Merge pull request #12972 from nsoranzo/misc_fixes

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"

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"

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
 
@@ -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

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"],

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

packages/data/requirements.txt

@@ -8,13 +8,14 @@ contextvars; python_version >= "3.6" and python_version < "3.7"
 h5py
 isa-rwval
 mrcfile
-parsley
 numpy
+parsley
 pycryptodome
 pydantic
 pysam
 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

packages/files/requirements.txt

@@ -1,3 +1,4 @@
 galaxy-util
 
 fs
+typing-extensions

packages/tool_util/requirements.txt

@@ -1,6 +1,7 @@
 galaxy-util>=20.1.0.dev0
 galaxy-containers
 lxml
-sortedcontainers
 pydantic
+pyyaml
+sortedcontainers
 typing-extensions

packages/util/requirements.txt

@@ -7,4 +7,5 @@ pycryptodome
 pyyaml
 requests
 routes
+typing-extensions
 zipstream-new

packages/webapps/requirements.txt

@@ -5,3 +5,4 @@ fastapi-utils
 Mako
 python-multipart  # required to support form parsing in FastAPI/Starlette
 starlette
+typing-extensions

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 = "*"