Merge branch 'dev' into remove_samples_000

client/galaxy/scripts/mvc/history/history-view.js

@@ -75,6 +75,9 @@ var HistoryView = _super.extend(
         // control contents/behavior based on where (and in what context) the panel is being used
         /** where should pages from links be displayed? (default to new tab/window) */
         this.linkTarget = attributes.linkTarget || '_blank';
+
+        /** timeout id for detailed fetch of collection counts, etc... */
+        this.detailedFetchTimeoutId = null;
     },
 
     /** create and return a collection for when none is initially passed */
@@ -89,9 +92,18 @@ var HistoryView = _super.extend(
         if( this.model ){
             this.model.clearUpdateTimeout();
         }
+        this._clearDetailedFetchTimeout();
         return this;
     },
 
+    /** clear the timeout and the cached timeout id */
+    _clearDetailedFetchTimeout : function(){
+        if( this.detailedFetchTimeoutId ){
+            clearTimeout( this.detailedFetchTimeoutId );
+            this.detailedFetchTimeoutId = null;
+        }
+    },
+
     /** create any event listeners for the panel
      *  @fires: rendered:initial    on the first render
      *  @fires: empty-history       when switching to a history with no contents or creating a new history
@@ -105,7 +117,8 @@ var HistoryView = _super.extend(
             'loading-done' : function(){
                 var self = this;
                 // after the initial load, decorate with more time consuming fields (like HDCA element_counts)
-                _.delay( function(){
+                self.detailedFetchTimeoutId = _.delay( function(){
+                    self.detailedFetchTimeoutId = null;
                     self.model.contents.fetchCollectionCounts();
                 }, self.FETCH_COLLECTION_COUNTS_DELAY );
             },

client/galaxy/scripts/mvc/library/library-folderlist-view.js

@@ -357,7 +357,7 @@ var FolderListView = Backbone.View.extend({
       '</ol>',
 
       // FOLDER CONTENT
-      '<table data-library-id="<%- parent_library_id  %>" id="folder_table" class="grid table table-condensed">',
+      '<table data-library-id="<%- parent_library_id  %>" class="grid table table-condensed">',
         '<thead>',
           '<th class="button_heading"></th>',
           '<th style="text-align: center; width: 20px; " title="Check to select all datasets"><input id="select-all-checkboxes" style="margin: 0;" type="checkbox"></th>',

client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js

@@ -207,8 +207,8 @@ var FolderToolbarView = Backbone.View.extend({
 
   // show bulk import modal
   modalBulkImport : function(){
-      var checkedValues = $('#folder_table').find(':checked');
-      if(checkedValues.length === 0){
+      var $checkedValues = this.findCheckedRows();
+      if($checkedValues.length === 0){
           mod_toastr.info('You must select some datasets first.');
       } else {
         var that = this;
@@ -268,7 +268,7 @@ var FolderToolbarView = Backbone.View.extend({
   processImportToHistory: function( history_id, history_name ){
     var dataset_ids = [];
     var folder_ids = [];
-    $('#folder_table').find(':checked').each(function(){
+    this.findCheckedRows().each(function(){
         var row_id = $(this).closest('tr').data('id');
         if (row_id.substring(0,1) == 'F'){
             folder_ids.push(row_id);
@@ -323,7 +323,7 @@ var FolderToolbarView = Backbone.View.extend({
   download : function( folder_id, format ){
     var dataset_ids = [];
     var folder_ids = [];
-        $( '#folder_table' ).find( ':checked' ).each( function(){
+        this.findCheckedRows().each( function(){
             var row_id = $(this).closest('tr').data('id');
             if (row_id.substring(0,1) == 'F'){
                 folder_ids.push(row_id);
@@ -997,7 +997,7 @@ var FolderToolbarView = Backbone.View.extend({
   deleteSelectedItems: function(){
     var dataset_ids = [];
     var folder_ids = [];
-    var $checkedValues = $('#folder_table').find(':checked');
+    var $checkedValues = this.findCheckedRows();
     if($checkedValues.length === 0){
         mod_toastr.info('You must select at least one item for deletion.');
     } else {
@@ -1116,6 +1116,10 @@ var FolderToolbarView = Backbone.View.extend({
     }
   },
 
+  findCheckedRows: function(){
+    return $('#folder_list_body').find(':checked');
+  },
+
   templateToolBar: function(){
     return _.template([
     // container start

client/galaxy/scripts/onload.js

@@ -184,13 +184,21 @@ $(document).ready( function() {
         }
     }
 
-    // Load all webhooks with the type 'onload'
-    $.getJSON( Galaxy.root + 'api/webhooks/onload/all', function(webhooks) {
-        _.each(webhooks, function(webhook) {
-            if (webhook.activate && webhook.script) {
-                $('<script/>', {type: 'text/javascript'}).text(webhook.script).appendTo('head');
-                $('<style/>', {type: 'text/css'}).text(webhook.styles).appendTo('head');
-            }
-        });
-    });
+    function onloadWebhooks() {
+        if (Galaxy.root !== undefined){
+            // Load all webhooks with the type 'onload'
+            $.getJSON( Galaxy.root + 'api/webhooks/onload/all', function(webhooks) {
+                _.each(webhooks, function(webhook) {
+                    if (webhook.activate && webhook.script) {
+                        $('<script/>', {type: 'text/javascript'}).text(webhook.script).appendTo('head');
+                        $('<style/>', {type: 'text/css'}).text(webhook.styles).appendTo('head');
+                    }
+                });
+            });
+        }
+        else {
+            setTimeout(onloadWebhooks, 100);
+        }
+    }
+    onloadWebhooks();
 });

config/datatypes_conf.xml.sample

@@ -234,6 +234,7 @@
     <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="postgresql" type="galaxy.datatypes.binary:PostgresqlArchive" subclass="True" display_in_upload="True"/>
     <datatype extension="searchgui_archive" type="galaxy.datatypes.binary:SearchGuiArchive" display_in_upload="true"/>
     <datatype extension="fast5.tar" type="galaxy.datatypes.binary:Fast5Archive" display_in_upload="true"/>
     <datatype extension="fast5.tar.gz" type="galaxy.datatypes.binary:Fast5ArchiveGz" display_in_upload="true"/>
@@ -679,6 +680,7 @@
     <sniffer type="galaxy.datatypes.binary:Fast5ArchiveGz" />
     <sniffer type="galaxy.datatypes.binary:Fast5ArchiveBz2" />
     <sniffer type="galaxy.datatypes.binary:Fast5Archive" />
+    <sniffer type="galaxy.datatypes.binary:PostgresqlArchive"/>
     <sniffer type="galaxy.datatypes.triples:Rdf"/>
     <sniffer type="galaxy.datatypes.blast:BlastXml"/>
     <sniffer type="galaxy.datatypes.xml:Phyloxml"/>

config/galaxy.ini.sample

@@ -779,6 +779,7 @@ nglims_config_file = tool-data/nglims.yaml
 
 # Verbosity of console log messages.  Acceptable values can be found here:
 # https://docs.python.org/2/library/logging.html#logging-levels
+# A custom debug level of "TRACE" is available for even more verbosity.
 #log_level = DEBUG
 
 # Print database operations to the server log (warning, quite verbose!).
@@ -978,7 +979,7 @@ use_interactive = True
 # Galaxy encodes various internal values when these values will be output in
 # some format (for example, in a URL or cookie).  You should set a key to be
 # used by the algorithm that encodes and decodes these values.  It can be any
-# string.
+# string up to 448 bits long.
 # One simple way to generate a value for this is with the shell command:
 #   python -c 'import time; print time.time()' | md5sum | cut -f 1 -d ' '
 #id_secret = USING THE DEFAULT IS NOT SECURE!

lib/galaxy/__init__.py

@@ -4,17 +4,3 @@
 
 from pkgutil import extend_path
 __path__ = extend_path(__path__, __name__)
-
-
-# compat: BadZipFile introduced in Python 2.7
-import zipfile
-if not hasattr(zipfile, 'BadZipFile'):
-    zipfile.BadZipFile = zipfile.error
-
-# compat: patch to add the NullHandler class to logging
-import logging
-if not hasattr(logging, 'NullHandler'):
-    class NullHandler(logging.Handler):
-        def emit(self, record):
-            pass
-    logging.NullHandler = NullHandler

lib/galaxy/app.py

@@ -226,7 +226,7 @@ def shutdown(self):
 
     def configure_fluent_log(self):
         if self.config.fluent_log:
-            from galaxy.util.log.fluent_log import FluentTraceLogger
+            from galaxy.util.logging.fluent_log import FluentTraceLogger
             self.trace_logger = FluentTraceLogger('galaxy', self.config.fluent_host, self.config.fluent_port)
         else:
             self.trace_logger = None

lib/galaxy/config.py

@@ -29,6 +29,7 @@
 from galaxy.util import string_as_bool
 from galaxy.util import unicodify
 from galaxy.util.dbkeys import GenomeBuilds
+from galaxy.util.logging import LOGLV_TRACE
 from galaxy.web.formatting import expand_pretty_datetime_format
 from galaxy.web.stack import register_postfork_function
 from .version import VERSION_MAJOR
@@ -876,6 +877,7 @@ def configure_logging(config):
     or a simple dictionary of configuration variables.
     """
     # Get root logger
+    logging.addLevelName(LOGLV_TRACE, "TRACE")
     root = logging.getLogger()
     # PasteScript will have already configured the logger if the
     # 'loggers' section was found in the config file, otherwise we do

lib/galaxy/datatypes/binary.py

@@ -1566,6 +1566,59 @@ def sniff(self, filename):
                                         OxliGraphLabels)
 
 
+class PostgresqlArchive(CompressedArchive):
+    """
+    Class describing a Postgresql database packed into a tar archive
+
+    >>> from galaxy.datatypes.sniff import get_test_fname
+    >>> fname = get_test_fname( 'postgresql_fake.tar.bz2' )
+    >>> PostgresqlArchive().sniff( fname )
+    True
+    >>> fname = get_test_fname( 'test.fast5.tar' )
+    >>> PostgresqlArchive().sniff( fname )
+    False
+    """
+    MetadataElement(name="version", default=None, param=MetadataParameter, desc="PostgreSQL database version",
+                    readonly=True, visible=True, no_value=None)
+    file_ext = "postgresql"
+
+    def set_meta(self, dataset, overwrite=True, **kwd):
+        super(PostgresqlArchive, self).set_meta(dataset, overwrite=overwrite, **kwd)
+        try:
+            if dataset and tarfile.is_tarfile(dataset.file_name):
+                with tarfile.open(dataset.file_name, 'r') as temptar:
+                    pg_version_file = temptar.extractfile('postgresql/db/PG_VERSION')
+                    dataset.metadata.version = pg_version_file.read().strip()
+        except Exception as e:
+            log.warning('%s, set_meta Exception: %s', self, e)
+
+    def sniff(self, filename):
+        if filename and tarfile.is_tarfile(filename):
+            try:
+                with tarfile.open(filename, 'r') as temptar:
+                    return 'postgresql/db/PG_VERSION' in temptar.getnames()
+            except Exception as e:
+                log.warning('%s, sniff Exception: %s', self, e)
+        return False
+
+    def set_peek(self, dataset, is_multi_byte=False):
+        if not dataset.dataset.purged:
+            dataset.peek = "PostgreSQL Archive (%s)" % (nice_size(dataset.get_size()))
+            dataset.blurb = "PostgreSQL version %s" % (dataset.metadata.version or 'unknown')
+        else:
+            dataset.peek = 'file does not exist'
+            dataset.blurb = 'file purged from disk'
+
+    def display_peek(self, dataset):
+        try:
+            return dataset.peek
+        except:
+            return "PostgreSQL Archive (%s)" % (nice_size(dataset.get_size()))
+
+
+Binary.register_sniffable_binary_format("postgresql_archiv", "postgresql", PostgresqlArchive)
+
+
 class Fast5Archive(CompressedArchive):
     """
     Class describing a FAST5 archive

lib/galaxy/datatypes/molecules.py

@@ -55,7 +55,7 @@ def count_lines(filename, non_empty=False):
 
 class GenericMolFile(data.Text):
     """
-        abstract class for most of the molecule files
+    Abstract class for most of the molecule files.
     """
     MetadataElement(name="number_of_molecules", default=0, desc="Number of molecules", readonly=True, visible=True, optional=True, no_value=0)
 
@@ -92,26 +92,53 @@ def sniff(self, filename):
         """
         Try to guess if the file is a SDF2 file.
 
+        An SDfile (structure-data file) can contain multiple compounds.
+
+        Each compound starts with a block in V2000 or V3000 molfile format,
+        which ends with a line equal to 'M  END'.
+        This is followed by a non-structural data block, which ends with a line
+        equal to '$$$$'.
+
         >>> from galaxy.datatypes.sniff import get_test_fname
         >>> fname = get_test_fname('drugbank_drugs.sdf')
         >>> SDF().sniff(fname)
         True
 
-        >>> fname = get_test_fname('drugbank_drugs.cml')
+        >>> fname = get_test_fname('github88.v3k.sdf')
+        >>> SDF().sniff(fname)
+        True
+
+        >>> fname = get_test_fname('chebi_57262.v3k.mol')
         >>> SDF().sniff(fname)
         False
         """
-        counter = count_special_lines("^M\s*END", filename) + count_special_lines("^\$\$\$\$", filename)
-        if counter > 0 and counter % 2 == 0:
-            return True
-        else:
-            return False
+        m_end_found = False
+        limit = 10000
+        idx = 0
+        with open(filename) as in_file:
+            for line in in_file:
+                idx += 1
+                line = line.rstrip('\n\r')
+                if idx < 4:
+                    continue
+                elif idx == 4:
+                    if len(line) != 39 or not(line.endswith(' V2000') or
+                            line.endswith(' V3000')):
+                        return False
+                elif not m_end_found:
+                    if line == 'M  END':
+                        m_end_found = True
+                elif line == '$$$$':
+                    return True
+                if idx == limit:
+                    break
+        return False
 
     def set_meta(self, dataset, **kwd):
         """
         Set the number of molecules in dataset.
         """
-        dataset.metadata.number_of_molecules = count_special_lines("^\$\$\$\$", dataset.file_name)
+        dataset.metadata.number_of_molecules = count_special_lines("^\$\$\$\$$", dataset.file_name)
 
     def split(cls, input_datasets, subdir_generator_function, split_params):
         """
@@ -180,10 +207,17 @@ def sniff(self, filename):
         >>> MOL2().sniff(fname)
         False
         """
-        if count_special_lines("@<TRIPOS>MOLECULE", filename) > 0:
-            return True
-        else:
-            return False
+        limit = 60
+        idx = 0
+        with open(filename) as in_file:
+            for line in in_file:
+                line = line.rstrip('\n\r')
+                if line == '@<TRIPOS>MOLECULE':
+                    return True
+                idx += 1
+                if idx == limit:
+                    break
+        return False
 
     def set_meta(self, dataset, **kwd):
         """
@@ -716,16 +750,13 @@ def sniff(self, filename):
         >>> CML().sniff(fname)
         True
         """
-        handle = open(filename)
-        line = handle.readline()
-        if line.strip() != '<?xml version="1.0"?>':
-            handle.close()
-            return False
-        line = handle.readline()
-        if line.strip().find('http://www.xml-cml.org/schema') == -1:
-            handle.close()
-            return False
-        handle.close()
+        with open(filename) as handle:
+            line = handle.readline()
+            if line.strip() != '<?xml version="1.0"?>':
+                return False
+            line = handle.readline()
+            if line.strip().find('http://www.xml-cml.org/schema') == -1:
+                return False
         return True
 
     def split(cls, input_datasets, subdir_generator_function, split_params):