From f23a6b8b903c115c925257fb2aa51d713903fcae Mon Sep 17 00:00:00 2001 From: Nicola Soranzo Date: Tue, 16 Nov 2021 02:06:28 +0000 Subject: [PATCH 1/4] Revert metaclass removed by mistake --- lib/galaxy/tool_util/cwl/parser.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lib/galaxy/tool_util/cwl/parser.py b/lib/galaxy/tool_util/cwl/parser.py index e29722fc3d87..9440e1e3193a 100644 --- a/lib/galaxy/tool_util/cwl/parser.py +++ b/lib/galaxy/tool_util/cwl/parser.py @@ -257,7 +257,7 @@ def check_requirements(rec, tool=True): check_requirements(d, tool=tool) -class ToolProxy(ABCMeta): +class ToolProxy(metaclass=ABCMeta): _class: str From 847ae6e14db04f47151c524e4cff67cec4cabad1 Mon Sep 17 00:00:00 2001 From: "Michael R. Crusoe" Date: Thu, 11 Nov 2021 13:32:54 +0100 Subject: [PATCH 2/4] fix for avro namespace leakage --- lib/galaxy/tool_util/cwl/representation.py | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/lib/galaxy/tool_util/cwl/representation.py b/lib/galaxy/tool_util/cwl/representation.py index 8fba8442d759..a9870f78926b 100644 --- a/lib/galaxy/tool_util/cwl/representation.py +++ b/lib/galaxy/tool_util/cwl/representation.py @@ -82,26 +82,32 @@ def uses_param(self): if not USE_FIELD_TYPES: CWL_TYPE_TO_REPRESENTATIONS = { "Any": ["integer", "float", "file", "boolean", "text", "record", "json"], + "org.w3id.cwl.salad.Any": ["integer", "float", "file", "boolean", "text", "record", "json"], "array": ["array"], "string": ["text"], "boolean": ["boolean"], "int": ["integer"], "float": ["float"], "File": ["file"], + "org.w3id.cwl.cwl.File": ["file"], "Directory": ["directory"], + "org.w3id.cwl.cwl.Directory": ["directory"], "null": ["null"], "record": ["record"], } else: CWL_TYPE_TO_REPRESENTATIONS = { "Any": ["field"], + "org.w3id.cwl.salad.Any": ["field"], "array": ["array"], "string": ["text"], "boolean": ["boolean"], "int": ["integer"], "float": ["float"], "File": ["file"], + "org.w3id.cwl.cwl.File": ["file"], "Directory": ["directory"], + "org.w3id.cwl.cwl.Directory": ["directory"], "null": ["null"], "record": ["record"], "enum": ["enum"], From 93b293a29f65644b6331aae38f23e6e39418e025 Mon Sep 17 00:00:00 2001 From: Nicola Soranzo Date: Tue, 23 Nov 2021 18:44:11 +0000 Subject: [PATCH 3/4] Remove unnecessary assert --- lib/galaxy/tool_util/cwl/parser.py | 1 - 1 file changed, 1 deletion(-) diff --git a/lib/galaxy/tool_util/cwl/parser.py b/lib/galaxy/tool_util/cwl/parser.py index 9440e1e3193a..8846efd7db11 100644 --- a/lib/galaxy/tool_util/cwl/parser.py +++ b/lib/galaxy/tool_util/cwl/parser.py @@ -293,7 +293,6 @@ def galaxy_id(self): # tool_id = os.path.splitext(os.path.basename(raw_id))[0] if not tool_id: return self._uuid - assert tool_id if tool_id.startswith("#"): tool_id = tool_id[1:] return tool_id From a65d8fade9a8117847b77072fdd05f0ff43e1cd2 Mon Sep 17 00:00:00 2001 From: Nicola Soranzo Date: Tue, 23 Nov 2021 19:27:10 +0000 Subject: [PATCH 4/4] Add missing typing-extensions requirement to `pyproject.toml` and packages' `requirements.txt` . We have been importing it explicitly since commit fc2ce457675a88c0a38457ffeb423e8bb1e48074 (December 2020). Also: - Remove now unnecessary minimum version for pygithub --- lib/galaxy/dependencies/dev-requirements.txt | 2 +- lib/galaxy/dependencies/pinned-requirements.txt | 2 +- packages/app/requirements.txt | 17 +++++++++-------- packages/data/requirements.txt | 3 ++- packages/files/requirements.txt | 1 + packages/tool_util/requirements.txt | 3 ++- packages/util/requirements.txt | 1 + packages/webapps/requirements.txt | 1 + pyproject.toml | 7 ++++--- 9 files changed, 22 insertions(+), 15 deletions(-) diff --git a/lib/galaxy/dependencies/dev-requirements.txt b/lib/galaxy/dependencies/dev-requirements.txt index 3f3234dd6127..fd2f27e8cfa8 100644 --- a/lib/galaxy/dependencies/dev-requirements.txt +++ b/lib/galaxy/dependencies/dev-requirements.txt @@ -251,7 +251,7 @@ tqdm==4.62.3; python_version >= "2.7" and python_full_version < "3.0.0" or pytho tuspy==0.2.5 tuswsgi==0.5.4 twill==3.0 -typing-extensions==3.10.0.2; python_version >= "3.6" and python_version < "3.7" and python_full_version >= "3.6.1" +typing-extensions==3.10.0.2 tzlocal==2.1; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version < "4" ubiquerg==0.6.2 unidecode==1.3.2; python_version >= "3.5" diff --git a/lib/galaxy/dependencies/pinned-requirements.txt b/lib/galaxy/dependencies/pinned-requirements.txt index 03df2c6cde47..3fe1994fd956 100644 --- a/lib/galaxy/dependencies/pinned-requirements.txt +++ b/lib/galaxy/dependencies/pinned-requirements.txt @@ -199,7 +199,7 @@ tifffile==2020.9.3; python_version >= "3.6" tornado==6.1; python_version >= "3.5" tqdm==4.62.3; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" tuswsgi==0.5.4 -typing-extensions==3.10.0.2; python_version >= "3.6" and python_version < "3.7" and python_full_version >= "3.6.1" +typing-extensions==3.10.0.2 tzlocal==2.1; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version < "4" ubiquerg==0.6.2 unidecode==1.3.2; python_version >= "3.5" diff --git a/packages/app/requirements.txt b/packages/app/requirements.txt index e46441c304ab..d82a936a763d 100644 --- a/packages/app/requirements.txt +++ b/packages/app/requirements.txt @@ -6,18 +6,19 @@ galaxy-tool-util[cwl] galaxy-web-framework galaxy-web-stack +Beaker celery cloudauthz==0.6.0 -kombu -Beaker -pykwalify -pulsar-galaxy-lib>=0.14.12 +Fabric3 gxformat2 +kombu +lagom Mako -sqlitedict -svgwrite Markdown +pulsar-galaxy-lib>=0.14.12 +pykwalify refgenconf>=0.12.0 -Fabric3 -lagom +sqlitedict +svgwrite tuswsgi +typing-extensions diff --git a/packages/data/requirements.txt b/packages/data/requirements.txt index ca5c0eb312df..de8d47437a76 100644 --- a/packages/data/requirements.txt +++ b/packages/data/requirements.txt @@ -8,8 +8,8 @@ contextvars; python_version >= "3.6" and python_version < "3.7" h5py isa-rwval mrcfile -parsley numpy +parsley pycryptodome pydantic pysam @@ -17,4 +17,5 @@ social-auth-core[openidconnect]==3.3.0 SQLAlchemy>=1.4.25,<2 sqlalchemy-migrate tifffile<=2020.9.3 # Last version compatible with python 3.6 +typing-extensions WebOb diff --git a/packages/files/requirements.txt b/packages/files/requirements.txt index 3bc702178e87..7447f74fc5dc 100644 --- a/packages/files/requirements.txt +++ b/packages/files/requirements.txt @@ -1,3 +1,4 @@ galaxy-util fs +typing-extensions diff --git a/packages/tool_util/requirements.txt b/packages/tool_util/requirements.txt index 85b882434409..5447c085e3c2 100644 --- a/packages/tool_util/requirements.txt +++ b/packages/tool_util/requirements.txt @@ -1,6 +1,7 @@ galaxy-util>=20.1.0.dev0 galaxy-containers lxml -sortedcontainers pydantic +pyyaml +sortedcontainers typing-extensions diff --git a/packages/util/requirements.txt b/packages/util/requirements.txt index e584c87673d3..ffffd7b7ee34 100644 --- a/packages/util/requirements.txt +++ b/packages/util/requirements.txt @@ -7,4 +7,5 @@ pycryptodome pyyaml requests routes +typing-extensions zipstream-new diff --git a/packages/webapps/requirements.txt b/packages/webapps/requirements.txt index 62d6fb043884..8392e9eb703f 100644 --- a/packages/webapps/requirements.txt +++ b/packages/webapps/requirements.txt @@ -5,3 +5,4 @@ fastapi-utils Mako python-multipart # required to support form parsing in FastAPI/Starlette starlette +typing-extensions diff --git a/pyproject.toml b/pyproject.toml index 055f086bc10e..b853d966a00d 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -81,6 +81,7 @@ starlette-context = {version = "*", python = ">=3.7"} svgwrite = "*" tifffile = "<=2020.9.3" # Last version compatible with python 3.6 tuswsgi = "*" +typing-extensions = "*" uvicorn = "*" WebOb = "*" Whoosh = "*" @@ -89,12 +90,12 @@ zipstream-new = "*" [tool.poetry.dev-dependencies] cwltest = "2.2.20210901154959" fluent-logger = "*" -httpx = "*" gunicorn = "*" +httpx = "*" lxml = "!=4.2.2" markdown-it-reporter = "*" NoseHTML = "*" -pygithub = ">=1.54.1" # prevent downgrade (depends on pyjwt(<2.0); pyjwt auto-upgrade to 2.0.1 causes pygithub downgrade to 1.53) +PyGithub = "*" pytest = "*" pytest-asyncio = "*" pytest-celery = "*" @@ -114,6 +115,6 @@ sphinx_markdown_tables = "*" sphinx_rtd_theme = "*" statsd = "*" testfixtures = "*" -twill = "*" tuspy = "*" +twill = "*" watchdog = "*"