initial commit

.gitignore

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+.idea/
+test.sh
+test176.sh
+/plugins/*jar
+/plugins/
+/xlsx/*xlsx
+/redcap_dict/*.csv
+/builder/__pycache__
+
+

README.md

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+Please read the wiki for instructions.
+
+## Updates
+**26 June 2023**:
+* Subforms added
+* Gradlew bug fixed - restarts gradle to clear cache, as can break if schema changed.
+* Date box and ynuo bugs fixed
+* Session/subject assessor label format changed to prevent same day clashes
+
+**22 March 2023**:
+* Redcap rewritten and improved - includeding calcsum and datediff
+* Bug fix: float textboxes did not work - came out string. Fixed
+* Project-specific field added
+* Using modified XNAT 1.8 Plugin Template (not working)
+* Tested on XNAT 1.8.7
+
+**22 March 2023**:
+* Redcap rewritten and improved - includeding calcsum and datediff
+* Bug fix: float textboxes did not work - came out string. Fixed
+* Project-specific field added
+* Using modified XNAT 1.8 Plugin Template
+* Tested on XNAT 1.8.7
+
+**26 Jan 2023**:
+* Subforms added (else potentially not buildable in gradle due to being too long)
+* Tested to XNATv1.8.6.1
+
+## Limitations
+
+* Redcap Calc fields are limited.
+* UK Date formats dd-MM-YYYY
+

builder/handle_csv.py

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+import os
+import shutil
+
+
+
+
+class CSVHandler(object):
+
+    def __init__(self, configData, deleteExistingFiles=False):
+        self.errors = []
+        self.log = []
+        self.configData = configData
+        self.schemaName = configData['schemaName']
+        self.csvDir = '{}/data'.format(configData['path_plugin_builder'])
+
+
+        if (deleteExistingFiles):
+            self.emptyTheDir()
+
+    def hasError(self):
+        return len(self.errors)
+
+    def errors(self):
+        return self.errors
+
+
+
+
+    def emptyTheDir(self):
+
+        thePath = ('{}/data/{}').format(self.configData['path_plugin_builder'], self.schemaName)
+        if os.path.exists(thePath):
+            self.log.append(' Delete Dir : {}'.format(thePath))
+            shutil.rmtree(thePath)
+        #make new dir
+
+        os.makedirs(thePath)
+
+
+    def getHeader(self, form):
+
+        out = 'ID,'
+        for i in form['inputs']:
+            el = '{}:{}/{}'.format(self.schemaName, form['ref'], i['dataName'])
+            if 'subform' in i['inputFormType']:
+
+                subform = i['options']
+                #insert questions later
+                out = '{}{}@{}@,'.format(out, el,subform)
+
+            elif len(i['children']) > 0:
+                elsub = '{}/{}'.format(el, i['subName'])
+                out = '{}{},'.format(out, elsub)
+                for ii in i['children']:
+                    elsub = '{}/{}'.format(el, ii['subName'])
+                    if 'subform' in ii['inputFormType']:
+                        subform = ii['options']
+                        # insert questions later
+                        out = '{}{}@{}@,'.format(out, elsub, subform)
+            else:
+                out = '{}{},'.format(out, el)
+        out = '{}subject_ID'.format(out )
+        return out
+
+    def getLineOfData(self, form, data):
+
+
+        form_label = '{}-{}'.format(form['ref'],data['subject_label'])
+        out = '{},'.format(form_label)
+
+        for i in data['inputs']:
+            out = '{},{},'.format(out, data[i])
+        out = '{},{}'.format(out, data['subject_label'] )
+        return out
+
+    def writeToFile(self, form):
+
+        head = self.getHeader(form)
+
+        if len(head) == 0:
+            self.errors.append('no inputs')
+            return
+
+        writeFileName = '{}/{}/{}_{}.csv'.format(self.csvDir,self.schemaName,self.schemaName, form['ref'])
+        #self.checkDir(writeFileName)
+        self.log.append(' write file : {}'.format(writeFileName))
+        f = open(writeFileName, "w")
+
+        f.write('{}'.format(head))
+
+        f.close()
+
+    def write_subforms(self, subform):
+        thePath = ('{}/data/{}').format(self.configData['path_plugin_builder'], self.schemaName)
+        subform_replace = '@{}@'.format(subform['ref'])
+        out = ''
+        if os.path.exists(thePath):
+            for filename in os.listdir(thePath):
+                filepath = os.path.join(thePath, filename)
+                with open(filepath) as f:
+                    header = f.readline()
+                    heads = header.split(',')
+                    for head in heads:
+                        print(head)
+                        if subform_replace in head:
+                            el = head.replace(subform_replace,'')
+                            print(el)
+                            for i in subform['inputs']:
+                                out = '{},{}/{}'.format(out,el, i['dataName'])
+
+                        else:
+                            out = '{},{}'.format(out,head)
+
+                with open(filepath, "w") as f:
+                    #get rid of first and last comma
+                    out = out[1:-1]
+                    f.write(out)
+

builder/handle_file_plugin.py

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+import os
+import shutil
+
+class PluginHandler(object):
+
+    def __init__(self, configData, deleteExistingFiles = False):
+
+        self.errors = []
+        self.log =[]
+        self.configData = configData
+        self.schemaName = configData['schemaName']
+
+        self.part_plugin_path = 'src/main/java/org/nrg/xnat/plugins/'
+
+    def hasError(self):
+        return len(self.errors)
+
+    def errors(self):
+        return self.errors
+
+
+
+
+    def copyTemplatesReplace(self,toDir):
+
+        fromDir = ('{}/plugin_template'.format(self.configData['path_builder_templates']))
+
+        self.log.append(' copy plugin template from : {}'.format(fromDir))
+        self.log.append(' copy plugin template to   : {}'.format(toDir))
+        if os.path.exists(toDir):
+            shutil.rmtree(toDir)
+
+        shutil.copytree( fromDir,toDir , symlinks=False, ignore=None)
+
+        for root, dirs, files in os.walk(toDir):
+            for file in files:
+                if file == '.DS_Store':
+                    continue
+                f_in = os.path.join(root, file)
+                # print ('File : ', f_in)
+                fxsd = open(f_in,"r")
+                lines = fxsd.readlines()
+                fxsd.close()
+                fxsd = open(f_in,"w")
+
+                for line in lines:
+                    fxsd.write(line.replace('[HERE_SCHEMANAME_LOWER]',self.schemaName.lower()).replace('[HERE_SCHEMANAME]',self.schemaName.title()))
+
+                fxsd.close()
+
+        for root, dirs, files in os.walk(toDir):
+            for file in files:
+                fo = os.path.join(root, file)
+                if 'Template' in file:                    
+                    print ('Renaming {} to {} '.format(file, file.replace('Template',self.schemaName.title()).replace('template',self.schemaName.lower())))
+                    os.rename(fo,os.path.join(root, file.replace('Template',self.schemaName.title()).replace('template',self.schemaName.lower())))
+                if 'template' in file:
+                    print ('Renaming {} to {} '.format(file, file.replace('Template',self.schemaName.title()).replace('template',self.schemaName.lower())))
+                    os.rename(fo,os.path.join(root, file.replace('template',self.schemaName.lower())))
+
+
+    def createFiles(self,forms):
+
+        toDir = ('{}/{}/{}{}').format(self.configData['path_builder_plugins'],self.schemaName, self.part_plugin_path,self.configData['schemaName'].lower())
+
+        self.copyTemplatesReplace(toDir)
+
+        HERE_IMPORT_BEANS =[]
+        HERE_XNAT_DATA_MODELS =[]
+
+        for f in forms:
+            sc = self.schemaName[:1].upper() + self.schemaName[1:].lower()
+            st = forms[f]['ref'][:1].upper() + forms[f]['ref'][1:].lower()
+            bean = '{}{}Bean'.format(sc,st)
+            formName = forms[f]['name']
+            md = '@XnatDataModel(value = {}.SCHEMA_ELEMENT_NAME, singular = "{}", plural = "{}")'.format(bean,formName,formName)
+
+            HERE_IMPORT_BEANS.append('import org.nrg.xdat.bean.{};'.format(bean) )
+            HERE_XNAT_DATA_MODELS.append(md)
+
+
+        file_plugin = ('{}/plugin/Xnat{}Plugin.java'.format(toDir,self.schemaName.title()))
+        print('FILE', file_plugin)
+        f = open(file_plugin,"r")
+        lines = f.readlines()
+        f.close()
+
+        # print(lines)
+        self.log.append(' replace file contents : {}'.format(file_plugin))
+
+        f = open(file_plugin,"w")
+        for line in lines:
+            # print(line)
+            if '[HERE_IMPORT_BEANS]' in line:
+                f.write(line.replace('[HERE_IMPORT_BEANS]','\n'.join(HERE_IMPORT_BEANS)))
+            elif '[HERE_XNAT_DATA_MODELS]' in line:
+                f.write(line.replace('[HERE_XNAT_DATA_MODELS]',','.join(HERE_XNAT_DATA_MODELS)))
+            elif '[HERE_CLASS_NAME]' in line:
+                f.write(line.replace('[HERE_CLASS_NAME]',sc))
+            elif '[HERE_SCHEMANAME_LOWER]' in line:
+                f.write(line.replace('[HERE_SCHEMANAME_LOWER]',self.configData['schemaName'].lower()))
+            elif '[HERE_PLUGIN_NAME]' in line:
+                f.write(line.replace('[HERE_PLUGIN_NAME]',self.configData['schemaName']))
+            else:
+                # print(line)
+                f.write(line)
+
+        f.close()
+
+
+

builder/handle_file_turbine.py

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+import errno
+import os
+import shutil
+
+class TurbineHandler(object):
+
+    def __init__(self, configData, deleteExistingFiles = False):
+
+        self.errors = []
+        self.log =[]
+        self.configData = configData
+        self.schemaName = configData['schemaName']
+
+        self.filesDir = 'src/main/java/org/apache/turbine/app/xnat/modules/screens/'
+        self.actionsDir = 'src/main/java/org/apache/turbine/app/xnat/modules/actions/'
+
+        if(deleteExistingFiles):
+            self.emptyTheDir()
+
+    def hasError(self):
+        return len(self.errors)
+
+
+    def checkDir(self,vmFile):
+
+        if not os.path.exists(os.path.dirname(vmFile)):
+            try:
+                os.makedirs(os.path.dirname(vmFile))
+            except OSError as exc: # Guard against race condition
+                if exc.errno != errno.EEXIST:
+                    raise
+
+    def emptyTheDir(self):
+
+        thePath = ('{}/{}/{}').format(self.configData['path_builder_plugins'],self.schemaName,self.filesDir)
+        if os.path.exists(thePath):
+            shutil.rmtree(thePath)
+
+            self.log.append(' Empty Dir : {}'.format(thePath))
+        thePath = ('{}/{}/{}').format(self.configData['path_builder_plugins'],self.schemaName,self.actionsDir)
+        if os.path.exists(thePath):
+            shutil.rmtree(thePath)
+
+            self.log.append(' Empty Dir : {}'.format(thePath))
+
+    def copyAndReplace(self,src,dst, form):
+        sc = self.schemaName[:1].upper() + self.schemaName[1:].lower()
+        st = form['ref'][:1].upper() + form['ref'][1:].lower()
+        om_name =  '{}{}'.format(sc, st)
+        class_name = 'XDATScreen_edit_{}_{}'.format(self.schemaName, form['ref'])
+        label_tag = form['ref']
+
+        f = open(src, "r")
+        lines = f.readlines()
+        f.close()
+
+        f = open(dst, "w")
+        for line in lines:
+            if '[SCHEMA_TITLE]'  in line or '[OM_NAME]' in line or '[CLASS_NAME]' in line or '[LABEL_TAG]' in line or '[FORM_NAME]' in line:
+                line = line.replace('[OM_NAME]', om_name)
+                line = line.replace('[CLASS_NAME]', class_name)
+                line = line.replace('[FORM_NAME]', form['ref'])
+                line = line.replace('[SCHEMA_TITLE]',self.schemaName.title())
+                f.write(line.replace('[LABEL_TAG]', str(label_tag)))
+            else:
+                f.write(line)
+
+        f.close()
+
+    def loadTemplateReplace(self, form):
+
+        fname = ('{}/turbine_java_template.java'.format(self.configData['path_builder_templates']))
+        if form['ext'] != 'subject':
+            #sesison level
+            fname = ('{}/turbine_java_template_session.java'.format(self.configData['path_builder_templates']))
+        self.log.append(' load file : {}'.format(fname))
+
+        return fname
+
+
+    def copyTemplateScreeen(self, form):
+        src = ('{}/TemplateScreen.java').format(self.configData['path_builder_templates'])
+        dst = ('{}/{}/{}/{}Screen.java').format(self.configData['path_builder_plugins'], self.schemaName, self.filesDir,self.schemaName.title() )
+        self.copyAndReplace(src,dst, form)
+
+    def copyModifyTemplateScreeen(self,form):
+        #under actions dir
+        #for subjects only as dunno about session
+        if 'ubject' in form['ext']:
+
+            dst = ('{}/{}/{}/').format(self.configData['path_builder_plugins'], self.schemaName,self.actionsDir)
+            if not os.path.exists(os.path.dirname(dst)):
+                try:
+                    os.makedirs(os.path.dirname(dst))
+                except OSError as exc: # Guard against race condition
+                    if exc.errno != errno.EEXIST:
+                        raise
+            self.log.append(' write file : {}'.format(dst))
+            #DONT USE title() - as does not work if form contains numbers
+            ref = form['ref'][:1].upper() + form['ref'][1:].lower()
+
+            dst = ('{}/{}/{}/Modify{}{}.java').format(self.configData['path_builder_plugins'], self.schemaName, self.actionsDir, self.schemaName.title(), ref)
+            src = ('{}/ModifyTemplateSample.java').format(self.configData['path_builder_templates'])
+            self.copyAndReplace(src,dst, form)
+
+
+    def pathTemplateReplaceOut(self,templateType,formRef):
+
+        fname = ('{}/{}/{}XDATScreen_{}').format(self.configData['path_builder_plugins'],self.schemaName,self.filesDir,templateType)
+        return fname + ('_{}_{}.java').format(self.configData['schemaName'],formRef)
+
+
+    def formEdit(self,form):
+
+
+        templateName = self.loadTemplateReplace(form)
+        writeFileName = self.pathTemplateReplaceOut('edit',form['ref'])
+
+        self.log.append(' write file : {}'.format(writeFileName))
+        self.checkDir(writeFileName)
+
+        self.copyAndReplace(templateName,writeFileName, form)