Merge branch 'dev' into fix_workflow_ui

galaxyproject · Jan 24, 2017 · 3911cb0 · 3911cb0
2 parents 9c9c4d2 + 3c4413d
commit 3911cb0
Show file tree

Hide file tree

Showing 160 changed files with 2,923 additions and 1,463 deletions.
diff --git a/.ci/flake8_lint_include_list.txt b/.ci/flake8_lint_include_list.txt
@@ -264,35 +264,7 @@ lib/galaxy/sample_tracking/__init__.py
 lib/galaxy/sample_tracking/sample.py
 lib/galaxy/security/validate_user_input.py
 lib/galaxy/tags/
-lib/galaxy/tools/actions/
-lib/galaxy/tools/cwl/
-lib/galaxy/tools/data_manager/__init__.py
-lib/galaxy/tools/deps/
-lib/galaxy/tools/exception_handling.py
-lib/galaxy/tools/execute.py
-lib/galaxy/tools/filters/
-lib/galaxy/tools/imp_exp/export_history.py
-lib/galaxy/tools/imp_exp/__init__.py
-lib/galaxy/tools/linters/
-lib/galaxy/tools/lint.py
-lib/galaxy/tools/lint_util.py
-lib/galaxy/tools/loader_directory.py
-lib/galaxy/tools/loader.py
-lib/galaxy/tools/parameters/dataset_matcher.py
-lib/galaxy/tools/parameters/history_query.py
-lib/galaxy/tools/parameters/__init__.py
-lib/galaxy/tools/parameters/input_translation.py
-lib/galaxy/tools/parameters/sanitize.py
-lib/galaxy/tools/parameters/validation.py
-lib/galaxy/tools/parameters/wrapped_json.py
-lib/galaxy/tools/parameters/wrapped.py
-lib/galaxy/tools/parser/
-lib/galaxy/tools/special_tools.py
-lib/galaxy/tools/test.py
-lib/galaxy/tools/toolbox/
-lib/galaxy/tools/util/galaxyops/
-lib/galaxy/tools/util/__init__.py
-lib/galaxy/tools/verify/
+lib/galaxy/tools/
 lib/galaxy/util/
 lib/galaxy_utils/__init__.py
 lib/galaxy/util/sleeper.py

diff --git a/.ci/jenkins/selenium/run_galaxy.bash b/.ci/jenkins/selenium/run_galaxy.bash
@@ -2,9 +2,12 @@
 
 set -e
 
-sleep 30  # TODO: wait on something instead of just sleeping...
-
-echo `df`
+echo "Waiting for postgres to become available"
+while ! nc -z postgres 5432;
+do
+    sleep 1
+    printf "."
+done
 
 echo "Creating postgres database for Galaxy"
 createdb -w -U postgres -h postgres galaxy

diff --git a/.ci/py3_sources.txt b/.ci/py3_sources.txt
@@ -40,26 +40,7 @@ lib/galaxy/quota/
 lib/galaxy/sample_tracking/
 lib/galaxy/security/
 lib/galaxy/tags/
-lib/galaxy/tools/actions/
-lib/galaxy/tools/cwl/
-lib/galaxy/tools/deps/
-lib/galaxy/tools/exception_handling.py
-lib/galaxy/tools/execute.py
-lib/galaxy/tools/lint.py
-lib/galaxy/tools/lint_util.py
-lib/galaxy/tools/linters/
-lib/galaxy/tools/loader.py
-lib/galaxy/tools/loader_directory.py
-lib/galaxy/tools/parameters/dataset_matcher.py
-lib/galaxy/tools/parameters/__init__.py
-lib/galaxy/tools/parameters/input_translation.py
-lib/galaxy/tools/parameters/sanitize.py
-lib/galaxy/tools/parameters/validation.py
-lib/galaxy/tools/parameters/wrapped_json.py
-lib/galaxy/tools/parameters/wrapped.py
-lib/galaxy/tools/parser/
-lib/galaxy/tools/test.py
-lib/galaxy/tools/toolbox/
+lib/galaxy/tools/
 lib/galaxy/tours/
 lib/galaxy/util/
 lib/galaxy/visualization/

diff --git a/README.rst b/README.rst
@@ -9,9 +9,13 @@ The latest information about Galaxy is available via `https://galaxyproject.org/
 
 .. image:: https://img.shields.io/badge/chat-irc.freenode.net%23galaxyproject-blue.svg
     :target: https://webchat.freenode.net/?channels=galaxyproject
-    :alt: Chat with us
+    :alt: Chat on irc
+
+.. image:: https://img.shields.io/badge/chat-gitter-blue.svg
+    :target: https://gitter.im/galaxyproject/Lobby
+    :alt: Chat on gitter
 
-.. image:: https://img.shields.io/badge/docs-release-green.svg
+.. image:: https://img.shields.io/badge/release-documentation-blue.svg
     :target: https://docs.galaxyproject.org/en/master/
     :alt: Release Documentation
 

diff --git a/client/galaxy/scripts/mvc/form/form-view.js b/client/galaxy/scripts/mvc/form/form-view.js
@@ -125,7 +125,7 @@ function( Utils, Portlet, Ui, FormSection, FormData ) {
         _renderForm: function() {
             $( '.tooltip' ).remove();
             var options = this.model.attributes;
-            this.message = new Ui.Message();
+            this.message = new Ui.UnescapedMessage();
             this.section = new FormSection.View( this, { inputs: options.inputs } );
             this.portlet = new Portlet.View({
                 icon            : options.icon,
@@ -145,4 +145,4 @@ function( Utils, Portlet, Ui, FormSection, FormData ) {
             Galaxy.emit.debug( 'form-view::initialize()', 'Completed' );
         }
     });
-});
+});
diff --git a/client/galaxy/scripts/mvc/ui/ui-misc.js b/client/galaxy/scripts/mvc/ui/ui-misc.js
@@ -62,7 +62,7 @@ define(['utils/utils',
                 this.$el.addClass( 'alert' ).addClass( 'alert-' + status );
             }
             if ( this.model.get( 'message' ) ) {
-                this.$el.html( this.model.get( 'message' ) );
+                this.$el.html( this.messageForDisplay() );
                 this.$el[ this.model.get( 'fade' ) ? 'fadeIn' : 'show' ]();
                 this.timeout && window.clearTimeout( this.timeout );
                 if ( !this.model.get( 'persistent' ) ) {
@@ -75,6 +75,15 @@ define(['utils/utils',
                 this.$el.fadeOut();
             }
             return this;
+        },
+        messageForDisplay: function() {
+            return _.escape( this.model.get( 'message' ) );
+        }
+    });
+
+    var UnescapedMessage = Message.extend({
+        messageForDisplay: function() {
+            return this.model.get( 'message' );
         }
     });
 
@@ -157,21 +166,22 @@ define(['utils/utils',
     });
 
     return {
-        Button      : Buttons.ButtonDefault,
-        ButtonIcon  : Buttons.ButtonIcon,
-        ButtonCheck : Buttons.ButtonCheck,
-        ButtonMenu  : Buttons.ButtonMenu,
-        ButtonLink  : Buttons.ButtonLink,
-        Input       : Input,
-        Label       : Label,
-        Message     : Message,
-        Modal       : Modal,
-        RadioButton : Options.RadioButton,
-        Checkbox    : Options.Checkbox,
-        Radio       : Options.Radio,
-        Select      : Select,
-        Hidden      : Hidden,
-        Slider      : Slider,
-        Drilldown   : Drilldown
+        Button           : Buttons.ButtonDefault,
+        ButtonIcon       : Buttons.ButtonIcon,
+        ButtonCheck      : Buttons.ButtonCheck,
+        ButtonMenu       : Buttons.ButtonMenu,
+        ButtonLink       : Buttons.ButtonLink,
+        Input            : Input,
+        Label            : Label,
+        Message          : Message,
+        UnescapedMessage : UnescapedMessage,
+        Modal            : Modal,
+        RadioButton      : Options.RadioButton,
+        Checkbox         : Options.Checkbox,
+        Radio            : Options.Radio,
+        Select           : Select,
+        Hidden           : Hidden,
+        Slider           : Slider,
+        Drilldown        : Drilldown
     }
-});
+});
diff --git a/client/galaxy/scripts/viz/trackster/tracks.js b/client/galaxy/scripts/viz/trackster/tracks.js
@@ -1222,18 +1222,23 @@ extend( TracksterView.prototype, DrawableCollection.prototype, {
                     view.reference_track = ref_track;
                 }
                 view.chrom_data = result.chrom_info;
-                var chrom_options = '<option value="">Select Chrom/Contig</option>';
+
+                view.chrom_select.html('');
+                view.chrom_select.append($('<option value="">Select Chrom/Contig</option>'));
+
                 for (var i = 0, len = view.chrom_data.length; i < len; i++) {
                     var chrom = view.chrom_data[i].chrom;
-                    chrom_options += '<option value="' + chrom + '">' + chrom + '</option>';
+                    var chrom_option  = $("<option>");
+                    chrom_option.text(chrom);
+                    chrom_option.val(chrom);
+                    view.chrom_select.append(chrom_option);
                 }
                 if (result.prev_chroms) {
-                    chrom_options += '<option value="previous">Previous ' + MAX_CHROMS_SELECTABLE + '</option>';
+                    view.chrom_select.append($('<option value="previous">Previous ' + MAX_CHROMS_SELECTABLE + '</option>'));
                 }
                 if (result.next_chroms) {
-                    chrom_options += '<option value="next">Next ' + MAX_CHROMS_SELECTABLE + '</option>';
+                    view.chrom_select.append($('<option value="next">Next ' + MAX_CHROMS_SELECTABLE + '</option>'));
                 }
-                view.chrom_select.html(chrom_options);
                 view.chrom_start_index = result.start_index;
 
                 chrom_data.resolve(result.chrom_info);

diff --git a/config/datatypes_conf.xml.sample b/config/datatypes_conf.xml.sample
@@ -38,6 +38,7 @@
     <datatype extension="len" type="galaxy.datatypes.chrominfo:ChromInfo" display_in_upload="true">
       <converter file="len_to_linecount.xml" target_datatype="linecount" />
     </datatype>
+    <datatype extension="dmnd" type="galaxy.datatypes.binary:Binary:DMND" subclass="True" display_in_upload="false"/>
     <datatype extension="bigbed" type="galaxy.datatypes.binary:BigBed" mimetype="application/octet-stream" display_in_upload="true">
       <display file="ucsc/bigbed.xml" />
       <display file="igb/bb.xml" />
@@ -87,6 +88,36 @@
     <datatype extension="fastqillumina" type="galaxy.datatypes.sequence:FastqIllumina" display_in_upload="true">
         <converter file="fastq_to_fqtoc.xml" target_datatype="fqtoc"/>
     </datatype>
+    <datatype extension="fastq.gz" type="galaxy.datatypes.sequence:FastqGz" display_in_upload="true">
+        <converter file="fastqgz_to_fastq.xml" target_datatype="fastq"/>
+    </datatype>
+    <datatype extension="fastqsanger.gz" type="galaxy.datatypes.sequence:FastqSangerGz" display_in_upload="true">
+        <converter file="fastqsangergz_to_fastqsanger.xml" target_datatype="fastqsanger"/>
+    </datatype>
+    <datatype extension="fastqsolexa.gz" type="galaxy.datatypes.sequence:FastqSolexaGz" display_in_upload="true">
+        <converter file="fastqsolexagz_to_fastqsolexa.xml" target_datatype="fastqsolexa"/>
+    </datatype>
+    <datatype extension="fastqcssanger.gz" type="galaxy.datatypes.sequence:FastqCSSangerGz" display_in_upload="true">
+        <converter file="fastqcssangergz_to_fastqcssanger.xml" target_datatype="fastqcssanger"/>
+    </datatype>
+    <datatype extension="fastqillumina.gz" type="galaxy.datatypes.sequence:FastqIlluminaGz" display_in_upload="true">
+        <converter file="fastqilluminagz_to_fastqillumina.xml" target_datatype="fastqillumina"/>
+    </datatype>
+    <datatype extension="fastq.bz2" type="galaxy.datatypes.sequence:FastqBz2" display_in_upload="true">
+        <converter file="fastqbz2_to_fastq.xml" target_datatype="fastq"/>
+    </datatype>
+    <datatype extension="fastqsanger.bz2" type="galaxy.datatypes.sequence:FastqSangerBz2" display_in_upload="true">
+        <converter file="fastqsangerbz2_to_fastqsanger.xml" target_datatype="fastqsanger"/>
+    </datatype>
+    <datatype extension="fastqsolexa.bz2" type="galaxy.datatypes.sequence:FastqSolexaBz2" display_in_upload="true">
+        <converter file="fastqsolexabz2_to_fastqsolexa.xml" target_datatype="fastqsolexa"/>
+    </datatype>
+    <datatype extension="fastqcssanger.bz2" type="galaxy.datatypes.sequence:FastqCSSangerBz2" display_in_upload="true">
+        <converter file="fastqcssangerbz2_to_fastqcssanger.xml" target_datatype="fastqcssanger"/>
+    </datatype>
+    <datatype extension="fastqillumina.bz2" type="galaxy.datatypes.sequence:FastqIlluminaBz2" display_in_upload="true">
+        <converter file="fastqilluminabz2_to_fastqillumina.xml" target_datatype="fastqillumina"/>
+    </datatype>
     <datatype extension="fqtoc" type="galaxy.datatypes.sequence:SequenceSplitLocations" display_in_upload="true"/>
     <datatype extension="eland" type="galaxy.datatypes.tabular:Eland" display_in_upload="true"/>
     <datatype extension="elandmulti" type="galaxy.datatypes.tabular:ElandMulti" display_in_upload="true"/>
@@ -606,6 +637,7 @@
     <sniffer type="galaxy.datatypes.binary:Sff"/>
     <sniffer type="galaxy.datatypes.binary:Sra"/>
     <sniffer type="galaxy.datatypes.binary:NetCDF"/>
+    <sniffer type="galaxy.datatypes.binary:DMND" />
     <sniffer type="galaxy.datatypes.triples:Rdf"/>
     <sniffer type="galaxy.datatypes.blast:BlastXml"/>
     <sniffer type="galaxy.datatypes.xml:Phyloxml"/>
@@ -642,6 +674,8 @@
     <!-- TODO: see molecules.py <sniffer type="galaxy.datatypes.molecules:SMILES"/>-->
     <sniffer type="galaxy.datatypes.sequence:Fasta"/>
     <sniffer type="galaxy.datatypes.sequence:Fastq"/>
+    <sniffer type="galaxy.datatypes.sequence:FastqGz"/>
+    <sniffer type="galaxy.datatypes.sequence:FastqBz2"/>
     <sniffer type="galaxy.datatypes.interval:Wiggle"/>
     <sniffer type="galaxy.datatypes.text:Html"/>
     <sniffer type="galaxy.datatypes.images:Pdf"/>

diff --git a/config/galaxy.ini.sample b/config/galaxy.ini.sample
@@ -210,7 +210,7 @@ paste.app_factory = galaxy.web.buildapp:app_factory
 #conda_auto_install = False
 # Set to True to instruct Galaxy to install Conda from the web automatically
 # if it cannot find a local copy and conda_exec is not configured.
-#conda_auto_init = False
+#conda_auto_init = True
 # You must set this to True if conda_prefix and job_working_directory are not on the same
 # volume, or some conda dependencies will fail to execute at job runtime.
 # Conda will copy packages content instead of creating hardlinks or symlinks.
@@ -909,6 +909,16 @@ use_interactive = True
 # results will appear.
 # tool_search_limit = 20
 
+# Enable/ disable Ngram-search for tools. It makes tool
+# search results tolerant for spelling mistakes in the query
+# by dividing the query into multiple ngrams and search for
+# each ngram
+#tool_enable_ngram_search = False
+
+# Set minimum and maximum sizes of ngrams
+#tool_ngram_minsize = 3
+#tool_ngram_maxsize = 4
+
 # -- Users and Security
 
 # Galaxy encodes various internal values when these values will be output in

diff --git a/config/local_conda_mapping.yml.sample b/config/local_conda_mapping.yml.sample
@@ -0,0 +1,2 @@
+# See $GALAXY_ROOT/lib/galaxy/tools/deps/default_conda_mapping.yml for example mapping - 
+# additional site-specific mappings can be added to config/conda_mapping.yml.
diff --git a/config/plugins/interactive_environments/rstudio/templates/rstudio.mako b/config/plugins/interactive_environments/rstudio/templates/rstudio.mako
@@ -33,7 +33,7 @@ ie_request.launch(
 # through proxy.
 notebook_pubkey_url = ie_request.url_template('${PROXY_URL}/rstudio/auth-public-key')
 notebook_access_url = ie_request.url_template('${PROXY_URL}/rstudio/')
-notebook_login_url =  ie_request.url_template('${PROXY_URL}/rstudio/auth-sign-in')
+notebook_login_url =  ie_request.url_template('${PROXY_URL}/rstudio/auth-do-sign-in')
 
 %>
 <html>

diff --git a/config/plugins/visualizations/charts/templates/charts.mako b/config/plugins/visualizations/charts/templates/charts.mako
@@ -8,7 +8,7 @@
 <html>
     <head>
         <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-        <title>${hda.name} | ${visualization_name}</title>
+        <title>${hda.name | h} | ${visualization_name}</title>
         ${h.js( 'libs/jquery/jquery',
                 'libs/jquery/jquery-ui',
                 'libs/jquery/select2',

diff --git a/config/plugins/visualizations/csg/templates/csg.mako b/config/plugins/visualizations/csg/templates/csg.mako
@@ -7,7 +7,7 @@
 <html>
     <head>
         <!-- CSG Viewer is a web application for 3D shape visualization. -->
-        <title>${hda.name} | ${visualization_name}</title>
+        <title>${hda.name | h} | ${visualization_name}</title>
         ${h.javascript_link( app_root + 'dat.gui.min.js' )}
         ${h.javascript_link( app_root + 'three.min.js' )}
         ${h.javascript_link( app_root + 'Detector.js' )}

diff --git a/config/plugins/visualizations/graphviz/templates/graphviz.mako b/config/plugins/visualizations/graphviz/templates/graphviz.mako
@@ -5,7 +5,7 @@
     <meta charset="utf-8">
     <meta name="viewport" content="width=device-width, user-scalable=no, minimum-scale=1.0, maximum-scale=1.0">
 
-    <title>${hda.name} | ${visualization_name}</title>
+    <title>${hda.name | h} | ${visualization_name}</title>
     <%
         root = h.url_for( '/' )
     %>

diff --git a/config/plugins/visualizations/scatterplot/templates/scatterplot.mako b/config/plugins/visualizations/scatterplot/templates/scatterplot.mako
@@ -16,7 +16,7 @@
 <html>
 <head>
 <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-<title>${title or default_title} | ${visualization_display_name}</title>
+<title>${title or default_title | h} | ${visualization_display_name}</title>
 
 ## ----------------------------------------------------------------------------
 ${h.css( 'base', 'jquery-ui/smoothness/jquery-ui')}

diff --git a/config/plugins/webhooks/demo/phdcomics/helper/__init__.py b/config/plugins/webhooks/demo/phdcomics/helper/__init__.py
@@ -8,15 +8,15 @@
 
 def main(trans, webhook):
     error = ''
-    data = {}
+    comic_src = ''
 
     try:
         # Third-party dependencies
         try:
             from bs4 import BeautifulSoup
         except ImportError as e:
             log.exception(e)
-            return {}
+            return {'success': False, 'error': str(e)}
 
         # Get latest id
         if 'latest_id' not in webhook.config.keys():
@@ -33,11 +33,16 @@ def main(trans, webhook):
         url = 'http://www.phdcomics.com/comics/archive.php?comicid=%d' % \
             random_id
         content = urllib.urlopen(url).read()
-        soap = BeautifulSoup(content, 'html.parser')
-        comics_src = soap.find_all('img', id='comic')[0].attrs.get('src')
-        data = {'src': comics_src}
+        soup = BeautifulSoup(content, 'html.parser')
+        comic_img = soup.find_all('img', id='comic2')
+
+        try:
+            comic_src = comic_img[0].attrs.get('src')
+        except IndexError:
+            pattern = '<img id=comic2 name=comic2 src=([\w:\/\.]+)'
+            comic_src = re.search(pattern, content).group(1)
 
     except Exception as e:
         error = str(e)
 
-    return {'success': not error, 'error': error, 'data': data}
+    return {'success': not error, 'error': error, 'src': comic_src}