From dd0702e89be9d5f2c01581cd87f8419a1a5ddcc2 Mon Sep 17 00:00:00 2001 From: Nuwan Goonasekera <2070605+nuwang@users.noreply.github.com> Date: Sun, 5 Jun 2022 02:30:37 +0530 Subject: [PATCH 1/7] Add root webapp to webapp package --- packages/webapps/setup.py | 1 + 1 file changed, 1 insertion(+) 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', From 635944aa5ba7c536fe73f3ebd016974fe7abd4ce Mon Sep 17 00:00:00 2001 From: Nuwan Goonasekera <2070605+nuwang@users.noreply.github.com> Date: Sun, 5 Jun 2022 12:17:47 +0530 Subject: [PATCH 2/7] Also add missing error_reports.plugins --- packages/app/setup.py | 1 + 1 file changed, 1 insertion(+) 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', From c61e3918d2f0c1a96f59628c89c6fd8d176c2c00 Mon Sep 17 00:00:00 2001 From: Nuwan Goonasekera <2070605+nuwang@users.noreply.github.com> Date: Sun, 5 Jun 2022 13:21:38 +0530 Subject: [PATCH 3/7] Add missing whoosh package to galaxy-app package requirements --- packages/app/requirements.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/packages/app/requirements.txt b/packages/app/requirements.txt index 67d71a8e1c7..dd6d4864bd4 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 From 6e434649798ee742d3cf4f7691ad9d4eddf02ee7 Mon Sep 17 00:00:00 2001 From: Nuwan Goonasekera <2070605+nuwang@users.noreply.github.com> Date: Sun, 5 Jun 2022 23:38:05 +0530 Subject: [PATCH 4/7] Update packages/app/requirements.txt Co-authored-by: Nicola Soranzo --- packages/app/requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/packages/app/requirements.txt b/packages/app/requirements.txt index dd6d4864bd4..d6f62fb68b1 100644 --- a/packages/app/requirements.txt +++ b/packages/app/requirements.txt @@ -19,4 +19,4 @@ refgenconf>=0.7.0,<0.10.0 # https://github.com/galaxyproject/galaxy/issues/11601 Fabric3 lagom fs -whoosh +Whoosh From 44bf638be79d80c4f46f0ebb34ab93d42dc9d440 Mon Sep 17 00:00:00 2001 From: davelopez <46503462+davelopez@users.noreply.github.com> Date: Tue, 12 Apr 2022 13:24:55 +0200 Subject: [PATCH 5/7] Fix mypy error --- lib/galaxy/util/bool_expressions.py | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/lib/galaxy/util/bool_expressions.py b/lib/galaxy/util/bool_expressions.py index 488e8687849..14fb641225b 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 = infixNotation( boolOperand, [ (NOT_OP, 1, opAssoc.RIGHT, BoolNot), From 9fdb5f2d8f2ea7e15b0b71c69f01b8521765221f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?David=20L=C3=B3pez?= <46503462+davelopez@users.noreply.github.com> Date: Tue, 12 Apr 2022 13:42:57 +0200 Subject: [PATCH 6/7] Add type hint suggestion Co-authored-by: Nicola Soranzo --- lib/galaxy/util/bool_expressions.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lib/galaxy/util/bool_expressions.py b/lib/galaxy/util/bool_expressions.py index 14fb641225b..162ca0f8562 100644 --- a/lib/galaxy/util/bool_expressions.py +++ b/lib/galaxy/util/bool_expressions.py @@ -131,7 +131,7 @@ class BooleanExpressionEvaluator: action.evaluator = evaluator boolOperand = TRUE | FALSE | Word(token_format or DEFAULT_TOKEN_FORMAT) boolOperand.setParseAction(action) - self.boolExpr = infixNotation( + self.boolExpr: ParserElement = infixNotation( boolOperand, [ (NOT_OP, 1, opAssoc.RIGHT, BoolNot), From 4a779c44ff9a4cb67d714d0abff95b1c24547aa5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= Date: Fri, 3 Jun 2022 11:04:59 +0200 Subject: [PATCH 7/7] try fixing the integration tests --- test/integration/objectstore/_base.py | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) 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)