Fixed upload when inputs is a list

models/SoftwareUpload.php

@@ -191,7 +191,7 @@ public function upload()
         $command=Software::sudoWrap(Yii::$app->params['scriptsFolder'] . "imageUploader.py ");
         $command.= implode(" ", $arguments) . " ";
         $command.= "2>&1";
-
+        
         Software::exec_log($command,$out,$ret);
 
         $errors='';
@@ -325,6 +325,11 @@ public function upload()
                 $errors.="One of the inputs does has an unknown type.";
                 $errors.="<br />Please correct the file syntax and try again or contact an administrator.";
                 break;
+            case 100:
+                $errors.="Error: code $ret. ";
+                $errors.="Your CWL definition has a format not recognized by the system";
+                $errors.="<br />Please contact an administrator to fix the issue.";
+                break;
             default:
                 $errors.="Error: code $ret. ";
                 $errors.="<br />An unexpected error occurred.";

scheduler_files/imageUploader.py

@@ -166,6 +166,12 @@ def quoteEnclose(string):
 if 'inputs' not in cwlContent:
     cwlContent['inputs']=[];
 
-exit_value=uf.inputStore(softName,softVersion, cwlContent['inputs'])
+if isinstance(cwlContent['inputs'],dict):
+    exit_value=uf.inputStoreDict(softName,softVersion, cwlContent['inputs'])
+elif isinstance(cwlContent['inputs'],list):
+    exit_value=uf.inputStoreList(softName,softVersion, cwlContent['inputs'])
+else:
+    exit_value=100
+
 exit(exit_value)
 

scheduler_files/uploadFunctions.py

@@ -139,7 +139,7 @@ def cwlReturnDockerImage(content):
         else:
             exit(23)
 
-def inputStore(softName,softVersion, inputs):
+def inputStoreDict(softName,softVersion, inputs):
     types=set(['string', 'int', 'long', 'float', 'double', 'null', 'File', 'Directory', 'Any','boolean'])
 
     #open db connection and get image id
@@ -278,6 +278,149 @@ def inputStore(softName,softVersion, inputs):
 
     return 0
 
+def inputStoreList(softName,softVersion, inputs):
+    types=set(['string', 'int', 'long', 'float', 'double', 'null', 'File', 'Directory', 'Any','boolean'])
+
+    #open db connection and get image id
+    conn=psg.connect(host=host, user=dbuser, password=passwd, dbname=dbname)
+    cur=conn.cursor()
+
+    query="SELECT id FROM software WHERE name='" + softName + "' AND version='" + softVersion + "'"
+    cur.execute(query)
+    result=cur.fetchall()
+    softId=str(result[0][0])
+
+    #save script in database and get its id
+    # print(inputs)
+    if len(inputs)==0:
+        exit(30)
+
+    #create queries for input insertion
+    query='INSERT INTO software_inputs(name, position, softwareid, field_type, prefix, separate, optional, default_value, is_array, array_separator, nested_array_binding) VALUES '
+
+    bindingFlag=False
+    positionFlag=False
+    separateInner=False
+    prefixInner=False
+
+
+    for inpt in inputs:
+        try:
+            inpt_name=inpt['id']
+        except:
+            deleteSavedSoftware(softName,softVersion)
+            return 100
+        is_array='f'
+        array_separator=''
+        nested_array_binding='f'
+        prefix=''
+        separate='t'
+        if 'type' not in inpt.keys():
+            #stop execution and return because this is serious
+            deleteSavedSoftware(softName,softVersion)
+            return 34
+        fieldType=inpt['type']
+        #field type is array
+        if isinstance(fieldType,dict):
+            if fieldType['type']!='array':
+                deleteSavedSoftware(softName,softVersion)
+                return 36
+            is_array='t'
+            if 'inputBinding' in fieldType:
+                nested_array_binding='t'
+                innerBinding=fieldType['inputBinding']
+                if 'separate' in binding:
+                    separateInner=True
+                    if innerBinding['separate']==False:
+                        separate='f'
+                if 'prefix' in binding:
+                    prefixInner=True
+                    prefix=innerBinding['prefix']
+            if 'items' not in fieldType:
+                deleteSavedSoftware(softName,softVersion)
+                return 37
+
+            fieldType=fieldType['items']
+
+        else:
+            fieldType=inpt['type'].strip()
+
+
+        if 'inputBinding' not in inpt.keys():
+                bindingFlag=True
+                continue
+                #exit(32)
+
+
+        outerBinding=inpt['inputBinding']
+        # Get position, separate and prefix from inputBinding.
+        # If it does not exist, ignore input
+        if 'position' not in outerBinding:
+            positionFlat=True
+            continue
+        position=outerBinding['position']
+
+        if ('separate' in outerBinding) and (separateInner==False):
+            if outerBinding['separate']=='false':
+                separate='f'
+            else:
+                separate='t'
+
+        if ('prefix' in outerBinding) and (prefixInner==False):
+            prefix=outerBinding['prefix'] 
+        if ('itemSeparator' in outerBinding):
+            array_separator=outerBinding['itemSeparator']     
+
+        # print(separate)
+
+        optional='f'
+        if fieldType[-1]=='?':
+            optional='t'
+            fieldType=fieldType[:-1]
+
+        if '[]' in fieldType:
+            is_array='t'
+            fieldType=fieldType[:-2]
+
+        if fieldType not in types:
+            #stop execution and return because this is serious
+            deleteSavedSoftware(softName,softVersion)
+            print("Field type: %s not in Types %s" % (fieldType,types))
+            return 35
+
+
+            #get default value
+        defaultValue=''
+        if (fieldType!='File') and (fieldType!='Directory') and (fieldType!='null'):
+            if 'default' in inpt.keys():
+                defaultValue=str(inpt['default'])
+
+        name=quoteEnclose(inpt_name)
+        fieldType=quoteEnclose(fieldType)
+        prefix=quoteEnclose(prefix)
+        defaultValue=quoteEnclose(defaultValue)
+        optional=quoteEnclose(optional)
+        separate=quoteEnclose(separate)
+        is_array=quoteEnclose(is_array)
+        array_separator=quoteEnclose(array_separator)
+        nested_array_binding=quoteEnclose(nested_array_binding)
+
+        query+='(' + name + ',' + str(position) + ',' + str(softId) + ',' + fieldType + ',' + prefix + ',' + separate + ',' + optional + ',' + defaultValue + ',' + is_array+ ',' + array_separator + ',' + nested_array_binding + '),'
+
+    query=query[:-1]
+    # print(query)
+    cur.execute(query)
+    conn.commit()
+
+    conn.close()
+
+    if bindingFlag:
+        return 32
+    if positionFlag:
+        return 33
+
+    return 0
+
 def imageStore(name,version,image,script,user,visibility,
                 workingDir,imountPoint,omountPoint, description,cwlPath,biotools,doiFile,mpi,original,docker_or_local,covid19,instructions,gpu):