Merge pull request #4799 from nsoranzo/python3

Python3: fix remaining print statements

.ci/flake8_lint_include_list.txt

@@ -57,6 +57,7 @@ lib/galaxy/managers/taggable.py
 lib/galaxy/model/
 lib/galaxy/objectstore/pulsar.py
 lib/galaxy/objectstore/s3_multipart_upload.py
+lib/galaxy/objectstore/s3.py
 lib/galaxy/openid/__init__.py
 lib/galaxy/quota/
 lib/galaxy/sample_tracking/data_transfer.py
@@ -81,6 +82,7 @@ lib/galaxy/visualization/tracks/
 lib/galaxy/web/base/
 lib/galaxy/web/buildapp.py
 lib/galaxy/web/formatting.py
+lib/galaxy/web/form_builder.py
 lib/galaxy/web/framework/base.py
 lib/galaxy/web/framework/decorators.py
 lib/galaxy/web/framework/helpers/grids.py
@@ -126,6 +128,7 @@ lib/galaxy/webapps/__init__.py
 lib/galaxy/webapps/reports/config.py
 lib/galaxy/webapps/reports/controllers/__init__.py
 lib/galaxy/webapps/reports/controllers/query.py
+lib/galaxy/webapps/reports/controllers/tools.py
 lib/galaxy/webapps/reports/__init__.py
 lib/galaxy/webapps/tool_shed/api/__init__.py
 lib/galaxy/webapps/tool_shed/controllers/groups.py

.ci/py3_sources.txt

@@ -70,6 +70,7 @@ scripts/communication/
 scripts/data_libraries/build_whoosh_index.py
 scripts/db_shell.py
 scripts/drmaa_external_runner.py
+scripts/metagenomics/
 scripts/secret_decoder_ring.py
 test/
 tool_list.py

contrib/galaxy_config_merger.py

@@ -80,9 +80,6 @@ def main():
         config_sample.write(outputfile)
         outputfile.close()
     else:
-        # print "----------"
-        # config_sample.write(sys.stdout)
-        # print "----------"
         logging.info("use -o OUTPUT to write the merged configuration into a file.")
 
     logging.info("read Galaxy galaxy.ini.sample for detailed information.")

lib/galaxy/datatypes/converters/bed_to_gff_converter.py

@@ -4,7 +4,7 @@ from __future__ import print_function
 
 import sys
 
-assert sys.version_info[:2] >= (2, 4)
+assert sys.version_info[:2] >= (2, 6)
 
 
 def __main__():

lib/galaxy/datatypes/converters/gff_to_bed_converter.py

@@ -3,7 +3,7 @@ from __future__ import print_function
 
 import sys
 
-assert sys.version_info[:2] >= (2, 4)
+assert sys.version_info[:2] >= (2, 6)
 
 
 def __main__():

lib/galaxy/datatypes/converters/interval_to_bed_converter.py

@@ -6,7 +6,7 @@ import sys
 
 import bx.intervals.io
 
-assert sys.version_info[:2] >= (2, 4)
+assert sys.version_info[:2] >= (2, 6)
 
 
 def stop_err(msg):

lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py

@@ -6,7 +6,7 @@ import sys
 
 import bx.intervals.io
 
-assert sys.version_info[:2] >= (2, 4)
+assert sys.version_info[:2] >= (2, 6)
 
 
 def stop_err(msg):

lib/galaxy/datatypes/converters/maf_to_fasta_converter.py

@@ -8,7 +8,7 @@ import bx.align.maf
 
 from galaxy.tools.util import maf_utilities
 
-assert sys.version_info[:2] >= (2, 4)
+assert sys.version_info[:2] >= (2, 6)
 
 
 def __main__():

lib/galaxy/datatypes/converters/maf_to_interval_converter.py

@@ -8,7 +8,7 @@ import bx.align.maf
 
 from galaxy.tools.util import maf_utilities
 
-assert sys.version_info[:2] >= (2, 4)
+assert sys.version_info[:2] >= (2, 6)
 
 
 def __main__():

lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.py

@@ -4,7 +4,7 @@ from __future__ import print_function
 
 import sys
 
-assert sys.version_info[:2] >= (2, 5)
+assert sys.version_info[:2] >= (2, 6)
 HEADER_STARTS_WITH = ('@')
 
 

lib/galaxy/datatypes/dataproviders/base.py

@@ -260,8 +260,6 @@ class LimitedOffsetDataProvider(FilteredDataProvider):
         parent_gen = super(LimitedOffsetDataProvider, self).__iter__()
         for datum in parent_gen:
             self.num_data_returned -= 1
-            # print 'self.num_data_returned:', self.num_data_returned
-            # print 'self.num_valid_data_read:', self.num_valid_data_read
 
             if self.num_valid_data_read > self.offset:
                 self.num_data_returned += 1

lib/galaxy/model/__init__.py

@@ -4242,7 +4242,6 @@ class MetadataFile(StorableObject):
             return path
         except AttributeError:
             # In case we're not working with the history_dataset
-            # print "Caught AttributeError"
             path = os.path.join(Dataset.file_path, '_metadata_files', *directory_hash_id(self.id))
             # Create directory if it does not exist
             try:

lib/galaxy/model/search.py

@@ -122,7 +122,6 @@ class ViewQueryBaseClass(object):
                     clazz, attribute = field.sqlalchemy_field
                     sqlalchemy_field_value = getattr(clazz, attribute)
                     if operator == "=":
-                        # print field.sqlalchemy_field == right, field.sqlalchemy_field, right
                         self.query = self.query.filter(sqlalchemy_field_value == right)
                     elif operator == "!=":
                         self.query = self.query.filter(sqlalchemy_field_value != right)
@@ -166,7 +165,6 @@ def library_extended_metadata_filter(view, left, operator, right):
         view.state['extended_metadata_joined'] = True
     alias = aliased(ExtendedMetadataIndex)
     field = "/%s" % ("/".join(left.split(".")[1:]))
-    # print "FIELD", field
     view.query = view.query.filter(
         and_(
             ExtendedMetadata.id == alias.extended_metadata_id,
@@ -313,7 +311,6 @@ def history_dataset_extended_metadata_filter(view, left, operator, right):
         view.state['extended_metadata_joined'] = True
     alias = aliased(ExtendedMetadataIndex)
     field = "/%s" % ("/".join(left.split(".")[1:]))
-    # print "FIELD", field
     view.query = view.query.filter(
         and_(
             ExtendedMetadata.id == alias.extended_metadata_id,

lib/galaxy/objectstore/s3.py

@@ -1,7 +1,6 @@
 """
 Object Store plugin for the Amazon Simple Storage Service (S3)
 """
-
 import logging
 import multiprocessing
 import os
@@ -9,9 +8,17 @@ import shutil
 import subprocess
 import threading
 import time
-
 from datetime import datetime
 
+try:
+    # Imports are done this way to allow objectstore code to be used outside of Galaxy.
+    import boto
+    from boto.exception import S3ResponseError
+    from boto.s3.connection import S3Connection
+    from boto.s3.key import Key
+except ImportError:
+    boto = None
+
 from galaxy.exceptions import ObjectInvalid, ObjectNotFound
 from galaxy.util import (
     directory_hash_id,
@@ -25,16 +32,6 @@ from galaxy.util.sleeper import Sleeper
 from .s3_multipart_upload import multipart_upload
 from ..objectstore import convert_bytes, ObjectStore
 
-try:
-    # Imports are done this way to allow objectstore code to be used outside of Galaxy.
-    import boto
-
-    from boto.exception import S3ResponseError
-    from boto.s3.key import Key
-    from boto.s3.connection import S3Connection
-except ImportError:
-    boto = None
-
 NO_BOTO_ERROR_MESSAGE = ("S3/Swift object store configured, but no boto dependency available."
                          "Please install and properly configure boto or modify object store configuration.")
 
@@ -296,21 +293,21 @@ class S3ObjectStore(ObjectStore):
         # creates, this check sould be implemented- in the mean time, it's not
         # looking likely to be implementable reliably.
         # if os.path.exists(cache_path):
-        #     # print "***1 %s exists" % cache_path
+        #     # print("***1 %s exists" % cache_path)
         #     if self._key_exists(rel_path):
-        #         # print "***2 %s exists in S3" % rel_path
+        #         # print("***2 %s exists in S3" % rel_path)
         #         # Make sure the size in cache is available in its entirety
-        #         # print "File '%s' cache size: %s, S3 size: %s" % (cache_path, os.path.getsize(cache_path), self._get_size_in_s3(rel_path))
+        #         # print("File '%s' cache size: %s, S3 size: %s" % (cache_path, os.path.getsize(cache_path), self._get_size_in_s3(rel_path)))
         #         if os.path.getsize(cache_path) == self._get_size_in_s3(rel_path):
-        #             # print "***2.1 %s exists in S3 and the size is the same as in cache (in_cache=True)" % rel_path
+        #             # print("***2.1 %s exists in S3 and the size is the same as in cache (in_cache=True)" % rel_path)
         #             exists = True
         #         else:
-        #             # print "***2.2 %s exists but differs in size from cache (in_cache=False)" % cache_path
+        #             # print("***2.2 %s exists but differs in size from cache (in_cache=False)" % cache_path)
         #             exists = False
         #     else:
         #         # Although not perfect decision making, this most likely means
         #         # that the file is currently being uploaded
-        #         # print "***3 %s found in cache but not in S3 (in_cache=True)" % cache_path
+        #         # print("***3 %s found in cache but not in S3 (in_cache=True)" % cache_path)
         #         exists = True
         # else:
         #     return False

lib/galaxy/tools/deps/containers.py

@@ -35,7 +35,13 @@ ALL_CONTAINER_TYPES = [DOCKER_CONTAINER_TYPE, SINGULARITY_CONTAINER_TYPE]
 
 LOAD_CACHED_IMAGE_COMMAND_TEMPLATE = '''
 python << EOF
-import re, tarfile, json, subprocess
+from __future__ import print_function
+
+import json
+import re
+import subprocess
+import tarfile
+
 t = tarfile.TarFile("${cached_image_file}")
 meta_str = t.extractfile('repositories').read()
 meta = json.loads(meta_str)
@@ -50,7 +56,7 @@ for line in stdo.split("\\n"):
     if tmp[0] == tag and tmp[1] == rev and tmp[2] == rev_value:
         found = True
 if not found:
-    print "Loading image"
+    print("Loading image")
     cmd = "cat ${cached_image_file} | ${load_cmd}"
     subprocess.check_call(cmd, shell=True)
 EOF

lib/galaxy/tools/imp_exp/__init__.py

@@ -271,14 +271,12 @@ class JobImportHistoryArchiveWrapper(object, UsesAnnotations):
                             input_hda = self.sa_session.query(model.HistoryDatasetAssociation) \
                                             .filter_by(history=new_history, hid=value.hid).first()
                             value = input_hda.id
-                        # print "added parameter %s-->%s to job %i" % ( name, value, imported_job.id )
                         imported_job.add_parameter(name, dumps(value, cls=HistoryDatasetAssociationIDEncoder))
 
                     # TODO: Connect jobs to input datasets.
 
                     # Connect jobs to output datasets.
                     for output_hid in job_attrs['output_datasets']:
-                        # print "%s job has output dataset %i" % (imported_job.id, output_hid)
                         output_hda = self.sa_session.query(model.HistoryDatasetAssociation) \
                             .filter_by(history=new_history, hid=output_hid).first()
                         if output_hda:

lib/galaxy/tools/parameters/__init__.py

@@ -1,6 +1,8 @@
 """
 Classes encapsulating Galaxy tool parameters.
 """
+from __future__ import print_function
+
 import re
 from json import dumps
 
@@ -49,7 +51,7 @@ def visit_input_values(inputs, input_values, callback, name_prefix='', label_pre
     >>> f.cases = [Bunch(value='true', inputs= { 'h': h }), Bunch(value='false', inputs= { 'i': i })]
     >>>
     >>> def visitor(input, value, prefix, prefixed_name, **kwargs):
-    ...     print 'name=%s, prefix=%s, prefixed_name=%s, value=%s' % (input.name, prefix, prefixed_name, value)
+    ...     print('name=%s, prefix=%s, prefixed_name=%s, value=%s' % (input.name, prefix, prefixed_name, value))
     >>> inputs = odict([('a',a),('b',b)])
     >>> nested = odict([('a', 1), ('b', [odict([('c', 3), ('d', [odict([('e', 5), ('f', odict([('g', True), ('h', 7)]))])])])])])
     >>> visit_input_values(inputs, nested, visitor)
@@ -249,13 +251,13 @@ def populate_state(request_context, inputs, incoming, state, errors={}, prefix='
     >>> flat = odict([('a', 1), ('b_0|c', 2), ('b_0|d_0|e', 3), ('b_0|d_0|f|h', 4), ('b_0|d_0|f|g', True)])
     >>> state = odict()
     >>> populate_state(trans, inputs, flat, state, check=False)
-    >>> print state['a']
+    >>> print(state['a'])
     1
-    >>> print state['b'][0]['c']
+    >>> print(state['b'][0]['c'])
     2
-    >>> print state['b'][0]['d'][0]['e']
+    >>> print(state['b'][0]['d'][0]['e'])
     3
-    >>> print state['b'][0]['d'][0]['f']['h']
+    >>> print(state['b'][0]['d'][0]['f']['h'])
     4
     """
     context = ExpressionContext(state, context)

lib/galaxy/tools/parameters/input_translation.py

@@ -1,6 +1,8 @@
 """
 Tool Input Translation.
 """
+from __future__ import print_function
+
 import logging
 
 from galaxy.util.bunch import Bunch
@@ -43,7 +45,7 @@ class ToolInputTranslator(object):
     ... '''))
     >>> params = Params({'db':'hg17', 'URL':'URL_value', 'org':'Human', 'hgta_outputType':'primaryTable'})
     >>> translator.translate(params)
-    >>> print sorted(list(params.__dict__.keys()))
+    >>> print(sorted(params.__dict__.keys()))
     ['URL', 'URL_method', 'data_type', 'db', 'dbkey', 'description', 'hgta_outputType', 'org', 'organism', 'table']
     >>> params.get('URL', None) in ['URL_value?GALAXY_URL=0&_export=1', 'URL_value?_export=1&GALAXY_URL=0']
     True

lib/galaxy/tools/util/maf_utilities.py

@@ -19,7 +19,7 @@ import bx.interval_index_file
 import bx.intervals
 from six.moves import xrange
 
-assert sys.version_info[:2] >= (2, 4)
+assert sys.version_info[:2] >= (2, 6)
 
 log = logging.getLogger(__name__)
 

lib/galaxy/util/jstree.py

@@ -1,8 +1,11 @@
-import os
+from __future__ import print_function
+
 import copy
-import dictobj
+import os
 from collections import namedtuple
 
+import dictobj
+
 Path = namedtuple('Path', ('path', 'id', 'options'))
 
 
@@ -46,23 +49,23 @@ class Node(dictobj.DictionaryObject):
     Example:
       >>> import jstree
       >>> node = jstree.Node('a', None)
-      >>> print node
+      >>> print(node)
       Node({'text': 'a', 'children': MutableDictionaryObject({})})
-      >>> print node.jsonData()
+      >>> print(node.jsonData())
       {'text': 'a'}
 
       >>> import jstree
       >>> node = jstree.Node('a', 1)
-      >>> print node
+      >>> print(node)
       Node({'text': 'a', 'children': MutableDictionaryObject({}), 'li_attr': DictionaryObject({'id': 1}), 'id': 1})
-      >>> print node.jsonData()
+      >>> print(node.jsonData())
       {'text': 'a', 'id': 1, 'li_attr': {'id': 1}}
 
       >>> import jstree
       >>> node = jstree.Node('a', 5, icon="folder", state = {'opened': True})
-      >>> print node
+      >>> print(node)
       Node({'text': 'a', 'id': 5, 'state': DictionaryObject({'opened': True}), 'children': MutableDictionaryObject({}), 'li_attr': DictionaryObject({'id': 5}), 'icon': 'folder'})
-      >>> print node.jsonData()
+      >>> print(node.jsonData())
       {'text': 'a', 'state': {'opened': True}, 'id': 5, 'li_attr': {'id': 5}, 'icon': 'folder'}
     """
     super(Node, self).__init__()

lib/galaxy/visualization/data_providers/basic.py

@@ -104,7 +104,6 @@ class ColumnDataProvider(BaseDataProvider):
                    (column >= 0)), (
                 "column index (%d) must be positive and less" % (column) +
                 " than the number of columns: %d" % (self.original_dataset.metadata.columns))
-        # print columns, start_val, max_vals, skip_comments, kwargs
 
         # set up the response, column lists
         response = {}

lib/galaxy/web/form_builder.py

@@ -1,10 +1,13 @@
 """
 Classes for generating HTML forms
 """
+from __future__ import print_function
+
 import logging
 
-from six import string_types
 from cgi import escape
+from six import string_types
+
 from galaxy.util import restore_text, unicodify
 
 log = logging.getLogger(__name__)
@@ -44,9 +47,9 @@ class TextField(BaseField):
     """
     A standard text input box.
 
-    >>> print TextField( "foo" ).get_html()
+    >>> print(TextField( "foo" ).get_html())
     <input type="text" name="foo" size="10" value="">
-    >>> print TextField( "bins", size=4, value="default" ).get_html()
+    >>> print(TextField( "bins", size=4, value="default" ).get_html())
     <input type="text" name="bins" size="4" value="default">
     """
 
@@ -72,9 +75,9 @@ class PasswordField(BaseField):
     """
     A password input box. text appears as "******"
 
-    >>> print PasswordField( "foo" ).get_html()
+    >>> print(PasswordField( "foo" ).get_html())
     <input type="password" name="foo" size="10" value="">
-    >>> print PasswordField( "bins", size=4, value="default" ).get_html()
+    >>> print(PasswordField( "bins", size=4, value="default" ).get_html())
     <input type="password" name="bins" size="4" value="default">
     """
 
@@ -101,9 +104,9 @@ class TextArea(BaseField):
     """
     A standard text area box.
 
-    >>> print TextArea( "foo" ).get_html()
+    >>> print(TextArea( "foo" ).get_html())
     <textarea name="foo" rows="5" cols="25"></textarea>
-    >>> print TextArea( "bins", size="4x5", value="default" ).get_html()
+    >>> print(TextArea( "bins", size="4x5", value="default" ).get_html())
     <textarea name="bins" rows="4" cols="5">default</textarea>
     """
     _DEFAULT_SIZE = "5x25"
@@ -136,9 +139,9 @@ class CheckboxField(BaseField):
     """
     A checkbox (boolean input)
 
-    >>> print CheckboxField( "foo" ).get_html()
+    >>> print(CheckboxField( "foo" ).get_html())
     <input type="checkbox" id="foo" name="foo" value="__CHECKED__"><input type="hidden" name="foo" value="__NOTHING__">
-    >>> print CheckboxField( "bar", checked="yes" ).get_html()
+    >>> print(CheckboxField( "bar", checked="yes" ).get_html())
     <input type="checkbox" id="bar" name="bar" value="__CHECKED__" checked="checked"><input type="hidden" name="bar" value="__NOTHING__">
     """
 
@@ -186,9 +189,9 @@ class FileField(BaseField):
     """
     A file upload input.
 
-    >>> print FileField( "foo" ).get_html()
+    >>> print(FileField( "foo" ).get_html())
     <input type="file" name="foo">
-    >>> print FileField( "foo", ajax = True ).get_html()
+    >>> print(FileField( "foo", ajax = True ).get_html())
     <input type="file" name="foo" galaxy-ajax-upload="true">
     """
 
@@ -233,7 +236,7 @@ class HiddenField(BaseField):
     """
     A hidden field.
 
-    >>> print HiddenField( "foo", 100 ).get_html()
+    >>> print(HiddenField( "foo", 100 ).get_html())
     <input type="hidden" name="foo" value="100">
     """
 
@@ -259,7 +262,7 @@ class SelectField(BaseField):
     >>> t = SelectField( "foo", multiple=True )
     >>> t.add_option( "tuti", 1 )
     >>> t.add_option( "fruity", "x" )
-    >>> print t.get_html()
+    >>> print(t.get_html())
     <select name="foo" multiple>
     <option value="1">tuti</option>
     <option value="x">fruity</option>
@@ -268,7 +271,7 @@ class SelectField(BaseField):
     >>> t = SelectField( "bar" )
     >>> t.add_option( "automatic", 3 )
     >>> t.add_option( "bazooty", 4, selected=True )
-    >>> print t.get_html()
+    >>> print(t.get_html())
     <select name="bar" last_selected_value="4">
     <option value="3">automatic</option>
     <option value="4" selected>bazooty</option>
@@ -277,14 +280,14 @@ class SelectField(BaseField):
     >>> t = SelectField( "foo", display="radio" )
     >>> t.add_option( "tuti", 1 )
     >>> t.add_option( "fruity", "x" )
-    >>> print t.get_html()
+    >>> print(t.get_html())
     <div><input type="radio" name="foo" value="1" id="foo|1"><label class="inline" for="foo|1">tuti</label></div>
     <div><input type="radio" name="foo" value="x" id="foo|x"><label class="inline" for="foo|x">fruity</label></div>
 
     >>> t = SelectField( "bar", multiple=True, display="checkboxes" )
     >>> t.add_option( "automatic", 3 )
     >>> t.add_option( "bazooty", 4, selected=True )
-    >>> print t.get_html()
+    >>> print(t.get_html())
     <div class="checkUncheckAllPlaceholder" checkbox_name="bar"></div>
     <div><input type="checkbox" name="bar" value="3" id="bar|3"><label class="inline" for="bar|3">automatic</label></div>
     <div><input type="checkbox" name="bar" value="4" id="bar|4" checked='checked'><label class="inline" for="bar|4">bazooty</label></div>

lib/galaxy/webapps/reports/controllers/tools.py

@@ -1,15 +1,15 @@
-
 import collections
 import logging
-import galaxy.model
-import sqlalchemy as sa
+from datetime import timedelta
 
+import sqlalchemy as sa
+from markupsafe import escape
+from sqlalchemy import and_
+
+import galaxy.model
 from galaxy import util
 from galaxy.web.base.controller import BaseUIController, web
 
-from sqlalchemy import and_
-from datetime import timedelta
-from markupsafe import escape
 
 log = logging.getLogger(__name__)
 
@@ -344,7 +344,6 @@ class Tools(BaseUIController):
                     if word in to_replace:
                         continue
                     if words.count(word) > 1:
-                        print word
                         to_replace.append(word)
                 for word in to_replace:
                     sentence = ("</br>" + word) * 2
@@ -352,7 +351,6 @@ class Tools(BaseUIController):
                     while sentence + "</br>" + word in new_key:
                         sentence += "</br>" + word
                         count += 1
-                    print sentence, count
                     if sentence in new_key:
                         new_key = new_key.replace(sentence, '</br>' + word + " [this line in %d times]" % (count))
             data[new_key] = counter[key]

lib/galaxy/webapps/tool_shed/model/migrate/versions/0001_initial_tables.py

@@ -1,6 +1,8 @@
 """
 Migration script to create initial tables.
 """
+from __future__ import print_function
+
 import datetime
 import logging
 import sys
@@ -145,7 +147,7 @@ ToolAnnotationAssociation_table = Table("tool_annotation_association", metadata,
 
 
 def upgrade(migrate_engine):
-    print __doc__
+    print(__doc__)
     metadata.bind = migrate_engine
     metadata.create_all()
     Index('ix_tool_annotation_association_annotation', ToolAnnotationAssociation_table.c.annotation, mysql_length=767).create()

lib/galaxy/webapps/tool_shed/model/migrate/versions/0002_add_tool_suite_column.py

@@ -1,6 +1,8 @@
 """
 Migration script to add the suite column to the tool table.
 """
+from __future__ import print_function
+
 import logging
 import sys
 
@@ -19,7 +21,7 @@ metadata = MetaData()
 
 def upgrade(migrate_engine):
     metadata.bind = migrate_engine
-    print __doc__
+    print(__doc__)
     metadata.reflect()
     # Create and initialize imported column in job table.
     Tool_table = Table("tool", metadata, autoload=True)
@@ -34,9 +36,8 @@ def upgrade(migrate_engine):
         elif migrate_engine.name in ['postgresql', 'postgres']:
             default_false = "false"
         migrate_engine.execute("UPDATE tool SET suite=%s" % default_false)
-    except Exception as e:
-        print "Adding suite column to the tool table failed: %s" % str(e)
-        log.debug("Adding suite column to the tool table failed: %s" % str(e))
+    except Exception:
+        log.exception("Adding suite column to the tool table failed.")
 
 
 def downgrade(migrate_engine):
@@ -46,6 +47,5 @@ def downgrade(migrate_engine):
     Tool_table = Table("tool", metadata, autoload=True)
     try:
         Tool_table.c.suite.drop()
-    except Exception as e:
-        print "Dropping column suite from the tool table failed: %s" % str(e)
-        log.debug("Dropping column suite from the tool table failed: %s" % str(e))
+    except Exception:
+        log.exception("Dropping column suite from the tool table failed.")

lib/galaxy/webapps/tool_shed/model/migrate/versions/0003_review_and_review_association_tables.py

@@ -1,6 +1,8 @@
 """
 Adds the tool_rating_association table, enabling tools to be rated along with review comments.
 """
+from __future__ import print_function
+
 import datetime
 import logging
 import sys
@@ -29,14 +31,14 @@ ToolRatingAssociation_table = Table("tool_rating_association", metadata,
 
 
 def upgrade(migrate_engine):
-    print __doc__
+    print(__doc__)
     metadata.bind = migrate_engine
     # Load existing tables
     metadata.reflect()
     try:
         ToolRatingAssociation_table.create()
-    except Exception as e:
-        log.debug("Creating tool_rating_association table failed: %s" % str(e))
+    except Exception:
+        log.exception("Creating tool_rating_association table failed.")
 
 
 def downgrade(migrate_engine):
@@ -45,5 +47,5 @@ def downgrade(migrate_engine):
     metadata.reflect()
     try:
         ToolRatingAssociation_table.drop()
-    except Exception as e:
-        log.debug("Dropping tool_rating_association table failed: %s" % str(e))
+    except Exception:
+        log.exception("Dropping tool_rating_association table failed.")

lib/galaxy/webapps/tool_shed/model/migrate/versions/0004_repository_tables.py

@@ -1,6 +1,8 @@
 """
 Adds the repository, repository_rating_association and repository_category_association tables.
 """
+from __future__ import print_function
+
 import datetime
 import logging
 import sys
@@ -47,22 +49,22 @@ RepositoryCategoryAssociation_table = Table("repository_category_association", m
 
 
 def upgrade(migrate_engine):
-    print __doc__
+    print(__doc__)
     # Load existing tables
     metadata.bind = migrate_engine
     metadata.reflect()
     try:
         Repository_table.create()
-    except Exception as e:
-        log.debug("Creating repository table failed: %s" % str(e))
+    except Exception:
+        log.exception("Creating repository table failed.")
     try:
         RepositoryRatingAssociation_table.create()
-    except Exception as e:
-        log.debug("Creating repository_rating_association table failed: %s" % str(e))
+    except Exception:
+        log.exception("Creating repository_rating_association table failed.")
     try:
         RepositoryCategoryAssociation_table.create()
-    except Exception as e:
-        log.debug("Creating repository_category_association table failed: %s" % str(e))
+    except Exception:
+        log.exception("Creating repository_category_association table failed.")
 
 
 def downgrade(migrate_engine):
@@ -71,13 +73,13 @@ def downgrade(migrate_engine):
     metadata.reflect()
     try:
         Repository_table.drop()
-    except Exception as e:
-        log.debug("Dropping repository table failed: %s" % str(e))
+    except Exception:
+        log.exception("Dropping repository table failed.")
     try:
         RepositoryRatingAssociation_table.drop()
-    except Exception as e:
-        log.debug("Dropping repository_rating_association table failed: %s" % str(e))
+    except Exception:
+        log.exception("Dropping repository_rating_association table failed.")
     try:
         RepositoryCategoryAssociation_table.drop()
-    except Exception as e:
-        log.debug("Dropping repository_category_association table failed: %s" % str(e))
+    except Exception:
+        log.exception("Dropping repository_category_association table failed.")

lib/galaxy/webapps/tool_shed/model/migrate/versions/0005_drop_tool_related_tables.py

@@ -3,6 +3,8 @@ Drops the tool, tool_category_association, event, tool_event_association, tool_r
 tool_tag_association and tool_annotation_association tables since they are no longer used in the
 next-gen tool shed.
 """
+from __future__ import print_function
+
 import datetime
 import logging
 import sys
@@ -26,7 +28,7 @@ metadata = MetaData()
 
 
 def upgrade(migrate_engine):
-    print __doc__
+    print(__doc__)
     # Load existing tables
     metadata.bind = migrate_engine
     metadata.reflect()
@@ -37,8 +39,8 @@ def upgrade(migrate_engine):
         log.debug("Failed loading table tool_category_association")
     try:
         ToolCategoryAssociation_table.drop()
-    except Exception as e:
-        log.debug("Dropping tool_category_association table failed: %s" % str(e))
+    except Exception:
+        log.exception("Dropping tool_category_association table failed.")
     # Load and then drop the tool_event_association table
     try:
         ToolEventAssociation_table = Table("tool_event_association", metadata, autoload=True)
@@ -46,8 +48,8 @@ def upgrade(migrate_engine):
         log.debug("Failed loading table tool_event_association")
     try:
         ToolEventAssociation_table.drop()
-    except Exception as e:
-        log.debug("Dropping tool_event_association table failed: %s" % str(e))
+    except Exception:
+        log.exception("Dropping tool_event_association table failed.")
     # Load and then drop the tool_rating_association table
     try:
         ToolRatingAssociation_table = Table("tool_rating_association", metadata, autoload=True)
@@ -55,8 +57,8 @@ def upgrade(migrate_engine):
         log.debug("Failed loading table tool_rating_association")
     try:
         ToolRatingAssociation_table.drop()
-    except Exception as e:
-        log.debug("Dropping tool_rating_association table failed: %s" % str(e))
+    except Exception:
+        log.exception("Dropping tool_rating_association table failed.")
     # Load and then drop the tool_tag_association table
     try:
         ToolTagAssociation_table = Table("tool_tag_association", metadata, autoload=True)
@@ -64,8 +66,8 @@ def upgrade(migrate_engine):
         log.debug("Failed loading table tool_tag_association")
     try:
         ToolTagAssociation_table.drop()
-    except Exception as e:
-        log.debug("Dropping tool_tag_association table failed: %s" % str(e))
+    except Exception:
+        log.exception("Dropping tool_tag_association table failed.")
     # Load and then drop the tool_annotation_association table
     try:
         ToolAnnotationAssociation_table = Table("tool_annotation_association", metadata, autoload=True)
@@ -73,8 +75,8 @@ def upgrade(migrate_engine):
         log.debug("Failed loading table tool_annotation_association")
     try:
         ToolAnnotationAssociation_table.drop()
-    except Exception as e:
-        log.debug("Dropping tool_annotation_association table failed: %s" % str(e))
+    except Exception:
+        log.exception("Dropping tool_annotation_association table failed.")
     # Load and then drop the event table
     try:
         Event_table = Table("event", metadata, autoload=True)
@@ -82,8 +84,8 @@ def upgrade(migrate_engine):
         log.debug("Failed loading table event")
     try:
         Event_table.drop()
-    except Exception as e:
-        log.debug("Dropping event table failed: %s" % str(e))
+    except Exception:
+        log.exception("Dropping event table failed.")
     # Load and then drop the tool table
     try:
         Tool_table = Table("tool", metadata, autoload=True)
@@ -91,8 +93,8 @@ def upgrade(migrate_engine):
         log.debug("Failed loading table tool")
     try:
         Tool_table.drop()
-    except Exception as e:
-        log.debug("Dropping tool table failed: %s" % str(e))
+    except Exception:
+        log.exception("Dropping tool table failed.")
 
 
 def downgrade(migrate_engine):
@@ -161,35 +163,35 @@ def downgrade(migrate_engine):
     # Create the event table
     try:
         Event_table.create()
-    except Exception as e:
-        log.debug("Creating event table failed: %s" % str(e))
+    except Exception:
+        log.exception("Creating event table failed.")
     # Create the tool table
     try:
         Tool_table.create()
-    except Exception as e:
-        log.debug("Creating tool table failed: %s" % str(e))
+    except Exception:
+        log.exception("Creating tool table failed.")
     # Create the tool_category_association table
     try:
         ToolCategoryAssociation_table.create()
-    except Exception as e:
-        log.debug("Creating tool_category_association table failed: %s" % str(e))
+    except Exception:
+        log.exception("Creating tool_category_association table failed.")
     # Create the tool_event_association table
     try:
         ToolEventAssociation_table.create()
-    except Exception as e:
-        log.debug("Creating tool_event_association table failed: %s" % str(e))
+    except Exception:
+        log.exception("Creating tool_event_association table failed.")
     # Create the tool_rating_association table
     try:
         ToolRatingAssociation_table.create()
-    except Exception as e:
-        log.debug("Creating tool_rating_association table failed: %s" % str(e))
+    except Exception:
+        log.exception("Creating tool_rating_association table failed.")
     # Create the tool_tag_association table
     try:
         ToolTagAssociation_table.create()
-    except Exception as e:
-        log.debug("Creating tool_tag_association table failed: %s" % str(e))
+    except Exception:
+        log.exception("Creating tool_tag_association table failed.")
     # Create the tool_annotation_association table
     try:
         ToolAnnotationAssociation_table.create()
-    except Exception as e:
-        log.debug("Creating tool_annotation_association table failed: %s" % str(e))
+    except Exception:
+        log.exception("Creating tool_annotation_association table failed.")

lib/galaxy/webapps/tool_shed/model/migrate/versions/0006_add_email_alerts_column.py

@@ -1,6 +1,8 @@
 """
 Migration script to add the email_alerts column to the repository table.
 """
+from __future__ import print_function
+
 import logging
 import sys
 
@@ -21,7 +23,7 @@ metadata = MetaData()
 
 
 def upgrade(migrate_engine):
-    print __doc__
+    print(__doc__)
     metadata.bind = migrate_engine
     metadata.reflect()
     # Create and initialize imported column in job table.
@@ -31,9 +33,8 @@ def upgrade(migrate_engine):
         # Create
         c.create(Repository_table)
         assert c is Repository_table.c.email_alerts
-    except Exception as e:
-        print "Adding email_alerts column to the repository table failed: %s" % str(e)
-        log.debug("Adding email_alerts column to the repository table failed: %s" % str(e))
+    except Exception:
+        log.exception("Adding email_alerts column to the repository table failed.")
 
 
 def downgrade(migrate_engine):
@@ -43,6 +44,5 @@ def downgrade(migrate_engine):
     Repository_table = Table("repository", metadata, autoload=True)
     try:
         Repository_table.c.email_alerts.drop()
-    except Exception as e:
-        print "Dropping column email_alerts from the repository table failed: %s" % str(e)
-        log.debug("Dropping column email_alerts from the repository table failed: %s" % str(e))
+    except Exception:
+        log.exception("Dropping column email_alerts from the repository table failed.")

lib/galaxy/webapps/tool_shed/model/migrate/versions/0007_add_long_description_times_downloaded_columns.py

@@ -1,6 +1,8 @@
 """
 Migration script to add the long_description and times_downloaded columns to the repository table.
 """
+from __future__ import print_function
+
 import logging
 import sys
 
@@ -18,7 +20,7 @@ metadata = MetaData()
 
 
 def upgrade(migrate_engine):
-    print __doc__
+    print(__doc__)
     metadata.bind = migrate_engine
     metadata.reflect()
     # Create and initialize imported column in job table.
@@ -28,18 +30,16 @@ def upgrade(migrate_engine):
         # Create
         c.create(Repository_table)
         assert c is Repository_table.c.long_description
-    except Exception as e:
-        print "Adding long_description column to the repository table failed: %s" % str(e)
-        log.debug("Adding long_description column to the repository table failed: %s" % str(e))
+    except Exception:
+        log.exception("Adding long_description column to the repository table failed.")
 
     c = Column("times_downloaded", Integer)
     try:
         # Create
         c.create(Repository_table)
         assert c is Repository_table.c.times_downloaded
-    except Exception as e:
-        print "Adding times_downloaded column to the repository table failed: %s" % str(e)
-        log.debug("Adding times_downloaded column to the repository table failed: %s" % str(e))
+    except Exception:
+        log.exception("Adding times_downloaded column to the repository table failed.")
 
     cmd = "UPDATE repository SET long_description = ''"
     migrate_engine.execute(cmd)
@@ -54,11 +54,9 @@ def downgrade(migrate_engine):
     Repository_table = Table("repository", metadata, autoload=True)
     try:
         Repository_table.c.long_description.drop()
-    except Exception as e:
-        print "Dropping column long_description from the repository table failed: %s" % str(e)
-        log.debug("Dropping column long_description from the repository table failed: %s" % str(e))
+    except Exception:
+        log.exception("Dropping column long_description from the repository table failed.")
     try:
         Repository_table.c.times_downloaded.drop()
-    except Exception as e:
-        print "Dropping column times_downloaded from the repository table failed: %s" % str(e)
-        log.debug("Dropping column times_downloaded from the repository table failed: %s" % str(e))
+    except Exception:
+        log.exception("Dropping column times_downloaded from the repository table failed.")

lib/galaxy/webapps/tool_shed/model/migrate/versions/0008_add_repository_metadata_table.py

@@ -1,6 +1,8 @@
 """
 Migration script to add the repository_metadata table.
 """
+from __future__ import print_function
+
 import datetime
 import logging
 import sys
@@ -31,15 +33,14 @@ RepositoryMetadata_table = Table("repository_metadata", metadata,
 
 
 def upgrade(migrate_engine):
-    print __doc__
+    print(__doc__)
     metadata.bind = migrate_engine
     metadata.reflect()
     # Create repository_metadata table.
     try:
         RepositoryMetadata_table.create()
-    except Exception as e:
-        print str(e)
-        log.debug("Creating repository_metadata table failed: %s" % str(e))
+    except Exception:
+        log.exception("Creating repository_metadata table failed.")
 
 
 def downgrade(migrate_engine):
@@ -48,6 +49,5 @@ def downgrade(migrate_engine):
     # Drop repository_metadata table.
     try:
         RepositoryMetadata_table.drop()
-    except Exception as e:
-        print str(e)
-        log.debug("Dropping repository_metadata table failed: %s" % str(e))
+    except Exception:
+        log.exception("Dropping repository_metadata table failed.")

lib/galaxy/webapps/tool_shed/model/migrate/versions/0009_add_malicious_column.py

@@ -1,6 +1,8 @@
 """
 Migration script to add the malicious column to the repository_metadata table.
 """
+from __future__ import print_function
+
 import logging
 import sys
 
@@ -18,7 +20,7 @@ metadata = MetaData()
 
 
 def upgrade(migrate_engine):
-    print __doc__
+    print(__doc__)
     metadata.bind = migrate_engine
     metadata.reflect()
     # Create and initialize imported column in job table.
@@ -34,9 +36,8 @@ def upgrade(migrate_engine):
         elif migrate_engine.name in ['postgresql', 'postgres']:
             default_false = "false"
         migrate_engine.execute("UPDATE repository_metadata SET malicious=%s" % default_false)
-    except Exception as e:
-        print "Adding malicious column to the repository_metadata table failed: %s" % str(e)
-        log.debug("Adding malicious column to the repository_metadata table failed: %s" % str(e))
+    except Exception:
+        log.exception("Adding malicious column to the repository_metadata table failed.")
 
 
 def downgrade(migrate_engine):
@@ -46,6 +47,5 @@ def downgrade(migrate_engine):
     Repository_metadata_table = Table("repository_metadata", metadata, autoload=True)
     try:
         Repository_metadata_table.c.malicious.drop()
-    except Exception as e:
-        print "Dropping column malicious from the repository_metadata table failed: %s" % str(e)
-        log.debug("Dropping column malicious from the repository_metadata table failed: %s" % str(e))
+    except Exception:
+        log.exception("Dropping column malicious from the repository_metadata table failed.")

lib/galaxy/webapps/tool_shed/model/migrate/versions/0010_add_new_repo_alert_column.py

@@ -1,6 +1,8 @@
 """
 Migration script to add the new_repo_alert column to the galaxy_user table.
 """
+from __future__ import print_function
+
 import logging
 import sys
 
@@ -18,7 +20,7 @@ metadata = MetaData()
 
 
 def upgrade(migrate_engine):
-    print __doc__
+    print(__doc__)
     metadata.bind = migrate_engine
     metadata.reflect()
     # Create and initialize imported column in job table.
@@ -36,9 +38,8 @@ def upgrade(migrate_engine):
         else:
             log.debug("unknown migrate_engine dialect")
         migrate_engine.execute("UPDATE galaxy_user SET new_repo_alert=%s" % default_false)
-    except Exception as e:
-        print "Adding new_repo_alert column to the galaxy_user table failed: %s" % str(e)
-        log.debug("Adding new_repo_alert column to the galaxy_user table failed: %s" % str(e))
+    except Exception:
+        log.exception("Adding new_repo_alert column to the galaxy_user table failed.")
 
 
 def downgrade(migrate_engine):
@@ -48,6 +49,5 @@ def downgrade(migrate_engine):
     User_table = Table("galaxy_user", metadata, autoload=True)
     try:
         User_table.c.new_repo_alert.drop()
-    except Exception as e:
-        print "Dropping column new_repo_alert from the galaxy_user table failed: %s" % str(e)
-        log.debug("Dropping column new_repo_alert from the galaxy_user table failed: %s" % str(e))
+    except Exception:
+        log.exception("Dropping column new_repo_alert from the galaxy_user table failed.")

lib/galaxy/webapps/tool_shed/model/migrate/versions/0011_add_tool_versions_column.py

@@ -1,6 +1,8 @@
 """
 Migration script to add the tool_versions column to the repository_metadata table.
 """
+from __future__ import print_function
+
 import datetime
 import logging
 import sys
@@ -23,7 +25,7 @@ metadata = MetaData()
 
 
 def upgrade(migrate_engine):
-    print __doc__
+    print(__doc__)
     metadata.bind = migrate_engine
     metadata.reflect()
     RepositoryMetadata_table = Table("repository_metadata", metadata, autoload=True)
@@ -32,8 +34,8 @@ def upgrade(migrate_engine):
         # Create
         c.create(RepositoryMetadata_table)
         assert c is RepositoryMetadata_table.c.tool_versions
-    except Exception as e:
-        print "Adding tool_versions column to the repository_metadata table failed: %s" % str(e)
+    except Exception:
+        log.exception("Adding tool_versions column to the repository_metadata table failed.")
 
 
 def downgrade(migrate_engine):
@@ -43,5 +45,5 @@ def downgrade(migrate_engine):
     RepositoryMetadata_table = Table("repository_metadata", metadata, autoload=True)
     try:
         RepositoryMetadata_table.c.tool_versions.drop()
-    except Exception as e:
-        print "Dropping column tool_versions from the repository_metadata table failed: %s" % str(e)
+    except Exception:
+        log.exception("Dropping column tool_versions from the repository_metadata table failed.")

lib/galaxy/webapps/tool_shed/model/migrate/versions/0012_add_downloadable_column.py

@@ -1,6 +1,8 @@
 """
 Migration script to add the downloadable column to the repository_metadata table.
 """
+from __future__ import print_function
+
 import logging
 import sys
 
@@ -18,7 +20,7 @@ metadata = MetaData()
 
 
 def upgrade(migrate_engine):
-    print __doc__
+    print(__doc__)
     metadata.bind = migrate_engine
     metadata.reflect()
     # Create and initialize imported column in job table.
@@ -34,8 +36,8 @@ def upgrade(migrate_engine):
         elif migrate_engine.name in ['postgresql', 'postgres']:
             default_true = "true"
         migrate_engine.execute("UPDATE repository_metadata SET downloadable=%s" % default_true)
-    except Exception as e:
-        print "Adding downloadable column to the repository_metadata table failed: %s" % str(e)
+    except Exception:
+        log.exception("Adding downloadable column to the repository_metadata table failed.")
 
 
 def downgrade(migrate_engine):
@@ -45,5 +47,5 @@ def downgrade(migrate_engine):
     RepositoryMetadata_table = Table("repository_metadata", metadata, autoload=True)
     try:
         RepositoryMetadata_table.c.downloadable.drop()
-    except Exception as e:
-        print "Dropping column downloadable from the repository_metadata table failed: %s" % str(e)
+    except Exception:
+        log.exception("Dropping column downloadable from the repository_metadata table failed.")

lib/galaxy/webapps/tool_shed/model/migrate/versions/0013_add_review_tables.py

@@ -1,6 +1,8 @@
 """
 Migration script to add the repository_review, component_review and component tables and the Repository Reviewer group and role.
 """
+from __future__ import print_function
+
 import datetime
 import logging
 import sys
@@ -83,25 +85,22 @@ Component_table = Table("component", metadata,
 
 
 def upgrade(migrate_engine):
-    print __doc__
+    print(__doc__)
     metadata.bind = migrate_engine
     metadata.reflect()
     # Create new review tables.
     try:
         Component_table.create()
-    except Exception as e:
-        print str(e)
-        log.debug("Creating component table failed: %s" % str(e))
+    except Exception:
+        log.exception("Creating component table failed.")
     try:
         RepositoryReview_table.create()
-    except Exception as e:
-        print str(e)
-        log.debug("Creating repository_review table failed: %s" % str(e))
+    except Exception:
+        log.exception("Creating repository_review table failed.")
     try:
         ComponentReview_table.create()
-    except Exception as e:
-        print str(e)
-        log.debug("Creating component_review table failed: %s" % str(e))
+    except Exception:
+        log.exception("Creating component_review table failed.")
     # Insert default Component values.
     names = ['Data types', 'Functional tests', 'README', 'Tool dependencies', 'Tools', 'Workflows']
     descriptions = ['Proprietary datatypes defined in a file named datatypes_conf.xml included in the repository',
@@ -170,19 +169,16 @@ def downgrade(migrate_engine):
     # Drop review tables.
     try:
         ComponentReview_table.drop()
-    except Exception as e:
-        print str(e)
-        log.debug("Dropping component_review table failed: %s" % str(e))
+    except Exception:
+        log.exception("Dropping component_review table failed.")
     try:
         RepositoryReview_table.drop()
-    except Exception as e:
-        print str(e)
-        log.debug("Dropping repository_review table failed: %s" % str(e))
+    except Exception:
+        log.exception("Dropping repository_review table failed.")
     try:
         Component_table.drop()
-    except Exception as e:
-        print str(e)
-        log.debug("Dropping component table failed: %s" % str(e))
+    except Exception:
+        log.exception("Dropping component table failed.")
     # Get the id of the REVIEWER group.
     cmd = "SELECT id FROM galaxy_group WHERE name = '%s';" % (IUC)
     row = migrate_engine.execute(cmd).fetchone()

lib/galaxy/webapps/tool_shed/model/migrate/versions/0014_add_deprecated_column.py

@@ -1,6 +1,8 @@
 """
 Migration script to add the deprecated column to the repository table.
 """
+from __future__ import print_function
+
 import logging
 import sys
 
@@ -18,7 +20,7 @@ metadata = MetaData()
 
 
 def upgrade(migrate_engine):
-    print __doc__
+    print(__doc__)
     metadata.bind = migrate_engine
     metadata.reflect()
     # Create and initialize imported column in job table.
@@ -34,9 +36,8 @@ def upgrade(migrate_engine):
         elif migrate_engine.name in ['postgresql', 'postgres']:
             default_false = "false"
         migrate_engine.execute("UPDATE repository SET deprecated=%s" % default_false)
-    except Exception as e:
-        print "Adding deprecated column to the repository table failed: %s" % str(e)
-        log.debug("Adding deprecated column to the repository table failed: %s" % str(e))
+    except Exception:
+        log.exception("Adding deprecated column to the repository table failed.")
 
 
 def downgrade(migrate_engine):
@@ -46,6 +47,5 @@ def downgrade(migrate_engine):
     Repository_table = Table("repository", metadata, autoload=True)
     try:
         Repository_table.c.deprecated.drop()
-    except Exception as e:
-        print "Dropping column deprecated from the repository table failed: %s" % str(e)
-        log.debug("Dropping column deprecated from the repository table failed: %s" % str(e))
+    except Exception:
+        log.exception("Dropping column deprecated from the repository table failed.")

lib/galaxy/webapps/tool_shed/model/migrate/versions/0015_add_api_keys_table.py

@@ -1,6 +1,8 @@
 """
 Migration script to add the api_keys table.
 """
+from __future__ import print_function
+
 import datetime
 import logging
 import sys
@@ -30,13 +32,13 @@ APIKeys_table = Table("api_keys", metadata,
 
 
 def upgrade(migrate_engine):
-    print __doc__
+    print(__doc__)
     metadata.bind = migrate_engine
     metadata.reflect()
     try:
         APIKeys_table.create()
-    except Exception as e:
-        log.debug("Creating api_keys table failed: %s" % str(e))
+    except Exception:
+        log.exception("Creating api_keys table failed.")
 
 
 def downgrade(migrate_engine):
@@ -45,5 +47,5 @@ def downgrade(migrate_engine):
     metadata.reflect()
     try:
         APIKeys_table.drop()
-    except Exception as e:
-        log.debug("Dropping api_keys table failed: %s" % str(e))
+    except Exception:
+        log.exception("Dropping api_keys table failed.")

lib/galaxy/webapps/tool_shed/model/migrate/versions/0016_add_do_not_test_tools_functionally_correct_errors_columns.py

@@ -1,6 +1,8 @@
 """
 Migration script to add the tool_test_errors, do_not_test, tools_functionally_correct, and time_last_tested columns to the repository_metadata table.
 """
+from __future__ import print_function
+
 import logging
 import sys
 
@@ -21,7 +23,7 @@ metadata = MetaData()
 
 
 def upgrade(migrate_engine):
-    print __doc__
+    print(__doc__)
     metadata.bind = migrate_engine
     metadata.reflect()
     # Create and initialize tools_functionally_correct, do_not_test, time_last_tested, and tool_test_errors columns in repository_metadata table.
@@ -37,9 +39,8 @@ def upgrade(migrate_engine):
         elif migrate_engine.name in ['postgresql', 'postgres']:
             default_false = "false"
         migrate_engine.execute("UPDATE repository_metadata SET tools_functionally_correct=%s" % default_false)
-    except Exception as e:
-        print "Adding tools_functionally_correct column to the repository_metadata table failed: %s" % str(e)
-        log.debug("Adding tools_functionally_correct column to the repository_metadata table failed: %s" % str(e))
+    except Exception:
+        log.exception("Adding tools_functionally_correct column to the repository_metadata table failed.")
     c = Column("do_not_test", Boolean, default=False, index=True)
     try:
         # Create do_not_test column
@@ -51,25 +52,22 @@ def upgrade(migrate_engine):
         elif migrate_engine.name in ['postgresql', 'postgres']:
             default_false = "false"
         migrate_engine.execute("UPDATE repository_metadata SET do_not_test=%s" % default_false)
-    except Exception as e:
-        print "Adding do_not_test column to the repository_metadata table failed: %s" % str(e)
-        log.debug("Adding do_not_test column to the repository_metadata table failed: %s" % str(e))
+    except Exception:
+        log.exception("Adding do_not_test column to the repository_metadata table failed.")
     c = Column("time_last_tested", DateTime, default=None, nullable=True)
     try:
         # Create time_last_tested column
         c.create(RepositoryMetadata_table, index_name="ix_repository_metadata_tlt")
         assert c is RepositoryMetadata_table.c.time_last_tested
-    except Exception as e:
-        print "Adding time_last_tested column to the repository_metadata table failed: %s" % str(e)
-        log.debug("Adding time_last_tested column to the repository_metadata table failed: %s" % str(e))
+    except Exception:
+        log.exception("Adding time_last_tested column to the repository_metadata table failed.")
     c = Column("tool_test_errors", JSONType, nullable=True)
     try:
         # Create tool_test_errors column
         c.create(RepositoryMetadata_table, index_name="ix_repository_metadata_tte")
         assert c is RepositoryMetadata_table.c.tool_test_errors
-    except Exception as e:
-        print "Adding tool_test_errors column to the repository_metadata table failed: %s" % str(e)
-        log.debug("Adding tool_test_errors column to the repository_metadata table failed: %s" % str(e))
+    except Exception:
+        log.exception("Adding tool_test_errors column to the repository_metadata table failed.")
 
 
 def downgrade(migrate_engine):
@@ -79,21 +77,17 @@ def downgrade(migrate_engine):
     RepositoryMetadata_table = Table("repository_metadata", metadata, autoload=True)
     try:
         RepositoryMetadata_table.c.tool_test_errors.drop()
-    except Exception as e:
-        print "Dropping column tool_test_errors from the repository_metadata table failed: %s" % str(e)
-        log.debug("Dropping column tool_test_errors from the repository_metadata table failed: %s" % str(e))
+    except Exception:
+        log.exception("Dropping column tool_test_errors from the repository_metadata table failed.")
     try:
         RepositoryMetadata_table.c.time_last_tested.drop()
-    except Exception as e:
-        print "Dropping column time_last_tested from the repository_metadata table failed: %s" % str(e)
-        log.debug("Dropping column time_last_tested from the repository_metadata table failed: %s" % str(e))
+    except Exception:
+        log.exception("Dropping column time_last_tested from the repository_metadata table failed.")
     try:
         RepositoryMetadata_table.c.do_not_test.drop()
-    except Exception as e:
-        print "Dropping column do_not_test from the repository_metadata table failed: %s" % str(e)
-        log.debug("Dropping column do_not_test from the repository_metadata table failed: %s" % str(e))
+    except Exception:
+        log.exception("Dropping column do_not_test from the repository_metadata table failed.")
     try:
         RepositoryMetadata_table.c.tools_functionally_correct.drop()
-    except Exception as e:
-        print "Dropping column tools_functionally_correct from the repository_metadata table failed: %s" % str(e)
-        log.debug("Dropping column tools_functionally_correct from the repository_metadata table failed: %s" % str(e))
+    except Exception:
+        log.exception("Dropping column tools_functionally_correct from the repository_metadata table failed.")

lib/galaxy/webapps/tool_shed/model/migrate/versions/0017_add_galaxy_utility_columns_to_repository_metadata_table.py

@@ -2,6 +2,8 @@
 Migration script to add the includes_datatypes, has_repository_dependencies, includes_tools, includes_tool_dependencies and includes_workflows
 columns to the repository_metadata table.
 """
+from __future__ import print_function
+
 import logging
 import sys
 
@@ -19,7 +21,7 @@ metadata = MetaData()
 
 
 def upgrade(migrate_engine):
-    print __doc__
+    print(__doc__)
     metadata.bind = migrate_engine
     metadata.reflect()
     # Initialize.
@@ -36,8 +38,8 @@ def upgrade(migrate_engine):
         c.create(RepositoryMetadata_table, index_name="ix_repository_metadata_inc_datatypes")
         assert c is RepositoryMetadata_table.c.includes_datatypes
         migrate_engine.execute("UPDATE repository_metadata SET includes_datatypes=%s" % default_false)
-    except Exception as e:
-        print "Adding includes_datatypes column to the repository_metadata table failed: %s" % str(e)
+    except Exception:
+        log.exception("Adding includes_datatypes column to the repository_metadata table failed.")
 
     # Create includes_datatypes column
     c = Column("has_repository_dependencies", Boolean, default=False, index=True)
@@ -45,8 +47,8 @@ def upgrade(migrate_engine):
         c.create(RepositoryMetadata_table, index_name="ix_repository_metadata_has_repo_deps")
         assert c is RepositoryMetadata_table.c.has_repository_dependencies
         migrate_engine.execute("UPDATE repository_metadata SET has_repository_dependencies=%s" % default_false)
-    except Exception as e:
-        print "Adding has_repository_dependencies column to the repository_metadata table failed: %s" % str(e)
+    except Exception:
+        log.exception("Adding has_repository_dependencies column to the repository_metadata table failed.")
 
     # Create includes_tools column
     c = Column("includes_tools", Boolean, default=False, index=True)
@@ -54,8 +56,8 @@ def upgrade(migrate_engine):
         c.create(RepositoryMetadata_table, index_name="ix_repository_metadata_inc_tools")
         assert c is RepositoryMetadata_table.c.includes_tools
         migrate_engine.execute("UPDATE repository_metadata SET includes_tools=%s" % default_false)
-    except Exception as e:
-        print "Adding includes_tools column to the repository_metadata table failed: %s" % str(e)
+    except Exception:
+        log.exception("Adding includes_tools column to the repository_metadata table failed.")
 
     # Create includes_tool_dependencies column
     c = Column("includes_tool_dependencies", Boolean, default=False, index=True)
@@ -63,8 +65,8 @@ def upgrade(migrate_engine):
         c.create(RepositoryMetadata_table, index_name="ix_repository_metadata_inc_tool_deps")
         assert c is RepositoryMetadata_table.c.includes_tool_dependencies
         migrate_engine.execute("UPDATE repository_metadata SET includes_tool_dependencies=%s" % default_false)
-    except Exception as e:
-        print "Adding includes_tool_dependencies column to the repository_metadata table failed: %s" % str(e)
+    except Exception:
+        log.exception("Adding includes_tool_dependencies column to the repository_metadata table failed.")
 
     # Create includes_workflows column
     c = Column("includes_workflows", Boolean, default=False, index=True)
@@ -72,8 +74,8 @@ def upgrade(migrate_engine):
         c.create(RepositoryMetadata_table, index_name="ix_repository_metadata_inc_workflows")
         assert c is RepositoryMetadata_table.c.includes_workflows
         migrate_engine.execute("UPDATE repository_metadata SET includes_workflows=%s" % default_false)
-    except Exception as e:
-        print "Adding includes_workflows column to the repository_metadata table failed: %s" % str(e)
+    except Exception:
+        log.exception("Adding includes_workflows column to the repository_metadata table failed.")
 
 
 def downgrade(migrate_engine):
@@ -85,29 +87,29 @@ def downgrade(migrate_engine):
     # Drop the includes_workflows column.
     try:
         RepositoryMetadata_table.c.includes_workflows.drop()
-    except Exception as e:
-        print "Dropping column includes_workflows from the repository_metadata table failed: %s" % str(e)
+    except Exception:
+        log.exception("Dropping column includes_workflows from the repository_metadata table failed.")
 
     # Drop the includes_tool_dependencies column.
     try:
         RepositoryMetadata_table.c.includes_tool_dependencies.drop()
-    except Exception as e:
-        print "Dropping column includes_tool_dependencies from the repository_metadata table failed: %s" % str(e)
+    except Exception:
+        log.exception("Dropping column includes_tool_dependencies from the repository_metadata table failed.")
 
     # Drop the includes_tools column.
     try:
         RepositoryMetadata_table.c.includes_tools.drop()
-    except Exception as e:
-        print "Dropping column includes_tools from the repository_metadata table failed: %s" % str(e)
+    except Exception:
+        log.exception("Dropping column includes_tools from the repository_metadata table failed.")
 
     # Drop the has_repository_dependencies column.
     try:
         RepositoryMetadata_table.c.has_repository_dependencies.drop()
-    except Exception as e:
-        print "Dropping column has_repository_dependencies from the repository_metadata table failed: %s" % str(e)
+    except Exception:
+        log.exception("Dropping column has_repository_dependencies from the repository_metadata table failed.")
 
     # Drop the includes_datatypes column.
     try:
         RepositoryMetadata_table.c.includes_datatypes.drop()
-    except Exception as e:
-        print "Dropping column includes_datatypes from the repository_metadata table failed: %s" % str(e)
+    except Exception:
+        log.exception("Dropping column includes_datatypes from the repository_metadata table failed.")

lib/galaxy/webapps/tool_shed/model/migrate/versions/0018_add_repository_metadata_flag_columns.py

@@ -2,6 +2,8 @@
 Migration script to alter the repository_metadata table by dropping the tool_test_errors column and adding columns
 tool_test_results, missing_test_components.
 """
+from __future__ import print_function
+
 import logging
 import sys
 
@@ -23,7 +25,7 @@ metadata = MetaData()
 
 
 def upgrade(migrate_engine):
-    print __doc__
+    print(__doc__)
     metadata.bind = migrate_engine
     metadata.reflect()
     # Initialize.
@@ -44,16 +46,16 @@ def upgrade(migrate_engine):
         try:
             col = RepositoryMetadata_table.c.tool_test_errors
             col.drop()
-        except Exception as e:
-            log.debug("Dropping column 'tool_test_errors' from repository_metadata table failed: %s" % (str(e)))
+        except Exception:
+            log.exception("Dropping column 'tool_test_errors' from repository_metadata table failed.")
 
         # Create the tool_test_results column to replace the ill-named tool_test_errors column just dropped above.
         c = Column("tool_test_results", JSONType, nullable=True)
         try:
             c.create(RepositoryMetadata_table)
             assert c is RepositoryMetadata_table.c.tool_test_results
-        except Exception as e:
-            print "Adding tool_test_results column to the repository_metadata table failed: %s" % str(e)
+        except Exception:
+            log.exception("Adding tool_test_results column to the repository_metadata table failed.")
 
         # Create the missing_test_components column.
         c = Column("missing_test_components", Boolean, default=False, index=True)
@@ -61,8 +63,8 @@ def upgrade(migrate_engine):
             c.create(RepositoryMetadata_table, index_name="ix_repository_metadata_mtc")
             assert c is RepositoryMetadata_table.c.missing_test_components
             migrate_engine.execute("UPDATE repository_metadata SET missing_test_components=%s" % default_false)
-        except Exception as e:
-            print "Adding missing_test_components column to the repository_metadata table failed: %s" % str(e)
+        except Exception:
+            log.exception("Adding missing_test_components column to the repository_metadata table failed.")
 
 
 def downgrade(migrate_engine):
@@ -74,19 +76,19 @@ def downgrade(migrate_engine):
     # Drop the missing_test_components column.
     try:
         RepositoryMetadata_table.c.missing_test_components.drop()
-    except Exception as e:
-        print "Dropping column missing_test_components from the repository_metadata table failed: %s" % str(e)
+    except Exception:
+        log.exception("Dropping column missing_test_components from the repository_metadata table failed.")
 
     # Drop the tool_test_results column.
     try:
         RepositoryMetadata_table.c.tool_test_results.drop()
-    except Exception as e:
-        print "Dropping column tool_test_results from the repository_metadata table failed: %s" % str(e)
+    except Exception:
+        log.exception("Dropping column tool_test_results from the repository_metadata table failed.")
 
     # Create the tool_test_errors column.
     c = Column("tool_test_errors", JSONType, nullable=True)
     try:
         c.create(RepositoryMetadata_table)
         assert c is RepositoryMetadata_table.c.tool_test_errors
-    except Exception as e:
-        print "Adding tool_test_errors column to the repository_metadata table failed: %s" % str(e)
+    except Exception:
+        log.exception("Adding tool_test_errors column to the repository_metadata table failed.")

lib/galaxy/webapps/tool_shed/model/migrate/versions/0019_add_skip_tool_test_table_and_test_install_error_column.py

@@ -1,6 +1,8 @@
 """
 Migration script to add the skip_tool_test table and add the test_install_error column to the repository_metadata table.
 """
+from __future__ import print_function
+
 import datetime
 import logging
 import sys
@@ -33,7 +35,7 @@ SkipToolTest_table = Table("skip_tool_test", metadata,
 
 
 def upgrade(migrate_engine):
-    print __doc__
+    print(__doc__)
     metadata.bind = migrate_engine
     metadata.reflect()
     # Initialize.
@@ -55,14 +57,14 @@ def upgrade(migrate_engine):
             c.create(RepositoryMetadata_table, index_name="ix_repository_metadata_ttie")
             assert c is RepositoryMetadata_table.c.test_install_error
             migrate_engine.execute("UPDATE repository_metadata SET test_install_error=%s" % default_false)
-        except Exception as e:
-            print "Adding test_install_error column to the repository_metadata table failed: %s" % str(e)
+        except Exception:
+            log.exception("Adding test_install_error column to the repository_metadata table failed.")
 
     # Create skip_tool_test table.
     try:
         SkipToolTest_table.create()
-    except Exception as e:
-        print "Creating the skip_tool_test table failed: %s" % str(e)
+    except Exception:
+        log.exception("Creating the skip_tool_test table failed.")
 
 
 def downgrade(migrate_engine):
@@ -72,12 +74,12 @@ def downgrade(migrate_engine):
     # Drop the skip_tool_test table.
     try:
         SkipToolTest_table.drop()
-    except Exception as e:
-        print "Dropping the skip_tool_test table failed: %s" % str(e)
+    except Exception:
+        log.exception("Dropping the skip_tool_test table failed.")
 
     # Drop test_install_error column from the repository_metadata table.
     RepositoryMetadata_table = Table("repository_metadata", metadata, autoload=True)
     try:
         RepositoryMetadata_table.c.test_install_error.drop()
-    except Exception as e:
-        print "Dropping column test_install_error from the repository_metadata table failed: %s" % str(e)
+    except Exception:
+        log.exception("Dropping column test_install_error from the repository_metadata table failed.")

lib/galaxy/webapps/tool_shed/model/migrate/versions/0020_add_repository_type_column.py

@@ -1,4 +1,6 @@
 """Migration script to add the type column to the repository table."""
+from __future__ import print_function
+
 import logging
 import sys
 
@@ -19,7 +21,7 @@ metadata = MetaData()
 
 
 def upgrade(migrate_engine):
-    print __doc__
+    print(__doc__)
     metadata.bind = migrate_engine
     metadata.reflect()
     Repository_table = Table("repository", metadata, autoload=True)
@@ -28,8 +30,8 @@ def upgrade(migrate_engine):
         # Create
         c.create(Repository_table, index_name="ix_repository_type")
         assert c is Repository_table.c.type
-    except Exception as e:
-        print "Adding type column to the repository table failed: %s" % str(e)
+    except Exception:
+        log.exception("Adding type column to the repository table failed.")
     # Update the type column to have the default unrestricted value.
     cmd = "UPDATE repository SET type = 'unrestricted'"
     migrate_engine.execute(cmd)
@@ -42,5 +44,5 @@ def downgrade(migrate_engine):
     Repository_table = Table("repository", metadata, autoload=True)
     try:
         Repository_table.c.type.drop()
-    except Exception as e:
-        print "Dropping column type from the repository table failed: %s" % str(e)
+    except Exception:
+        log.exception("Dropping column type from the repository table failed.")

lib/galaxy/webapps/tool_shed/model/migrate/versions/0021_change_repository_type_value.py

@@ -1,4 +1,6 @@
 """Migration script to change repository.type column value from generic to unrestricted."""
+from __future__ import print_function
+
 import logging
 import sys
 
@@ -16,7 +18,7 @@ metadata = MetaData()
 
 
 def upgrade(migrate_engine):
-    print __doc__
+    print(__doc__)
     metadata.bind = migrate_engine
     metadata.reflect()
     # Update the type column to have the default unrestricted value.

lib/galaxy/webapps/tool_shed/model/migrate/versions/0022_add_repository_admin_roles.py

@@ -3,6 +3,8 @@ Migration script to create the repository_role_association table, insert name-sp
 repository administrative roles into the role table and associate each repository and
 owner with the appropriate name-spaced role.
 """
+from __future__ import print_function
+
 import datetime
 import logging
 import sys
@@ -59,15 +61,14 @@ def boolean_false(migrate_engine):
 
 
 def upgrade(migrate_engine):
-    print __doc__
+    print(__doc__)
     metadata.bind = migrate_engine
     metadata.reflect()
     # Create the new repository_role_association table.
     try:
         RepositoryRoleAssociation_table.create()
-    except Exception as e:
-        print str(e)
-        log.debug("Creating repository_role_association table failed: %s" % str(e))
+    except Exception:
+        log.exception("Creating repository_role_association table failed.")
     # Select the list of repositories and associated public user names for their owners.
     user_ids = []
     repository_ids = []
@@ -159,5 +160,5 @@ def downgrade(migrate_engine):
         log.debug("Failed loading table repository_role_association")
     try:
         RepositoryRoleAssociation_table.drop()
-    except Exception as e:
-        log.debug("Dropping repository_role_association table failed: %s" % str(e))
+    except Exception:
+        log.exception("Dropping repository_role_association table failed.")

lib/galaxy/webapps/tool_shed/model/migrate/versions/0023_add_repository_url_and_hompeage_url.py

@@ -2,6 +2,8 @@
 Migration script to add the remote_repository_url and homepage_url
 columns to the repository table.
 """
+from __future__ import print_function
+
 import logging
 import sys
 
@@ -21,7 +23,7 @@ metadata = MetaData()
 
 
 def upgrade(migrate_engine):
-    print __doc__
+    print(__doc__)
     metadata.bind = migrate_engine
     metadata.reflect()
     Repository_table = Table("repository", metadata, autoload=True)
@@ -33,8 +35,8 @@ def upgrade(migrate_engine):
         c_homepage.create(Repository_table)
         assert c_remote is Repository_table.c.remote_repository_url
         assert c_homepage is Repository_table.c.homepage_url
-    except Exception as e:
-        print "Adding remote_repository_url and homepage_url columns to the repository table failed: %s" % str(e)
+    except Exception:
+        log.exception("Adding remote_repository_url and homepage_url columns to the repository table failed.")
 
 
 def downgrade(migrate_engine):
@@ -45,5 +47,5 @@ def downgrade(migrate_engine):
     try:
         Repository_table.c.remote_repository_url.drop()
         Repository_table.c.homepage_url.drop()
-    except Exception as e:
-        print "Dropping columns remote_repository_url and homepage_url from the repository table failed: %s" % str(e)
+    except Exception:
+        log.exception("Dropping columns remote_repository_url and homepage_url from the repository table failed.")

lib/galaxy/webapps/tool_shed/model/migrate/versions/0024_password_reset.py

@@ -1,6 +1,8 @@
 """
 Migration script for the password reset table
 """
+from __future__ import print_function
+
 import datetime
 import logging
 
@@ -18,12 +20,11 @@ PasswordResetToken_table = Table("password_reset_token", metadata,
 
 def upgrade(migrate_engine):
     metadata.bind = migrate_engine
-    print __doc__
+    print(__doc__)
     metadata.reflect()
     try:
         PasswordResetToken_table.create()
-    except Exception as e:
-        print str(e)
+    except Exception:
         log.exception("Creating %s table failed", PasswordResetToken_table.name)
 
 
@@ -32,6 +33,5 @@ def downgrade(migrate_engine):
     metadata.reflect()
     try:
         PasswordResetToken_table.drop()
-    except Exception as e:
-        print str(e)
+    except Exception:
         log.exception("Dropping %s table failed", PasswordResetToken_table.name)

lib/galaxy/webapps/tool_shed/model/migrate/versions/0025_session_timeout.py

@@ -1,6 +1,8 @@
 """
 Migration script to add session update time (used for timeouts)
 """
+from __future__ import print_function
+
 import datetime
 import logging
 
@@ -13,7 +15,7 @@ metadata = MetaData()
 
 def upgrade(migrate_engine):
     metadata.bind = migrate_engine
-    print __doc__
+    print(__doc__)
     metadata.reflect()
 
     lastaction_column = Column("last_action", DateTime)
@@ -31,8 +33,7 @@ def __add_column(column, table_name, metadata, **kwds):
     try:
         table = Table(table_name, metadata, autoload=True)
         column.create(table, **kwds)
-    except Exception as e:
-        print str(e)
+    except Exception:
         log.exception("Adding column %s failed.", column)
 
 
@@ -40,6 +41,5 @@ def __drop_column(column_name, table_name, metadata):
     try:
         table = Table(table_name, metadata, autoload=True)
         getattr(table.c, column_name).drop()
-    except Exception as e:
-        print str(e)
+    except Exception:
         log.exception("Dropping column %s failed.", column_name)

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

@@ -1807,7 +1807,7 @@ class SetupVirtualEnv(Download, RecipeStep):
         # to subprocess.Popen.
         for site_packages_command in [r"""%s -c 'import site; site.getsitepackages()[0]'""" %
                                       os.path.join(venv_directory, "bin", "python"),
-                                      r"""%s -c 'import os, sys; print os.path.join( sys.prefix, "lib", "python" + sys.version[:3], "site-packages" )'""" %
+                                      r"""%s -c 'from __future__ import print_function; import os, sys; print(os.path.join(sys.prefix, "lib", "python" + sys.version[:3], "site-packages"))'""" %
                                       os.path.join(venv_directory, "bin", "python")]:
             output = install_environment.handle_command(tool_dependency=tool_dependency,
                                                         cmd=site_packages_command,

scripts/api/copy_hda_to_library_folder.py

@@ -1,4 +1,6 @@
 #!/usr/bin/env python
+from __future__ import print_function
+
 import sys
 
 from common import submit
@@ -22,7 +24,7 @@ def copy_hda_to_library_folder(base_url, key, hda_id, library_id, folder_id, mes
 if __name__ == '__main__':
     num_args = len(sys.argv)
     if num_args < 6:
-        print >> sys.stderr, usage
+        print(usage, file=sys.stderr)
         sys.exit(1)
 
     (base_url, key, hda_id, library_id, folder_id) = sys.argv[1:6]
@@ -31,5 +33,5 @@ if __name__ == '__main__':
     if num_args >= 7:
         message = sys.argv[6]
 
-    print >> sys.stderr, base_url, key, hda_id, library_id, folder_id, message
+    print(base_url, key, hda_id, library_id, folder_id, message, file=sys.stderr)
     returned = copy_hda_to_library_folder(base_url, key, hda_id, library_id, folder_id, message)

scripts/api/library_upload_dir.py

@@ -1,4 +1,6 @@
 #!/usr/bin/env python
+from __future__ import print_function
+
 import argparse
 import os
 import sys
@@ -66,14 +68,11 @@ class Uploader:
 
         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]
@@ -84,7 +83,7 @@ class Uploader:
             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
+        # getting the IDs of each folder per path component
         ids = self.recursively_build_path(path_parts, base_folder)
 
         # These are then associated with the paths.
@@ -102,7 +101,6 @@ class Uploader:
         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

scripts/api/workflow_import.py

@@ -24,7 +24,6 @@ def main():
     except IndexError:
         print('usage: %s key galaxy_url workflow_file' % os.path.basename(sys.argv[0]))
         sys.exit(1)
-    # print display( api_key, api_base_url + "/api/workflows" )
     submit(api_key, api_url, data, return_formatted=False)
 
 

scripts/cleanup_datasets/admin_cleanup_datasets.py

@@ -63,7 +63,7 @@ log = logging.getLogger()
 log.setLevel(logging.INFO)
 log.addHandler(logging.StreamHandler(sys.stdout))
 
-assert sys.version_info[:2] >= (2, 4)
+assert sys.version_info[:2] >= (2, 6)
 
 
 def main():

scripts/cleanup_datasets/cleanup_datasets.py

@@ -27,7 +27,7 @@ log = logging.getLogger()
 log.setLevel(logging.INFO)
 log.addHandler(logging.StreamHandler(sys.stdout))
 
-assert sys.version_info[:2] >= (2, 4)
+assert sys.version_info[:2] >= (2, 6)
 
 
 def main():

scripts/cleanup_datasets/populate_uuid.py

@@ -14,7 +14,7 @@ import uuid
 from galaxy.model import mapping
 from galaxy.model.orm.scripts import get_config
 
-assert sys.version_info[:2] >= (2, 4)
+assert sys.version_info[:2] >= (2, 6)
 
 
 def usage(prog):

scripts/cleanup_datasets/remove_renamed_datasets_from_disk.py

@@ -8,7 +8,7 @@ from __future__ import print_function
 import os
 import sys
 
-assert sys.version_info[:2] >= (2, 4)
+assert sys.version_info[:2] >= (2, 6)
 
 
 def usage(prog):

scripts/cleanup_datasets/rename_purged_datasets.py

@@ -8,7 +8,7 @@ from __future__ import print_function
 import os
 import sys
 
-assert sys.version_info[:2] >= (2, 4)
+assert sys.version_info[:2] >= (2, 6)
 
 
 def usage(prog):

scripts/cleanup_datasets/update_dataset_size.py

@@ -12,7 +12,7 @@ from six.moves import configparser
 
 import galaxy.app
 
-assert sys.version_info[:2] >= (2, 4)
+assert sys.version_info[:2] >= (2, 6)
 
 
 def usage(prog):

scripts/cleanup_datasets/update_metadata.py

@@ -17,7 +17,7 @@ sys.path.insert(1, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pa
 import galaxy.app
 import galaxy.datatypes.tabular
 
-assert sys.version_info[:2] >= (2, 4)
+assert sys.version_info[:2] >= (2, 6)
 
 
 def usage(prog):

scripts/db_shell.py

@@ -41,7 +41,7 @@ sa_session = init('/tmp/', db_url).context
 # http://stackoverflow.com/questions/5631078/sqlalchemy-print-the-actual-query
 def printquery(statement, bind=None):
     """
-    print a query, with values filled in
+    Print a query, with values filled in
     for debugging purposes *only*
     for security, you should always separate queries from their values
     please also note that this function is quite slow

scripts/extract_toolbox_sections.py

@@ -123,9 +123,8 @@ def getfnl(startdir):
             if fn.endswith('.xml'):
                 try:
                     doc = ET.parse(fullfn)
-                except:
-                    print "Oops, bad xml in: ", fullfn
-                    raise
+                except Exception as e:
+                    raise Exception("Oops, bad XML in '%s': %s" % (fullfn, e))
                 rootelement = doc.getroot()
                 # here we check if this xml file actually is a tool conf xml!
                 if rootelement.tag == 'tool':

scripts/get_platforms.py

@@ -1,11 +1,13 @@
 #!/usr/bin/env python
+from __future__ import print_function
+
 import os
 import sys
 
-assert sys.version_info[:2] >= (2, 4)
+assert sys.version_info[:2] >= (2, 6)
 
 lib = os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, "lib"))
 sys.path.insert(1, lib)
 
 import pkg_resources
-print pkg_resources.get_platform()
+print(pkg_resources.get_platform())

scripts/helper.py

@@ -4,6 +4,8 @@ A command line helper for common operations performed by Galaxy maintainers.
 Encodes and decodes IDs, returns Dataset IDs if provided an HDA or LDDA id,
 returns the disk path of a dataset.
 """
+from __future__ import print_function
+
 import os
 import sys
 from ConfigParser import ConfigParser
@@ -41,10 +43,10 @@ helper = security.SecurityHelper(id_secret=config.get('app:main', 'id_secret'))
 model = mapping.init(config.get('app:main', 'file_path'), config.get('app:main', 'database_connection'), create_tables=False)
 
 if options.encode_id:
-    print 'Encoded "%s": %s' % (options.encode_id, helper.encode_id(options.encode_id))
+    print('Encoded "%s": %s' % (options.encode_id, helper.encode_id(options.encode_id)))
 
 if options.decode_id:
-    print 'Decoded "%s": %s' % (options.decode_id, helper.decode_id(options.decode_id))
+    print('Decoded "%s": %s' % (options.decode_id, helper.decode_id(options.decode_id)))
 
 if options.hda_id:
     try:
@@ -52,7 +54,7 @@ if options.hda_id:
     except:
         hda_id = int(helper.decode_id(options.hda_id))
     hda = model.context.current.query(model.HistoryDatasetAssociation).get(hda_id)
-    print 'HDA "%s" is Dataset "%s" at: %s' % (hda.id, hda.dataset.id, hda.file_name)
+    print('HDA "%s" is Dataset "%s" at: %s' % (hda.id, hda.dataset.id, hda.file_name))
 
 if options.ldda_id:
     try:
@@ -60,4 +62,4 @@ if options.ldda_id:
     except:
         ldda_id = int(helper.decode_id(options.ldda_id))
     ldda = model.context.current.query(model.HistoryDatasetAssociation).get(ldda_id)
-    print 'LDDA "%s" is Dataset "%s" at: %s' % (ldda.id, ldda.dataset.id, ldda.file_name)
+    print('LDDA "%s" is Dataset "%s" at: %s' % (ldda.id, ldda.dataset.id, ldda.file_name))

scripts/loc_files/create_all_fasta_loc.py

@@ -23,6 +23,8 @@ usage: %prog [options]
    -a, --append=a: Append to existing all_fasta.loc file rather than create new
    -p, --sample-text=p: Copy over text from all_fasta.loc.sample file (false if set to append)
 """
+from __future__ import print_function
+
 import optparse
 import os
 import sys
@@ -199,16 +201,16 @@ def __main__():
         paths_to_look_in = [os.path.join(options.genome_dir, '%s')]
 
     # say what we're looking in
-    print '\nLooking in:\n\t%s' % '\n\t'.join([p % '<build_name>' for p in paths_to_look_in])
+    print('\nLooking in:\n\t%s' % '\n\t'.join(p % '<build_name>' for p in paths_to_look_in))
     poss_names = ['<build_name>%s' % _ for _ in variants]
-    print 'for files that are named %s' % ', '.join(poss_names[:-1]),
+    print('for files that are named %s' % ', '.join(poss_names[:-1]), end=' ')
     if len(poss_names) > 1:
-        print 'or %s' % poss_names[-1],
+        print('or %s' % poss_names[-1], end=' ')
     if len(options.fasta_exts) == 1:
-        print 'with the extension %s.' % ', '.join(fasta_exts[:-1])
+        print('with the extension %s.' % ', '.join(fasta_exts[:-1]))
     else:
-        print 'with the extension %s or %s.' % (', '.join(fasta_exts[:-1]), fasta_exts[-1])
-    print '\nSkipping the following:\n\t%s' % '\n\t'.join(exemptions)
+        print('with the extension %s or %s.' % (', '.join(fasta_exts[:-1]), fasta_exts[-1]))
+    print('\nSkipping the following:\n\t%s' % '\n\t'.join(exemptions))
 
     # get column names
     col_values = []
@@ -265,8 +267,8 @@ def __main__():
                             del fasta_locs[tr]
 
     # output results
-    print '\nThere were %s fasta files found that were not included because they did not have the expected file names.' % len(unmatching_fasta_paths)
-    print '%s fasta files were found and listed.\n' % len(fasta_locs.keys())
+    print('\nThere were %s fasta files found that were not included because they did not have the expected file names.' % len(unmatching_fasta_paths))
+    print('%s fasta files were found and listed.\n' % len(fasta_locs.keys()))
 
     # output unmatching fasta files
     if options.unmatching_fasta and unmatching_fasta_paths:

scripts/manage_tools.py

@@ -1,3 +1,5 @@
+from __future__ import print_function
+
 import logging
 import os.path
 import sys
@@ -14,7 +16,7 @@ log = logging.getLogger(__name__)
 
 config_file = read_config_file_arg(sys.argv, 'config/galaxy.ini', 'universe_wsgi.ini')
 if not os.path.exists(config_file):
-    print "Galaxy config file does not exist (hint: use '-c config.ini' for non-standard locations): %s" % config_file
+    print("Galaxy config file does not exist (hint: use '-c config.ini' for non-standard locations): %s" % config_file)
     sys.exit(1)
 repo = 'lib/tool_shed/galaxy_install/migrate'
 

scripts/metagenomics/convert_title.py

@@ -1,9 +1,9 @@
 #!/usr/bin/env python
-
 """
 convert nt and wgs data (fasta format) to giNumber_seqLen
 run formatdb in the command line: gunzip -c nt.gz |formatdb -i stdin -p F -n "nt.chunk" -v 2000
 """
+from __future__ import print_function
 
 import sys
 
@@ -19,8 +19,8 @@ if __name__ == '__main__':
             if len_seq > 0:
                 if gi is None:
                     raise Exception('The first sequence does not have an header.')
-                print ">%s_%d" % (gi, len_seq)
-                print "\n".join(seq)
+                print(">%s_%d" % (gi, len_seq))
+                print("\n".join(seq))
             title = line
             fields = title.split('|')
             if len(fields) >= 2 and fields[0] == '>gi':
@@ -34,7 +34,7 @@ if __name__ == '__main__':
             seq.append(line)
             len_seq += len(line)
     if len_seq > 0:
-        print ">%s_%d" % (gi, len_seq)
-        print "\n".join(seq)
+        print(">%s_%d" % (gi, len_seq))
+        print("\n".join(seq))
 
-    print >> sys.stderr, "Unable to find gi number for %d sequences, the title is replaced as giunknown" % (invalid_lines)
+    print("Unable to find gi number for %d sequences, the title is replaced as giunknown" % (invalid_lines), file=sys.stderr)

scripts/microbes/BeautifulSoup.py

@@ -42,6 +42,7 @@ documentation:
 http://www.crummy.com/software/BeautifulSoup/documentation.html
 """
 from __future__ import generators
+from __future__ import print_function
 
 import codecs
 import re
@@ -1807,4 +1808,4 @@ class UnicodeDammit:
 # By default, act as an HTML pretty-printer.
 if __name__ == '__main__':
     soup = BeautifulSoup(sys.stdin.read())
-    print soup.prettify()
+    print(soup.prettify())

scripts/microbes/create_bacteria_loc_file.py

@@ -1,9 +1,11 @@
 #!/usr/bin/env python
 # Dan Blankenberg
+from __future__ import print_function
+
 import os
 import sys
 
-assert sys.version_info[:2] >= (2, 4)
+assert sys.version_info[:2] >= (2, 6)
 
 
 def __main__():
@@ -12,7 +14,6 @@ def __main__():
         base_dir = sys.argv[1]
     except:
         pass
-        # print "using default base_dir:", base_dir
 
     organisms = {}
     for result in os.walk(base_dir):
@@ -47,26 +48,26 @@ def __main__():
             continue
         if 'build' in org:
             build = org['build']
-            print "ORG\t%s\t%s\t%s\t%s\t%s\t%s\tUCSC" % (build, org['name'], org['kingdom'], org['group'], org['chromosomes'], org['info url'])
+            print("ORG\t%s\t%s\t%s\t%s\t%s\t%s\tUCSC" % (build, org['name'], org['kingdom'], org['group'], org['chromosomes'], org['info url']))
         else:
-            print "ORG\t%s\t%s\t%s\t%s\t%s\t%s\tNone" % (build, org['name'], org['kingdom'], org['group'], org['chromosomes'], org['info url'])
+            print("ORG\t%s\t%s\t%s\t%s\t%s\t%s\tNone" % (build, org['name'], org['kingdom'], org['group'], org['chromosomes'], org['info url']))
 
         for chr in org['chrs']:
             chr = org['chrs'][chr]
-            print "CHR\t%s\t%s\t%s\t%s\t%s\t%s\t%s" % (build, chr['chromosome'], chr['name'], chr['length'], chr['gi'], chr['gb'], "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=" + chr['refseq'])
+            print("CHR\t%s\t%s\t%s\t%s\t%s\t%s\t%s" % (build, chr['chromosome'], chr['name'], chr['length'], chr['gi'], chr['gb'], "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=" + chr['refseq']))
             for feature in ['CDS', 'tRNA', 'rRNA']:
-                print "DATA\t%s_%s_%s\t%s\t%s\t%s\t%s\t%s" % (build, chr['chromosome'], feature, build, chr['chromosome'], feature, "bed", os.path.join(org['base_dir'], "%s.%s.bed" % (chr['chromosome'], feature)))
+                print("DATA\t%s_%s_%s\t%s\t%s\t%s\t%s\t%s" % (build, chr['chromosome'], feature, build, chr['chromosome'], feature, "bed", os.path.join(org['base_dir'], "%s.%s.bed" % (chr['chromosome'], feature))))
             # FASTA
-            print "DATA\t%s_%s_%s\t%s\t%s\t%s\t%s\t%s" % (build, chr['chromosome'], "seq", build, chr['chromosome'], "sequence", "fasta", os.path.join(org['base_dir'], "%s.fna" % chr['chromosome']))
+            print("DATA\t%s_%s_%s\t%s\t%s\t%s\t%s\t%s" % (build, chr['chromosome'], "seq", build, chr['chromosome'], "sequence", "fasta", os.path.join(org['base_dir'], "%s.fna" % chr['chromosome'])))
             # GeneMark
             if os.path.exists(os.path.join(org['base_dir'], "%s.GeneMark.bed" % chr['chromosome'])):
-                print "DATA\t%s_%s_%s\t%s\t%s\t%s\t%s\t%s" % (build, chr['chromosome'], "GeneMark", build, chr['chromosome'], "GeneMark", "bed", os.path.join(org['base_dir'], "%s.GeneMark.bed" % chr['chromosome']))
+                print("DATA\t%s_%s_%s\t%s\t%s\t%s\t%s\t%s" % (build, chr['chromosome'], "GeneMark", build, chr['chromosome'], "GeneMark", "bed", os.path.join(org['base_dir'], "%s.GeneMark.bed" % chr['chromosome'])))
             # GenMarkHMM
             if os.path.exists(os.path.join(org['base_dir'], "%s.GeneMarkHMM.bed" % chr['chromosome'])):
-                print "DATA\t%s_%s_%s\t%s\t%s\t%s\t%s\t%s" % (build, chr['chromosome'], "GeneMarkHMM", build, chr['chromosome'], "GeneMarkHMM", "bed", os.path.join(org['base_dir'], "%s.GeneMarkHMM.bed" % chr['chromosome']))
+                print("DATA\t%s_%s_%s\t%s\t%s\t%s\t%s\t%s" % (build, chr['chromosome'], "GeneMarkHMM", build, chr['chromosome'], "GeneMarkHMM", "bed", os.path.join(org['base_dir'], "%s.GeneMarkHMM.bed" % chr['chromosome'])))
             # Glimmer3
             if os.path.exists(os.path.join(org['base_dir'], "%s.Glimmer3.bed" % chr['chromosome'])):
-                print "DATA\t%s_%s_%s\t%s\t%s\t%s\t%s\t%s" % (build, chr['chromosome'], "Glimmer3", build, chr['chromosome'], "Glimmer3", "bed", os.path.join(org['base_dir'], "%s.Glimmer3.bed" % chr['chromosome']))
+                print("DATA\t%s_%s_%s\t%s\t%s\t%s\t%s\t%s" % (build, chr['chromosome'], "Glimmer3", build, chr['chromosome'], "Glimmer3", "bed", os.path.join(org['base_dir'], "%s.Glimmer3.bed" % chr['chromosome'])))
 
 
 if __name__ == "__main__":

scripts/microbes/create_bacteria_table.py

@@ -1,9 +1,11 @@
 #!/usr/bin/env python
 # Dan Blankenberg
+from __future__ import print_function
+
 import os
 import sys
 
-assert sys.version_info[:2] >= (2, 4)
+assert sys.version_info[:2] >= (2, 6)
 
 
 def __main__():
@@ -12,7 +14,6 @@ def __main__():
         base_dir = sys.argv[1]
     except:
         pass
-        # print "using default base_dir:", base_dir
 
     organisms = {}
     for result in os.walk(base_dir):
@@ -55,7 +56,7 @@ def __main__():
         if swap_test is False:
             break
 
-    print "||'''Organism'''||'''Kingdom'''||'''Group'''||'''Links to UCSC Archaea Browser'''||"
+    print("||'''Organism'''||'''Kingdom'''||'''Group'''||'''Links to UCSC Archaea Browser'''||")
 
     for org in orgs:
         org = organisms[org]
@@ -72,7 +73,7 @@ def __main__():
         if at_ucsc:
             out_str = out_str + "Yes"
         out_str = out_str + "||"
-        print out_str
+        print(out_str)
 
 
 if __name__ == "__main__":

scripts/microbes/create_nib_seq_loc_file.py

@@ -1,9 +1,11 @@
 #!/usr/bin/env python
 # Dan Blankenberg
+from __future__ import print_function
+
 import os
 import sys
 
-assert sys.version_info[:2] >= (2, 4)
+assert sys.version_info[:2] >= (2, 6)
 
 
 def __main__():
@@ -11,13 +13,13 @@ def __main__():
     try:
         base_dir = sys.argv[1]
     except:
-        print "using default base_dir:", base_dir
+        print("using default base_dir:", base_dir)
 
     loc_out = os.path.join(base_dir, "seq.loc")
     try:
         loc_out = os.path.join(base_dir, sys.argv[2])
     except:
-        print "using default seq.loc:", loc_out
+        print("using default seq.loc:", loc_out)
 
     organisms = {}
 
@@ -63,12 +65,12 @@ def __main__():
         try:
             os.mkdir(seq_path)
         except:
-            print "Skipping", build
+            print("Skipping", build)
             # continue
 
         loc_out.write("seq %s %s\n" % (build, seq_path))
 
-        # print org info
+        # Print org info
 
         for chr in org['chrs']:
             chr = org['chrs'][chr]

scripts/microbes/get_builds_lengths.py

@@ -1,9 +1,11 @@
 #!/usr/bin/env python
 # Dan Blankenberg
+from __future__ import print_function
+
 import os
 import sys
 
-assert sys.version_info[:2] >= (2, 4)
+assert sys.version_info[:2] >= (2, 6)
 
 
 def __main__():
@@ -12,7 +14,6 @@ def __main__():
         base_dir = sys.argv[1]
     except:
         pass
-        # print "using default base_dir:", base_dir
 
     organisms = {}
     for result in os.walk(base_dir):
@@ -53,7 +54,7 @@ def __main__():
         for chrom in org['chrs']:
             chrom = org['chrs'][chrom]
             chrs.append("%s=%s" % (chrom['chromosome'], chrom['length']))
-        print "%s\t%s\t%s" % (build, org['name'], ",".join(chrs))
+        print("%s\t%s\t%s" % (build, org['name'], ",".join(chrs)))
 
 
 if __name__ == "__main__":

scripts/microbes/harvest_bacteria.py

@@ -4,6 +4,8 @@
 # Harvest Bacteria
 # Connects to NCBI's Microbial Genome Projects website and scrapes it for information.
 # Downloads and converts annotations for each Genome
+from __future__ import print_function
+
 import os
 import sys
 import time
@@ -19,7 +21,7 @@ from util import (
     get_bed_from_glimmer3
 )
 
-assert sys.version_info[:2] >= (2, 4)
+assert sys.version_info[:2] >= (2, 6)
 
 # this defines the types of ftp files we are interested in, and how to process/convert them to a form for our use
 desired_ftp_files = {'GeneMark': {'ext': 'GeneMark-2.5f', 'parser': 'process_GeneMark'},
@@ -55,7 +57,7 @@ def iter_genome_projects(url="http://www.ncbi.nlm.nih.gov/genomes/lproks.cgi?vie
         try:
             ftp_url = fields[22].split("href=\"")[1].split("\"")[0]
         except:
-            print "FAILED TO AQUIRE FTP ADDRESS:", org_num, info_url
+            print("FAILED TO AQUIRE FTP ADDRESS:", org_num, info_url)
             ftp_url = None
 
         chroms = get_chroms_by_project_id(org_num)
@@ -72,7 +74,7 @@ def get_chroms_by_project_id(org_num, base_url="http://www.ncbi.nlm.nih.gov/entr
         try:
             html = requests.get(url).text
         except:
-            print "GENOME PROJECT FAILED:", html_count, "org:", org_num, url
+            print("GENOME PROJECT FAILED:", html_count, "org:", org_num, url)
             html = None
             time.sleep(1)  # Throttle Connection
     if html is None:
@@ -131,7 +133,7 @@ def scrape_ftp(ftp_contents, org_dir, org_num, refseq, ftp_url):
             if items['parser'] is not None:
                 globals()[items['parser']](target_filename, org_num, refseq)
         else:
-            print "FTP filetype:", file_type, "not found for", org_num, refseq
+            print("FTP filetype:", file_type, "not found for", org_num, refseq)
     # FTP Files have been Loaded
 
 
@@ -169,14 +171,14 @@ def process_Genbank(filename, org_num, refseq):
         feature_file = open(os.path.join(os.path.split(filename)[0], "%s.%s.bed" % (refseq, feature)), 'wb+')
         feature_file.write('\n'.join(features[feature]))
         feature_file.close()
-    print "Genbank extraction finished for chrom:", refseq, "file:", filename
+    print("Genbank extraction finished for chrom:", refseq, "file:", filename)
 
 
 def process_Glimmer3(filename, org_num, refseq):
     try:
         glimmer3_bed = get_bed_from_glimmer3(filename, refseq)
     except Exception as e:
-        print "Converting Glimmer3 to bed FAILED! For chrom:", refseq, "file:", filename, e
+        print("Converting Glimmer3 to bed FAILED! For chrom:", refseq, "file:", filename, e)
         glimmer3_bed = []
     glimmer3_bed_file = open(os.path.join(os.path.split(filename)[0], "%s.Glimmer3.bed" % refseq), 'wb+')
     glimmer3_bed_file.write('\n'.join(glimmer3_bed))
@@ -187,7 +189,7 @@ def process_GeneMarkHMM(filename, org_num, refseq):
     try:
         geneMarkHMM_bed = get_bed_from_GeneMarkHMM(filename, refseq)
     except Exception as e:
-        print "Converting GeneMarkHMM to bed FAILED! For chrom:", refseq, "file:", filename, e
+        print("Converting GeneMarkHMM to bed FAILED! For chrom:", refseq, "file:", filename, e)
         geneMarkHMM_bed = []
     geneMarkHMM_bed_bed_file = open(os.path.join(os.path.split(filename)[0], "%s.GeneMarkHMM.bed" % refseq), 'wb+')
     geneMarkHMM_bed_bed_file.write('\n'.join(geneMarkHMM_bed))
@@ -198,7 +200,7 @@ def process_GeneMark(filename, org_num, refseq):
     try:
         geneMark_bed = get_bed_from_GeneMark(filename, refseq)
     except Exception as e:
-        print "Converting GeneMark to bed FAILED! For chrom:", refseq, "file:", filename, e
+        print("Converting GeneMark to bed FAILED! For chrom:", refseq, "file:", filename, e)
         geneMark_bed = []
     geneMark_bed_bed_file = open(os.path.join(os.path.split(filename)[0], "%s.GeneMark.bed" % refseq), 'wb+')
     geneMark_bed_bed_file.write('\n'.join(geneMark_bed))
@@ -211,13 +213,13 @@ def __main__():
     try:
         base_dir = sys.argv[1]
     except:
-        print "using default base_dir:", base_dir
+        print("using default base_dir:", base_dir)
 
     try:
         os.mkdir(base_dir)
-        print "path '%s' has been created" % base_dir
+        print("path '%s' has been created" % base_dir)
     except:
-        print "path '%s' seems to already exist" % base_dir
+        print("path '%s' seems to already exist" % base_dir)
 
     for org_num, name, chroms, kingdom, group, org_genbank, org_refseq, info_url, ftp_url in iter_genome_projects():
         if chroms is None:
@@ -227,7 +229,7 @@ def __main__():
             org_dir = os.path.join(base_dir, org_num)
             os.mkdir(org_dir)
         except:
-            print "Organism %s already exists on disk, skipping" % org_num
+            print("Organism %s already exists on disk, skipping" % org_num)
             continue
 
         # get ftp contents
@@ -238,7 +240,7 @@ def __main__():
             for refseq in chroms:
                 scrape_ftp(ftp_contents, org_dir, org_num, refseq, ftp_url)
                 # FTP Files have been Loaded
-                print "Org:", org_num, "chrom:", refseq, "[", time.time() - start_time, "seconds elapsed. ]"
+                print("Org:", org_num, "chrom:", refseq, "[", time.time() - start_time, "seconds elapsed. ]")
 
         # Create org info file
         info_file = open(os.path.join(org_dir, "%s.info" % org_num), 'wb+')
@@ -251,9 +253,9 @@ def __main__():
         info_file.write("ftp url=%s\n" % ftp_url)
         info_file.close()
 
-    print "Finished Harvesting", "[", time.time() - start_time, "seconds elapsed. ]"
-    print "[", (time.time() - start_time) / 60, "minutes. ]"
-    print "[", (time.time() - start_time) / 60 / 60, "hours. ]"
+    print("Finished Harvesting", "[", time.time() - start_time, "seconds elapsed. ]")
+    print("[", (time.time() - start_time) / 60, "minutes. ]")
+    print("[", (time.time() - start_time) / 60 / 60, "hours. ]")
 
 
 if __name__ == "__main__":

scripts/microbes/ncbi_to_ucsc.py

@@ -3,6 +3,8 @@
 Walk downloaded Genome Projects and Convert, in place, IDs to match the UCSC Archaea browser, where applicable.
 Uses UCSC Archaea DSN.
 """
+from __future__ import print_function
+
 import os
 import sys
 import urllib
@@ -15,7 +17,7 @@ def __main__():
     try:
         base_dir = sys.argv[1]
     except:
-        print "using default base_dir:", base_dir
+        print("using default base_dir:", base_dir)
 
     organisms = {}
     for result in os.walk(base_dir):
@@ -46,28 +48,26 @@ def __main__():
     try:
         page = urllib.urlopen(URL)
     except:
-        print "#Unable to open " + URL
-        print "?\tunspecified (?)"
+        print("#Unable to open " + URL)
+        print("?\tunspecified (?)")
         sys.exit(1)
 
     text = page.read()
     try:
         tree = ElementTree.fromstring(text)
     except:
-        print "#Invalid xml passed back from " + URL
-        print "?\tunspecified (?)"
+        print("#Invalid xml passed back from " + URL)
+        print("?\tunspecified (?)")
         sys.exit(1)
 
     builds = {}
 
-    # print "#Harvested from http://archaea.ucsc.edu/cgi-bin/das/dsn"
-    # print "?\tunspecified (?)"
     for dsn in tree:
         build = dsn.find("SOURCE").attrib['id']
         try:
             org_page = urllib.urlopen("http://archaea.ucsc.edu/cgi-bin/hgGateway?db=" + build).read().replace("\n", "").split("<table border=2 cellspacing=2 cellpadding=2>")[1].split("</table>")[0].split("</tr>")
         except:
-            print "NO CHROMS FOR", build
+            print("NO CHROMS FOR", build)
             continue
         org_page.pop(0)
         if org_page[-1] == "":
@@ -82,12 +82,11 @@ def __main__():
                         if org not in builds:
                             builds[org] = {'chrs': {}, 'build': build}
                         builds[org]['chrs'][refseq] = chr
-                        # print build,org,chr,refseq
 
-    print
+    print()
     ext_to_edit = ['bed', 'info', ]
     for org in builds:
-        print org, "changed to", builds[org]['build']
+        print(org, "changed to", builds[org]['build'])
 
         # org info file
         info_file_old = os.path.join(base_dir + org, org + ".info")

scripts/migrate_tools/migrate_tools.py

@@ -7,6 +7,8 @@ migrated_tools_conf.xml for tools outside tool panel sections as well as tools i
 layout of the local tool_conf.xml file.  Entries will not be created in migrated_tools_conf.xml for tools included in the tool
 shed repository but not defined in tool_conf.xml.
 """
+from __future__ import print_function
+
 import os
 import sys
 
@@ -24,6 +26,6 @@ else:
     file_names = ', '.join(non_shed_tool_confs)
 msg = "\nThe installation process is finished.  All tools associated with this migration that were defined in your file%s named\n" % plural
 msg += "%s, have been removed.  You may now start your Galaxy server.\n" % file_names
-print msg
+print(msg)
 app.shutdown()
 sys.exit(0)

scripts/others/incorrect_gops_jobs.py

@@ -3,6 +3,8 @@
 Fetch jobs using gops_intersect, gops_merge, gops_subtract, gops_complement, gops_coverage
 wherein the second dataset doesn't have chr, start and end in standard columns 1, 2 and 3.
 """
+from __future__ import print_function
+
 import ConfigParser
 import os
 import sys
@@ -13,13 +15,13 @@ import sqlalchemy as sa
 import galaxy.app
 import galaxy.model.mapping
 
-assert sys.version_info[:2] >= (2, 4)
+assert sys.version_info[:2] >= (2, 6)
 
 
 class TestApplication(object):
     """Encapsulates the state of a Universe application"""
     def __init__(self, database_connection=None, file_path=None):
-        print >> sys.stderr, "python path is: " + ", ".join(sys.path)
+        print("python path is: " + ", ".join(sys.path), file=sys.stderr)
         if database_connection is None:
             raise Exception("CleanupDatasetsApplication requires a database_connection value")
         if file_path is None:
@@ -51,16 +53,16 @@ def main():
                                                        sa.and_(sa.or_(app.model.Job.table.c.tool_id == 'gops_complement_1',
                                                                       app.model.Job.table.c.tool_id == 'gops_merge_1'),
                                                                sa.not_(app.model.Job.table.c.command_line.like('%-1 1,2,3%')))))).all():
-            print "# processing job id %s" % str(job.id)
+            print("# processing job id %s" % str(job.id))
             for jtoda in job.output_datasets:
-                print "# --> processing JobToOutputDatasetAssociation id %s" % str(jtoda.id)
+                print("# --> processing JobToOutputDatasetAssociation id %s" % str(jtoda.id))
                 hda = app.model.HistoryDatasetAssociation.get(jtoda.dataset_id)
-                print "# ----> processing HistoryDatasetAssociation id %s" % str(hda.id)
+                print("# ----> processing HistoryDatasetAssociation id %s" % str(hda.id))
                 if not hda.deleted:
                     # Probably don't need this check, since the job state should suffice, but...
                     if hda.dataset.state == 'ok':
                         history = app.model.History.get(hda.history_id)
-                        print "# ------> processing history id %s" % str(history.id)
+                        print("# ------> processing history id %s" % str(history.id))
                         if history.user_id:
                             cmd_line = str(job.command_line)
                             new_output = tempfile.NamedTemporaryFile('w')
@@ -77,7 +79,7 @@ def main():
                             diff_status = os.system('diff %s %s >> /dev/null' % (new_output.name, job_output))
                             if diff_status == 0:
                                 continue
-                            print "# --------> Outputs differ"
+                            print("# --------> Outputs differ")
                             user = app.model.User.get(history.user_id)
                             jobs[job.id] = {}
                             jobs[job.id]['hda_id'] = hda.id
@@ -88,20 +90,20 @@ def main():
                             jobs[job.id]['history_update_time'] = history.update_time
                             jobs[job.id]['user_email'] = user.email
     except Exception as e:
-        print "# caught exception: %s" % str(e)
+        print("# caught exception: %s" % e)
 
-    print "\n\n# Number of incorrect Jobs: %d\n\n" % (len(jobs))
-    print "#job_id\thda_id\thda_name\thda_info\thistory_id\thistory_name\thistory_update_time\tuser_email"
+    print("\n\n# Number of incorrect Jobs: %d\n\n" % (len(jobs)))
+    print("#job_id\thda_id\thda_name\thda_info\thistory_id\thistory_name\thistory_update_time\tuser_email")
     for jid in jobs:
-        print '%s\t%s\t"%s"\t"%s"\t%s\t"%s"\t"%s"\t%s' % \
+        print('%s\t%s\t"%s"\t"%s"\t%s\t"%s"\t"%s"\t%s' %
             (str(jid),
-              str(jobs[jid]['hda_id']),
-              jobs[jid]['hda_name'],
-              jobs[jid]['hda_info'],
-              str(jobs[jid]['history_id']),
-              jobs[jid]['history_name'],
-              jobs[jid]['history_update_time'],
-              jobs[jid]['user_email'])
+             str(jobs[jid]['hda_id']),
+             jobs[jid]['hda_name'],
+             jobs[jid]['hda_info'],
+             str(jobs[jid]['history_id']),
+             jobs[jid]['history_name'],
+             jobs[jid]['history_update_time'],
+             jobs[jid]['user_email']))
     sys.exit(0)
 
 

scripts/others/incorrect_gops_join_jobs.py

@@ -2,6 +2,8 @@
 """
 Fetch gops_join wherein the use specified minimum coverage is not 1.
 """
+from __future__ import print_function
+
 import ConfigParser
 import os
 import sys
@@ -12,13 +14,13 @@ import sqlalchemy as sa
 import galaxy.app
 import galaxy.model.mapping
 
-assert sys.version_info[:2] >= (2, 4)
+assert sys.version_info[:2] >= (2, 6)
 
 
 class TestApplication(object):
     """Encapsulates the state of a Universe application"""
     def __init__(self, database_connection=None, file_path=None):
-        print >> sys.stderr, "python path is: " + ", ".join(sys.path)
+        print("python path is: " + ", ".join(sys.path), file=sys.stderr)
         if database_connection is None:
             raise Exception("CleanupDatasetsApplication requires a database_connection value")
         if file_path is None:
@@ -45,16 +47,16 @@ def main():
                                                 app.model.Job.table.c.state == 'ok',
                                                 app.model.Job.table.c.tool_id == 'gops_join_1',
                                                 sa.not_(app.model.Job.table.c.command_line.like('%-m 1 %')))).all():
-            print "# processing job id %s" % str(job.id)
+            print("# processing job id %s" % str(job.id))
             for jtoda in job.output_datasets:
-                print "# --> processing JobToOutputDatasetAssociation id %s" % str(jtoda.id)
+                print("# --> processing JobToOutputDatasetAssociation id %s" % str(jtoda.id))
                 hda = app.model.HistoryDatasetAssociation.get(jtoda.dataset_id)
-                print "# ----> processing HistoryDatasetAssociation id %s" % str(hda.id)
+                print("# ----> processing HistoryDatasetAssociation id %s" % str(hda.id))
                 if not hda.deleted:
                     # Probably don't need this check, since the job state should suffice, but...
                     if hda.dataset.state == 'ok':
                         history = app.model.History.get(hda.history_id)
-                        print "# ------> processing history id %s" % str(history.id)
+                        print("# ------> processing history id %s" % str(history.id))
                         if history.user_id:
                             cmd_line = str(job.command_line)
                             new_output = tempfile.NamedTemporaryFile('w')
@@ -67,7 +69,7 @@ def main():
                             diff_status = os.system('diff %s %s >> /dev/null' % (new_output.name, job_output))
                             if diff_status == 0:
                                 continue
-                            print "# --------> Outputs differ"
+                            print("# --------> Outputs differ")
                             user = app.model.User.get(history.user_id)
                             jobs[job.id] = {}
                             jobs[job.id]['hda_id'] = hda.id
@@ -78,20 +80,20 @@ def main():
                             jobs[job.id]['history_update_time'] = history.update_time
                             jobs[job.id]['user_email'] = user.email
     except Exception as e:
-        print "# caught exception: %s" % str(e)
+        print("# caught exception: %s" % e)
 
-    print "\n\n# Number of incorrect Jobs: %d\n\n" % (len(jobs))
-    print "#job_id\thda_id\thda_name\thda_info\thistory_id\thistory_name\thistory_update_time\tuser_email"
+    print("\n\n# Number of incorrect Jobs: %d\n\n" % (len(jobs)))
+    print("#job_id\thda_id\thda_name\thda_info\thistory_id\thistory_name\thistory_update_time\tuser_email")
     for jid in jobs:
-        print '%s\t%s\t"%s"\t"%s"\t%s\t"%s"\t"%s"\t%s' % \
+        print('%s\t%s\t"%s"\t"%s"\t%s\t"%s"\t"%s"\t%s' %
             (str(jid),
-              str(jobs[jid]['hda_id']),
-              jobs[jid]['hda_name'],
-              jobs[jid]['hda_info'],
-              str(jobs[jid]['history_id']),
-              jobs[jid]['history_name'],
-              jobs[jid]['history_update_time'],
-              jobs[jid]['user_email'])
+             str(jobs[jid]['hda_id']),
+             jobs[jid]['hda_name'],
+             jobs[jid]['hda_info'],
+             str(jobs[jid]['history_id']),
+             jobs[jid]['history_name'],
+             jobs[jid]['history_update_time'],
+             jobs[jid]['user_email']))
     sys.exit(0)
 
 

scripts/set_dataset_sizes.py

@@ -1,4 +1,6 @@
 #!/usr/bin/env python
+from __future__ import print_function
+
 import os
 import sys
 from ConfigParser import ConfigParser
@@ -36,15 +38,15 @@ def init():
 
 
 if __name__ == '__main__':
-    print 'Loading Galaxy model...'
+    print('Loading Galaxy model...')
     model, object_store = init()
     sa_session = model.context.current
 
     set = 0
     dataset_count = sa_session.query(model.Dataset).count()
-    print 'Processing %i datasets...' % dataset_count
+    print('Processing %i datasets...' % dataset_count)
     percent = 0
-    print 'Completed %i%%' % percent,
+    print('Completed %i%%' % percent, end=' ')
     sys.stdout.flush()
     for i, dataset in enumerate(sa_session.query(model.Dataset).enable_eagerloads(False).yield_per(1000)):
         if dataset.total_size is None:
@@ -55,8 +57,8 @@ if __name__ == '__main__':
         new_percent = int(float(i) / dataset_count * 100)
         if new_percent != percent:
             percent = new_percent
-            print '\rCompleted %i%%' % percent,
+            print('\rCompleted %i%%' % percent, end=' ')
             sys.stdout.flush()
     sa_session.flush()
-    print 'Completed 100%%'
+    print('\rCompleted 100%')
     object_store.shutdown()

scripts/set_user_disk_usage.py

@@ -1,4 +1,6 @@
 #!/usr/bin/env python
+from __future__ import print_function
+
 import os
 import sys
 from ConfigParser import ConfigParser
@@ -50,25 +52,25 @@ def init():
 def quotacheck(sa_session, users, engine):
     sa_session.refresh(user)
     current = user.get_disk_usage()
-    print user.username, '<' + user.email + '>:',
+    print(user.username, '<' + user.email + '>:', end=' ')
     if engine not in ('postgres', 'postgresql'):
         new = user.calculate_disk_usage()
         sa_session.refresh(user)
         # usage changed while calculating, do it again
         if user.get_disk_usage() != current:
-            print 'usage changed while calculating, trying again...'
+            print('usage changed while calculating, trying again...')
             return quotacheck(sa_session, user, engine)
     else:
         new = pgcalc(sa_session, user.id, dryrun=options.dryrun)
     # yes, still a small race condition between here and the flush
-    print 'old usage:', nice_size(current), 'change:',
+    print('old usage:', nice_size(current), 'change:', end=' ')
     if new in (current, None):
-        print 'none'
+        print('none')
     else:
         if new > current:
-            print '+%s' % (nice_size(new - current))
+            print('+%s' % (nice_size(new - current)))
         else:
-            print '-%s' % (nice_size(current - new))
+            print('-%s' % (nice_size(current - new)))
         if not options.dryrun and engine not in ('postgres', 'postgresql'):
             user.set_disk_usage(new)
             sa_session.add(user)
@@ -76,17 +78,17 @@ def quotacheck(sa_session, users, engine):
 
 
 if __name__ == '__main__':
-    print 'Loading Galaxy model...'
+    print('Loading Galaxy model...')
     model, object_store, engine = init()
     sa_session = model.context.current
 
     if not options.username and not options.email:
         user_count = sa_session.query(model.User).count()
-        print 'Processing %i users...' % user_count
+        print('Processing %i users...' % user_count)
         for i, user in enumerate(sa_session.query(model.User).enable_eagerloads(False).yield_per(1000)):
-            print '%3i%%' % int(float(i) / user_count * 100),
+            print('%3i%%' % int(float(i) / user_count * 100), end=' ')
             quotacheck(sa_session, user, engine)
-        print '100% complete'
+        print('100% complete')
         object_store.shutdown()
         sys.exit(0)
     elif options.username:
@@ -94,7 +96,7 @@ if __name__ == '__main__':
     elif options.email:
         user = sa_session.query(model.User).enable_eagerloads(False).filter_by(email=options.email).first()
     if not user:
-        print 'User not found'
+        print('User not found')
         sys.exit(1)
     object_store.shutdown()
     quotacheck(sa_session, user, engine)

scripts/slideshow/build_slideshow.py

@@ -1,3 +1,5 @@
+from __future__ import print_function
+
 import os
 import string
 import sys
@@ -20,7 +22,7 @@ def main(argv=None):
         'title': title,
         'content': content,
     })
-    print html
+    print(html)
     open(output, "w").write(html)
 
 

scripts/tool_shed/api/add_repository_registry_entry.py

@@ -5,6 +5,7 @@ Add appropriate entries to the Tool Shed's repository registry for a specified r
 Here is a working example of how to use this script.
 python ./add_repository_registry_entry.py -a <api key> -u <tool shed url> -n <repository name> -o <repository owner>
 """
+from __future__ import print_function
 
 import argparse
 
@@ -22,11 +23,11 @@ def main(options):
             data['owner'] = options.owner
             url = '%s%s' % (base_tool_shed_url, '/api/repositories/add_repository_registry_entry')
             response_dict = submit(url, data, api_key=api_key, return_formatted=False)
-            print response_dict
+            print(response_dict)
         else:
-            print "Invalid tool_shed: ", base_tool_shed_url, " name: ", options.name, " or owner: ", options.owner, "."
+            print("Invalid tool_shed: ", base_tool_shed_url, " name: ", options.name, " or owner: ", options.owner, ".")
     else:
-        print "An API key for an admin user in the Tool Shed is required to add entries into the Tool Shed's repository registry."
+        print("An API key for an admin user in the Tool Shed is required to add entries into the Tool Shed's repository registry.")
 
 
 if __name__ == '__main__':

scripts/tool_shed/api/common.py

@@ -1,3 +1,5 @@
+from __future__ import print_function
+
 import json
 import os
 import sys
@@ -62,15 +64,15 @@ def delete(api_key, url, data, return_formatted=True):
         response = json.loads(delete_request.read())
     except urllib2.HTTPError as e:
         if return_formatted:
-            print e
-            print e.read(1024)
+            print(e)
+            print(e.read(1024))
             sys.exit(1)
         else:
             return dict(status='error', message=str(e.read(1024)))
     if return_formatted:
-        print 'Response'
-        print '--------'
-        print response
+        print('Response')
+        print('--------')
+        print(response)
     else:
         return response
 
@@ -80,40 +82,40 @@ def display(url, api_key=None, return_formatted=True):
     try:
         r = get(url, api_key=api_key)
     except urllib2.HTTPError as e:
-        print e
+        print(e)
         # Only return the first 1K of errors.
-        print e.read(1024)
+        print(e.read(1024))
         sys.exit(1)
     if type(r) == unicode:
-        print 'error: %s' % r
+        print('error: %s' % r)
         return None
     if not return_formatted:
         return r
     elif type(r) == list:
         # Response is a collection as defined in the REST style.
-        print 'Collection Members'
-        print '------------------'
+        print('Collection Members')
+        print('------------------')
         for n, i in enumerate(r):
             # All collection members should have a name in the response.
             # url is optional
             if 'url' in i:
-                print '#%d: %s' % (n + 1, i.pop('url'))
+                print('#%d: %s' % (n + 1, i.pop('url')))
             if 'name' in i:
-                print '  name: %s' % i.pop('name')
+                print('  name: %s' % i.pop('name'))
             for k, v in i.items():
-                print '  %s: %s' % (k, v)
-        print ''
-        print '%d element(s) in collection' % len(r)
+                print('  %s: %s' % (k, v))
+        print()
+        print('%d element(s) in collection' % len(r))
     elif type(r) == dict:
         # Response is an element as defined in the REST style.
-        print 'Member Information'
-        print '------------------'
+        print('Member Information')
+        print('------------------')
         for k, v in r.items():
-            print '%s: %s' % (k, v)
+            print('%s: %s' % (k, v))
     elif type(r) == str:
-        print r
+        print(r)
     else:
-        print 'response is unknown type: %s' % type(r)
+        print('response is unknown type: %s' % type(r))
 
 
 def get(url, api_key=None):
@@ -195,7 +197,7 @@ def json_from_url(url):
         parsed_json = json.loads(url_contents)
     except Exception as e:
         error_message = str(url_contents)
-        print 'Error parsing JSON data in json_from_url(): ', str(e)
+        print('Error parsing JSON data in json_from_url():', e)
         return None, error_message
     return parsed_json, error_message
 
@@ -242,32 +244,32 @@ def submit(url, data, api_key=None, return_formatted=True):
         response = post(url, data, api_key=api_key)
     except urllib2.HTTPError as e:
         if return_formatted:
-            print e
-            print e.read(1024)
+            print(e)
+            print(e.read(1024))
             sys.exit(1)
         else:
             return dict(status='error', message=str(e.read(1024)))
     if not return_formatted:
         return response
-    print 'Response'
-    print '--------'
+    print('Response')
+    print('--------')
     if type(response) == list:
         # Currently the only implemented responses are lists of dicts, because submission creates
         # some number of collection elements.
         for i in response:
             if type(i) == dict:
                 if 'url' in i:
-                    print i.pop('url')
+                    print(i.pop('url'))
                 else:
-                    print '----'
+                    print('----')
                 if 'name' in i:
-                    print '  name: %s' % i.pop('name')
+                    print('  name: %s' % i.pop('name'))
                 for k, v in i.items():
-                    print '  %s: %s' % (k, v)
+                    print('  %s: %s' % (k, v))
             else:
-                print i
+                print(i)
     else:
-        print response
+        print(response)
 
 
 def update(api_key, url, data, return_formatted=True):
@@ -279,14 +281,14 @@ def update(api_key, url, data, return_formatted=True):
         response = put(url, data, api_key=api_key)
     except urllib2.HTTPError as e:
         if return_formatted:
-            print e
-            print e.read(1024)
+            print(e)
+            print(e.read(1024))
             sys.exit(1)
         else:
             return dict(status='error', message=str(e.read(1024)))
     if return_formatted:
-        print 'Response'
-        print '--------'
-        print response
+        print('Response')
+        print('--------')
+        print(response)
     else:
         return response

scripts/tool_shed/api/create_categories.py

@@ -17,6 +17,7 @@ available in the test public Tool Shed and create each of them in a local develo
 
 ./create_categories.py -a <api key> -f http://testtoolshed.g2.bx.psu.edu -t http://localhost:9009
 """
+from __future__ import print_function
 
 import argparse
 
@@ -42,7 +43,7 @@ def main(options):
                 response = submit(url, data, api_key)
             except Exception as e:
                 response = str(e)
-                print "Error attempting to create category using URL: ", url, " exception: ", str(e)
+                print("Error attempting to create category using URL: ", url, " exception: ", e)
             create_response_dict = dict(response=response)
             create_response_dicts.append(create_response_dict)
 

scripts/tool_shed/api/create_users.py

@@ -18,6 +18,7 @@ are available in the test public Tool Shed and create each of them in a local de
 
 ./create_users.py -a <api key> -f http://testtoolshed.g2.bx.psu.edu -t http://localhost:9009
 """
+from __future__ import print_function
 
 import argparse
 
@@ -45,7 +46,7 @@ def main(options):
                 response = submit(url, data, api_key)
             except Exception as e:
                 response = str(e)
-                print "Error attempting to create user using URL: ", url, " exception: ", str(e)
+                print("Error attempting to create user using URL: ", url, " exception: ", e)
             create_response_dict = dict(response=response)
             create_response_dicts.append(create_response_dict)
 

scripts/tool_shed/api/export.py

@@ -6,6 +6,7 @@ dependencies from the tool shed into a compressed archive.
 Here is a working example of how to use this script to export a repository from the tool shed.
 ./export.py --url http://testtoolshed.g2.bx.psu.edu --name chemicaltoolbox --owner bgruening --revision 4133dbf7ff4d --export_repository_dependencies True --download_dir /tmp
 """
+from __future__ import print_function
 
 import argparse
 import os
@@ -85,7 +86,7 @@ def main(options):
         export_dict = submit(url, data, return_formatted=False)
         error_messages = export_dict['error_messages']
         if error_messages:
-            print "Error attempting to export revision ", options.changeset_revision, " of repository ", options.name, " owned by ", options.owner, ":\n", error_messages
+            print("Error attempting to export revision ", options.changeset_revision, " of repository ", options.name, " owned by ", options.owner, ":\n", error_messages)
         else:
             export_repository_dependencies = string_as_bool(options.export_repository_dependencies)
             repositories_archive_filename = \
@@ -104,10 +105,10 @@ def main(options):
                 for chunk in src.iter_content(chunk_size=CHUNK_SIZE):
                     if chunk:
                         dst.write(chunk)
-            print "Successfully exported revision ", options.changeset_revision, " of repository ", options.name, " owned by ", options.owner
-            print "to location ", file_path
+            print("Successfully exported revision ", options.changeset_revision, " of repository ", options.name, " owned by ", options.owner)
+            print("to location ", file_path)
     else:
-        print "Invalid tool_shed / name / owner ."
+        print("Invalid tool_shed / name / owner .")
 
 
 if __name__ == '__main__':

scripts/tool_shed/api/get_filtered_repository_revisions.py

@@ -19,6 +19,7 @@ This script is useful for analyzing the Tool Shed's install and test framework.
 Here is a working example of how to use this script.
 ./get_filtered_repository_revisions.py --url http://testtoolshed.g2.bx.psu.edu
 """
+from __future__ import print_function
 
 import argparse
 import os
@@ -54,7 +55,7 @@ def main(options):
     api_url = get_api_url(base=base_tool_shed_url, parts=parts, params=params)
     baseline_repository_dicts, error_message = json_from_url(api_url)
     if baseline_repository_dicts is None or error_message:
-        print error_message
+        print(error_message)
     else:
         repository_dicts = []
         for baseline_repository_dict in baseline_repository_dicts:
@@ -62,7 +63,7 @@ def main(options):
             # module that will generate the install methods.
             repository_dict, error_message = get_repository_dict(base_tool_shed_url, baseline_repository_dict)
             if error_message:
-                print 'Error getting additional details from the API: ', error_message
+                print('Error getting additional details from the API: ', error_message)
                 repository_dicts.append(baseline_repository_dict)
             else:
                 # Don't test empty repositories.
@@ -76,8 +77,8 @@ def main(options):
                             repository_dicts.append(dict(repository_dict.items() + baseline_repository_dict.items()))
                     else:
                         repository_dicts.append(dict(repository_dict.items() + baseline_repository_dict.items()))
-        print '\n\n', repository_dicts
-        print '\nThe url:\n\n', api_url, '\n\nreturned ', len(repository_dicts), ' repository dictionaries...'
+        print('\n\n', repository_dicts)
+        print('\nThe url:\n\n', api_url, '\n\nreturned ', len(repository_dicts), ' repository dictionaries...')
 
 
 if __name__ == '__main__':

scripts/tool_shed/api/remove_repository_registry_entry.py

@@ -5,6 +5,7 @@ Remove appropriate entries from the Tool Shed's repository registry for a specif
 Here is a working example of how to use this script.
 python ./remove_repository_registry_entry.py -a <api key> -u <tool shed url> -n <repository name> -o <repository owner>
 """
+from __future__ import print_function
 
 import argparse
 
@@ -22,11 +23,11 @@ def main(options):
             data['owner'] = options.owner
             url = '%s%s' % (base_tool_shed_url, '/api/repositories/remove_repository_registry_entry')
             response_dict = submit(url, data, api_key=api_key, return_formatted=False)
-            print response_dict
+            print(response_dict)
         else:
-            print "Invalid tool_shed: ", base_tool_shed_url, " name: ", options.name, " or owner: ", options.owner, "."
+            print("Invalid tool_shed: ", base_tool_shed_url, " name: ", options.name, " or owner: ", options.owner, ".")
     else:
-        print "An API key for an admin user in the Tool Shed is required to remove entries from the Tool Shed's repository registry."
+        print("An API key for an admin user in the Tool Shed is required to remove entries from the Tool Shed's repository registry.")
 
 
 if __name__ == '__main__':

scripts/tool_shed/api/reset_metadata_on_repositories.py

@@ -11,6 +11,8 @@ usage: reset_metadata_on_repositories.py key <my_writable>
 Here is a working example of how to use this script to reset metadata on certain repositories in a specified Tool Shed.
 python ./reset_metadata_on_repositories.py -a 22be3b -m True -u http://localhost:9009/
 """
+from __future__ import print_function
+
 import argparse
 import logging
 import os
@@ -56,9 +58,9 @@ def main(options):
         repository_ids = get(url, api_key)
         for repository_id in repository_ids:
             if repository_id in encoded_ids_to_skip:
-                print "--------"
-                print "Skipping repository with id %s because it is in skip file %s" % (str(repository_id), str(skip_file))
-                print "--------"
+                print("--------")
+                print("Skipping repository with id %s because it is in skip file %s" % (repository_id, skip_file))
+                print("--------")
             else:
                 data = dict(repository_id=repository_id)
                 url = '%s/api/repositories/reset_metadata_on_repository' % base_tool_shed_url

scripts/tool_shed/bootstrap_tool_shed/bootstrap_util.py

@@ -1,4 +1,6 @@
 #!/usr/bin/python
+from __future__ import print_function
+
 import ConfigParser
 import optparse
 import os
@@ -75,7 +77,7 @@ def admin_user_info():
     email = None
     password = None
     if tree is None:
-        print "The XML file ", user_info_config, " seems to be invalid, using defaults."
+        print("The XML file ", user_info_config, " seems to be invalid, using defaults.")
         email = 'admin@test.org'
         password = 'testuser'
         username = 'admin'
@@ -97,7 +99,7 @@ def get_local_tool_shed_url(config_parser):
         if config_parser.has_option('server:main', 'port'):
             port = config_parser.get('server:main', 'port')
     host = '127.0.0.1'
-    print 'http://%s:%s' % (host, port)
+    print('http://%s:%s' % (host, port))
     return 0
 
 
@@ -113,7 +115,7 @@ def main(args):
         return check_db(config_parser)
     elif args.method == 'admin_user_info':
         (username, email, password) = admin_user_info()
-        print '%s__SEP__%s__SEP__%s' % (username, email, password)
+        print('%s__SEP__%s__SEP__%s' % (username, email, password))
         return 0
     elif args.method == 'get_url':
         return get_local_tool_shed_url(config_parser)

scripts/tool_shed/bootstrap_tool_shed/create_user_with_api_key.py

@@ -1,4 +1,5 @@
 #!/usr/bin/env python
+from __future__ import print_function
 
 import ConfigParser
 import logging
@@ -33,7 +34,7 @@ class BootstrapApplication(object):
         self.config = config
         if not self.config.database_connection:
             self.config.database_connection = "sqlite:///%s?isolation_level=IMMEDIATE" % str(config.database)
-        print 'Using database connection: ', self.config.database_connection
+        print('Using database connection: ', self.config.database_connection)
         # Setup the database engine and ORM
         self.model = mapping.init(self.config.file_path,
                                   self.config.database_connection,
@@ -42,7 +43,7 @@ class BootstrapApplication(object):
         self.security = security.SecurityHelper(id_secret=self.config.id_secret)
         self.hgweb_config_manager = self.model.hgweb_config_manager
         self.hgweb_config_manager.hgweb_config_dir = self.config.hgweb_config_dir
-        print 'Using hgweb.config file: ', self.hgweb_config_manager.hgweb_config
+        print('Using hgweb.config file: ', self.hgweb_config_manager.hgweb_config)
 
     @property
     def sa_session(self):
@@ -68,7 +69,7 @@ def create_user(app):
     if email and password and username:
         invalid_message = validate(email, password, username)
         if invalid_message:
-            print invalid_message
+            print(invalid_message)
         else:
             user = app.model.User(email=email)
             user.set_password_cleartext(password)
@@ -78,7 +79,7 @@ def create_user(app):
             app.model.security_agent.create_private_user_role(user)
             return user
     else:
-        print "Missing required values for email: ", email, ", password: ", password, ", username: ", username
+        print("Missing required values for email: ", email, ", password: ", password, ", username: ", username)
     return None
 
 
@@ -124,7 +125,7 @@ if __name__ == "__main__":
     (args, options) = parser.parse_args()
     ini_file = args.config
     config_parser = ConfigParser.ConfigParser({'here': os.getcwd()})
-    print "Reading ini file: ", ini_file
+    print("Reading ini file: ", ini_file)
     config_parser.read(ini_file)
     config_dict = {}
     for key, value in config_parser.items("app:main"):
@@ -134,7 +135,7 @@ if __name__ == "__main__":
     user = create_user(app)
     if user is not None:
         api_key = create_api_key(app, user)
-        print "Created new user with public username '", user.username, ".  An API key was also created and associated with the user."
+        print("Created new user with public username '", user.username, ".  An API key was also created and associated with the user.")
         sys.exit(0)
     else:
         sys.exit("Problem creating a new user and an associated API key.")

scripts/tool_shed/build_ts_whoosh_index.py

@@ -10,6 +10,8 @@ Make sure you adjusted your config to:
 
 This script expects the Tool Shed's runtime virtualenv to be active.
 """
+from __future__ import print_function
+
 import ConfigParser
 import logging
 import os
@@ -97,7 +99,6 @@ def build_index(sa_session, whoosh_index_dir, path_to_repositories):
                              full_last_updated=repo.get('full_last_updated'))
         #  Tools get their own index
         for tool in repo.get('tools_list'):
-            # print tool
             tool_index_writer.add_document(id=to_unicode(tool.get('id')),
                                            name=to_unicode(tool.get('name')),
                                            version=to_unicode(tool.get('version')),
@@ -107,16 +108,16 @@ def build_index(sa_session, whoosh_index_dir, path_to_repositories):
                                            repo_name=to_unicode(repo.get('name')),
                                            repo_id=repo.get('id'))
             tools_indexed += 1
-            print tools_indexed, 'tools (', tool.get('id'), ')'
+            print(tools_indexed, 'tools (', tool.get('id'), ')')
 
         repos_indexed += 1
-        print repos_indexed, 'repos (', repo.get('id'), ')'
+        print(repos_indexed, 'repos (', repo.get('id'), ')')
 
     tool_index_writer.commit()
     repo_index_writer.commit()
 
-    print "TOTAL repos indexed: ", repos_indexed
-    print "TOTAL tools indexed: ", tools_indexed
+    print("TOTAL repos indexed: ", repos_indexed)
+    print("TOTAL tools indexed: ", tools_indexed)
 
 
 def get_repos(sa_session, path_to_repositories):

scripts/tool_shed/check_download_urls.py

@@ -2,6 +2,8 @@
 # Dan Blankenberg
 # Script that checks toolshed tags to see if URLs are accessible.
 # Does not currently handle 'download_binary'
+from __future__ import print_function
+
 import os
 import urllib2
 import xml.etree.ElementTree as ET
@@ -30,9 +32,9 @@ def main():
                             try:
                                 urllib2.urlopen(urllib2.Request(url))
                             except Exception as e:
-                                print "Bad URL '%s' in file '%s': %s" % (url, path, e)
+                                print("Bad URL '%s' in file '%s': %s" % (url, path, e))
                 except Exception as e:
-                    print "Unable to check XML file '%s': %s" % (path, e)
+                    print("Unable to check XML file '%s': %s" % (path, e))
 
 
 if __name__ == "__main__":

scripts/tool_shed/check_filesystem_for_empty_tool_dependency_installation_paths.py

@@ -1,3 +1,5 @@
+from __future__ import print_function
+
 import argparse
 import os
 import shutil
@@ -11,9 +13,9 @@ from tool_shed.util.basic_util import INSTALLATION_LOG
 def main(args):
     empty_installation_paths = []
     if not os.path.exists(args.basepath):
-        print 'Tool dependency path %s does not exist.' % str(args.basepath)
+        print('Tool dependency path "%s" does not exist.' % args.basepath)
         return 1
-    print 'Checking path %s for empty tool dependency installation directories.' % args.basepath
+    print('Checking path "%s" for empty tool dependency installation directories.' % args.basepath)
     for root, dirs, files in os.walk(args.basepath):
         path_parts = root.replace(args.basepath, '').lstrip('/').split(os.sep)
         # Skip certain special directories.
@@ -35,18 +37,18 @@ def main(args):
         if no_files and no_dirs and root not in empty_installation_paths:
             empty_installation_paths.append(root)
     if len(empty_installation_paths) > 0:
-        print 'The following %d tool dependency installation directories were found to be empty or contain only the file %s.' % \
-            (len(empty_installation_paths), INSTALLATION_LOG)
+        print('The following %d tool dependency installation directories were found to be empty or contain only the file %s.' %
+            (len(empty_installation_paths), INSTALLATION_LOG))
         if args.delete:
             for path in empty_installation_paths:
                 if os.path.exists(path):
                     shutil.rmtree(path)
-                    print 'Deleted %s.' % path
+                    print('Deleted %s.' % path)
         else:
             for empty_installation_path in empty_installation_paths:
-                print empty_installation_path
+                print(empty_installation_path)
     else:
-        print 'No empty tool dependency installation directories found.'
+        print('No empty tool dependency installation directories found.')
     return 0
 
 

scripts/tool_shed/check_s3_for_empty_tool_dependency_installation_paths.py

@@ -1,3 +1,5 @@
+from __future__ import print_function
+
 import argparse
 import os
 import sys
@@ -23,15 +25,15 @@ class BucketList(object):
 
     def display_empty_installation_paths(self):
         for empty_installation_path in self.empty_installation_paths:
-            print empty_installation_path
+            print(empty_installation_path)
 
     def delete_empty_installation_paths(self):
-        print 'Deleting empty installation paths.'
+        print('Deleting empty installation paths.')
         for empty_installation_path in self.empty_installation_paths:
             # Get all keys in the S3 bucket that start with the installation path, and delete each one.
             for path_to_delete in self.bucket.list(prefix=empty_installation_path):
                 self.bucket.delete_key(path_to_delete.key)
-                print 'Deleted empty path %s' % str(empty_installation_path)
+                print('Deleted empty path %s' % empty_installation_path)
 
     def get_tool_dependency_install_paths(self):
         found_paths = []
@@ -92,22 +94,22 @@ def main(args):
         if args.s3passwd is not None and os.path.exists(args.s3passwd):
             awsid, secret = open(args.s3passwd, 'r').read().rstrip('\n').split(':')
         else:
-            print 'Amazon ID and secret not provided, and no s3passwd file found.'
+            print('Amazon ID and secret not provided, and no s3passwd file found.')
             return 1
     else:
         awsid = args.id
         secret = args.secret
     dependency_cleaner = BucketList(awsid, secret, args.bucket)
     if len(dependency_cleaner.empty_installation_paths) == 0:
-        print 'No empty installation paths found, exiting.'
+        print('No empty installation paths found, exiting.')
         return 0
-    print 'The following %d tool dependency installation paths were found to be empty or contain only the file %s.' % \
-        (len(dependency_cleaner.empty_installation_paths), INSTALLATION_LOG)
+    print('The following %d tool dependency installation paths were found to be empty or contain only the file %s.' %
+        (len(dependency_cleaner.empty_installation_paths), INSTALLATION_LOG))
     if asbool(args.delete):
         dependency_cleaner.delete_empty_installation_paths()
     else:
         for empty_installation_path in dependency_cleaner.empty_installation_paths:
-            print empty_installation_path
+            print(empty_installation_path)
     return 0
 
 

scripts/tool_shed/clean_up_tool_dependency_directory.py

@@ -1,3 +1,5 @@
+from __future__ import print_function
+
 import argparse
 import os
 import shutil
@@ -6,12 +8,12 @@ import sys
 
 def main(args):
     if not os.path.exists(args.tool_dependency_dir):
-        print 'Tool dependency base path %s does not exist, creating.' % str(args.tool_dependency_dir)
+        print('Tool dependency base path "%s" does not exist, creating.' % args.tool_dependency_dir)
         os.mkdir(args.tool_dependency_dir)
         return 0
     else:
         for content in os.listdir(args.tool_dependency_dir):
-            print 'Deleting directory %s from %s.' % (content, args.tool_dependency_dir)
+            print('Deleting directory "%s" from "%s" .' % (content, args.tool_dependency_dir))
             full_path = os.path.join(args.tool_dependency_dir, content)
             if os.path.isdir(full_path):
                 shutil.rmtree(full_path)

scripts/tool_shed/deprecate_repositories_without_metadata.py

@@ -1,4 +1,5 @@
 #!/usr/bin/env python
+from __future__ import print_function
 
 import ConfigParser
 import logging
@@ -26,7 +27,7 @@ from galaxy.util import (
 log = logging.getLogger()
 log.setLevel(10)
 log.addHandler(logging.StreamHandler(sys.stdout))
-assert sys.version_info[:2] >= (2, 4)
+assert sys.version_info[:2] >= (2, 6)
 
 
 def build_citable_url(host, repository):
@@ -56,11 +57,11 @@ def main():
     app = DeprecateRepositoriesApplication(config)
     cutoff_time = datetime.utcnow() - timedelta(days=options.days)
     now = strftime("%Y-%m-%d %H:%M:%S")
-    print "\n####################################################################################"
-    print "# %s - Handling stuff older than %i days" % (now, options.days)
+    print("\n####################################################################################")
+    print("# %s - Handling stuff older than %i days" % (now, options.days))
 
     if options.info_only:
-        print "# Displaying info only ( --info_only )"
+        print("# Displaying info only ( --info_only )")
 
     deprecate_repositories(app, cutoff_time, days=options.days, info_only=options.info_only, verbose=options.verbose)
 
@@ -75,10 +76,10 @@ def send_mail_to_owner(app, name, owner, email, repositories_deprecated, days=14
     # an environment variable named TOOL_SHED_CANONICAL_URL be set, pointing to the tool shed that is being checked.
     url = os.environ.get('TOOL_SHED_CANONICAL_URL', None)
     if None in [smtp_server, from_address]:
-        print '# Mail not configured, not sending email to repository owner.'
+        print('# Mail not configured, not sending email to repository owner.')
         return
     elif url is None:
-        print '# Environment variable TOOL_SHED_CANONICAL_URL not set, not sending email to repository owner.'
+        print('# Environment variable TOOL_SHED_CANONICAL_URL not set, not sending email to repository owner.')
         return
     subject = "Regarding your tool shed repositories at %s" % url
     message_body_template = 'The tool shed automated repository checker has discovered that one or more of your repositories hosted ' + \
@@ -91,10 +92,10 @@ def send_mail_to_owner(app, name, owner, email, repositories_deprecated, days=14
     body += '\n'.join([build_citable_url(url, repository) for repository in repositories_deprecated])
     try:
         galaxy_send_mail(from_address, repository.user.email, subject, body, app.config)
-        print "# An email has been sent to %s, the owner of %s." % (repository.user.username, ', '.join([repository.name for repository in repositories_deprecated]))
+        print("# An email has been sent to %s, the owner of %s." % (repository.user.username, ', '.join([repository.name for repository in repositories_deprecated])))
         return True
     except Exception as e:
-        print "# An error occurred attempting to send email: %s" % str(e)
+        print("# An error occurred attempting to send email: %s" % e)
         return False
 
 
@@ -129,10 +130,10 @@ def deprecate_repositories(app, cutoff_time, days=14, info_only=False, verbose=F
             .filter(app.model.Repository.table.c.id == repository_id).one()
         owner = repository.user
         if info_only:
-            print '# Repository %s owned by %s would have been deprecated, but info_only was set.' % (repository.name, repository.user.username)
+            print('# Repository %s owned by %s would have been deprecated, but info_only was set.' % (repository.name, repository.user.username))
         else:
             if verbose:
-                print '# Deprecating repository %s owned by %s.' % (repository.name, owner.username)
+                print('# Deprecating repository %s owned by %s.' % (repository.name, owner.username))
             if owner.username not in repositories_by_owner:
                 repositories_by_owner[owner.username] = dict(owner=owner, repositories=[])
             repositories_by_owner[owner.username]['repositories'].append(repository)
@@ -146,9 +147,9 @@ def deprecate_repositories(app, cutoff_time, days=14, info_only=False, verbose=F
         owner = repositories_by_owner[repository_owner]['owner']
         send_mail_to_owner(app, repository.name, owner.username, owner.email, repositories_by_owner[repository_owner]['repositories'], days)
     stop = time.time()
-    print '# Deprecated %d repositories.' % len(repositories)
-    print "# Elapsed time: ", stop - start
-    print "####################################################################################"
+    print('# Deprecated %d repositories.' % len(repositories))
+    print("# Elapsed time: ", stop - start)
+    print("####################################################################################")
 
 
 class DeprecateRepositoriesApplication(object):

scripts/tool_shed/migrate_tools_to_repositories.py

@@ -18,6 +18,8 @@ enable_next_gen_tool_shed = True
 
 To run this script, use "sh migrate_tools_to_repositories.sh" from this directory
 '''
+from __future__ import print_function
+
 import ConfigParser
 import os
 import shutil
@@ -32,7 +34,7 @@ sys.path.insert(1, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pa
 
 import galaxy.webapps.tool_shed.app
 
-assert sys.version_info[:2] >= (2, 4)
+assert sys.version_info[:2] >= (2, 6)
 
 
 def directory_hash_id(id):
@@ -83,7 +85,7 @@ def create_repository_from_tool(app, sa_session, tool):
     # Make the repository name a form of the tool's tool_id by
     # lower-casing everything and replacing any blank spaces with underscores.
     repo_name = tool.tool_id.lower().replace(' ', '_')
-    print "Creating repository '%s' in database" % (repo_name)
+    print("Creating repository '%s' in database" % (repo_name))
     repository = app.model.Repository(name=repo_name,
                                       description=tool.description,
                                       user_id=tool.user_id)
@@ -101,19 +103,19 @@ def create_repository_from_tool(app, sa_session, tool):
     if not os.path.exists(repository_path):
         os.makedirs(repository_path)
     # Create the local hg repository
-    print "Creating repository '%s' on disk" % (os.path.abspath(repository_path))
+    print("Creating repository '%s' on disk" % (os.path.abspath(repository_path)))
     hg.repository(ui.ui(), os.path.abspath(repository_path), create=True)
     # Add an entry in the hgweb.config file for the new repository - this enables calls to repository.repo_path
     add_hgweb_config_entry(repository, repository_path)
     # Migrate tool categories
     for tca in tool.categories:
         category = tca.category
-        print "Associating category '%s' with repository '%s' in database" % (category.name, repository.name)
+        print("Associating category '%s' with repository '%s' in database" % (category.name, repository.name))
         rca = app.model.RepositoryCategoryAssociation(repository, category)
         sa_session.add(rca)
     sa_session.flush()
     # Migrate tool ratings
-    print "Associating ratings for tool '%s' with repository '%s'" % (tool.name, repository.name)
+    print("Associating ratings for tool '%s' with repository '%s'" % (tool.name, repository.name))
     for tra in tool.ratings:
         rra = app.model.RepositoryRatingAssociation(user=tra.user,
                                                     rating=tra.rating,
@@ -167,8 +169,8 @@ def add_tool_files_to_repository(app, sa_session, tool):
     # Get all valid versions of the tool
     tool_versions = get_versions(app, tool)
     for tool_version in tool_versions:
-        print "------------------------------"
-        print "Migrating tool '%s' version '%s' from archive to repository '%s'" % (tool_version.tool_id, tool_version.version, repo_path)
+        print("------------------------------")
+        print("Migrating tool '%s' version '%s' from archive to repository '%s'" % (tool_version.tool_id, tool_version.version, repo_path))
         # Make a temporary working directory
         tmp_dir = tempfile.mkdtemp()
         tmp_archive_dir = os.path.join(tmp_dir, 'tmp_archive_dir')
@@ -208,13 +210,13 @@ def add_tool_files_to_repository(app, sa_session, tool):
             for dir in dirs:
                 os.system("hg add %s" % dir)
             for name in files:
-                print "Adding file '%s' to cloned repository at %s" % (name, str(os.getcwd()))
+                print("Adding file '%s' to cloned repository at %s" % (name, os.getcwd()))
                 os.system("hg add %s" % name)
-        print "Committing change set to cloned repository at %s" % str(os.getcwd())
+        print("Committing change set to cloned repository at %s" % os.getcwd())
         os.system("hg commit -m 'Migrated tool version %s from old tool shed archive to new tool shed repository'" % tool_version.version)
-        print "Pushing changeset from cloned repository '%s' to repository '%s'" % (cloned_repo_dir, repo_path)
+        print("Pushing changeset from cloned repository '%s' to repository '%s'" % (cloned_repo_dir, repo_path))
         cmd = "hg push %s" % repo_path
-        print "cmd is: ", cmd
+        print("cmd is: ", cmd)
         os.system(cmd)
         # The tool shed includes a repository source file browser, which currently depends upon
         # copies of the hg repository file store in the repo_path for browsing.  We'll do the
@@ -266,12 +268,12 @@ def tool_archive_file_name(tool, file_name):
 
 def main():
     if len(sys.argv) < 2:
-        print "Usage: python %s <Tool shed config file>" % sys.argv[0]
+        print("Usage: python %s <Tool shed config file>" % sys.argv[0])
         sys.exit(0)
     now = strftime("%Y-%m-%d %H:%M:%S")
-    print " "
-    print "##########################################"
-    print "%s - Migrating current tool archives to new tool repositories" % now
+    print()
+    print("##########################################")
+    print("%s - Migrating current tool archives to new tool repositories" % now)
     # tool_shed_wsgi.ini file
     ini_file = sys.argv[1]
     conf_parser = ConfigParser.ConfigParser({'here': os.getcwd()})
@@ -280,7 +282,7 @@ def main():
         db_conn_str = conf_parser.get("app:main", "database_connection")
     except ConfigParser.NoOptionError:
         db_conn_str = conf_parser.get("app:main", "database_file")
-    print 'DB Connection: ', db_conn_str
+    print('DB Connection: ', db_conn_str)
     # Instantiate app
     configuration = {}
     for key, value in conf_parser.items("app:main"):
@@ -290,7 +292,7 @@ def main():
     # Remove the hgweb.config file if it exists
     hgweb_config = "%s/hgweb.config" % os.getcwd()
     if os.path.exists(hgweb_config):
-        print "Removing old file: ", hgweb_config
+        print("Removing old file: ", hgweb_config)
         os.remove(hgweb_config)
     repo_records = 0
     rca_records = 0
@@ -300,11 +302,11 @@ def main():
         # tool files exist in app.config.file_path/tools and we don't want to delete them
         dir = os.path.join(app.config.file_path, *directory_hash_id(repo.id))
         if os.path.exists(dir):
-            print "Removing old repository file directory: ", dir
+            print("Removing old repository file directory: ", dir)
             shutil.rmtree(dir)
         # Delete all records from db tables:
         # repository_category_association, repository_rating_association, repository
-        print "Deleting db records for repository: ", repo.name
+        print("Deleting db records for repository: ", repo.name)
         for rca in repo.categories:
             sa_session.delete(rca)
             rca_records += 1
@@ -314,9 +316,9 @@ def main():
         sa_session.delete(repo)
         repo_records += 1
     sa_session.flush()
-    print "Deleted %d rows from the repository table" % repo_records
-    print "Deleted %d rows from the repository_category_association table" % rca_records
-    print "Deleted %d rows from the repository_rating_association table" % rra_records
+    print("Deleted %d rows from the repository table" % repo_records)
+    print("Deleted %d rows from the repository_category_association table" % rca_records)
+    print("Deleted %d rows from the repository_rating_association table" % rra_records)
     # Migrate database tool, tool category and tool rating records to new
     # database repository, repository category and repository rating records
     # and create the hg repository on disk for each.
@@ -327,9 +329,9 @@ def main():
     for tool in get_approved_tools(app, sa_session):
         add_tool_files_to_repository(app, sa_session, tool)
     app.shutdown()
-    print ' '
-    print 'Migration to next gen tool shed complete...'
-    print "##########################################"
+    print()
+    print('Migration to next gen tool shed complete...')
+    print("##########################################")
     sys.exit(0)
 
 

scripts/tool_shed/show_tool_dependency_installation_dir_contents.py

@@ -1,3 +1,5 @@
+from __future__ import print_function
+
 import argparse
 import os
 import sys
@@ -28,17 +30,17 @@ class CleanUpDependencyApplication(object):
 
 def main(args, app):
     if not os.path.exists(args.basepath):
-        print 'Tool dependency base path %s does not exist.' % str(args.basepath)
+        print('Tool dependency base path "%s" does not exist.' % args.basepath)
         return
-    print 'Checking tool dependency path %s' % args.basepath
+    print('Checking tool dependency path %s' % args.basepath)
     tool_dependency_dirs = get_tool_dependency_dirs(app)
     for tool_dependency_dir in tool_dependency_dirs:
         path = os.path.join(args.basepath, tool_dependency_dir)
         if os.path.exists(path):
             path_contents = os.listdir(path)
             if len(path_contents) > 0:
-                print 'Found non-empty tool dependency installation directory %s.' % path
-                print 'Directory has the following contents: \n   %s' % '\n   '.join(path_contents)
+                print('Found non-empty tool dependency installation directory %s.' % path)
+                print('Directory has the following contents: \n   %s' % '\n   '.join(path_contents))
 
 
 def get_tool_dependency_dirs(app):

scripts/tools/maf/check_loc_file.py

@@ -1,13 +1,15 @@
 # Dan Blankenberg
 # This script checks maf_index.loc file for inconsistencies between what is listed as available and what is really available.
 # Make sure that required dependencies (e.g. galaxy_root/lib) are included in your PYTHONPATH
+from __future__ import print_function
+
 import sys
 
 import bx.align.maf
 
 from galaxy.tools.util import maf_utilities
 
-assert sys.version_info[:2] >= (2, 4)
+assert sys.version_info[:2] >= (2, 6)
 
 
 def __main__():
@@ -39,19 +41,19 @@ def __main__():
             # indexed species
             for spec in indexed_for_species:
                 if spec not in species_indexed_in_maf:
-                    print "Line %i, %s claims to be indexed for %s, but indexes do not exist." % (i, uid, spec)
+                    print("Line %i, %s claims to be indexed for %s, but indexes do not exist." % (i, uid, spec))
             for spec in species_indexed_in_maf:
                 if spec not in indexed_for_species:
-                    print "Line %i, %s is indexed for %s, but is not listed in loc file." % (i, uid, spec)
+                    print("Line %i, %s is indexed for %s, but is not listed in loc file." % (i, uid, spec))
             # existing species
             for spec in species_exist:
                 if spec not in species_found_in_maf:
-                    print "Line %i, %s claims to have blocks for %s, but was not found in MAF files." % (i, uid, spec)
+                    print("Line %i, %s claims to have blocks for %s, but was not found in MAF files." % (i, uid, spec))
             for spec in species_found_in_maf:
                 if spec not in species_exist:
-                    print "Line %i, %s contains %s, but is not listed in loc file." % (i, uid, spec)
+                    print("Line %i, %s contains %s, but is not listed in loc file." % (i, uid, spec))
         except Exception as e:
-            print "Line %i is invalid: %s" % (i, e)
+            print("Line %i is invalid: %s" % (i, e))
 
 
 if __name__ == "__main__":

scripts/update_shed_config_path.py

@@ -1,3 +1,5 @@
+from __future__ import print_function
+
 import argparse
 import ConfigParser
 import os
@@ -34,7 +36,7 @@ def create_database(config_file):
     if database_connection is None:
         database_connection = 'sqlite:///%s' % parser.get('app:main', 'database_file')
     if database_connection is None:
-        print 'Unable to determine correct database connection.'
+        print('Unable to determine correct database connection.')
         exit(1)
 
     '''Initialize the database file.'''
@@ -54,7 +56,7 @@ if __name__ == '__main__':
     parser.add_argument('--force', dest='force', action='store_true', help="Use this flag to set the new path even if the file does not (yet) exist there.")
     opts = parser.parse_args()
     if not os.path.exists(opts.good_filename) and not opts.force:
-        print 'The file %s does not exist, use the --force option to proceed.' % opts.good_filename
+        print('The file %s does not exist, use the --force option to proceed.' % opts.good_filename)
         exit(1)
     session, model = create_database(opts.config_file)
     exit(main(opts, session, model))

test/unit/managers/test_CollectionManager.py

@@ -49,10 +49,6 @@ class DatasetCollectionManagerTestCase(BaseTestCase, CreatesCollectionsMixin):
         self.assertFalse(hdca.deleted)
         self.assertTrue(hdca.visible)
 
-        # print 'hdca dir:'
-        # for k in dir( hdca ):
-        #     print k, getattr( hdca, k, '(?)' )
-
         self.log("should contain an underlying, well-formed DatasetCollection")
         self.assertIsInstance(hdca.collection, model.DatasetCollection)
         collection = hdca.collection
@@ -61,15 +57,6 @@ class DatasetCollectionManagerTestCase(BaseTestCase, CreatesCollectionsMixin):
         self.assertEqual(len(collection.dataset_instances), 3)
         self.assertEqual(len(collection.elements), 3)
 
-        # print 'hdca.collection dir:'
-        # for k in dir( hdca.collection ):
-        #     print k, getattr( hdca.collection, k, '(?)' )
-
-        # elements = collection.elements
-        # print 'hdca.collection element dir:'
-        # for k in dir( elements[0] ):
-        #     print k, getattr( elements[0], k, '(?)' )
-
         self.log("and that collection should have three well-formed Elements")
         self.assertIsInstance(collection.elements[0], model.DatasetCollectionElement)
         self.assertEqual(collection.elements[0].element_identifier, 'one')