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Lint only realized tools during shed linting. #628

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merged 1 commit into from Feb 6, 2017
Merged

Lint only realized tools during shed linting. #628

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58 changes: 34 additions & 24 deletions planemo/shed_lint.py
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Expand Up @@ -58,7 +58,6 @@ def lint_repository(ctx, realized_repository, **kwds):
See :module:`planemo.shed` for details on constructing a realized
repository data structure.
"""
# TODO: this really needs to start working with realized path.
failed = False
path = realized_repository.real_path
info("Linting repository %s" % path)
Expand All @@ -76,22 +75,22 @@ def lint_repository(ctx, realized_repository, **kwds):
lint_ctx.lint(
"lint_tool_dependencies_xsd",
lint_tool_dependencies_xsd,
path,
realized_repository,
)
lint_ctx.lint(
"lint_tool_dependencies_sha256sum",
lint_tool_dependencies_sha256sum,
path,
realized_repository,
)
lint_ctx.lint(
"lint_tool_dependencies_actions",
lint_tool_dependencies_actions,
path,
realized_repository,
)
lint_ctx.lint(
"lint_repository_dependencies",
lint_repository_dependencies,
path,
realized_repository,
)
lint_ctx.lint(
"lint_shed_yaml",
Expand All @@ -101,7 +100,7 @@ def lint_repository(ctx, realized_repository, **kwds):
lint_ctx.lint(
"lint_readme",
lint_readme,
path,
realized_repository,
)
if kwds["urls"]:
lint_ctx.lint(
Expand All @@ -110,17 +109,8 @@ def lint_repository(ctx, realized_repository, **kwds):
path,
)
if kwds["tools"]:
for (tool_path, tool_source) in yield_tool_sources(ctx, path,
recursive=True):
info("+Linting tool %s" % tool_path)
if handle_tool_load_error(tool_path, tool_source):
failed = True
continue
lint_tool_source_with(
lint_ctx,
tool_source,
extra_modules=lint_args["extra_modules"]
)
tools_failed = lint_repository_tools(ctx, realized_repository, lint_ctx, lint_args)
failed = failed or tools_failed
if kwds["ensure_metadata"]:
lint_ctx.lint(
"lint_shed_metadata",
Expand All @@ -130,6 +120,21 @@ def lint_repository(ctx, realized_repository, **kwds):
return handle_lint_complete(lint_ctx, lint_args, failed=failed)


def lint_repository_tools(ctx, realized_repository, lint_ctx, lint_args):
path = realized_repository.path
for (tool_path, tool_source) in yield_tool_sources(ctx, path,
recursive=True):
original_path = tool_path.replace(path, realized_repository.real_path)
info("+Linting tool %s" % original_path)
if handle_tool_load_error(tool_path, tool_source):
return True
lint_tool_source_with(
lint_ctx,
tool_source,
extra_modules=lint_args["extra_modules"]
)


def lint_expansion(realized_repository, lint_ctx):
missing = realized_repository.missing
if missing:
Expand All @@ -154,7 +159,8 @@ def lint_shed_metadata(realized_repository, lint_ctx):
)


def lint_readme(path, lint_ctx):
def lint_readme(realized_repository, lint_ctx):
path = realized_repository.real_path
readme_rst = os.path.join(path, "README.rst")
readme = os.path.join(path, "README")
readme_txt = os.path.join(path, "README.txt")
Expand Down Expand Up @@ -190,7 +196,8 @@ def lint_readme(path, lint_ctx):
lint_ctx.info("README found containing plain text.")


def lint_tool_dependencies_urls(path, lint_ctx):
def lint_tool_dependencies_urls(realized_repository, lint_ctx):
path = realized_repository.real_path
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This had broken planemo:

  File "/home/travis/virtualenv/python2.7.9/lib/python2.7/site-packages/planemo/shed_lint.py", line 200, in lint_tool_dependencies_urls
    path = realized_repository.real_path
AttributeError: 'str' object has no attribute 'real_path'

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No test coverage for --urls it would seem - sorry about that @bgruening.

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sorry for not fixing it myself, busy with the training here

tool_dependencies = os.path.join(path, "tool_dependencies.xml")
if not os.path.exists(tool_dependencies):
lint_ctx.info("No tool_dependencies.xml, skipping.")
Expand All @@ -200,8 +207,8 @@ def lint_tool_dependencies_urls(path, lint_ctx):
lint_urls(root, lint_ctx)


def lint_tool_dependencies_sha256sum(path, lint_ctx):
tool_dependencies = os.path.join(path, "tool_dependencies.xml")
def lint_tool_dependencies_sha256sum(realized_repository, lint_ctx):
tool_dependencies = os.path.join(realized_repository.real_path, "tool_dependencies.xml")
if not os.path.exists(tool_dependencies):
lint_ctx.info("No tool_dependencies.xml, skipping.")
return
Expand All @@ -227,15 +234,17 @@ def lint_tool_dependencies_sha256sum(path, lint_ctx):
lint_ctx.info("Found %i download action(s) with SHA256 checksums" % count)


def lint_tool_dependencies_xsd(path, lint_ctx):
def lint_tool_dependencies_xsd(realized_repository, lint_ctx):
path = realized_repository.real_path
tool_dependencies = os.path.join(path, "tool_dependencies.xml")
if not os.path.exists(tool_dependencies):
lint_ctx.info("No tool_dependencies.xml, skipping.")
return
lint_xsd(lint_ctx, TOOL_DEPENDENCIES_XSD, tool_dependencies)


def lint_tool_dependencies_actions(path, lint_ctx):
def lint_tool_dependencies_actions(realized_repository, lint_ctx):
path = realized_repository.real_path
tool_dependencies = os.path.join(path, "tool_dependencies.xml")
if not os.path.exists(tool_dependencies):
lint_ctx.info("No tool_dependencies.xml, skipping.")
Expand Down Expand Up @@ -267,7 +276,8 @@ def lint_expected_files(realized_repository, lint_ctx):
"repository_dependencies.xml file.")


def lint_repository_dependencies(path, lint_ctx):
def lint_repository_dependencies(realized_repository, lint_ctx):
path = realized_repository.real_path
repo_dependencies = os.path.join(path, "repository_dependencies.xml")
if not os.path.exists(repo_dependencies):
lint_ctx.info("No repository_dependencies.xml, skipping.")
Expand Down