make some stuff looks better

bin/jflow_cli.py

@@ -142,9 +142,14 @@ if __name__ == '__main__':
         else:
             workflows = wfmanager.get_workflows()
             if len(workflows) > 0:
+                workflows_by_id, wfids = {}, []
+                # first sort workflow by ID
+                for workflow in workflows:
+                    wfids.append(workflow.id)
+                    workflows_by_id[workflow.id] = workflow
                 status = "ID\tNAME\tSTATUS\tELAPSED_TIME\tSTART_TIME\tEND_TIME\n"
-                for i, workflow in enumerate(workflows):
-                    status += workflow.get_status_under_text_format()
+                for i, wfid in enumerate(sorted(wfids)):
+                    status += workflows_by_id[wfid].get_status_under_text_format()
                     if i<len(workflows)-1: status += "\n"
             else: status = "no workflow available"
             print status

bin/jflow_server.py

@@ -23,7 +23,6 @@ import sys
 import datetime
 from functools import wraps
 import time
-import datetime
 import os
 import argparse
 import logging

src/jflow/component.py

@@ -24,7 +24,7 @@ import types
 from jflow.workflows_manager import WorkflowsManager
 from jflow.config_reader import JFlowConfigReader
 from jflow.dataset import ArrayList
-from jflow.utils import which
+from jflow.utils import which, display_error_message
 from jflow.parameter import *
 from weaver.util import parse_string_list
 
@@ -308,13 +308,11 @@ class Component(object):
         elif exec_path is None and os.path.isfile(os.path.join(os.path.dirname(inspect.getfile(self.__class__)), "bin", software)):
             exec_path = os.path.join(os.path.dirname(inspect.getfile(self.__class__)), "bin", software)
         elif exec_path is None and which(software) == None:
-            sys.stderr.write("Error: '" + software + "' path connot be retrieved either in the PATH and in the application.properties file!\n")
-            sys.exit(1)
+            display_error_message("'" + software + "' path connot be retrieved either in the PATH and in the application.properties file!")
         elif exec_path is None and which(software) != None: 
             exec_path = software
         elif exec_path != None and not os.path.isfile(exec_path):
-            sys.stderr.write("Error: '" + exec_path + "' set for '" + software + "' does not exists, please provide a valid path!\n")
-            sys.exit(1)
+            display_error_message("'" + exec_path + "' set for '" + software + "' does not exists, please provide a valid path!")
         return exec_path
     
     def get_nameid(self):

src/jflow/config_reader.py

@@ -21,7 +21,7 @@ import inspect
 
 from ConfigParser import ConfigParser, NoOptionError
 
-from jflow.utils import which
+from jflow.utils import which, display_error_message
 
 
 class JFlowConfigReader(object):
@@ -70,8 +70,7 @@ class JFlowConfigReader(object):
             exec_path = None
         if exec_path is None: exec_path = "makeflow"
         if which(exec_path) == None:
-            sys.stderr.write("Error: 'makeflow' path connot be retrieved either in the PATH and in the application.properties file!\n")
-            sys.exit(1)
+            display_error_message("'makeflow' path connot be retrieved either in the PATH and in the application.properties file!")
         return exec_path
 
     def get_date_format(self):

src/jflow/parameter.py

@@ -30,7 +30,7 @@ import copy as _copy
 from urlparse import urlparse
 
 from jflow.config_reader import JFlowConfigReader
-from jflow.utils import get_octet_string_representation, get_nb_octet
+from jflow.utils import get_octet_string_representation, get_nb_octet, display_error_message
 
 # import custom types and custom formats
 from workflows.types import *
@@ -745,11 +745,9 @@ class AbstractInputFile(AbstractIOFile):
             try: 
                 eval(self.file_format)(ifile)
             except jflow.InvalidFormatError as e:
-                sys.stderr.write(str(e)+"\n")
-                sys.exit(1)
+                display_error_message(str(e))
         else:
-            sys.stderr.write("Error: Invalid file format '" + self.file_format + "'!\n")
-            sys.exit(1)
+            display_error_message("Invalid file format '" + self.file_format + "'!")
 
 class AbstractOutputFile(AbstractIOFile):
     """

src/jflow/utils.py

@@ -16,6 +16,7 @@
 #
 
 import re
+import sys
 import smtplib
 import socket
 import math
@@ -27,6 +28,14 @@ except:
     DNS = None
     class ServerError(Exception): pass
 
+def display_error_message(msg):
+    sys.stderr.write("\033[91mError: "+msg+"\n\033[0m")
+    sys.exit(1)
+
+def display_info_message(msg, with_exit=False):
+    sys.stderr.write("\033[93mInfo: "+msg+"\n\033[0m")
+    if with_exit: sys.exit(1)
+
 def which(program):
     """
     Return if the asked program exist in the user path

src/jflow/workflow.py

@@ -27,6 +27,7 @@ import time
 import threading
 import types
 import logging
+import datetime
 
 from logging import FileHandler
 from ConfigParser import ConfigParser, NoOptionError
@@ -323,6 +324,7 @@ class Workflow(threading.Thread):
         if self.start_time and self.end_time: elapsed_time = str(self.end_time-self.start_time)
         elif self.start_time: elapsed_time = str(time.time()-self.start_time)
         else: elapsed_time = "-"
+        elapsed_time = "-" if elapsed_time == "-" else str(datetime.timedelta(seconds=int(str(elapsed_time).split(".")[0])))
         if self.end_time: end_time = time.asctime(time.localtime(self.end_time))
         else: end_time = "-"
         if detailed:
@@ -388,8 +390,20 @@ class Workflow(threading.Thread):
             if html: return pretty_str.replace("\n", "<br />")
             else: return pretty_str
         else:
-            return utils.get_nb_string(self.id) + "\t" + self.name + "\t" + self.get_status() + \
-                "\t" + elapsed_time + "\t" + start_time + "\t" + end_time
+            pretty_str = utils.get_nb_string(self.id) + "\t" + self.name + "\t"
+            if self.get_status() == self.STATUS_STARTED:
+                pretty_str += "\033[94m"
+            elif self.get_status() == self.STATUS_COMPLETED:
+                pretty_str += "\033[92m"
+            elif self.get_status() == self.STATUS_FAILED:
+                pretty_str += "\033[91m"
+            elif self.get_status() == self.STATUS_ABORTED:
+                pretty_str += "\033[91m"
+            elif self.get_status() == self.STATUS_RESETED:
+                pretty_str += "\033[3m"
+            pretty_str += self.get_status() + "\033[0m"
+            pretty_str += "\t" + elapsed_time + "\t" + start_time + "\t" + end_time
+            return pretty_str
     
     def get_errors(self):
         error = {
@@ -523,13 +537,11 @@ class Workflow(threading.Thread):
         elif exec_path is None and os.path.isfile(os.path.join(os.path.dirname(inspect.getfile(self.__class__)), "bin", software)):
             exec_path = os.path.join(os.path.dirname(inspect.getfile(self.__class__)), "bin", software)
         elif exec_path is None and utils.which(software) == None:
-            sys.stderr.write("Error: '" + software + "' path connot be retrieved either in the PATH and in the application.properties file!\n")
-            sys.exit(1)
+            utils.display_error_message("'" + software + "' path connot be retrieved either in the PATH and in the application.properties file!")
         elif exec_path is None and utils.which(software) != None: 
             exec_path = software
         elif exec_path != None and not os.path.isfile(exec_path):
-            sys.stderr.write("Error: '" + exec_path + "' set for '" + software + "' does not exists, please provide a valid path!\n")
-            sys.exit(1)
+            utils.display_error_message("'" + exec_path + "' set for '" + software + "' does not exists, please provide a valid path!")
         return exec_path
     
     def add_component(self, component_name, args=[], kwargs={}, component_prefix="default"):
@@ -765,8 +777,7 @@ class Workflow(threading.Thread):
                 cpt.reset()
                 found = True
         if not found:
-            sys.stderr.write("Impossible to reset component '" + component_name + "'! This one is not part of the workflow\n")
-            sys.exit(1)
+            utils.display_error_message("Impossible to reset component '" + component_name + "'! This one is not part of the workflow")
         self.reseted_components.append(component_name)
         self.status = self.STATUS_RESETED
         self._serialize()

src/jflow/workflows_manager.py

@@ -154,8 +154,7 @@ class WorkflowsManager(object):
             workflow = pickle.load(workflow_dump)
             workflow_dump.close()
         else:
-            sys.stderr.write("Error: Workflow with id " + str(rworkflow_id) + " cannot be retrived!\n")
-            sys.exit(1)
+            utils.display_error_message("Workflow with id " + str(rworkflow_id) + " cannot be retrived")
         return workflow
 
     def get_workflow_directory(self, wname, wid):

src/js/jflow-wfform.js

@@ -581,7 +581,11 @@ jQuery.validator.addMethod("mparam", function(value, element, params) {
 			'{{else param.type.indexOf("inputfile") === 0}}',
 			'  <div class="input-group">',
 			'    <div class="input-group-btn">',
+			'      {{if param.action == "append"}}',
+			'      <button type="button" style="padding-top:23px; padding-bottom:22px;" class="btn btn-default dropdown-toggle" data-toggle="dropdown">',
+			'      {{else}}',
 			'      <button type="button" class="btn btn-default dropdown-toggle" data-toggle="dropdown">',
+			'      {{/if}}',
 			'        <span id="inputfile_${param.name}">server file</span>',
 			'        <span class="caret"></span>',
 			'      </button>',
@@ -600,7 +604,11 @@ jQuery.validator.addMethod("mparam", function(value, element, params) {
 			'    <input id="${param.name}" name="${param.name}" class="form-control ${param.group}" type="text" value="${param.default}">',
 			'    {{/if}}',
 			'    <span class="input-group-btn">',
+			'      {{if param.action == "append"}}',
+			'      <button id="urlfile_btn_${param.name}" style="display: none; padding-top:23px; padding-bottom:22px;" class="btn btn-default" type="button"><span class="glyphicon glyphicon-folder-open"></span></button>',
+			'      {{else}}',
 			'      <button id="urlfile_btn_${param.name}" style="display: none;" class="btn btn-default" type="button"><span class="glyphicon glyphicon-folder-open"></span></button>',
+			'      {{/if}}',
 			'    </span>',
 			'  </div>',
 			// if param is a browsefile