diff --git a/lib/galaxy/util/bool_expressions.py b/lib/galaxy/util/bool_expressions.py index 488e8687849..162ca0f8562 100644 --- a/lib/galaxy/util/bool_expressions.py +++ b/lib/galaxy/util/bool_expressions.py @@ -14,7 +14,6 @@ from typing import ( from pyparsing import ( alphanums, CaselessKeyword, - Forward, infixNotation, Keyword, opAssoc, @@ -132,7 +131,7 @@ class BooleanExpressionEvaluator: action.evaluator = evaluator boolOperand = TRUE | FALSE | Word(token_format or DEFAULT_TOKEN_FORMAT) boolOperand.setParseAction(action) - self.boolExpr: Forward = infixNotation( + self.boolExpr: ParserElement = infixNotation( boolOperand, [ (NOT_OP, 1, opAssoc.RIGHT, BoolNot), diff --git a/packages/app/requirements.txt b/packages/app/requirements.txt index 67d71a8e1c7..d6f62fb68b1 100644 --- a/packages/app/requirements.txt +++ b/packages/app/requirements.txt @@ -19,3 +19,4 @@ refgenconf>=0.7.0,<0.10.0 # https://github.com/galaxyproject/galaxy/issues/11601 Fabric3 lagom fs +Whoosh diff --git a/packages/app/setup.py b/packages/app/setup.py index f0b961fea2a..852e3427b0b 100644 --- a/packages/app/setup.py +++ b/packages/app/setup.py @@ -56,6 +56,7 @@ PACKAGES = [ 'galaxy.tools.data', 'galaxy.tools.data_manager', 'galaxy.tools.error_reports', + 'galaxy.tools.error_reports.plugins', 'galaxy.tools.expressions', 'galaxy.tools.filters', 'galaxy.tools.imp_exp', diff --git a/packages/webapps/setup.py b/packages/webapps/setup.py index bc8ab520f0c..d799ca7661f 100644 --- a/packages/webapps/setup.py +++ b/packages/webapps/setup.py @@ -50,6 +50,7 @@ PACKAGES = [ 'tool_shed.tools', 'tool_shed.util', 'tool_shed.utility_containers', + 'tool_shed.webapp', 'tool_shed.webapp.api', 'tool_shed.webapp.controllers', 'tool_shed.webapp.framework', diff --git a/test/integration/objectstore/_base.py b/test/integration/objectstore/_base.py index 734d6f3780c..186b521a68e 100644 --- a/test/integration/objectstore/_base.py +++ b/test/integration/objectstore/_base.py @@ -38,10 +38,11 @@ def start_minio(container_name): '-d', '--name', container_name, - '--rm', - 'minio/minio:latest', - 'server', - '/tmp/data'] + "--rm", + "minio/minio:latest", + "server", + "/data", + ] subprocess.check_call(minio_start_args)