Merge branch 'dev' into remove_toolshed_grids

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 );
             },

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!).

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/jobs/actions/post.py

@@ -3,14 +3,14 @@
 immediate_actions listed below.  Currently only used in workflows.
 """
 import datetime
-import logging
 import socket
 
 from markupsafe import escape
 
 from galaxy.util import send_mail
+from galaxy.util.logging import get_logger
 
-log = logging.getLogger(__name__)
+log = get_logger(__name__)
 
 
 class DefaultJobAction(object):
@@ -308,6 +308,7 @@ def execute(cls, app, sa_session, action, job, replacement_dict):
                     safe_to_delete = True
                     for job_to_check in [d_j.job for d_j in input_dataset.dependent_jobs]:
                         if job_to_check != job and job_to_check.state not in [job.states.OK, job.states.DELETED]:
+                            log.trace("Workflow Intermediates cleanup attempted, but non-terminal state '%s' detected for job %s" % (job_to_check.state, job_to_check.id))
                             safe_to_delete = False
                     if safe_to_delete:
                         # Support purging here too.