Merge -dev.

client/galaxy/scripts/mvc/tools/tools-form-base.js

@@ -61,26 +61,20 @@ define(['utils/utils', 'utils/deferred', 'mvc/ui/ui-misc', 'mvc/form/form-view',
         /** Builds a new model through api call and recreates the entire form
         */
         _buildModel: function(options, hide_message) {
-            // link this
             var self = this;
-
-            // update current version
             this.options.id = options.id;
             this.options.version = options.version;
 
+            // build request url
+            var build_url = '';
+            var build_data = {};
             if ( options.job_id ) {
                 build_url = Galaxy.root + 'api/jobs/' + options.job_id + '/build_for_rerun';
             } else {
-                var build_url = Galaxy.root + 'api/tools/' + options.id + '/build?';
-                if ( options.version ) {
-                    build_url += 'tool_version=' + options.version + '&';
-                }
+                build_url = Galaxy.root + 'api/tools/' + options.id + '/build';
                 if ( Galaxy.params && Galaxy.params.tool_id == options.id ) {
-                    _.each( Galaxy.params, function ( item, key ) {
-                        if ( [ 'tool_version', 'tool_id' ].indexOf( key ) == -1 ) {
-                            build_url += key + '=' + item + '&';
-                        }
-                    } );
+                    build_data = $.extend( {}, Galaxy.params );
+                    options.version && ( build_data[ 'tool_version' ] = options.version );
                 }
             }
 
@@ -91,6 +85,7 @@ define(['utils/utils', 'utils/deferred', 'mvc/ui/ui-misc', 'mvc/form/form-view',
             Utils.request({
                 type    : 'GET',
                 url     : build_url,
+                data    : build_data,
                 success : function(new_model) {
                     // rebuild form
                     self._buildForm(new_model['tool_model'] || new_model);

config/datatypes_conf.xml.sample

@@ -179,7 +179,7 @@
     <datatype extension="sf3" type="galaxy.datatypes.proteomics:Sf3" display_in_upload="true" />
     <datatype extension="cps" type="galaxy.datatypes.binary:Binary" subclass="True" display_in_upload="true" />
     <datatype extension="ct" type="galaxy.datatypes.tabular:ConnectivityTable" display_in_upload="True"/>
-    <datatype extension="searchgui_archive" type="galaxy.datatypes.binary:CompressedArchive" subclass="True" display_in_upload="True"/>
+    <datatype extension="searchgui_archive" type="galaxy.datatypes.binary:SearchGuiArchive" display_in_upload="True"/>
     <datatype extension="peptideshaker_archive" type="galaxy.datatypes.binary:CompressedArchive" subclass="True" display_in_upload="True"/>
     <!-- End Proteomics Datatypes -->
     <datatype extension="eps" type="galaxy.datatypes.images:Eps" mimetype="image/eps"/>

doc/source/admin/index.rst

@@ -9,3 +9,5 @@ documentation. These resources should be used together.
    :maxdepth: 3
 
    interactive_environments.rst
+
+   useful_scripts.rst

doc/source/admin/useful_scripts.rst

@@ -0,0 +1,19 @@
+Useful Scripts and Administration Tricks
+========================================
+
+This page aims to help ease the burden of administration with some easy to use scripts and documentation on what is available for admins to use.
+
+Uploading a directory into a Data Library
+-----------------------------------------
+
+Data libraries can really ease the use of Galaxy for your administrators and end users. They provide a form of shared folders that users can copy datasets from into their history.
+
+This script was developed to be as general as possible, allowing you to pipe the output of a much more complex find command to this script, uploading all of the files into a data library:
+
+.. code-block:: console
+
+    $ find /path/to/sequencing-data/ -name '*.fastq' -or -name '*.fa' | python $GALAXY_ROOT/scripts/api/library_upload_dir.py
+
+Find has an extremely expressive command line for selecting specific files that are of interest to you. These will then be recursively uploaded into Galaxy, maintaining the folder hierarchy, a useful feature when moving legacy data into Galaxy. For a complete description of the options of this script, you can run ``python $GALAXY_ROOT/scripts/api/library_upload_dir.py --help``
+
+This tool will not overwrite or re-upload already uploaded datasets. As a result, one can imagine running this on a cron job to keep an "incoming sequencing data" directory synced with a data library.

doc/source/dev/faq.rst

@@ -2,7 +2,7 @@ How Do I...
 ===========
 
 This section contains a number of smaller topics with links and examples meant
-to provide relatively concrete answers for specific tool development scenarios.
+to provide relatively concrete answers for specific Galaxy development scenarios.
 
 ... interact with the Galaxy codebase interactively?
 ----------------------------------------------------

lib/galaxy/datatypes/binary.py

@@ -1053,3 +1053,56 @@ class OxliGraphLabels(OxliBinary):
 
 Binary.register_sniffable_binary_format("oxli.graphlabels", "oxligl",
                                         OxliGraphLabels)
+
+
+class SearchGuiArchive ( CompressedArchive ):
+    """Class describing a SearchGUI archive """
+    MetadataElement( name="searchgui_version", default='1.28.0' , param=MetadataParameter, desc="SearchGui Version",
+                     readonly=True, visible=True, no_value=None )
+    MetadataElement( name="searchgui_major_version", default='1' , param=MetadataParameter, desc="SearchGui Major Version",
+                     readonly=True, visible=True, no_value=None )
+    file_ext = "searchgui_archive"
+
+    def set_meta( self, dataset, overwrite=True, **kwd ):
+        super( SearchGuiArchive, self ).set_meta( dataset, overwrite=overwrite, **kwd )
+        try:
+            if dataset and zipfile.is_zipfile( dataset.file_name ):
+                tempzip = zipfile.ZipFile( dataset.file_name )
+                if 'searchgui.properties' in tempzip.namelist():
+                    fh = tempzip.open('searchgui.properties')
+                    for line in fh:
+                        if line.startswith('searchgui.version'):
+                            version = line.split('=')[1].strip()
+                            dataset.metadata.searchgui_version = version
+                            dataset.metadata.searchgui_major_version = version.split('.')[0]
+                    fh.close()
+                tempzip.close()
+        except Exception as e:
+            log.warn( '%s, set_meta Exception: %s', self, e )
+
+    def sniff( self, filename ):
+        try:
+            if filename and zipfile.is_zipfile( filename ):
+                tempzip = zipfile.ZipFile( filename, 'r' )
+                is_searchgui = 'searchgui.properties' in tempzip.namelist()
+                tempzip.close()
+                return is_searchgui
+        except Exception as e:
+            log.warn( '%s, sniff Exception: %s', self, e )
+        return False
+
+    def set_peek( self, dataset, is_multi_byte=False ):
+        if not dataset.dataset.purged:
+            dataset.peek = "SearchGUI Archive, version %s" % ( dataset.metadata.searchgui_version or 'unknown' )
+            dataset.blurb = nice_size( dataset.get_size() )
+        else:
+            dataset.peek = 'file does not exist'
+            dataset.blurb = 'file purged from disk'
+
+    def display_peek( self, dataset ):
+        try:
+            return dataset.peek
+        except:
+            return "SearchGUI Archive, version %s" % ( dataset.metadata.searchgui_version or 'unknown' )
+
+Binary.register_sniffable_binary_format("searchgui_archive", "searchgui_archive", SearchGuiArchive)

lib/galaxy/tools/loader_directory.py

@@ -1,5 +1,6 @@
 import glob
 import os
+import re
 from ..tools import loader
 
 import sys
@@ -9,6 +10,7 @@ log = logging.getLogger(__name__)
 
 PATH_DOES_NOT_EXIST_ERROR = "Could not load tools from path [%s] - this path does not exist."
 LOAD_FAILURE_ERROR = "Failed to load tool with path %s."
+TOOL_REGEX = re.compile(r"<tool\s")
 
 
 def load_exception_handler(path, exc_info):
@@ -40,7 +42,7 @@ def __looks_like_a_tool(path):
                 line = f.next()
             except StopIteration:
                 break
-            if "<tool" in line:
+            if TOOL_REGEX.search(line):
                 return True
     return False
 

lib/galaxy/web/framework/middleware/remoteuser.py

@@ -4,6 +4,8 @@ Middleware for handling $REMOTE_USER if use_remote_user is enabled.
 
 import socket
 from galaxy.util import safe_str_cmp
+import logging
+log = logging.getLogger(__name__)
 
 errorpage = """
 <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
@@ -163,6 +165,10 @@ class RemoteUser( object ):
             # The API handles its own authentication via keys
             return self.app( environ, start_response )
         else:
+            log.debug("Unable to identify user.  %s not found" % self.remote_user_header)
+            for k, v in environ.iteritems():
+                log.debug("%s = %s" , k, v)
+
             title = "Access to Galaxy is denied"
             message = """
                 Galaxy is configured to authenticate users via an external

lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py

@@ -53,7 +53,7 @@ class CompressedFile( object ):
     def extract( self, path ):
         '''Determine the path to which the archive should be extracted.'''
         contents = self.getmembers()
-        extraction_path = os.path.join( path )
+        extraction_path = path
         common_prefix = ''
         if len( contents ) == 1:
             # The archive contains a single file, return the extraction path.
@@ -84,8 +84,11 @@ class CompressedFile( object ):
                 external_attributes = self.archive.getinfo( filename ).external_attr
                 # The 2 least significant bytes are irrelevant, the next two contain unix permissions.
                 unix_permissions = external_attributes >> 16
-                if unix_permissions != 0 and os.path.exists( absolute_filepath ):
-                    os.chmod( absolute_filepath, unix_permissions )
+                if unix_permissions != 0:
+                    if os.path.exists( absolute_filepath ):
+                        os.chmod( absolute_filepath, unix_permissions )
+                    else:
+                        log.warn("Unable to change permission on extracted file '%s' as it does not exist" % absolute_filepath)
         return os.path.abspath( os.path.join( extraction_path, common_prefix ) )
 
     def getmembers_tar( self ):
@@ -1372,7 +1375,7 @@ class SetupREnvironment( Download, RecipeStep ):
                     # Use raw strings so that python won't automatically unescape the quotes before passing the command
                     # to subprocess.Popen.
                     cmd = r'''PATH=$PATH:$R_HOME/bin; export PATH; R_LIBS=$INSTALL_DIR:$R_LIBS; export R_LIBS;
-                        Rscript -e "tryCatch( install.packages(c('%s'),lib='$INSTALL_DIR', repos=NULL, dependencies=FALSE), error = quit(status = 1))"''' % \
+                        Rscript -e "tryCatch( { install.packages(c('%s'), lib = '$INSTALL_DIR', repos = NULL, dependencies = FALSE) }, error = function(e) { print(e); quit(status = 1) }, warning = function(w) { if ( grepl('had non-zero exit status|is not writable|installation of one of more packages failed', as.character(w)) ) { print(w); quit(status = 1) } } )"''' % \
                         ( str( tarball_name ) )
                     cmd = install_environment.build_command( basic_util.evaluate_template( cmd, install_environment ) )
                     return_code = install_environment.handle_command( tool_dependency=tool_dependency,

run_tests.sh

@@ -3,8 +3,6 @@
 pwd_dir=$(pwd)
 cd `dirname $0`
 
-./scripts/common_startup.sh
-
 # A good place to look for nose info: http://somethingaboutorange.com/mrl/projects/nose/
 rm -f run_functional_tests.log
 
@@ -72,6 +70,8 @@ ensure_grunt() {
 }
 
 
+DOCKER_DEFAULT_IMAGE='galaxy/testing-base:15.10.0'
+
 test_script="./scripts/functional_tests.py"
 report_file="run_functional_tests.html"
 xunit_report_file=""
@@ -85,7 +85,7 @@ then
     shift
     DOCKER_EXTRA_ARGS=${DOCKER_ARGS:-""}
     DOCKER_RUN_EXTRA_ARGS=${DOCKER_RUN_EXTRA_ARGS:-""}
-    DOCKER_IMAGE=${DOCKER_IMAGE:-"galaxy/testing-base"}
+    DOCKER_IMAGE=${DOCKER_IMAGE:-${DOCKER_DEFAULT_IMAGE}}
     if [ "$1" = "--db" ]; then
        db_type=$2
        shift 2
@@ -286,6 +286,12 @@ do
           watch=1
           shift
           ;;
+      --skip-common-startup)
+          # Don't run ./scripts/common_startup.sh (presumably it has already
+          # been done, or you know what you're doing).
+          skip_common_startup=1
+          shift
+          ;;
       --) 
           shift
           break
@@ -301,6 +307,10 @@ do
     esac
 done
 
+if [ -z "$skip_common_startup" ]; then
+    ./scripts/common_startup.sh
+fi
+
 if [ -n "$migrated_test" ] ; then
     [ -n "$test_id" ] && class=":TestForTool_$test_id" || class=""
     extra_args="functional.test_toolbox$class -migrated"

scripts/api/library_upload_dir.py

@@ -0,0 +1,169 @@
+#!/usr/bin/env python
+import sys
+import argparse
+import os
+from bioblend import galaxy
+
+
+class Uploader:
+
+    def __init__(self, url, api, library_id, folder_id, should_link,
+                 non_local):
+        self.gi = galaxy.GalaxyInstance(url=url, key=api)
+        self.library_id = library_id
+        self.folder_id = folder_id
+        self.should_link = should_link
+        self.non_local = non_local
+
+        self.memo_path = {}
+        self.prepopulate_memo()
+
+    def prepopulate_memo(self):
+        """
+        Because the Galaxy Data Libraries API/system does not act like any
+        other file system in existence, and allows multiple files/folders with
+        identical names in the same parent directory, we have to prepopulate
+        the memoization cache with everything currently in the target
+        directory.
+
+        Because the Galaxy Data Libraries API does not work from a perspective
+        of "show me what is in this directory", we are forced to get the entire
+        contents of the data library, and then filter out things that are
+        interesting to us based on a folder prefix.
+        """
+        existing = self.gi.libraries.show_library(self.library_id, contents=True)
+
+        uploading_to = [x for x in existing if x['id'] == self.folder_id]
+        if len(uploading_to) == 0:
+            raise Exception("Unknown folder [%s] in library [%s]" %
+                            (self.folder_id, self.library_id))
+        else:
+            uploading_to = uploading_to[0]
+
+        for x in existing:
+            # We only care if it's a subdirectory of where we're uploading to
+            if not x['name'].startswith(uploading_to['name']):
+                continue
+
+            name_part = x['name'].split(uploading_to['name'], 1)[-1]
+            if name_part.startswith('/'):
+                name_part = name_part[1:]
+            self.memo_path[name_part] = x['id']
+
+    def memoized_path(self, path_parts, base_folder=None):
+        """Get the folder ID for a given folder path specified by path_parts.
+
+        If the folder does not exist, it will be created ONCE (during the
+        instantiation of this Uploader object). After that it is stored and
+        recycled. If the Uploader object is re-created, it is not aware of
+        previously existing paths and will not respect those. TODO: handle
+        existing paths.
+        """
+        if base_folder is None:
+            base_folder = self.folder_id
+        dropped_prefix = []
+
+        fk = '/'.join(path_parts)
+        if fk in self.memo_path:
+            # print "Cache hit %s" % fk
+            return self.memo_path[fk]
+        else:
+            # print "Cache miss %s" % fk
+            for i in reversed(range(len(path_parts))):
+                fk = '/'.join(path_parts[0:i + 1])
+                if fk in self.memo_path:
+                    # print "Parent folder hit %s" % fk
+                    dropped_prefix = path_parts[0:i + 1]
+                    path_parts = path_parts[i + 1:]
+                    base_folder = self.memo_path[fk]
+                    break
+
+        nfk = []
+        for i in range(len(path_parts)):
+            nfk.append('/'.join(list(dropped_prefix) + list(path_parts[0:i + 1])))
+
+        # Recursively create the path from our base_folder starting points,
+        # gettting the IDs of each folder per path component
+        ids = self.recursively_build_path(path_parts, base_folder)
+
+        # These are then associated with the paths.
+        for (key, fid) in zip(nfk, ids):
+            self.memo_path[key] = fid
+        return ids[-1]
+
+    def recursively_build_path(self, path_parts, parent_folder_id, ids=None):
+        """Given an iterable of path components and a parent folder id, recursively
+        create directories below parent_folder_id"""
+        if ids is None:
+            ids = []
+        if len(path_parts) == 0:
+            return ids
+        else:
+            pf = self.gi.libraries.create_folder(self.library_id, path_parts[0], base_folder_id=parent_folder_id)
+            ids.append(pf[0]['id'])
+            # print "create_folder(%s, %s, %s) = %s" % (self.library_id, path_parts[0], parent_folder_id, pf[0]['id'])
+            return self.recursively_build_path(path_parts[1:], pf[0]['id'], ids=ids)
+
+    # http://stackoverflow.com/questions/13505819/python-split-path-recursively/13505966#13505966
+    def rec_split(self, s):
+        if s == '/':
+            return ()
+
+        rest, tail = os.path.split(s)
+        if tail == '.':
+            return ()
+        if rest == '':
+            return tail,
+        return self.rec_split(rest) + (tail,)
+
+    def upload(self):
+        all_files = [x.strip() for x in list(sys.stdin.readlines())]
+
+        for idx, path in enumerate(all_files):
+            (dirName, fname) = path.rsplit(os.path.sep, 1)
+            if not os.path.exists(os.path.join(dirName, fname)):
+                continue
+            # Figure out what the memo key will be early
+            basepath = self.rec_split(dirName)
+            if len(basepath) == 0:
+                memo_key = fname
+            else:
+                memo_key = os.path.join(os.path.join(*basepath), fname)
+
+            # So that we can check if it really needs to be uploaded.
+            already_uploaded = memo_key in self.memo_path.keys()
+            fid = self.memoized_path(basepath, base_folder=self.folder_id)
+            print('[%s/%s] %s/%s uploaded=%' % (idx + 1, len(all_files), fid, fname, already_uploaded))
+
+            if not already_uploaded:
+                if self.non_local:
+                    self.gi.libraries.upload_file_from_local_path(
+                        self.library_id,
+                        os.path.join(dirName, fname),
+                        folder_id=fid,
+                    )
+                else:
+                    self.gi.libraries.upload_from_galaxy_filesystem(
+                        self.library_id,
+                        os.path.join(dirName, fname),
+                        folder_id=fid,
+                        link_data_only='link_to_files' if self.should_link else 'copy_files',
+                    )
+
+
+if __name__ == '__main__':
+    parser = argparse.ArgumentParser(description='Upload a directory into a data library')
+    parser.add_argument( "-u", "--url", dest="url", required=True, help="Galaxy URL" )
+    parser.add_argument( "-a", "--api", dest="api", required=True, help="API Key" )
+
+    parser.add_argument( "-l", "--lib", dest="library_id", required=True, help="Library ID" )
+    parser.add_argument( "-f", "--folder", dest="folder_id", help="Folder ID. If not specified, will go to root of library." )
+
+    parser.add_argument( "--nonlocal", dest="non_local", action="store_true", default=False,
+                        help="Set this flag if you are NOT running this script on your Galaxy head node with access to the full filesystem" )
+    parser.add_argument( "--link", dest="should_link", action="store_true", default=False,
+                        help="Link datasets only, do not upload to Galaxy. ONLY Avaialble if you run 'locally' relative to your Galaxy head node/filesystem ")
+    args = parser.parse_args()
+
+    u = Uploader(**vars(args))
+    u.upload()

static/scripts/mvc/tools/tools-form-base.js

@@ -1,2 +1,2 @@
-define(["utils/utils","utils/deferred","mvc/ui/ui-misc","mvc/form/form-view","mvc/tools/tools-template","mvc/citation/citation-model","mvc/citation/citation-view"],function(a,b,c,d,e,f,g){return Backbone.View.extend({initialize:function(c){this.options=a.merge(c,{}),this.setElement("<div/>"),this.deferred=new b,c.inputs?this._buildForm(c):this._buildModel(c,!0)},_buildForm:function(b){var c=this;this.options=a.merge(b,this.options),this.options=a.merge({icon:"fa-wrench",title:"<b>"+b.name+"</b> "+b.description+" (Galaxy Tool Version "+b.version+")",operations:this._operations(),onchange:function(){c.deferred.reset(),c.deferred.execute(function(){c._updateModel()})}},this.options),this.options.customize&&this.options.customize(this.options),this.form=new d(this.options),this._footer(),this.$el.empty(),this.$el.append(this.form.$el)},_buildModel:function(b,d){var e=this;if(this.options.id=b.id,this.options.version=b.version,b.job_id)f=Galaxy.root+"api/jobs/"+b.job_id+"/build_for_rerun";else{var f=Galaxy.root+"api/tools/"+b.id+"/build?";b.version&&(f+="tool_version="+b.version+"&"),Galaxy.params&&Galaxy.params.tool_id==b.id&&_.each(Galaxy.params,function(a,b){-1==["tool_version","tool_id"].indexOf(b)&&(f+=b+"="+a+"&")})}var g=this.deferred.register();a.request({type:"GET",url:f,success:function(a){e._buildForm(a.tool_model||a),!d&&e.form.message.update({status:"success",message:"Now you are using '"+e.options.name+"' version "+e.options.version+".",persistent:!1}),e.deferred.done(g),console.debug("tools-form::initialize() - Initial tool model ready."),console.debug(a)},error:function(a){e.deferred.done(g),console.debug("tools-form::initialize() - Initial tool model request failed."),console.debug(a);var b=a&&a.err_msg||"Uncaught error.";e.$el.is(":empty")?e.$el.prepend(new c.Message({message:b,status:"danger",persistent:!0,large:!0}).$el):Galaxy.modal.show({title:"Tool request failed",body:b,buttons:{Close:function(){Galaxy.modal.hide()}}})}})},_updateModel:function(){var b=this.options.update_url||Galaxy.root+"api/tools/"+this.options.id+"/build",c=this,d=this.form,e={tool_id:this.options.id,tool_version:this.options.version,inputs:$.extend(!0,{},c.form.data.create())};d.wait(!0);var f=this.deferred.register();console.debug("tools-form-base::_updateModel() - Sending current state (see below)."),console.debug(e),a.request({type:"POST",url:b,data:e,success:function(a){c.form.update(a.tool_model||a),c.options.update&&c.options.update(a),d.wait(!1),console.debug("tools-form-base::_updateModel() - Received new model (see below)."),console.debug(a),c.deferred.done(f)},error:function(a){c.deferred.done(f),console.debug("tools-form-base::_updateModel() - Refresh request failed."),console.debug(a)}})},_operations:function(){var a=this,b=this.options,d=new c.ButtonMenu({icon:"fa-cubes",title:!b.narrow&&"Versions"||null,tooltip:"Select another tool version"});if(!b.is_workflow&&b.versions&&b.versions.length>1)for(var f in b.versions){var g=b.versions[f];g!=b.version&&d.addMenu({title:"Switch to "+g,version:g,icon:"fa-cube",onclick:function(){var c=b.id.replace(b.version,this.version),d=this.version;a.deferred.reset(),a.deferred.execute(function(){a._buildModel({id:c,version:d})})}})}else d.$el.hide();var h=new c.ButtonMenu({icon:"fa-caret-down",title:!b.narrow&&"Options"||null,tooltip:"View available options"});return b.biostar_url&&(h.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(b.biostar_url+"/p/new/post/")}}),h.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(b.biostar_url+"/local/search/page/?q="+b.name)}})),h.addMenu({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+Galaxy.root+"root?tool_id="+b.id)}}),Galaxy.user&&Galaxy.user.get("is_admin")&&h.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=Galaxy.root+"api/tools/"+b.id+"/download"}}),b.requirements&&b.requirements.length>0&&h.addMenu({icon:"fa-info-circle",title:"Requirements",tooltip:"Display tool requirements",onclick:function(){this.visible?(this.visible=!1,a.form.message.update({message:""})):(this.visible=!0,a.form.message.update({persistent:!0,message:e.requirements(b),status:"info"}))}}),b.sharable_url&&h.addMenu({icon:"fa-external-link",title:"See in Tool Shed",tooltip:"Access the repository",onclick:function(){window.open(b.sharable_url)}}),{menu:h,versions:d}},_footer:function(){var a=this.options;if(""!=a.help&&this.form.$el.append(e.help(a)),a.citations){var b=$("<div/>"),c=new f.ToolCitationCollection;c.tool_id=a.id;var d=new g.CitationListView({el:b,collection:c});d.render(),c.fetch(),this.form.$el.append(b)}}})});
+define(["utils/utils","utils/deferred","mvc/ui/ui-misc","mvc/form/form-view","mvc/tools/tools-template","mvc/citation/citation-model","mvc/citation/citation-view"],function(a,b,c,d,e,f,g){return Backbone.View.extend({initialize:function(c){this.options=a.merge(c,{}),this.setElement("<div/>"),this.deferred=new b,c.inputs?this._buildForm(c):this._buildModel(c,!0)},_buildForm:function(b){var c=this;this.options=a.merge(b,this.options),this.options=a.merge({icon:"fa-wrench",title:"<b>"+b.name+"</b> "+b.description+" (Galaxy Tool Version "+b.version+")",operations:this._operations(),onchange:function(){c.deferred.reset(),c.deferred.execute(function(){c._updateModel()})}},this.options),this.options.customize&&this.options.customize(this.options),this.form=new d(this.options),this._footer(),this.$el.empty(),this.$el.append(this.form.$el)},_buildModel:function(b,d){var e=this;this.options.id=b.id,this.options.version=b.version;var f="",g={};b.job_id?f=Galaxy.root+"api/jobs/"+b.job_id+"/build_for_rerun":(f=Galaxy.root+"api/tools/"+b.id+"/build",Galaxy.params&&Galaxy.params.tool_id==b.id&&(g=$.extend({},Galaxy.params),b.version&&(g.tool_version=b.version)));var h=this.deferred.register();a.request({type:"GET",url:f,data:g,success:function(a){e._buildForm(a.tool_model||a),!d&&e.form.message.update({status:"success",message:"Now you are using '"+e.options.name+"' version "+e.options.version+".",persistent:!1}),e.deferred.done(h),console.debug("tools-form::initialize() - Initial tool model ready."),console.debug(a)},error:function(a){e.deferred.done(h),console.debug("tools-form::initialize() - Initial tool model request failed."),console.debug(a);var b=a&&a.err_msg||"Uncaught error.";e.$el.is(":empty")?e.$el.prepend(new c.Message({message:b,status:"danger",persistent:!0,large:!0}).$el):Galaxy.modal.show({title:"Tool request failed",body:b,buttons:{Close:function(){Galaxy.modal.hide()}}})}})},_updateModel:function(){var b=this.options.update_url||Galaxy.root+"api/tools/"+this.options.id+"/build",c=this,d=this.form,e={tool_id:this.options.id,tool_version:this.options.version,inputs:$.extend(!0,{},c.form.data.create())};d.wait(!0);var f=this.deferred.register();console.debug("tools-form-base::_updateModel() - Sending current state (see below)."),console.debug(e),a.request({type:"POST",url:b,data:e,success:function(a){c.form.update(a.tool_model||a),c.options.update&&c.options.update(a),d.wait(!1),console.debug("tools-form-base::_updateModel() - Received new model (see below)."),console.debug(a),c.deferred.done(f)},error:function(a){c.deferred.done(f),console.debug("tools-form-base::_updateModel() - Refresh request failed."),console.debug(a)}})},_operations:function(){var a=this,b=this.options,d=new c.ButtonMenu({icon:"fa-cubes",title:!b.narrow&&"Versions"||null,tooltip:"Select another tool version"});if(!b.is_workflow&&b.versions&&b.versions.length>1)for(var f in b.versions){var g=b.versions[f];g!=b.version&&d.addMenu({title:"Switch to "+g,version:g,icon:"fa-cube",onclick:function(){var c=b.id.replace(b.version,this.version),d=this.version;a.deferred.reset(),a.deferred.execute(function(){a._buildModel({id:c,version:d})})}})}else d.$el.hide();var h=new c.ButtonMenu({icon:"fa-caret-down",title:!b.narrow&&"Options"||null,tooltip:"View available options"});return b.biostar_url&&(h.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(b.biostar_url+"/p/new/post/")}}),h.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(b.biostar_url+"/local/search/page/?q="+b.name)}})),h.addMenu({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+Galaxy.root+"root?tool_id="+b.id)}}),Galaxy.user&&Galaxy.user.get("is_admin")&&h.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=Galaxy.root+"api/tools/"+b.id+"/download"}}),b.requirements&&b.requirements.length>0&&h.addMenu({icon:"fa-info-circle",title:"Requirements",tooltip:"Display tool requirements",onclick:function(){this.visible?(this.visible=!1,a.form.message.update({message:""})):(this.visible=!0,a.form.message.update({persistent:!0,message:e.requirements(b),status:"info"}))}}),b.sharable_url&&h.addMenu({icon:"fa-external-link",title:"See in Tool Shed",tooltip:"Access the repository",onclick:function(){window.open(b.sharable_url)}}),{menu:h,versions:d}},_footer:function(){var a=this.options;if(""!=a.help&&this.form.$el.append(e.help(a)),a.citations){var b=$("<div/>"),c=new f.ToolCitationCollection;c.tool_id=a.id;var d=new g.CitationListView({el:b,collection:c});d.render(),c.fetch(),this.form.$el.append(b)}}})});
 //# sourceMappingURL=../../../maps/mvc/tools/tools-form-base.js.map

test/docker/base/run_test_wrapper.sh

@@ -7,7 +7,7 @@ then
     su -c '/usr/lib/postgresql/9.3/bin/pg_ctl -o "-F" start -D /opt/galaxy/db' postgres
     sleep 3
     GALAXY_TEST_INSTALL_DB_MERGED="true"
-    GALAXY_TEST_DBURI="postgres://root@localhost:5930/galaxy"
+    GALAXY_TEST_DBURI="postgres://root@localhost:5930/galaxy?client_encoding=utf8"
     TOOL_SHED_TEST_DBURI="postgres://root@localhost:5930/toolshed"
 elif [ "$GALAXY_TEST_DATABASE_TYPE" = "mysql" ];
 then
@@ -32,11 +32,16 @@ cd /galaxy
 GALAXY_CONFIG_OVERRIDE_DATABASE_CONNECTION="$GALAXY_TEST_DBURI";
 export GALAXY_CONFIG_OVERRIDE_DATABASE_CONNECTION
 
+./scripts/common_startup.sh || { echo "common_startup.sh failed"; exit 1; }
+
+dev_requirements=./lib/galaxy/dependencies/dev-requirements.txt
+[ -f $dev_requirements ] && ./.venv/bin/pip install -r $dev_requirements
+
 sh manage_db.sh upgrade
 
 if [ -z "$GALAXY_NO_TESTS" ];
 then
-    sh run_tests.sh $@
+    sh run_tests.sh --skip-common-startup $@
 else
     GALAXY_CONFIG_MASTER_API_KEY=${GALAXY_CONFIG_MASTER_API_KEY:-"testmasterapikey"}
     GALAXY_CONFIG_FILE=${GALAXY_CONFIG_FILE:-config/galaxy.ini.sample}