From c1fab91e3ab04b19973e9fc63cb296f86059ac13 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Fri, 1 Sep 2023 13:35:18 +0200
Subject: [PATCH] Switch out conditional requirement parser

Fixes
```
Traceback (most recent call last):
  File "/storage/srv/galaxy/server/.venv/lib64/python3.9/site-packages/pkg_resources/_vendor/packaging/requirements.py", line 35, in __init__
    parsed = _parse_requirement(requirement_string)
  File "/storage/srv/galaxy/server/.venv/lib64/python3.9/site-packages/pkg_resources/_vendor/packaging/_parser.py", line 64, in parse_requirement
    return _parse_requirement(Tokenizer(source, rules=DEFAULT_RULES))
  File "/storage/srv/galaxy/server/.venv/lib64/python3.9/site-packages/pkg_resources/_vendor/packaging/_parser.py", line 73, in _parse_requirement
    name_token = tokenizer.expect(
  File "/storage/srv/galaxy/server/.venv/lib64/python3.9/site-packages/pkg_resources/_vendor/packaging/_tokenizer.py", line 140, in expect
    raise self.raise_syntax_error(f"Expected {expected}")
  File "/storage/srv/galaxy/server/.venv/lib64/python3.9/site-packages/pkg_resources/_vendor/packaging/_tokenizer.py", line 165, in raise_syntax_error
    raise ParserSyntaxError(
pkg_resources.extern.packaging._tokenizer.ParserSyntaxError: Expected package name at the start of dependency specifier
    "git+https://github.com/jakobmerljak/pyarcrest.git@dev"
    ^

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/storage/srv/galaxy/server/lib/galaxy/dependencies/__init__.py", line 312, in optional
    conditional = ConditionalDependencies(config_file)
  File "/storage/srv/galaxy/server/lib/galaxy/dependencies/__init__.py", line 45, in __init__
    self.get_conditional_requirements()
  File "/storage/srv/galaxy/server/lib/galaxy/dependencies/__init__.py", line 176, in get_conditional_requirements
    for req in pkg_resources.parse_requirements(open(crfile).readlines()):
  File "/storage/srv/galaxy/server/.venv/lib64/python3.9/site-packages/pkg_resources/__init__.py", line 3174, in __init__
    super(Requirement, self).__init__(requirement_string)
  File "/storage/srv/galaxy/server/.venv/lib64/python3.9/site-packages/pkg_resources/_vendor/packaging/requirements.py", line 37, in __init__
    raise InvalidRequirement(str(e)) from e
pkg_resources.extern.packaging.requirements.InvalidRequirement: Expected package name at the start of dependency specifier
    "git+https://github.com/jakobmerljak/pyarcrest.git@dev"
    ^

```

for advanced package specifiers that might be used during development.
---
 lib/galaxy/dependencies/__init__.py             | 14 ++++++++------
 lib/galaxy/dependencies/pinned-requirements.txt |  1 +
 pyproject.toml                                  |  1 +
 3 files changed, 10 insertions(+), 6 deletions(-)

diff --git a/lib/galaxy/dependencies/__init__.py b/lib/galaxy/dependencies/__init__.py
index eb484b9dcbd..1530b48fb3c 100644
--- a/lib/galaxy/dependencies/__init__.py
+++ b/lib/galaxy/dependencies/__init__.py
@@ -10,8 +10,8 @@ from os.path import (
     join,
 )
 
-import pkg_resources
 import yaml
+from dparse import parse
 
 from galaxy.util import (
     asbool,
@@ -173,8 +173,10 @@ class ConditionalDependencies:
 
     def get_conditional_requirements(self):
         crfile = join(dirname(__file__), "conditional-requirements.txt")
-        for req in pkg_resources.parse_requirements(open(crfile).readlines()):
-            self.conditional_reqs.append(req)
+        with open(crfile) as fh:
+            dependency_file = parse(fh.read(), file_type="requirements.txt")
+            for dep in dependency_file.dependencies:
+                self.conditional_reqs.append(dep)
 
     def check(self, name):
         try:
@@ -307,7 +309,7 @@ def optional(config_file=None):
         return []
     rval = []
     conditional = ConditionalDependencies(config_file)
-    for opt in conditional.conditional_reqs:
-        if conditional.check(opt.key):
-            rval.append(str(opt))
+    for dependency in conditional.conditional_reqs:
+        if conditional.check(dependency.name):
+            rval.append(dependency.line)
     return rval
diff --git a/lib/galaxy/dependencies/pinned-requirements.txt b/lib/galaxy/dependencies/pinned-requirements.txt
index 2985546ff68..f754ad8be39 100644
--- a/lib/galaxy/dependencies/pinned-requirements.txt
+++ b/lib/galaxy/dependencies/pinned-requirements.txt
@@ -61,6 +61,7 @@ dictobj==0.4 ; python_version >= "3.7" and python_version < "3.12"
 dnspython==2.3.0 ; python_version >= "3.7" and python_version < "3.12"
 docopt==0.6.2 ; python_version >= "3.7" and python_version < "3.12"
 docutils==0.18.1 ; python_version >= "3.7" and python_version < "3.12"
+dparse==0.6.3 ; python_version >= "3.7" and python_version < "3.12"
 ecdsa==0.18.0 ; python_version >= "3.7" and python_version < "3.12"
 edam-ontology==1.25.2 ; python_version >= "3.7" and python_version < "3.12"
 email-validator==2.0.0.post2 ; python_version >= "3.7" and python_version < "3.12"
diff --git a/pyproject.toml b/pyproject.toml
index 0d96d9c7502..44f2cd221b9 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -49,6 +49,7 @@ conda-package-streaming = "*"
 dictobj = "*"
 dnspython = "*"
 docutils = "!=0.17, !=0.17.1"
+dparse = "*"
 edam-ontology = "*"
 fastapi = ">=0.71.0, !=0.89.0, <0.99"  # https://github.com/tiangolo/fastapi/issues/4041 https://github.com/tiangolo/fastapi/issues/5861
 fastapi-utils = "*"