Uploader can now specify a workingdir

models/Software.php

@@ -822,7 +822,7 @@ public function runJob()
         $executor=[];
         $executor['image']=$this->image;
         $executor['command']=$this->container_command;
-        $executor['workdir']=empty($this->omountpoint) ? $this->imountpoint : $this->omountpoint;
+        $executor['workdir']=empty($this->workingdir) ? $this->omountpoint : $this->workingdir;
         $data['executors']=[$executor];
         // var_dump($data);
         // exit(0);

models/SoftwareUpload.php

@@ -113,7 +113,7 @@ public function attributeLabels()
             'visibility' => 'Visible to',
             'imountpoint'=>'Input folder mount point (where users can provide input data inside the container). Leave empty if no mount is required',
             'omountpoint'=>'Output folder mount point (folder inside the container where users can find the output). Leave empty if no mount is required',
-            'workingdir'=>'Working directory (inside the container). If left empty, /data will be used.',
+            'workingdir'=>'Working directory (inside the container). If left empty, the output mountpoint will be used.',
             'description'=> 'Software description * ',
             'imageInDockerHub'=>'Image exists in DockerHub and is specified in the CWL file',
             'iomount' => 'Image requires disk I/O',
@@ -180,18 +180,18 @@ public function upload()
         $imageFileName=$this->quotes($imageFileName);
         $this->name=$this->quotes($this->name);
         $this->version=$this->quotes($this->version);
-        $mpi=($this->mpi=='1') ? $this->quotes('t') : $this->quotes('f');
+        $this->workingdir=$this->quotes($this->workingdir);
         $username=$this->quotes($username);
 
         $arguments=[$this->name, $this->version, $imageFileName, $imageFileExt, $cwlFileName, 
                     $username, $this->visibility, $this->imountpoint, $this->omountpoint,
-                    $this->description, $this->biotools, $doiFile, $mpi, $this->covid19, $this->instructions,$this->gpu];
+                    $this->description, $this->biotools, $doiFile, $this->workingdir, $this->covid19, $this->instructions,$this->gpu];
 
 
         $command=Software::sudoWrap(Yii::$app->params['scriptsFolder'] . "imageUploader.py ");
         $command.= implode(" ", $arguments) . " ";
         $command.= "2>&1";
-
+        print_r($command);exit(0);
         Software::exec_log($command,$out,$ret);
 
         $errors='';

models/SoftwareUploadExisting.php

@@ -114,7 +114,7 @@ public function attributeLabels()
             'visibility' => 'Visible to',
             'imountpoint'=>'Input folder mount point (where users can provide input data inside the container). Leave empty if no mount is required',
             'omountpoint'=>'Output folder mount point (folder inside the container where users can find the output). Leave empty if no mount is required',
-            'workingdir'=>'Working directory (inside the container). If left empty, /data will be used.',
+            'workingdir'=>'Working directory (inside the container). If left empty, the output mountpoint a will be used.',
             'description'=> 'Software description * ',
             'imageInDockerHub'=>'Image exists in DockerHub and is specified in the CWL file',
             'iomount' => 'Image requires disk I/O',
@@ -140,12 +140,13 @@ public function upload()
         $workingdir=$previous->workingdir;
         $original=$previous->original_image;
         $dockerhub=($previous->docker_or_local) ? "'t'" : "'f'";
-        $workingdir=$this->quotes($workingdir);
+        $this->workingdir=$this->quotes($this->workingdir);
         $original=$this->quotes($original);
         $this->covid19=($this->covid19=='1') ? "'t'" : "'f'";
         $this->biotools=$this->quotes($this->biotools);
         $this->instructions=$this->quotes($this->instructions);
         $this->gpu=$this->quotes($this->gpu);
+        $this->workingdir=$this->quotes($this->workingdir);
 
         //add dois string in a file and pass it on to python
         $dataFolder=Yii::$app->params['tmpImagePath'] . $username . '/' . str_replace(' ','-',$this->name) . '/' . str_replace(' ','-',$this->version) . '/';
@@ -178,13 +179,12 @@ public function upload()
 
         $this->name=$this->quotes($this->name);
         $this->version=$this->quotes($this->version);
-        $mpi=($this->mpi=='1') ? $this->quotes('t') : $this->quotes('f');
         $username=$this->quotes($username);
 
         $arguments=[
             $this->name, $this->version, $this->image, $cwlFileName, 
             $username, $this->visibility, $this->imountpoint, $this->omountpoint,
-            $this->description, $this->biotools, $doiFile, $mpi, $workingdir,
+            $this->description, $this->biotools, $doiFile, $this->workingdir,
             $original,$dockerhub,$this->covid19, $this->instructions,$this->gpu];
 
         $command=Software::sudoWrap(Yii::$app->params['scriptsFolder'] . "existingImageUploader.py ");

scheduler_files/existingImageUploader.py

@@ -39,13 +39,12 @@
 description=sys.argv[9]
 biotools=sys.argv[10]
 doiFile=sys.argv[11]
-mpi=sys.argv[12]
-workingDir=sys.argv[13]
-original=sys.argv[14]
-docker_or_local=sys.argv[15]
-covid19=sys.argv[16]
-instructions=sys.argv[17]
-gpu=sys.argv[18]
+workingDir=sys.argv[12]
+original=sys.argv[13]
+docker_or_local=sys.argv[14]
+covid19=sys.argv[15]
+instructions=sys.argv[16]
+gpu=sys.argv[17]
 
 def quoteEnclose(string):
     return "'" + string + "'"
@@ -77,11 +76,16 @@ def quoteEnclose(string):
     workingDir='/'
 
 uf.imageStore(softName,softVersion, image,script,user,visibility,
-    workingDir,imountPoint,omountPoint,description,cwlPath,biotools,doiFile,mpi,original,docker_or_local,covid19,instructions,gpu)
+    workingDir,imountPoint,omountPoint,description,cwlPath,biotools,doiFile,original,docker_or_local,covid19,instructions,gpu)
 
 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/imageUploader.py

@@ -44,7 +44,7 @@
 description=sys.argv[10]
 biotools=sys.argv[11]
 doiFile=sys.argv[12]
-mpi=sys.argv[13]
+workingDir=sys.argv[13]
 covid19=sys.argv[14]
 instructions=sys.argv[15]
 gpu=sys.argv[16]
@@ -121,7 +121,6 @@ def quoteEnclose(string):
 # imageName=softName.lower()
 # imageVersion=softVersion.lower()
 
-workingDir='/'
 
 
 if (dockerHub=='t'):
@@ -161,7 +160,7 @@ def quoteEnclose(string):
     conn.commit()
 
 uf.imageStore(softName,softVersion, imageFull,script,user,visibility,
-    workingDir,imountPoint,omountPoint,description,cwlPath,biotools,doiFile,mpi,original,dockerHub,covid19,instructions,gpu)
+    workingDir,imountPoint,omountPoint,description,cwlPath,biotools,doiFile,original,dockerHub,covid19,instructions,gpu)
 
 if 'inputs' not in cwlContent:
     cwlContent['inputs']=[];

scheduler_files/uploadFunctions.py

@@ -422,7 +422,7 @@ def inputStoreList(softName,softVersion, inputs):
     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):
+                workingDir,imountPoint,omountPoint, description,cwlPath,biotools,doiFile,original,docker_or_local,covid19,instructions,gpu):
 
     softFull=name+ '-' + version
     name=quoteEnclose(name)
@@ -437,7 +437,6 @@ def imageStore(name,version,image,script,user,visibility,
     description=quoteEnclose(description)
     cwlPath=quoteEnclose(cwlPath)
     biotools=quoteEnclose(biotools)
-    mpi=quoteEnclose(mpi)
     original=quoteEnclose(original)
     docker_or_local=quoteEnclose(docker_or_local)
     covid19=quoteEnclose(covid19)
@@ -459,19 +458,19 @@ def imageStore(name,version,image,script,user,visibility,
     date="NOW()"
 
     values=[name,version,image,script,user, date, visibility, workingDir, imountPoint, 
-                omountPoint, description, cwlPath,biotools,dois,mpi,original,docker_or_local,covid19, instructions,gpu]
+                omountPoint, description, cwlPath,biotools,dois,original,docker_or_local,covid19, instructions,gpu]
 
     sql1='INSERT INTO software_upload (name,version, image,script,uploaded_by, date, visibility, workingdir, imountpoint, omountpoint,\
-    description, cwl_path,biotools,dois,mpi,original_image,docker_or_local,covid19, instructions,gpu) '
+    description, cwl_path,biotools,dois,original_image,docker_or_local,covid19, instructions,gpu) '
     sql1+='VALUES (' + ','.join(values) + ')'
 
 
 
     values=[name,version,image,script,user, visibility, workingDir, imountPoint, omountPoint,description,cwlPath,biotools,
-                    dois,mpi,original,docker_or_local,covid19, instructions,gpu]
+                    dois,original,docker_or_local,covid19, instructions,gpu]
     sql2='INSERT INTO software (name,version,image,script,uploaded_by,\
             visibility, workingdir, imountpoint, omountpoint, description,\
-            cwl_path,biotools,dois,mpi,original_image,docker_or_local,covid19, instructions,gpu) '
+            cwl_path,biotools,dois,original_image,docker_or_local,covid19, instructions,gpu) '
     sql2+='VALUES (' + ','.join(values) + ')'
 
     # print()

views/software/software_edit.php

@@ -75,6 +75,7 @@
         </div>
 
     <?= ($superadmin)? $form->field($model, 'shared') -> checkbox(['id'=>'shared', "uncheck"=>'0',]):'' ?>
+    <?=$form->field($model, 'workingdir')?>
     <?= $form->field($model, 'gpu') -> checkbox(['id'=>'gpu', "uncheck"=>'0']) ?>
 
     <?=$form->field($model, 'biotools')->textInput() ?>

views/software/software_upload.php

@@ -76,6 +76,7 @@
             <?= $form->field($model, 'imountpoint') ?>
             <?= $form->field($model, 'omountpoint') ?>
         </div>
+        <?=$form->field($model, 'workingdir')?>
         <?= $form->field($model, 'gpu') -> checkbox(['id'=>'gpu', "uncheck"=>'0']) ?>
 
         <?= $form->field($model, 'biotools') ?>

views/software/software_upload_existing.php

@@ -74,6 +74,7 @@
             <?= $form->field($model, 'imountpoint') ?>
             <?= $form->field($model, 'omountpoint') ?>
         </div>
+        <?=$form->field($model, 'workingdir')?>
         <?= $form->field($model, 'gpu') -> checkbox(['id'=>'gpu', "uncheck"=>'0']) ?>
         <?= $form->field($model, 'biotools') ?>
         <div class="doi-container">