "field_type": "file",
+      "field_type": "folder",
       "level": "prescription",
       "allowed": [
         "text/plain",
@@ -60,14 +60,14 @@
     "planned_dicom_pres": {
       "path": "/{clinical_trial}/{test_centre}/Dose Reconstruction/DICOM/Patient {centre_patient_no}/",
       "display_name": "Planned DICOM (prescription level)",
-      "field_type": "file",
+      "field_type": "folder",
       "level": "prescription",
       "allowed": ["application/dicom"]
     },
     "centroid_pres": {
       "path": "/{clinical_trial}/{test_centre}/Patient Files/Patient {centre_patient_no}/",
       "display_name": "Centroid (prescription level)",
-      "field_type": "file",
+      "field_type": "folder",
       "level": "prescription",
       "allowed": [
         "text/plain"
@@ -88,36 +88,44 @@
     "rt_dose_fraction": {
       "path": "/{clinical_trial}/{test_centre}/Patient Plans/Patient {centre_patient_no}/Dose/",
       "display_name": "RT Dose (fraction level)",
-      "field_type": "file",
+      "field_type": "folder",
       "level": "fraction",
       "allowed": [
         "application/dicom"
       ],
       "file_name": []
     },
     "rt_plan_fraction": {
-      "path": "",
-      "display_name": "",
-      "field_type": "file",
-      "level": "",
-      "allowed": []
+      "path": "/{clinical_trial}/{test_centre}/Patient Plans/Patient {centre_patient_no}/Plan/",
+      "display_name": "RT Dose (fraction level)",
+      "field_type": "folder",
+      "level": "fraction",
+      "allowed": [
+        "application/dicom"
+      ],
+      "file_name": []
     },
     "rt_structure_fraction": {
-      "path": "",
-      "display_name": "",
-      "field_type": "file",
-      "level": "",
-      "allowed": []
+      "path": "/{clinical_trial}/{test_centre}/Patient Structure Sets/Patient {centre_patient_no}/",
+      "display_name": "RT Structure (fraction level)",
+      "field_type": "folder",
+      "level": "fraction",
+      "allowed": [
+        "application/dicom"
+      ],
+      "file_name": []
     },
     "centroid_fraction": {
       "path": "/{clinical_trial}/{test_centre}/Patient Files/Patient {centre_patient_no}/",
       "display_name": "Centroid (fraction level)",
-      "field_type": "file",
+      "field_type": "folder",
       "level": "fraction",
       "allowed": [
         "text/plain",
         "text/csv",
-        "text/xlsx"
+        "application/vnd.ms-excel",
+        "application/vnd.openxmlformats-officedocument.spreadsheetml.sheet",
+        "application/vnd.oasis.opendocument.spreadsheet"
       ],
       "file_name": [
         "Centroid"
@@ -126,7 +134,7 @@
     "KIM threshold": {
       "path": "/{clinical_trial}/{test_centre}/Patient Files/Patient {centre_patient_no}/",
       "display_name": "KIM threshold (fraction level)",
-      "field_type": "file",
+      "field_type": "folder",
       "level": "fraction",
       "allowed": ["text/plain"]
     },
@@ -152,12 +160,11 @@
         "image/his",
         "image/jpg",
         "image/png",
-        "image/dicom",
         "application/dicom",
         "application/octet-stream",
         "text/plain",
-        "text/xml"
-        "text/csv",
+        "text/xml",
+        "text/csv"
       ]
     },
     "mv_images_path": {
@@ -176,14 +183,14 @@
         "application/dicom",
         "application/octet-stream",
         "text/plain",
-        "text/xml"
-        "text/csv",
+        "text/xml",
+        "text/csv"
       ]
     },
     "metrics_path": {
       "path": "/{clinical_trial}/{test_centre}/Triangulation/Patient {centre_patient_no}/",
       "display_name": "Metrics",
-      "field_type": "file",
+      "field_type": "folder",
       "level": "fraction",
       "allowed": [
         "text/plain",
@@ -196,7 +203,7 @@
     "triangulation_path": {
       "path": "/{clinical_trial}/{test_centre}/Triangulation/Patient {centre_patient_no}/",
       "display_name": "Triangulation Files",
-      "field_type": "file",
+      "field_type": "folder",
       "level": "fraction",
       "allowed": [
         "text/plain",
@@ -223,7 +230,7 @@
     "dvh_track_path": {
       "path": "/{clinical_trial}/{test_centre}/Dose Reconstruction/DVH/Patient {centre_patient_no}/",
       "display_name": "DVH Track",
-      "field_type": "file",
+      "field_type": "folder",
       "level": "fraction",
       "allowed": [
         "text/plain",
@@ -233,7 +240,7 @@
     "dvh_no_track_path": {
       "path": "/{clinical_trial}/{test_centre}/Dose Reconstruction/DVH/Patient {centre_patient_no}/",
       "display_name": "DVH No Track",
-      "field_type": "file",
+      "field_type": "folder",
       "level": "fraction",
       "allowed": [
         "text/plain",
@@ -243,8 +250,8 @@
     "planned_dvh_fraction": {
       "path": "/{clinical_trial}/{test_centre}/Dose Reconstruction/DVH/Patient {centre_patient_no}/",
       "display_name": "Planned DVH (fraction level)",
-      "field_type": "file",
-      "level": "prescription",
+      "field_type": "folder",
+      "level": "fraction",
       "allowed": [
         "text/plain",
         "text/csv"
@@ -253,14 +260,14 @@
     "planned_dicom_fraction": {
       "path": "/{clinical_trial}/{test_centre}/Dose Reconstruction/DICOM/Patient {centre_patient_no}/",
       "display_name": "Planned DICOM (fraction level)",
-      "field_type": "file",
+      "field_type": "folder",
       "level": "fraction",
       "allowed": ["application/dicom"]
     },
     "dicom_track_plan_path": {
       "path": "/{clinical_trial}/{test_centre}/Dose Reconstruction/DICOM/Patient {centre_patient_no}/",
       "display_name": "DICOM Track Plan",
-      "field_type": "file",
+      "field_type": "folder",
       "level": "fraction",
       "allowed": [
         "application/dicom"
@@ -272,13 +279,14 @@
       "field_type": "folder",
       "level": "fraction",
       "allowed": [
-        "application/plain text"
+        "application/dicom",
+        "plain/text"
       ]
     },
     "dicom_no_track_plan_path": {
       "path": "/{clinical_trial}/{test_centre}/Dose Reconstruction/DICOM/Patient {centre_patient_no}/",
       "display_name": "DICOM No Track Plan",
-      "field_type": "file",
+      "field_type": "folder",
       "level": "fraction",
       "allowed": [
         "application/dicom"

src/content_uploader/ContentUploader.py

@@ -316,6 +316,15 @@ def getFileTypes(self) -> Dict:
     def updateFileTypes(self, trialFileType) -> None:
         self.fileTypes = trialFileType
 
+    def getUploadFormatForFileType(self, fileType:str) -> str:
+        if fileType not in self.fileTypes:
+            return None
+        if self.fileTypes[fileType]["field_type"] == "file":
+            return "File (Please only uplaod one file)"
+        elif self.fileTypes[fileType]["field_type"] == "folder":
+            return "Folder (Please drag the entire file folder)"
+        return self.fileTypes[fileType]["field_type"]
+
 class LoginScreen(QWidget):
     authorisationRequested:SignalInstance = Signal()
 
@@ -876,6 +885,7 @@ def __init__(self, parent: Optional[QWidget]=None) -> None:
         self.cancelRequest = False
         self.isPatientIdValidated = False
         self.currentProfile = None
+        self.currentUploadFormatDisplay = None
         self._initGUI()
 
         self.loginScreen = LoginScreen()
@@ -929,8 +939,12 @@ def _initGUI(self):
         addTestCentreBtn.setMaximumSize(30, addTestCentreBtn.height())
         addTestCentreBtn.clicked.connect(self.showNewTestCentreScreen)
 
+        self.fileLevelSelector = QComboBox()
+        self.fileLevelSelector.addItems(["Prescription", "Fraction"])
+        self.fileLevelSelector.currentTextChanged.connect(self.changeFileType)
+
         self.fileTypeSelector = QComboBox()
-        fileTypesItems = self.dbClient.getFileTypesForTrial(self.trialSelector.currentText())
+        fileTypesItems = self.dbClient.getFileTypesForTrial(self.trialSelector.currentText(), self.fileLevelSelector.currentText())
         self.trialsMetaData.updateFileTypes(fileTypesItems)
         self.fileTypeSelector.addItems(self.trialsMetaData.getFileTypesSupported())
         self.fileTypeSelector.setMaximumWidth(200)
@@ -968,6 +982,9 @@ def _initGUI(self):
 
         self.patientSequenceInput = QSpinBox()
 
+        self.uploadForamtLabel = QLabel()
+        self.uploadForamtLabel.setText(f"Upload Format: {self.currentUploadFormatDisplay}")
+
         patientIdLayout = QHBoxLayout()
         patientIdLayout.addWidget(QLabel("Patient clinical trial ID:"))
         patientIdLayout.addWidget(self.patientIdVerifiedIndicator)
@@ -1000,6 +1017,12 @@ def _initGUI(self):
         fileTypeLayout.addWidget(typeofFileLabel)
         fileTypeLayout.addWidget(self.fileTypeSelector)
 
+        fileLevelLayout = QHBoxLayout()
+        fileLevelLabel = QLabel("Level:")
+        fileLevelLabel.setSizePolicy(QSizePolicy.Fixed, QSizePolicy.Preferred)
+        fileLevelLayout.addWidget(fileLevelLabel)
+        fileLevelLayout.addWidget(self.fileLevelSelector)
+
         mainFractionLayout = QHBoxLayout()
         fractionLabel = QLabel("Fraction:")
         fractionLabel.setSizePolicy(QSizePolicy.Fixed, QSizePolicy.Preferred)
@@ -1014,9 +1037,11 @@ def _initGUI(self):
         subFractionLayout.addWidget(self.subFractionSelector)
         subFractionLayout.addWidget(addSubFractionPushBtn)
 
-        inputLayout.addLayout(fileTypeLayout, 0, 0)
-        inputLayout.addLayout(mainFractionLayout, 1, 0)
-        inputLayout.addLayout(subFractionLayout, 1, 1)
+        inputLayout.addLayout(fileLevelLayout, 0, 0)
+        inputLayout.addLayout(fileTypeLayout, 0, 1)
+        inputLayout.addWidget(self.uploadForamtLabel, 1, 0, 1, 2)
+        inputLayout.addLayout(mainFractionLayout, 2, 0)
+        inputLayout.addLayout(subFractionLayout, 2, 1)
         inputLayout.setVerticalSpacing(0)
 
         self.dropArea = DropArea()
@@ -1516,6 +1541,8 @@ def removeEntryFromUploadTable(self):
 
     @Slot(str)
     def fileTypeSelected(self, fileType:str):
+        self.currentUploadFormatDisplay = self.trialsMetaData.getUploadFormatForFileType(fileType)
+        self.uploadForamtLabel.setText(f"Upload Format: {self.currentUploadFormatDisplay}")
         if self.trialsMetaData.getLevelofFileType(fileType) == "fraction":
             self.fractionSelector.setEnabled(True)
         else:
@@ -1527,7 +1554,7 @@ def fileTypeSelected(self, fileType:str):
     @Slot(str)
     def changeFileType(self):
         self.fileTypeSelector.clear()
-        fileTypes = self.dbClient.getFileTypesForTrial(self.trialSelector.currentText())
+        fileTypes = self.dbClient.getFileTypesForTrial(self.trialSelector.currentText(), self.fileLevelSelector.currentText())
         self.trialsMetaData.updateFileTypes(fileTypes)
         self.fileTypeSelector.addItems(self.trialsMetaData.getFileTypesSupported())
 

src/content_uploader/ImagingDBClient/Clients.py

@@ -249,7 +249,7 @@ def addSiteAndTrial(self, newDetails:Dict) -> Result:
             return Result(success=True, message="Added site and trial successfully")
         return Result(success=False, message=f"data service retured {req.status_code}")
 
-    def getFileTypesForTrial(self, trialName:str) -> Dict:
+    def getFileTypesForTrial(self, trialName:str, levelName:str) -> Dict:
         if not trialName:
             return {}
         try:
@@ -258,5 +258,7 @@ def getFileTypesForTrial(self, trialName:str) -> Dict:
         except (Exception, InvalidSchema) as ex:
             return {}
         if req.status_code == 200:
-            return req.json()
+            level = levelName.lower()
+            if level in req.json():
+                return req.json()[level]
         return {}

src/data_service/AccessManager.py

@@ -512,16 +512,19 @@ def getContentUploaderTrial(trialName:str) ->Dict:
         return {}
     strucutre = rows[0][0]
     result = {}
-    for key in strucutre.keys():
-        if strucutre[key]:
-            displayName = strucutre[key]["display_name"]
-            contentInfo = {
-                "level": strucutre[key]["level"],
-                "key": key,
-                "field_type": strucutre[key]["field_type"],
-                "allowed": strucutre[key]["allowed"],
-            }
-            result[displayName] = contentInfo
+    for level in strucutre.keys():
+        for key in strucutre[level].keys():
+            if strucutre[level][key]:
+                displayName = strucutre[level][key]["display_name"]
+                contentInfo = {
+                    "level": strucutre[level][key]["level"],
+                    "key": key,
+                    "field_type": strucutre[level][key]["field_type"],
+                    "allowed": strucutre[level][key]["allowed"],
+                }
+                if level not in result:
+                    result[level] = {}
+                result[level][displayName] = contentInfo
     return result
 
 def addTrialStructure(trialPack:Dict) -> Tuple[bool, str]: