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raise report level for some shed linting #1111

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raise report level for some shed linting #1111

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02a2411
raise report level for some shed linting
bernt-matthias Dec 15, 2020
bc43d59
add .shed.yml to bad_invalid_tool_xml
bernt-matthias Dec 15, 2020
4db71af
add shed.yml to multi_repos_nested
bernt-matthias Dec 15, 2020
fb169b4
fix category
bernt-matthias Dec 15, 2020
5c687a4
add type to shed.yml
bernt-matthias Dec 15, 2020
cee8cfb
lint type only if present
bernt-matthias Dec 15, 2020
c5602de
skip shed.yml check only for unrestricted repos
bernt-matthias Dec 16, 2020
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19 changes: 12 additions & 7 deletions planemo/shed_lint.py
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Original file line number Diff line number Diff line change
Expand Up @@ -290,14 +290,14 @@ def lint_repository_dependencies(realized_repository, lint_ctx):
def lint_shed_yaml(realized_repository, lint_ctx):
path = realized_repository.real_path
shed_yaml = os.path.join(path, ".shed.yml")
if not os.path.exists(shed_yaml):
lint_ctx.info("No .shed.yml file found, skipping.")
if not os.path.exists(shed_yaml) and realized_repository.repository_type != REPO_TYPE_UNRESTRICTED:
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Not sure I understand this change?

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Was an attempt to fix the testing error for https://github.com/galaxyproject/planemo/tree/master/tests/data/repos/suite_1 which fails because there is no .shed.yml .. which is OK in this case .. or isn't it?

lint_ctx.error("No .shed.yml file found, skipping.")
return
try:
with open(shed_yaml, "r") as fh:
yaml.safe_load(fh)
except Exception as e:
lint_ctx.warn("Failed to parse .shed.yml file [%s]" % unicodify(e))
lint_ctx.error("Failed to parse .shed.yml file [%s]" % unicodify(e))
return
lint_ctx.info(".shed.yml found and appears to be valid YAML.")
_lint_shed_contents(lint_ctx, realized_repository)
Expand All @@ -311,12 +311,17 @@ def _lint_if_present(key, func, *args):
if value is not None:
msg = func(value, *args)
if msg:
lint_ctx.warn(msg)
lint_ctx.error(msg)
return value

_lint_if_present("owner", validate_repo_owner)
_lint_if_present("name", validate_repo_name)
def _lint(key, func, *args):
if _lint_if_present(key, func, *args) is None:
lint_ctx.error("Repository does not define: %s" % key)
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I think this is going against the original intent of the method _lint_if_present ? E.g. type is unrestricted by default, so probably no need to give an error if it's not present.

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@bernt-matthias bernt-matthias Dec 15, 2020 •
edited
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Maybe we can rename the function? My aim it to error in cases where shed_lint upload to the toolshed will error ... and I guess this is the case here.

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OK. I see .. the type does not need to be defined in .shed.yml.

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Is this also the case for name, owner, and categories?

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name and owner can be specified on the command-line with e.g. shed_update. name defaults to the directory name if it's not specified in other ways. Categories I think are optional? I suppose these can all be warnings if not present.

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I think name and owner should also be in the realized repo if given on the command line:

planemo/planemo/shed/__init__.py

Line 1022 in 157cace

config = self._realize_config(name)
(but I do not understand the code for setting name ..)


_lint("owner", validate_repo_owner)
_lint("name", validate_repo_name)
_lint_if_present("type", _validate_repo_type, config["name"])
_lint_if_present("categories", _validate_categories, realized_repository)
_lint("categories", _validate_categories, realized_repository)


def _validate_repo_type(repo_type, name):
Expand Down
5 changes: 5 additions & 0 deletions tests/data/repos/bad_invalid_tool_xml/.shed.yml
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Original file line number Diff line number Diff line change
@@ -0,0 +1,5 @@
name: cat
owner: iuc
description: cat1 tool
categories:
- Text Manipulation
2 changes: 2 additions & 0 deletions tests/data/repos/multi_repos_nested/cat1/.shed.yml
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Original file line number Diff line number Diff line change
@@ -1,3 +1,5 @@
name: cat1
owner: iuc
description: cat1 tool
categories:
- Text Manipulation
2 changes: 2 additions & 0 deletions tests/data/repos/multi_repos_nested/cat2/.shed.yml
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Original file line number Diff line number Diff line change
@@ -1,3 +1,5 @@
name: cat2
owner: iuc
description: cat2 tool
categories:
- Text Manipulation