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Commit 79ab67bb authored by Penom Nom's avatar Penom Nom
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application.properties
View file @ 79ab67bb
......@@ -63,12 +63,9 @@ work_directory = <path>/work
# accessible by all cluster nodes
tmp_directory = <path>/tmp
[local]
# This is a space separated list of workflows Class names that will not be available
# for adding a run
runwf_filter = AddAnalysis AddProject AddFiles RADseq DownloadArchive DownloadSymlink DownloadURL
[ui]
# This must be an absolute path of a directory mounted and accessible by the server
server_directory = /work/
user_base_directory = /work/
# where could be find binaries
[softwares]
......@@ -108,7 +105,7 @@ server_directory = /work/
#junction_saturation.py = /usr/local/bin/junction_saturation.py
#RPKM_saturation.py = /usr/local/bin/scripts/RPKM_saturation.py
#junction_annotation.py = /usr/local/bin/junction_annotation.py
#NormalizeFasta.jar = /home/inabihoudin/save/src/picard-tools-1.113/NormalizeFasta.jar
#NormalizeFasta.jar = /usr/local/bin/NormalizeFasta.jar
# radseq
......@@ -139,6 +136,25 @@ server_directory = /work/
#AlignmentStats.batch_options = -q unlimitq
#ContaminationSearch.batch_options = -q unlimitq
# Set workflows group
[workflows]
# download workflows
DownloadArchive.group = download
DownloadSymlink.group = download
DownloadURL.group = download
# run workflows
AddRun.group = addrun
GeneDiversity.group = addrun
IlluminaDiversityQC.group = addrun
IlluminaMatePair.group = addrun
IlluminaQualityCheck.group = addrun
RnaSeqQualityCheck.group = addrun
Methylseq.group = addrun
PacBioQualityCheck.group = addrun
PhiXCheck.group = addrun
R454QualityCheck.group = addrun
[resources]
typo3_src = http://prdownloads.sourceforge.net/typo3/typo3_src+dummy-4.7.12.zip
#phix_bwa = /bank/bwadb/phi.fa
......
src/jflow/config_reader.py
View file @ 79ab67bb
......@@ -119,4 +119,11 @@ class JFlowConfigReader(object):
return self.reader.get("components", component_class+".batch_options")
except:
return ""
\ No newline at end of file
def get_workflow_group(self, workflow_class):
try:
return self.reader.get("workflows", workflow_class+".group")
except:
return ""
\ No newline at end of file
src/jflow/server.py
View file @ 79ab67bb
......@@ -36,7 +36,6 @@ from workflows.types import *
from . import utils
from cctools.util import time_format
from .utils import get_octet_string_representation
from ng6.config_reader import NG6ConfigReader
# function in charge to upload large files
class UploadFieldStorage(cgi.FieldStorage):
......@@ -118,7 +117,6 @@ class JFlowServer (object):
# Create a workflow manager to get access to our workflows
self.wfmanager = WorkflowsManager()
self.jflow_config_reader = JFlowConfigReader()
self.ng6_config_reader = NG6ConfigReader()
@staticmethod
def quickstart(server_class, config=None, daemon=False):
......@@ -224,7 +222,12 @@ class JFlowServer (object):
@jsonify
def get_available_workflows(self, **kwargs):
workflows = []
wf_instances, wf_methodes = self.wfmanager.get_available_workflows()
filter_groups = None
select = False
if 'filter_groups' in kwargs : filter_groups = kwargs['filter_groups'].split(',')
if 'select' in kwargs : select = kwargs['select'] in ['True', 'true', '1', 1]
wf_instances, wf_methodes = self.wfmanager.get_available_workflows(filter_groups = filter_groups , select = select)
for instance in wf_instances:
parameters, parameters_per_groups, groups = [], {}, ["default"]
for param in instance.get_parameters():
......@@ -498,11 +501,6 @@ class JFlowServer (object):
on_web_outputs[cpt_name][outf] = self._webify_outputs(JFlowServer.JFLOW_WDATA, on_disk_outputs[cpt_name][outf])
return on_web_outputs
@cherrypy.expose
@jsonify
def get_workflow_filters(self, **kwargs):
return self.ng6_config_reader.get_workflow_filters()
@cherrypy.expose
@jsonify
def validate_field(self, **kwargs):
......
src/jflow/workflow.py
View file @ 79ab67bb
......@@ -35,7 +35,6 @@ from inspect import getcallargs
from datetime import date as ddate
import jflow
import workflows
import jflow.utils as utils
from jflow.utils import validate_email
from pygraph.classes.digraph import digraph
......@@ -90,6 +89,7 @@ class Workflow(threading.Thread):
STDERR_FILE_NAME = "wf_stderr.txt"
WORKING = ".working"
OLD_EXTENSION = ".old"
DEFAULT_GROUP = "default"
STATUS_STARTED = "started"
STATUS_COMPLETED = "completed"
......@@ -140,6 +140,7 @@ class Workflow(threading.Thread):
self.id = id
self.name = self.get_name()
self.description = self.get_description()
self.__group = self.jflow_config_reader.get_workflow_group(self.__class__.__name__) or self.DEFAULT_GROUP
# define the parameters
self.params_order = []
......@@ -159,6 +160,8 @@ class Workflow(threading.Thread):
self.internal_components = self._import_internal_components()
self.external_components = self._import_external_components()
def get_workflow_group(self):
return self.__group
def add_input_directory(self, name, help, default=None, required=False, flag=None,
group="default", display_name=None, get_files_fn=None, add_to=None):
......@@ -1072,7 +1075,7 @@ class Workflow(threading.Thread):
except Exception as e:
self._log("Component <{0}> cannot be loaded: {1}".format(modname, e), level="debug", traceback=traceback.format_exc(chain=False))
# finally import workflows shared packages
workflows_dir = os.path.dirname(workflows.__file__)
workflows_dir = os.path.dirname(os.path.dirname(inspect.getfile(self.__class__)))
for importer, modname, ispkg in pkgutil.iter_modules([os.path.join(workflows_dir, "components")], "workflows.components."):
try:
m = __import__(modname)
......@@ -1087,7 +1090,7 @@ class Workflow(threading.Thread):
pckge = {}
parsers = []
# get exparsers
extparsers_dir = os.path.join( os.path.dirname(workflows.__file__), 'extparsers' )
extparsers_dir = os.path.join( os.path.dirname(os.path.dirname(inspect.getfile(self.__class__))), 'extparsers' )
for importer, modname, ispkg in pkgutil.iter_modules([extparsers_dir], "workflows.extparsers.") :
try :
m = __import__(modname)
......@@ -1121,65 +1124,4 @@ class Workflow(threading.Thread):
# Import symbols from module into global namespace, which we store as
# an attribute for later use (i.e. during compile)
for symbol in symbols:
self.globals[symbol] = getattr(m, symbol)
def get_classname(self):
return self.__class__.__name__
class ComponentWorkflow(Workflow):
"""
A workflow with a single component
"""
def __init__(self, comp_object, *args, **kwargs):
self._comp_object = comp_object
Workflow.__init__(self, *args, **kwargs)
def get_description(self):
return "%sWorkflow"%self._comp_object.__name__
def get_name(self):
return self._comp_object.__name__.lower()
def process(self):
argspec = inspect.getargspec(self._comp_object.define_parameters)
args = argspec[0][1:]
kwargs = {}
for param in args:
for attribute_value in self.__dict__.values():
if (issubclass(attribute_value.__class__, AbstractParameter)) and param == attribute_value.name:
kwargs[param] = attribute_value
self.add_component(self._comp_object.__name__, [], kwargs)
def get_classname(self):
return self._comp_object.__name__
def define_parameters(self, function="process"):
argspec = inspect.getargspec(self._comp_object.define_parameters)
args = argspec[0][1:]
varargs = argspec[1] or []
keywords = argspec[2] or {}
defaults = argspec[3]
if defaults :
for i,e in enumerate(defaults) :
args[-1*(i+1)] = e
for i,e in enumerate(args) :
if defaults and e not in defaults:
args[i] = None
args.extend( varargs )
try :
self._comp_object.__dict__['define_parameters'](self, *args , **keywords)
except AttributeError as e: pass
def _serialize(self):
self.dump_path = os.path.join(self.directory, self.DUMP_FILE_NAME)
workflow_dump = open(self.dump_path, "wb")
pickle.dump(self, workflow_dump)
workflow_dump.close()
def get_comp_object(self):
return self._comp_object
\ No newline at end of file
self.globals[symbol] = getattr(m, symbol)
\ No newline at end of file
src/jflow/workflows_manager.py
View file @ 79ab67bb
......@@ -63,12 +63,15 @@ class WorkflowsManager(object):
workflows_ids = [wf.id for wf in workflows]
concurrent.exec_on_shared( dump_func, self.dump_file, self.config_reader.get_tmp_directory(), 1, 200, {"action": "Add wf", "wf_id": workflows_ids} )
def get_available_workflows(self, function="process"):
def get_available_workflows(self, function="process", filter_groups = [], select = False ):
if function.__class__.__name__ == "str":
functions = [function]
else:
functions = set(function)
wf_instances, wf_methodes = [], []
if isinstance(filter_groups, str): filter_groups = [filter_groups]
# Load all modules within the workflow module
for importer, modname, ispkg in pkgutil.iter_modules(workflows.__path__, workflows.__name__ + "."):
__import__(modname)
......@@ -82,8 +85,14 @@ class WorkflowsManager(object):
if ifunction[0] == function:
# try to build the workflow
try:
wf_instances.append(obj(function=function))
wf_methodes.append(function)
select_workflow = True
inst = obj(function=function)
if filter_groups :
select_workflow = (inst.get_workflow_group() in filter_groups) == select
if select_workflow:
wf_instances.append(inst)
wf_methodes.append(function)
except: pass
return [wf_instances, wf_methodes]
......
src/ng6/config_reader.py
View file @ 79ab67bb
......@@ -136,13 +136,13 @@ class NG6ConfigReader(object):
return []
def get_server_directory(self):
def get_user_base_directory(self):
"""
Return an absolute path of a directory mounted on the web server
@return: string
"""
try:
return self.reader.get('local', 'server_directory')
return self.reader.get('ui', 'user_base_directory')
except :
raise Error("Could not retrieve server directory !")
......
src/ng6/ng6workflow.py
View file @ 79ab67bb
......@@ -24,7 +24,7 @@ import datetime
import argparse
import xml.etree.ElementTree as ET
from jflow.workflow import Workflow, ComponentWorkflow
from jflow.workflow import Workflow
from jflow.utils import display_error_message
from jflow.parameter import *
......@@ -126,63 +126,6 @@ class DownloadWorkflow(BasicNG6Workflow):
self.add_parameter_list('data_id', 'Ids of a run from which rawdata will be retrieved', type = 'existingrun')
self.add_parameter_list('run_id', 'Ids of run from which all data will be retrieved', type = 'existingrun')
self.add_parameter_list('analysis_id', 'Ids of analysis to retrieve', type = 'existinganalysis')
class AnalysisWorkflow(BasicNG6Workflow, ComponentWorkflow):
"""
A workflow with a single analysis
"""
def __init__(self, comp_object, args={}, id=None, function= "process"):
self._comp_object = comp_object
ComponentWorkflow.__init__(self, comp_object, args, id, function)
BasicNG6Workflow.__init__(self, args, id, function)
self.add_parameter("project_id", "The project id the analysis belongs to", type = 'int', required = True)
self.add_parameter("run_id", "The run id the analysis belongs to", type = 'int', required = True)
self.add_parameter("parent_analysis", "The id of an analysis to be used as a parent analysis", type= 'int')
self.add_exclusion_rule( "project_id", "run_id" )
def process(self):
self.project = None
self.runobj = None
# Check if user provided a project or a run
if self.project_id :
self.project = Project.get_from_id(self.project_id)
self.metadata.append("project_id="+str(self.project_id))
# if user is not allowed to add data on project (is not admin)
if self.project is not None and not self.project.is_admin(self.admin_login):
display_error_message( "The user login '" + self.admin_login + "' is not allowed to add data on project '" + self.project.name + "'.\n" )
elif self.run_id :
self.runobj = Run.get_from_id(self.run_id)
self.metadata.append("run_id="+str(self.run_id))
addto = "project" if self.project else "run"
parent = None
if self.parent_analysis :
parent = Analysis.get_from_id(self.parent_analysis)
if self.project :
analyses_ids = [ o.id for o in self.project.get_analysis()]
else :
analyses_ids = [ o.id for o in self.runobj.get_analysis()]
if parent.id not in analyses_ids :
display_error_message("The parent analysis associated with id '%s' does not belong to the %s id '%s' " % (parent.id, addto, self.project_id or self.run_id) )
argspec = inspect.getargspec(self._comp_object.define_parameters)
args = argspec[0][1:]
kwargs = {}
for param in args:
for attribute_value in self.__dict__.values():
if (issubclass(attribute_value.__class__, AbstractParameter)) and param == attribute_value.name:
kwargs[param] = attribute_value
self.add_component(self._comp_object.__name__, [], kwargs, addto=addto, parent = parent)
def post_process(self):
if self.runobj:
self.runobj.sync()
elif self.project:
self.project.sync()
class NG6Workflow (BasicNG6Workflow):
......
ui/nG6/res/js/jflow.min.js
View file @ 79ab67bb
......@@ -182,7 +182,7 @@ function(){function a(a){this._value=a}function b(a,b,c,d){var e,f,g=Math.pow(10
//activewf
!function(t){"use strict";var e=function(e,a){this.$element=t(e),this.options=t.extend({},t.fn.activewf.defaults,a),""==this.options.serverURL&&(this.options.serverURL=t.fn.activewf.defaults.serverURL),this.reload()};e.prototype.reload=function(){var e=this,a=['<div class="container-fluid"><div class="row"><div class="col-md-1 col-md-offset-2"><div class="inline floatingBarsG">','<div class="blockG" id="rotateG_01"></div>','<div class="blockG" id="rotateG_02"></div>','<div class="blockG" id="rotateG_03"></div>','<div class="blockG" id="rotateG_04"></div>','<div class="blockG" id="rotateG_05"></div>','<div class="blockG" id="rotateG_06"></div>','<div class="blockG" id="rotateG_07"></div>','<div class="blockG" id="rotateG_08"></div>','</div></div> <div class="col-md-8">Please wait until modul is being loaded!</div></div></div>'].join("\n"),s=this.options.serverURL+"/get_workflows_status?";this.options.metadataFilter.length>0&&(s+="metadata_filter="+this.options.metadataFilter.join(",")+"&"),s+="callback=?",e.$element.html(a),t.ajax({url:s,dataType:"json",timeout:2e4,error:function(){var t=['<div class="alert alert-danger" role="alert">',"<strong>Error!</strong>","Jflow failed to connect to the specified server <strong>"+e.options.serverURL+"</strong>","</div>"].join("\n");e.$element.html(t)},success:function(a){var s={},l=new Array,i=new Array;for(var o in a)s[a[o].id]=a[o],l.push(a[o].id);l.sort(function(t,e){return e-t});for(var o in l)i.push(s[l[o]]);e.$element.html(""),t.tmpl(e.options.template,{workflows:i}).appendTo(e.$element),t("[id^=activewf_btn_]").click(function(){var a=t(this).attr("id").split("activewf_btn_")[1];e.$element.trigger("select.activewf",s[a])}),t("[id^=activewf_refresh_]").click(function(){e.reload()}),t("[id^=activewf_delete_]").click(function(){var a=t(this).attr("id").split("activewf_delete_")[1];t.ajax({url:e.options.serverURL+"/delete_workflow?workflow_id="+a+"&callback=?",dataType:"json",timeout:2e4,error:function(){var t=['<div class="alert alert-danger" role="alert">',"<strong>Error!</strong>","Jflow failed to connect to the specified server <strong>"+e.options.serverURL+"</strong>","</div>"].join("\n");e.$element.html(t)},success:function(){e.reload()}})})}})};t.fn.activewf;t.fn.activewf=function(a){return this.each(function(){var s=t(this),l=s.data("activewf"),i=t.extend({},t.fn.activewf.defaults,"object"==typeof a&&a),o="string"==typeof a?a:null;l||s.data("activewf",l=new e(this,i)),o&&l[o]()})},t.fn.activewf.defaults={serverURL:"http://localhost:8080",template:['<table class="table table-striped table-striped">',"<thead>","<tr>","<th>ID<th>","<th>Name</th>","<th>Status</th>","<th>Start time</th>","<th>End time</th>","<th>Actions</th>","</tr>","</thead>","{{each(index, workflow) workflows}}","<tr>",'<td><a id="activewf_btn_${workflow.id}" href="#">${workflow.id}</a><td>',"<td>${workflow.name}</td>",'{{if workflow.status == "completed"}}','<td> <span class="label label-success">${workflow.status}</span></td>','{{else workflow.status == "failed"}}','<td> <span class="label label-danger">${workflow.status}</span></td>','{{else workflow.status == "aborted"}}','<td> <span class="label label-danger">${workflow.status}</span></td>','{{else workflow.status == "started"}}','<td> <span class="label label-info">${workflow.status}</span></td>','{{else workflow.status == "reseted"}}','<td> <span class="label label-default">${workflow.status}</span></td>',"{{else}}","<td>${workflow.status}</td>","{{/if}}","<td>${workflow.start_time}</td>","<td>${workflow.end_time}</td>","<td>",' <div class="btn-group">',' {{if workflow.status == "started"}}',' <button type="button" id="activewf_refresh_${workflow.id}" class="btn btn-default btn-xs" aria-label="Left Align">'," {{else}}",' <button type="button" id="activewf_refresh_${workflow.id}" disabled class="btn btn-default btn-xs" aria-label="Left Align">'," {{/if}}",' <span class="glyphicon glyphicon-refresh"></span>'," </button>",' {{if workflow.status == "started"}}',' <button type="button" id="activewf_delete_${workflow.id}" disabled class="btn btn-default btn-xs" aria-label="Left Align">'," {{else}}",' <button type="button" id="activewf_delete_${workflow.id}" class="btn btn-default btn-xs" aria-label="Left Align">'," {{/if}}",' <span class="glyphicon glyphicon-remove"></span>'," </button>"," </div>","</td>","</tr>","{{/each}}","</table>"].join("\n"),metadataFilter:[]},t.fn.activewf.Constructor=e}(window.jQuery);
//availablewf
!function(t){"use strict";var e=function(e,a){this.$element=t(e),this.options=t.extend({},t.fn.availablewf.defaults,a),""==this.options.serverURL&&(this.options.serverURL=t.fn.availablewf.defaults.serverURL),this.reload()};e.prototype.reload=function(){var e=this,a=['<div class="container-fluid"><div class="row"><div class="col-md-1 col-md-offset-2"><div class="inline floatingBarsG">','<div class="blockG" id="rotateG_01"></div>','<div class="blockG" id="rotateG_02"></div>','<div class="blockG" id="rotateG_03"></div>','<div class="blockG" id="rotateG_04"></div>','<div class="blockG" id="rotateG_05"></div>','<div class="blockG" id="rotateG_06"></div>','<div class="blockG" id="rotateG_07"></div>','<div class="blockG" id="rotateG_08"></div>','</div></div> <div class="col-md-8">Please wait until modul is being loaded!</div></div></div>'].join("\n");e.$element.html(a),t.ajax({url:this.options.serverURL+"/get_available_workflows?callback=?",dataType:"json",timeout:2e4,error:function(){var t=['<div class="alert alert-danger" role="alert">',"<strong>Error!</strong>","Jflow failed to connect to the specified server <strong>"+e.options.serverURL+"</strong>","</div>"].join("\n");e.$element.html(t)},success:function(a){var l={};for(var i in a)l[a[i]["class"]]=a[i];e.$element.html(""),t.tmpl(e.options.template,{workflows:a,filters:e.options.filters}).appendTo(e.$element),t("[id^=availablewf_btn_]").click(function(){var a=t(this).attr("id").split("availablewf_btn_")[1];e.$element.trigger("select.availablewf",l[a])})}})};t.fn.availablewf;t.fn.availablewf=function(a){return this.each(function(){var l=t(this),i=l.data("availablewf"),s=t.extend({},t.fn.availablewf.defaults,"object"==typeof a&&a),o="string"==typeof a?a:null;i||l.data("availablewf",i=new e(this,s)),o&&i[o]()})},t.fn.availablewf.defaults={serverURL:"http://localhost:8080",template:['<table class="table table-striped table-striped">',"<thead>","<tr>","<th>Name</th>","<th>Description</th>","</tr>","</thead>","{{each(index, workflow) workflows}}"," {{if filters.indexOf(workflow.class) == -1 }}"," <tr>",' <td><a id="availablewf_btn_${workflow.class}" href="#">${workflow.name}</a></td>'," <td>${workflow.help}</td>"," </tr>"," {{/if}}","{{/each}}","</dl>"].join("\n"),filters:[]},t.fn.availablewf.Constructor=e}(window.jQuery);
!function(t){"use strict";var e=function(e,i){this.$element=t(e),this.options=t.extend({},t.fn.availablewf.defaults,i),""==this.options.serverURL&&(this.options.serverURL=t.fn.availablewf.defaults.serverURL),this.reload()};e.prototype.reload=function(){var e=this,i=['<div class="container-fluid"><div class="row"><div class="col-md-1 col-md-offset-2"><div class="inline floatingBarsG">','<div class="blockG" id="rotateG_01"></div>','<div class="blockG" id="rotateG_02"></div>','<div class="blockG" id="rotateG_03"></div>','<div class="blockG" id="rotateG_04"></div>','<div class="blockG" id="rotateG_05"></div>','<div class="blockG" id="rotateG_06"></div>','<div class="blockG" id="rotateG_07"></div>','<div class="blockG" id="rotateG_08"></div>','</div></div> <div class="col-md-8">Please wait until modul is being loaded!</div></div></div>'].join("\n");e.$element.html(i),t.ajax({url:this.options.serverURL+"/get_available_workflows?filter_groups="+this.options.filter_groups.join(",")+"&select="+this.options.select+"&callback=?",dataType:"json",timeout:2e4,error:function(t,i,l){var a=['<div class="alert alert-danger" role="alert">',"<strong>Error!</strong>","Jflow failed to connect to the specified server <strong>"+e.options.serverURL+"</strong>","</div>"].join("\n");e.$element.html(a)},success:function(i){var l={};for(var a in i)l[i[a]["class"]]=i[a];e.$element.html(""),t.tmpl(e.options.template,{workflows:i,filters:e.options.filters}).appendTo(e.$element),t("[id^=availablewf_btn_]").click(function(){var i=t(this).attr("id").split("availablewf_btn_")[1];e.$element.trigger("select.availablewf",l[i])})}})};t.fn.availablewf;t.fn.availablewf=function(i){return this.each(function(){var l=t(this),a=l.data("availablewf"),s=t.extend({},t.fn.availablewf.defaults,"object"==typeof i&&i),o="string"==typeof i?i:null;a||l.data("availablewf",a=new e(this,s)),o&&a[o]()})},t.fn.availablewf.defaults={serverURL:"http://localhost:8080",template:['<table class="table table-striped table-striped">',"<thead>","<tr>","<th>Name</th>","<th>Description</th>","</tr>","</thead>","{{each(index, workflow) workflows}}"," {{if filters.indexOf(workflow.class) == -1 }}"," <tr>",' <td><a id="availablewf_btn_${workflow.class}" href="#">${workflow.name}</a></td>'," <td>${workflow.help}</td>"," </tr>"," {{/if}}","{{/each}}","</dl>"].join("\n"),filters:[],filter_groups:[],select:!1},t.fn.availablewf.Constructor=e}(window.jQuery);
//wfoutputs
!function(t){"use strict";var o=function(o,e){this.$element=t(o),this.options=t.extend({},t.fn.wfoutputs.defaults,e),""==this.options.serverURL&&(this.options.serverURL=t.fn.wfoutputs.defaults.serverURL)};o.prototype.reload=function(){var o=this,e="",l=['<div class="container-fluid"><div class="row"><div class="col-md-1 col-md-offset-2"><div class="inline floatingBarsG">','<div class="blockG" id="rotateG_01"></div>','<div class="blockG" id="rotateG_02"></div>','<div class="blockG" id="rotateG_03"></div>','<div class="blockG" id="rotateG_04"></div>','<div class="blockG" id="rotateG_05"></div>','<div class="blockG" id="rotateG_06"></div>','<div class="blockG" id="rotateG_07"></div>','<div class="blockG" id="rotateG_08"></div>','</div></div> <div class="col-md-8">Please wait until modul is being loaded!</div></div></div>'].join("\n");o.$element.html(l),this.options.workflowID&&(e="workflow_id="+this.options.workflowID+"&"),t.ajax({url:this.options.serverURL+"/get_workflow_outputs?"+e+"callback=?",dataType:"json",timeout:2e4,error:function(){var t=['<div class="alert alert-danger" role="alert">',"<strong>Error!</strong>","Jflow failed to connect to the specified server <strong>"+o.options.serverURL+"</strong>","</div>"].join("\n");o.$element.html(t)},success:function(e){o.$element.html(""),t.tmpl(o.options.template,{data:e}).appendTo(o.$element);var l=new Array;t.each(e,function(e,s){t.each(s,function(e,s){-1==t.inArray(s.extension,l)&&-1==t.inArray(s.extension,o.options.logFile)&&l.push(s.extension)})}),t.each(l,function(o,e){t("#jflow_file_type").append(t("<option>",{text:e}))}),t(".output-file").each(function(){var e=t(this).find("A").text().substr(t(this).find("A").text().lastIndexOf("."));-1==t.inArray(e,o.options.logFile)?t(this).addClass("output"):(t(this).addClass("log"),t(this).hide())}),t("#jflow_log_on").click(function(){t(".log").each(function(){t(this).fadeIn(500)}),t("#jflow_log_on").hide(),t("#jflow_log_off").show()}),t("#jflow_log_off").click(function(){t(".log").each(function(){t(this).fadeOut(500)}),t("#jflow_log_off").hide(),t("#jflow_log_on").show()}),t("#jflow_file_type").on("change",function(){var o=t("#jflow_file_type option:selected").val(),e=new RegExp(o);t(".output").each(function(){"all"==o?t(this).fadeIn(500):e.test(t(this).text())?t(this).fadeIn(500):t(this).fadeOut(500)})})}})};t.fn.wfoutputs;t.fn.wfoutputs=function(e){return this.each(function(){var l=t(this),s=l.data("wfoutputs"),i=t.extend({},t.fn.wfoutputs.defaults,"object"==typeof e&&e),n="string"==typeof e?e:null;s?i.workflowID&&(s.options.workflowID=i.workflowID):l.data("wfoutputs",s=new o(this,i)),n?s[n]():s.reload()})},t.fn.wfoutputs.defaults={serverURL:"http://localhost:8080",template:['<div style="float:right;margin-bottom:14px">',' <button id="jflow_log_on" class="btn btn-default btn-xs" type="button"><span class="glyphicon glyphicon-eye-open"></span> View log files</button>',' <button id="jflow_log_off" style="display:none" class="btn btn-default btn-xs" type="button"><span class="glyphicon glyphicon-eye-close"></span> Mask log files</button>',' <span class="btn-xs">- View:</span>',' <select id="jflow_file_type" class="btn btn-default btn-xs" style="width:auto">'," view: <option>all</option>",' </select><span class="btn-xs"> files.</span>',"</div>",'<div style="clear:both;">',' <dl "style=margin-bottom:15px">'," {{each(component_name, files) data}}",' <div style="clear:both"></div>',' <dt style="margin-top:15px;background-color: #eee">',' <span class="glyphicon glyphicon-play" style="color:white;left:-3px"></span>'," ${component_name}"," </dt>"," {{each(file_name, href) files}}",' <dd class="output-file" style="float:left;margin-left:20px;width:265px;overflow:hidden;white-space: nowrap;text-overflow:ellipsis;">',' <span class="glyphicon glyphicon-file"></span>',' <a href="${href.url}" download>${file_name}</a>',' <span style="color:grey">| ${href.size}</span>'," </dd>"," {{/each}}"," {{/each}}</dl>","</div>"].join("\n"),logFile:[".stderr",".stdout",".log"],workflowID:null},t.fn.wfoutputs.Constructor=o}(window.jQuery);
//wfform
......
ui/nG6/res/js/tx_nG6_pi1.js
View file @ 79ab67bb
......@@ -1919,19 +1919,12 @@ function addRunHandler() {
$('#availableWorkflows').html("wait");
$('#setAndRunModal').modal();
$.ajax({
url: $("#server_url").val() + "/get_workflow_filters?",
dataType: "jsonp",
error: function () {
$('#availableWorkflows').html('<div class="alert alert-danger"><strong>Error!</strong> An error occured when attempting to get workflows.</div>');
},
success: function(data) {
$('#availableWorkflows').availablewf({
filters : data,
serverURL: $("#server_url").val()
});
}
$('#availableWorkflows').availablewf({
filter_groups : ['addrun'],
select : true,
serverURL: $("#server_url").val()
});
$('#availableWorkflows').on('select.availablewf', function(event, workflow) {
$("#myCarousel").carousel('next');
$("#myCarousel").carousel('pause');
......
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