directory in db start again with a /

src/ng6/analysis.py

@@ -105,7 +105,7 @@ class Analysis (Component):
     """
 
     # The directories structure into ng6
-    DIRECTORIES_STRUCTURE = "analyze/"
+    DIRECTORIES_STRUCTURE = "analyze"
     ANALYSIS_CONFIG_FILE_NAME = "analysis.cfg"
 
     def __init__(self, name="", description="", software="",
@@ -183,7 +183,7 @@ class Analysis (Component):
                 break
             directory_name = uuid.uuid4().hex[:9]
 
-        self.directory = os.path.join(ng6conf.get_space_directory(self.space_id), self.DIRECTORIES_STRUCTURE, directory_name)
+        self.directory = "/" + os.path.join(ng6conf.get_space_directory(self.space_id), self.DIRECTORIES_STRUCTURE, directory_name)
 
         # first create the output directory
         if not os.path.isdir(self.output_directory):
@@ -649,7 +649,7 @@ class Analysis (Component):
         Return the full path of the analysis directory into the save dir
         """
         ng6conf = NG6ConfigReader()
-        return os.path.join( ng6conf.get_save_directory(), self.directory)
+        return ng6conf.get_save_directory() + self.directory
 
 
     def __get_work_directory(self):
@@ -657,7 +657,7 @@ class Analysis (Component):
         Return the full path of the analysis directory into the work dir
         """
         ng6conf = NG6ConfigReader()
-        return os.path.join( ng6conf.get_work_directory(), self.directory)
+        return ng6conf.get_work_directory() + self.directory
 
 
     @staticmethod

src/ng6/run.py

@@ -41,7 +41,7 @@ class Run(object):
     """
 
     # The directories structure into ng6
-    DIRECTORIES_STRUCTURE = "run/"
+    DIRECTORIES_STRUCTURE = "run"
     SEQUENCERS = ["454", "454 GS FLX Titanium", "454 GS FLX+", "454 GS FLX XL+", "HiSeq 2000", "MiSeq"]
 
     def __init__(self, name, date, species, data_nature, type, description, sequencer, space_id="default", id = None ):
@@ -82,15 +82,19 @@ class Run(object):
             uniq = False
             directory_name = uuid.uuid4().hex[:9]
             while True:
-                save_dir = os.path.join(ng6conf.get_save_directory(), ng6conf.get_space_directory(self.space_id), self.DIRECTORIES_STRUCTURE, directory_name)
-                work_dir = os.path.join(ng6conf.get_work_directory(), ng6conf.get_space_directory(self.space_id), self.DIRECTORIES_STRUCTURE, directory_name)
+                save_dir = os.path.join(ng6conf.get_save_directory(), \
+                            ng6conf.get_space_directory(self.space_id), self.DIRECTORIES_STRUCTURE, directory_name)
+                work_dir = os.path.join(ng6conf.get_work_directory(), ng6conf.get_space_directory(self.space_id), \
+                        self.DIRECTORIES_STRUCTURE, directory_name)
+                print (work_dir)
+                print (os.path.isdir(work_dir))
                 if not os.path.isdir(save_dir) and not os.path.isdir(work_dir):
                     break
                 directory_name = uuid.uuid4().hex[:9]
+
             # Then make directories
-            work_dir = os.path.join(ng6conf.get_work_directory(), ng6conf.get_space_directory(self.space_id), self.DIRECTORIES_STRUCTURE, directory_name)
             os.makedirs(work_dir, 0o751)
-            self.directory = os.path.join(ng6conf.get_space_directory(self.space_id), self.DIRECTORIES_STRUCTURE, directory_name)
+            self.directory = "/" + os.path.join(ng6conf.get_space_directory(self.space_id),self.DIRECTORIES_STRUCTURE, directory_name)
 
     def process_raw_files(self, total_size, total_seq):
         """
@@ -370,21 +374,21 @@ class Run(object):
         Return the full path of the run directory into the work dir
         """
         ng6conf = NG6ConfigReader()
-        return os.path.join(ng6conf.get_work_directory(), self.directory)
+        return ng6conf.get_work_directory() + self.directory
 
     def get_work_directory(self):
         """
         Return the full path of the run directory into the work dir
         """
         ng6conf = NG6ConfigReader()
-        return os.path.join(ng6conf.get_work_directory(), self.directory)
+        return self.__get_work_directory()
 
     def __get_save_directory(self):
         """
         Return the full path of the run directory into the save dir
         """
         ng6conf = NG6ConfigReader()
-        return os.path.join(ng6conf.get_save_directory(), self.directory)
+        return ng6conf.get_save_directory() + self.directory
 
     @staticmethod
     def get_from_id (id):

ui/nG6/pi1/analyzes/Adaptorcleaner.tpl

@@ -138,11 +138,11 @@ along with this program.  If not, see <http://www.gnu.org/licenses/>.
 			{block name=download}
 				{if $nb_files != 0}
 					<p><ul>
-						{$dir=$data_folder|cat:'/'|cat:$analyse.directory}
+						{$dir=$data_folder|cat:$analyse.directory}
 						{assign var="nb_files" value=0}
 						{foreach $dir|scandir as $file}
 						{if $file != "." and $file != "" and $file != ".." and ($file|substr:-strlen(".png")) != ".png"}
-							{$link=(('fileadmin'|cat:'/'|cat:$analyse.directory)|cat:'/')|cat:$file}
+							{$link=(('fileadmin'|cat:$analyse.directory)|cat:'/')|cat:$file}
 							<li class="filelist"><a href="{$link}">{$file}</a> </li>
 							{$nb_files = $nb_files + 1}
 						{/if}

ui/nG6/pi1/analyzes/AnalysisTemplate.tpl

@@ -109,9 +109,9 @@ along with this program.  If not, see <http://www.gnu.org/licenses/>.
 				<div class="tab-pane fade" id="downloads">
 					{block name=download}
 						{assign var="nb_files" value=0}
-						{$dir=$data_folder|cat:'/'|cat:$analyse.directory}
+						{$dir=$data_folder|cat:$analyse.directory}
 						{foreach $dir|scandir as $file}
-							{assign var="link" value=(('fileadmin'|cat:'/'|cat:$analyse.directory)|cat:'/')|cat:$file}
+							{assign var="link" value=(('fileadmin'|cat:$analyse.directory)|cat:'/')|cat:$file}
 							{if $file != "." and $file != "" and $file != ".." and ($file|substr:-strlen(".png")) != ".png" and !is_dir($link)}
 								{$nb_files = $nb_files + 1}
 							{/if}

ui/nG6/pi1/analyzes/MothurOTU.tpl

@@ -173,11 +173,11 @@ along with this program.  If not, see <http://www.gnu.org/licenses/>.
 			{block name=download}
 				{if $nb_files != 0}
 					<p><ul>
-						{$dir=$data_folder|cat:'/'|cat:$analyse.directory}
+						{$dir=$data_folder|cat:$analyse.directory}
 						{assign var="nb_files" value=0}
 						{foreach $dir|scandir as $file}
 						{if $file != "." and $file != "" and $file != ".." and ($file|substr:-strlen(".png")) != ".png"}
-							{$link=(('fileadmin'|cat:'/'|cat:$analyse.directory)|cat:'/')|cat:$file}
+							{$link=(('fileadmin'|cat:$analyse.directory)|cat:'/')|cat:$file}
 							<li class="filelist"><a href="{$link}">{$file}</a> </li>
 							{$nb_files = $nb_files + 1}
 						{/if}

ui/nG6/pi1/analyzes/MothurOTUAnalysis.tpl

@@ -249,9 +249,9 @@ along with this program.  If not, see <http://www.gnu.org/licenses/>.
 		<div class="tab-pane fade" id="downloads">
 			{block name=download}
 				{assign var="nb_files" value=0}
-				{$dir=$data_folder|cat:'/'|cat:$analyse.directory}
+				{$dir=$data_folder|cat:$analyse.directory}
 				{foreach $dir|scandir as $file}
-					{assign var="link" value=(('fileadmin'|cat:'/'|cat:$analyse.directory)|cat:'/')|cat:$file}
+					{assign var="link" value=(('fileadmin'|cat:$analyse.directory)|cat:'/')|cat:$file}
 					{if $file != "." and $file != "" and $file != ".." and ($file|substr:-strlen(".png")) != ".png" and !is_dir($link)}
 						{$nb_files = $nb_files + 1}
 					{/if}
@@ -263,7 +263,7 @@ along with this program.  If not, see <http://www.gnu.org/licenses/>.
 				{else}
 					<ul>
 						{foreach $dir|scandir as $file}
-						{assign var="link" value=(('fileadmin'|cat:'/'|cat:$analyse.directory)|cat:'/')|cat:$file}
+						{assign var="link" value=(('fileadmin'|cat:$analyse.directory)|cat:'/')|cat:$file}
 						{if $file != "." and $file != "" and $file != ".." and ($file|substr:-strlen(".png")) != ".png" and !is_dir($link)}
 							<li class="filelist"><a href="{$link}">{$file}</a> </li>
 						{/if}

ui/nG6/pi1/analyzes/RunAssembly.tpl

@@ -391,11 +391,11 @@ along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
 		<div class="tab-pane fade" id="downloads">
 			<ul>
-				{$dir=$data_folder|cat:'/'|cat:$analyse.directory}
+				{$dir=$data_folder|cat:$analyse.directory}
 				{assign var="nb_files" value=0}
 				{foreach $dir|scandir as $file}
 				{if $file != "." and $file != "" and $file != ".." and ($file|substr:-strlen(".png")) != ".png"}
-					{$link=(('fileadmin'|cat:'/'|cat:$analyse.directory)|cat:'/')|cat:$file}
+					{$link=(('fileadmin'|cat:$analyse.directory)|cat:'/')|cat:$file}
 					<li class="filelist"><a href="{$link}">{$file}</a> </li>
 					{$nb_files = $nb_files + 1}
 				{/if}

ui/nG6/pi1/run_view.tpl

@@ -120,12 +120,12 @@ along with this program.  If not, see <http://www.gnu.org/licenses/>.
 	 		</div>
 
 	 		<div class="tab-pane fade" id="downloads">
-	 			{$dir=$data_folder|cat:'/'|cat:$runs[key($runs)].directory}
+	 			{$dir=$data_folder|cat:$runs[key($runs)].directory}
 				{assign var="nb_files" value=0}
 				<ul>
 				{foreach $dir|scandir as $file}
 					{if $file != "." and $file !="" and $file != ".." and ($file|substr:-strlen(".png")) != ".png"}
-						{$link=(('fileadmin'|cat:'/'|cat:$runs[key($runs)].directory)|cat:'/')|cat:$file}
+						{$link=(('fileadmin'|cat:$runs[key($runs)].directory)|cat:'/')|cat:$file}
 						<li class="filelist"><a href="{$link}">{$file}</a> <br /></li>
 						{$nb_files = $nb_files + 1}
 					{/if}