mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
branch merge
This commit is contained in:
Ross Lazarus
@@ -212,9 +212,16 @@ class DRMAAJobRunner( AsynchronousJobRunner ):
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try:
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assert external_job_id not in ( None, 'None' ), '(%s/%s) Invalid job id' % ( galaxy_id_tag, external_job_id )
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state = self.ds.jobStatus( external_job_id )
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# TODO: probably need to keep track of InvalidJobException count and remove after it exceeds some configurable
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except ( drmaa.DrmCommunicationException, drmaa.InternalException, drmaa.InvalidJobException ), e:
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log.warning( "(%s/%s) job check resulted in %s: %s", galaxy_id_tag, external_job_id, e.__class__.__name__, e )
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# InternalException was reported to be necessary on some DRMs, but
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# this could cause failures to be detected as completion! Please
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# report if you experience problems with this.
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except ( drmaa.InvalidJobException, drmaa.InternalException ), e:
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# we should only get here if an orphaned job was put into the queue at app startup
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log.info( "(%s/%s) job left DRM queue with following message: %s" % ( galaxy_id_tag, external_job_id, e ) )
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self.work_queue.put( ( self.finish_job, ajs ) )
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continue
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except drmaa.DrmCommunicationException, e:
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log.warning( "(%s/%s) unable to communicate with DRM: %s" % ( galaxy_id_tag, external_job_id, e ))
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new_watched.append( ajs )
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continue
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except Exception, e:
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@@ -9,7 +9,6 @@ import urllib2
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import zipfile
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import tool_shed.util.shed_util_common as suc
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from galaxy.datatypes import checkers
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from urllib2 import HTTPError
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log = logging.getLogger( __name__ )
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@@ -21,6 +21,7 @@ from tool_shed.util import common_util
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from tool_shed.util import encoding_util
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from tool_shed.util import xml_util
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from xml.etree import ElementTree as XmlET
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from urllib2 import HTTPError
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from galaxy import eggs
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eggs.require( 'mercurial' )
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@@ -1232,10 +1233,25 @@ def get_tool_shed_status_for_installed_repository( app, repository ):
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try:
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encoded_tool_shed_status_dict = common_util.tool_shed_get( app, tool_shed_url, url )
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tool_shed_status_dict = encoding_util.tool_shed_decode( encoded_tool_shed_status_dict )
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return tool_shed_status_dict
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except HTTPError, e:
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# This should handle backward compatility to the Galaxy 12/20/12 release. We used to only handle updates for an installed revision
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# using a boolean value.
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log.debug( "Error attempting to get tool shed status for installed repository %s: %s\nAttempting older 'check_for_updates' method.\n" % \
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( str( repository.name ), str( e ) ) )
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url = url_join( tool_shed_url,
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'repository/check_for_updates?name=%s&owner=%s&changeset_revision=%s&from_update_manager=True' % \
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( repository.name, repository.owner, repository.changeset_revision ) )
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try:
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# The value of text will be 'true' or 'false', depending upon whether there is an update available for the installed revision.
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text = common_util.tool_shed_get( app, tool_shed_url, url )
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return dict( revision_update=text )
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except Exception, e:
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# The required tool shed may be unavailable, so default the revision_update value to 'false'.
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return dict( revision_update='false' )
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except Exception, e:
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log.exception( "Error attempting to get tool shed status for installed repository %s: %s" % ( str( repository.name ), str( e ) ) )
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return {}
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return tool_shed_status_dict
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def get_updated_changeset_revisions( trans, name, owner, changeset_revision ):
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"""
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@@ -57,6 +57,10 @@ var GalaxyUpload = Backbone.View.extend(
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return;
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}
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// check if logged in
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if (!Galaxy.currUser.get('id'))
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return;
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// add activate icon
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var self = this;
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this.button_show = new mod_master.GalaxyMasterIcon (
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@@ -24,7 +24,8 @@
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error_filesize : "File exceeds 2GB. Please use an FTP client.",
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error_default : "Please make sure the file is available.",
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error_server : "The server is unavailable.",
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error_toomany : "You can only queue <20 files per upload session."
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error_toomany : "You can only queue <20 files per upload session.",
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error_login : "Uploads require you to log in."
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}
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// options
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@@ -158,6 +159,9 @@
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// process an upload, recursive
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function process()
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{
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// log
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//console.log("Processing queue..." + queue_length + " (" + queue_running + " / " + queue_pause + ")");
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// validate
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if (queue_length == 0 || queue_pause)
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{
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@@ -167,6 +171,9 @@
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return;
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} else
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queue_running = true;
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// log
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//console.log("Looking for file...");
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// get an identifier from the queue
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var index = -1;
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@@ -181,52 +188,23 @@
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// remove from queue
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remove(index)
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// log
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//console.log("Initializing ('" + file.name + "').");
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// start
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var data = opts.initialize(index, file);
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// identify maximum file size
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var filesize = file.size;
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var maxfilesize = 1048576 * opts.maxfilesize;
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// add file to queue
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try
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// check file size
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if (filesize < maxfilesize)
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{
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// load file read
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var reader = new FileReader();
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// identify maximum file size
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var filesize = file.size;
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var maxfilesize = 1048576 * opts.maxfilesize;
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// set index
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reader.index = index;
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if (filesize < maxfilesize)
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{
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// link load
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reader.onload = function(e)
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{
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send(index, file, data)
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};
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// link error
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reader.onerror = function(e)
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{
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error(index, file, opts.error_default);
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};
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// link abort
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reader.onabort = function(e)
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{
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error(index, file, opts.error_default);
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};
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// read data
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reader.readAsDataURL(file);
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} else {
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// skip file
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error(index, file, opts.error_filesize);
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}
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} catch (err)
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{
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// parse error
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error(index, file, err);
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// send data
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var data = opts.initialize(index, file);
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send(index, file, data)
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} else {
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// skip file
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error(index, file, opts.error_filesize);
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}
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}
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@@ -241,10 +219,17 @@
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// prepare request
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xhr = new XMLHttpRequest();
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xhr.open('POST', opts.url, true);
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xhr.setRequestHeader('Accept', 'application/json');
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xhr.setRequestHeader('Cache-Control', 'no-cache');
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xhr.setRequestHeader('X-Requested-With', 'XMLHttpRequest');
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// captures state changes
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xhr.onreadystatechange = function()
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{
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// status change
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//console.log("Status changed: " + xhr.readyState + ".");
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// check for request completed, server connection closed
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if (xhr.readyState != xhr.DONE)
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return;
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@@ -264,14 +249,14 @@
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// pass any error to the error option
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if (xhr.status < 200 || xhr.status > 299)
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{
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// format error
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// format status
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var text = xhr.statusText;
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if (!xhr.statusText) {
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if (xhr.status == 0)
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text = opts.error_server;
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else
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text = opts.error_default;
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}
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if (xhr.status == 403)
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text = opts.error_login;
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else if (xhr.status == 0)
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text = opts.error_server;
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else if (!text)
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text = opts.error_default;
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// request error
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error(index, file, text + " (" + xhr.status + ")");
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@@ -284,13 +269,12 @@
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xhr.upload.index = index;
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xhr.upload.file = file;
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xhr.upload.addEventListener('progress', progress, false);
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// open request
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xhr.open('POST', opts.url, true);
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xhr.setRequestHeader('Accept', 'application/json');
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xhr.setRequestHeader('Cache-Control', 'no-cache');
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xhr.setRequestHeader('X-Requested-With', 'XMLHttpRequest');
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// send request
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xhr.send(formData);
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// sending file
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//console.log("Sending file ('" + file.name + "').");
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}
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// success
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@@ -360,7 +344,7 @@
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// verify browser compatibility
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function compatible()
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{
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return window.File && window.FileReader && window.FormData && window.XMLHttpRequest && window.FileList;
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return window.File && window.FormData && window.XMLHttpRequest && window.FileList;
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}
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// export functions
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@@ -1851,3 +1851,9 @@ div.toolTitleNoSection
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.icon-button.chevron-expand {
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.sprite(@chevron-expand-bw);
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}
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// honeypot for registration form
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#for_bears {
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display: none;
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}
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@@ -37,25 +37,82 @@
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subscribe_check_box = CheckboxField( 'subscribe' )
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%>
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<script type="text/javascript">
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$(document).ready(function() {
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function validateString(test_string, type) {
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var mail_re = /^(([^<>()[\]\\.,;:\s@\"]+(\.[^<>()[\]\\.,;:\s@\"]+)*)|(\".+\"))@((\[[0-9]{1,3}\.[0-9]{1,3}\.[0-9]{1,3}\.[0-9]{1,3}\])|(([a-zA-Z\-0-9]+\.)+[a-zA-Z]{2,}))$/;
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//var mail_re_RFC822 = /^([^\x00-\x20\x22\x28\x29\x2c\x2e\x3a-\x3c\x3e\x40\x5b-\x5d\x7f-\xff]+|\x22([^\x0d\x22\x5c\x80-\xff]|\x5c[\x00-\x7f])*\x22)(\x2e([^\x00-\x20\x22\x28\x29\x2c\x2e\x3a-\x3c\x3e\x40\x5b-\x5d\x7f-\xff]+|\x22([^\x0d\x22\x5c\x80-\xff]|\x5c[\x00-\x7f])*\x22))*\x40([^\x00-\x20\x22\x28\x29\x2c\x2e\x3a-\x3c\x3e\x40\x5b-\x5d\x7f-\xff]+|\x5b([^\x0d\x5b-\x5d\x80-\xff]|\x5c[\x00-\x7f])*\x5d)(\x2e([^\x00-\x20\x22\x28\x29\x2c\x2e\x3a-\x3c\x3e\x40\x5b-\x5d\x7f-\xff]+|\x5b([^\x0d\x5b-\x5d\x80-\xff]|\x5c[\x00-\x7f])*\x5d))*$/;
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var username_re = /^[a-z0-9\-]{3,255}$/;
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if (type === 'email') {
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return mail_re.test(test_string);
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} else if (type === 'username'){
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return username_re.test(test_string);
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}
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}
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function renderError(message) {
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if ($(".errormessage").length === 1) {
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$(".errormessage").html(message)
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} else {
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var div = document.createElement("div");
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div.className = "errormessage"
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div.innerHTML = message;
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document.body.insertBefore(div, document.body.firstChild);
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}
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}
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$('#registration').bind('submit', function(e) {
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$('#send').attr('disabled', 'disabled');
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// we need this value to detect submitting at backend
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var hidden_input = '<input type="hidden" id="create_user_button" name="create_user_button" value="Submit"/>';
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$("#email_input").before(hidden_input);
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var error_text_email= 'Please enter your valid email address';
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var error_text_email_long= 'Email cannot be more than 255 characters in length';
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var error_text_username_characters = 'Public name must contain only lowercase letters, numbers and "-". It also has to be shorter than 255 characters but longer than 3.';
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var error_text_password_short = 'Please use a password of at least 6 characters';
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var error_text_password_match = "Passwords don't match";
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var validForm = true;
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var email = $('#email_input').val();
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var name = $('#name_input').val()
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if (email.length > 255){ renderError(error_text_email_long); validForm = false;}
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else if (!validateString(email,"email")){ renderError(error_text_email); validForm = false;}
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else if (!($('#password_input').val() === $('#password_check_input').val())){ renderError(error_text_password_match); validForm = false;}
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else if ($('#password_input').val().length < 6 ){ renderError(error_text_password_short); validForm = false;}
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else if (!(validateString(name,"username"))){ renderError(error_text_username_characters); validForm = false;}
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|
||||
if (!validForm) {
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e.preventDefault();
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||||
// reactivate the button if the form wasn't submitted
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$('#send').removeAttr('disabled');
|
||||
}
|
||||
});
|
||||
});
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||||
|
||||
</script>
|
||||
<div class="toolForm">
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||||
<form name="registration" id="registration" action="${form_action}" method="post" >
|
||||
<div class="toolFormTitle">Create account</div>
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||||
<div class="form-row">
|
||||
<label>Email address:</label>
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||||
<input type="text" name="email" value="${email | h}" size="40"/>
|
||||
<input id="email_input" type="text" name="email" value="${email | h}" size="40"/>
|
||||
<input type="hidden" name="redirect" value="${redirect | h}" size="40"/>
|
||||
</div>
|
||||
<div class="form-row">
|
||||
<label>Password:</label>
|
||||
<input type="password" name="password" value="" size="40"/>
|
||||
<input id="password_input" type="password" name="password" value="" size="40"/>
|
||||
</div>
|
||||
<div class="form-row">
|
||||
<label>Confirm password:</label>
|
||||
<input type="password" name="confirm" value="" size="40"/>
|
||||
<input id="password_check_input" type="password" name="confirm" value="" size="40"/>
|
||||
</div>
|
||||
<div class="form-row">
|
||||
<label>Public name:</label>
|
||||
<input type="text" name="username" size="40" value="${username |h}"/>
|
||||
<input id="name_input" type="text" name="username" size="40" value="${username |h}"/>
|
||||
%if t.webapp.name == 'galaxy':
|
||||
<div class="toolParamHelp" style="clear: both;">
|
||||
Your public name is an identifier that will be used to generate addresses for information
|
||||
@@ -103,8 +160,12 @@
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||||
<input type="hidden" name="user_type_fd_id" value="${trans.security.encode_id( user_type_form_definition.id )}"/>
|
||||
%endif
|
||||
%endif
|
||||
<div id="for_bears">
|
||||
If you see this, please leave following field blank.
|
||||
<input type="text" name="please leave this field blank" size="1" value=""/>
|
||||
</div>
|
||||
<div class="form-row">
|
||||
<input type="submit" name="create_user_button" value="Submit"/>
|
||||
<input type="submit" id="send" name="create_user_button" value="Submit"/>
|
||||
</div>
|
||||
</form>
|
||||
%if registration_warning_message:
|
||||
|
||||
@@ -952,11 +952,11 @@ class TwillTestCase( unittest.TestCase ):
|
||||
# HACK: don't use panels because late_javascripts() messes up the twill browser and it
|
||||
# can't find form fields (and hence user can't be logged in).
|
||||
self.visit_url( "%s/user/create?cntrller=%s&use_panels=False" % ( self.url, cntrller ) )
|
||||
tc.fv( '1', 'email', email )
|
||||
tc.fv( '1', 'redirect', redirect )
|
||||
tc.fv( '1', 'password', password )
|
||||
tc.fv( '1', 'confirm', password )
|
||||
tc.fv( '1', 'username', username )
|
||||
tc.fv( 'registration', 'email', email )
|
||||
tc.fv( 'registration', 'redirect', redirect )
|
||||
tc.fv( 'registration', 'password', password )
|
||||
tc.fv( 'registration', 'confirm', password )
|
||||
tc.fv( 'registration', 'username', username )
|
||||
tc.submit( 'create_user_button' )
|
||||
previously_created = False
|
||||
username_taken = False
|
||||
|
||||
@@ -8,39 +8,59 @@ log = logging.getLogger(__name__)
|
||||
def delete_obj( obj ):
|
||||
sa_session.delete( obj )
|
||||
sa_session.flush()
|
||||
|
||||
def delete_user_roles( user ):
|
||||
for ura in user.roles:
|
||||
sa_session.delete( ura )
|
||||
sa_session.flush()
|
||||
|
||||
def flush( obj ):
|
||||
sa_session.add( obj )
|
||||
sa_session.flush()
|
||||
|
||||
def get_repository( repository_id ):
|
||||
return sa_session.query( model.ToolShedRepository ) \
|
||||
.filter( model.ToolShedRepository.table.c.id == repository_id ) \
|
||||
.first()
|
||||
|
||||
def get_installed_repository_by_name_owner_changeset_revision( name, owner, changeset_revision ):
|
||||
return sa_session.query( model.ToolShedRepository ) \
|
||||
.filter( and_( model.ToolShedRepository.table.c.name == name,
|
||||
model.ToolShedRepository.table.c.owner == owner,
|
||||
model.ToolShedRepository.table.c.installed_changeset_revision == changeset_revision ) ) \
|
||||
.one()
|
||||
|
||||
def get_private_role( user ):
|
||||
for role in user.all_roles():
|
||||
if role.name == user.email and role.description == 'Private Role for %s' % user.email:
|
||||
return role
|
||||
raise AssertionError( "Private role not found for user '%s'" % user.email )
|
||||
|
||||
def get_tool_dependencies_for_installed_repository( repository_id, status=None ):
|
||||
if status is not None:
|
||||
return sa_session.query( model.ToolDependency ) \
|
||||
.filter( and_( model.ToolDependency.table.c.tool_shed_repository_id == repository_id,
|
||||
model.ToolDependency.table.c.status == status ) ) \
|
||||
.all()
|
||||
else:
|
||||
return sa_session.query( model.ToolDependency ) \
|
||||
.filter( model.ToolDependency.table.c.tool_shed_repository_id == repository_id ) \
|
||||
.all()
|
||||
|
||||
def mark_obj_deleted( obj ):
|
||||
obj.deleted = True
|
||||
sa_session.add( obj )
|
||||
sa_session.flush()
|
||||
|
||||
def refresh( obj ):
|
||||
sa_session.refresh( obj )
|
||||
|
||||
def get_private_role( user ):
|
||||
for role in user.all_roles():
|
||||
if role.name == user.email and role.description == 'Private Role for %s' % user.email:
|
||||
return role
|
||||
raise AssertionError( "Private role not found for user '%s'" % user.email )
|
||||
|
||||
def get_user( email ):
|
||||
return sa_session.query( model.User ) \
|
||||
.filter( model.User.table.c.email==email ) \
|
||||
|
||||
@@ -149,4 +149,20 @@ class InstallTestRepository( TwillTestCase ):
|
||||
strings_displayed.append( 'has been deactivated' )
|
||||
else:
|
||||
strings_displayed.append( 'has been uninstalled' )
|
||||
self.check_for_strings( strings_displayed, strings_not_displayed=[] )
|
||||
self.check_for_strings( strings_displayed, strings_not_displayed=[] )
|
||||
# Get all tool dependencies that are in an error state and uninstall them explicitly, so that the next installation attempt
|
||||
# may succeed.
|
||||
error_state = model.ToolDependency.installation_status.ERROR
|
||||
tool_dependencies = test_db_util.get_tool_dependencies_for_installed_repository( installed_repository.id, status=error_state )
|
||||
if len( tool_dependencies ) > 0:
|
||||
encoded_tool_dependency_ids = [ self.security.encode_id( tool_dependency.id ) for tool_dependency in tool_dependencies ]
|
||||
self.uninstall_tool_dependencies( self.security.encode_id( installed_repository.id ), encoded_tool_dependency_ids )
|
||||
|
||||
def uninstall_tool_dependencies( self, encoded_repository_id, encoded_tool_dependency_ids ):
|
||||
tool_dependency_ids = ','.join( encoded_tool_dependency_ids )
|
||||
url = '/admin_toolshed/uninstall_tool_dependencies?repository_id=%s&inst_td_ids=%s&operation=uninstall' % \
|
||||
( encoded_repository_id, tool_dependency_ids )
|
||||
self.visit_url( url )
|
||||
tc.fv( 'uninstall_tool_dependencies', 'tool_dependency_ids', tool_dependency_ids )
|
||||
tc.submit( 'uninstall_tool_dependencies_button' )
|
||||
|
||||
Reference in New Issue
Block a user