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Implement repository readme validation as part of shed_lint.

Check restructured text if a README.rst is found. Warn the user if they have accidently used a README.md file. Otherwise just present INFO about the readme detected.

Closes #91
Closes #89
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jmchilton committed Apr 23, 2015
1 parent 988de1d commit d26929e18bbd61f43650336f02a70f2899f5b63b
@@ -2,6 +2,7 @@
import re
import yaml
from galaxy.tools.lint import LintContext
from galaxy.tools.linters.help import rst_invalid
from planemo.lint import lint_xsd
from planemo.shed import (
path_to_repo_name,
@@ -55,6 +56,11 @@ def lint_repository(ctx, path, **kwds):
lint_shed_yaml,
path,
)
lint_ctx.lint(
"readme",
lint_readme,
path,
)
if kwds["tools"]:
for (tool_path, tool_xml) in yield_tool_xmls(ctx, path):
info("+Linting tool %s" % tool_path)
@@ -69,6 +75,41 @@ def lint_repository(ctx, path, **kwds):
return 1 if failed else 0


def lint_readme(path, lint_ctx):
readme_rst = os.path.join(path, "README.rst")
readme = os.path.join(path, "README")
readme_txt = os.path.join(path, "README.txt")

readme_found = False
for readme in [readme_rst, readme, readme_txt]:
if os.path.exists(readme):
readme_found = readme

if not readme_found and os.path.exists("README.md"):
lint_ctx.warn("Tool Shed doesn't render markdown, "
"README.md is invalid readme.")
return

if not readme_found:
# TODO: filter on TYPE and make this a warning if
# unrestricted repository - need to update iuc standards
# first though.
lint_ctx.info("No README found skipping.")
return

if readme_found.endswith(".rst"):
readme_text = open(readme_found, "r").read()
invalid_rst = rst_invalid(readme_text)
if invalid_rst:
template = "Invalid restructured text found in README [%s]."
msg = template % invalid_rst
lint_ctx.warn(msg)
return
lint_ctx.info("README found containing valid reStructuredText.")
else:
lint_ctx.info("README found containing plain text.")


def lint_tool_dependencies(path, lint_ctx):
tool_dependencies = os.path.join(path, "tool_dependencies.xml")
if not os.path.exists(tool_dependencies):
@@ -18,11 +18,7 @@ def lint_help(tool_xml, lint_ctx):
return

lint_ctx.valid("Tool contains help section.")
invalid_rst = False
try:
rst_to_html(help)
except Exception as e:
invalid_rst = str(e)
invalid_rst = rst_invalid(help)

if "TODO" in help:
lint_ctx.warn("Help contains TODO text.")
@@ -31,3 +27,12 @@ def lint_help(tool_xml, lint_ctx):
lint_ctx.warn("Invalid reStructuredText found in help - [%s]." % invalid_rst)
else:
lint_ctx.valid("Help contains valid reStructuredText.")


def rst_invalid(text):
invalid_rst = False
try:
rst_to_html(text)
except Exception as e:
invalid_rst = str(e)
return invalid_rst
@@ -0,0 +1,8 @@
name: "single_tool"
owner: "iuc"
description: "a simple tool"
type: "unrestricted"
remote_repository_url: "https://github.com/galaxyproject/planemo/tree/master/tests/data/repos/single_tool"
homepage_url: "http://planemo.readthedocs.org/en/latest/"
categories:
- "Text Manipulation"
@@ -0,0 +1,2 @@
This is fine markdown but tool shed doesn't implement markdown so this won't show up and should result in a shed_lint warning.

@@ -0,0 +1,23 @@
<tool id="cat" name="Concatenate datasets (for test workflows)" version="1.0">
<description>tail-to-head</description>
<command>
cat $input1 #for $q in $queries# ${q.input2} #end for# > $out_file1
</command>
<inputs>
<param name="input1" type="data" label="Concatenate Dataset"/>
<repeat name="queries" title="Dataset">
<param name="input2" type="data" label="Select" />
</repeat>
</inputs>
<outputs>
<data name="out_file1" format="input" metadata_source="input1"/>
</outputs>
<tests>
<test>
<param name="input1" value="1.bed"/>
<output name="out_file1" file="1.bed"/>
</test>
</tests>
<help>
</help>
</tool>
@@ -0,0 +1,2 @@
A related non-tool file.

@@ -0,0 +1,65 @@
chr1 147962192 147962580 CCDS989.1_cds_0_0_chr1_147962193_r 0 -
chr1 147984545 147984630 CCDS990.1_cds_0_0_chr1_147984546_f 0 +
chr1 148078400 148078582 CCDS993.1_cds_0_0_chr1_148078401_r 0 -
chr1 148185136 148185276 CCDS996.1_cds_0_0_chr1_148185137_f 0 +
chr10 55251623 55253124 CCDS7248.1_cds_0_0_chr10_55251624_r 0 -
chr11 116124407 116124501 CCDS8374.1_cds_0_0_chr11_116124408_r 0 -
chr11 116206508 116206563 CCDS8377.1_cds_0_0_chr11_116206509_f 0 +
chr11 116211733 116212337 CCDS8378.1_cds_0_0_chr11_116211734_r 0 -
chr11 1812377 1812407 CCDS7726.1_cds_0_0_chr11_1812378_f 0 +
chr12 38440094 38440321 CCDS8736.1_cds_0_0_chr12_38440095_r 0 -
chr13 112381694 112381953 CCDS9526.1_cds_0_0_chr13_112381695_f 0 +
chr14 98710240 98712285 CCDS9949.1_cds_0_0_chr14_98710241_r 0 -
chr15 41486872 41487060 CCDS10096.1_cds_0_0_chr15_41486873_r 0 -
chr15 41673708 41673857 CCDS10097.1_cds_0_0_chr15_41673709_f 0 +
chr15 41679161 41679250 CCDS10098.1_cds_0_0_chr15_41679162_r 0 -
chr15 41826029 41826196 CCDS10101.1_cds_0_0_chr15_41826030_f 0 +
chr16 142908 143003 CCDS10397.1_cds_0_0_chr16_142909_f 0 +
chr16 179963 180135 CCDS10401.1_cds_0_0_chr16_179964_r 0 -
chr16 244413 244681 CCDS10402.1_cds_0_0_chr16_244414_f 0 +
chr16 259268 259383 CCDS10403.1_cds_0_0_chr16_259269_r 0 -
chr18 23786114 23786321 CCDS11891.1_cds_0_0_chr18_23786115_r 0 -
chr18 59406881 59407046 CCDS11985.1_cds_0_0_chr18_59406882_f 0 +
chr18 59455932 59456337 CCDS11986.1_cds_0_0_chr18_59455933_r 0 -
chr18 59600586 59600754 CCDS11988.1_cds_0_0_chr18_59600587_f 0 +
chr19 59068595 59069564 CCDS12866.1_cds_0_0_chr19_59068596_f 0 +
chr19 59236026 59236146 CCDS12872.1_cds_0_0_chr19_59236027_r 0 -
chr19 59297998 59298008 CCDS12877.1_cds_0_0_chr19_59297999_f 0 +
chr19 59302168 59302288 CCDS12878.1_cds_0_0_chr19_59302169_r 0 -
chr2 118288583 118288668 CCDS2120.1_cds_0_0_chr2_118288584_f 0 +
chr2 118394148 118394202 CCDS2121.1_cds_0_0_chr2_118394149_r 0 -
chr2 220190202 220190242 CCDS2441.1_cds_0_0_chr2_220190203_f 0 +
chr2 220229609 220230869 CCDS2443.1_cds_0_0_chr2_220229610_r 0 -
chr20 33330413 33330423 CCDS13249.1_cds_0_0_chr20_33330414_r 0 -
chr20 33513606 33513792 CCDS13255.1_cds_0_0_chr20_33513607_f 0 +
chr20 33579500 33579527 CCDS13256.1_cds_0_0_chr20_33579501_r 0 -
chr20 33593260 33593348 CCDS13257.1_cds_0_0_chr20_33593261_f 0 +
chr21 32707032 32707192 CCDS13614.1_cds_0_0_chr21_32707033_f 0 +
chr21 32869641 32870022 CCDS13615.1_cds_0_0_chr21_32869642_r 0 -
chr21 33321040 33322012 CCDS13620.1_cds_0_0_chr21_33321041_f 0 +
chr21 33744994 33745040 CCDS13625.1_cds_0_0_chr21_33744995_r 0 -
chr22 30120223 30120265 CCDS13897.1_cds_0_0_chr22_30120224_f 0 +
chr22 30160419 30160661 CCDS13898.1_cds_0_0_chr22_30160420_r 0 -
chr22 30665273 30665360 CCDS13901.1_cds_0_0_chr22_30665274_f 0 +
chr22 30939054 30939266 CCDS13903.1_cds_0_0_chr22_30939055_r 0 -
chr5 131424298 131424460 CCDS4149.1_cds_0_0_chr5_131424299_f 0 +
chr5 131556601 131556672 CCDS4151.1_cds_0_0_chr5_131556602_r 0 -
chr5 131621326 131621419 CCDS4152.1_cds_0_0_chr5_131621327_f 0 +
chr5 131847541 131847666 CCDS4155.1_cds_0_0_chr5_131847542_r 0 -
chr6 108299600 108299744 CCDS5061.1_cds_0_0_chr6_108299601_r 0 -
chr6 108594662 108594687 CCDS5063.1_cds_0_0_chr6_108594663_f 0 +
chr6 108640045 108640151 CCDS5064.1_cds_0_0_chr6_108640046_r 0 -
chr6 108722976 108723115 CCDS5067.1_cds_0_0_chr6_108722977_f 0 +
chr7 113660517 113660685 CCDS5760.1_cds_0_0_chr7_113660518_f 0 +
chr7 116512159 116512389 CCDS5771.1_cds_0_0_chr7_116512160_r 0 -
chr7 116714099 116714152 CCDS5773.1_cds_0_0_chr7_116714100_f 0 +
chr7 116945541 116945787 CCDS5774.1_cds_0_0_chr7_116945542_r 0 -
chr8 118881131 118881317 CCDS6324.1_cds_0_0_chr8_118881132_r 0 -
chr9 128764156 128764189 CCDS6914.1_cds_0_0_chr9_128764157_f 0 +
chr9 128787519 128789136 CCDS6915.1_cds_0_0_chr9_128787520_r 0 -
chr9 128882427 128882523 CCDS6917.1_cds_0_0_chr9_128882428_f 0 +
chr9 128937229 128937445 CCDS6919.1_cds_0_0_chr9_128937230_r 0 -
chrX 122745047 122745924 CCDS14606.1_cds_0_0_chrX_122745048_f 0 +
chrX 152648964 152649196 CCDS14733.1_cds_0_0_chrX_152648965_r 0 -
chrX 152691446 152691471 CCDS14735.1_cds_0_0_chrX_152691447_f 0 +
chrX 152694029 152694263 CCDS14736.1_cds_0_0_chrX_152694030_r 0 -
@@ -0,0 +1 @@
chr5 131424298 131424460 CCDS4149.1_cds_0_0_chr5_131424299_f 0 +
@@ -0,0 +1,8 @@
name: "single_tool"
owner: "iuc"
description: "a simple tool"
type: "unrestricted"
remote_repository_url: "https://github.com/galaxyproject/planemo/tree/master/tests/data/repos/single_tool"
homepage_url: "http://planemo.readthedocs.org/en/latest/"
categories:
- "Text Manipulation"
@@ -0,0 +1,6 @@

.. header invalid since top and bottom don't match
==========
Mooo
=========
@@ -0,0 +1,23 @@
<tool id="cat" name="Concatenate datasets (for test workflows)" version="1.0">
<description>tail-to-head</description>
<command>
cat $input1 #for $q in $queries# ${q.input2} #end for# > $out_file1
</command>
<inputs>
<param name="input1" type="data" label="Concatenate Dataset"/>
<repeat name="queries" title="Dataset">
<param name="input2" type="data" label="Select" />
</repeat>
</inputs>
<outputs>
<data name="out_file1" format="input" metadata_source="input1"/>
</outputs>
<tests>
<test>
<param name="input1" value="1.bed"/>
<output name="out_file1" file="1.bed"/>
</test>
</tests>
<help>
</help>
</tool>
@@ -0,0 +1,2 @@
A related non-tool file.

@@ -0,0 +1,65 @@
chr1 147962192 147962580 CCDS989.1_cds_0_0_chr1_147962193_r 0 -
chr1 147984545 147984630 CCDS990.1_cds_0_0_chr1_147984546_f 0 +
chr1 148078400 148078582 CCDS993.1_cds_0_0_chr1_148078401_r 0 -
chr1 148185136 148185276 CCDS996.1_cds_0_0_chr1_148185137_f 0 +
chr10 55251623 55253124 CCDS7248.1_cds_0_0_chr10_55251624_r 0 -
chr11 116124407 116124501 CCDS8374.1_cds_0_0_chr11_116124408_r 0 -
chr11 116206508 116206563 CCDS8377.1_cds_0_0_chr11_116206509_f 0 +
chr11 116211733 116212337 CCDS8378.1_cds_0_0_chr11_116211734_r 0 -
chr11 1812377 1812407 CCDS7726.1_cds_0_0_chr11_1812378_f 0 +
chr12 38440094 38440321 CCDS8736.1_cds_0_0_chr12_38440095_r 0 -
chr13 112381694 112381953 CCDS9526.1_cds_0_0_chr13_112381695_f 0 +
chr14 98710240 98712285 CCDS9949.1_cds_0_0_chr14_98710241_r 0 -
chr15 41486872 41487060 CCDS10096.1_cds_0_0_chr15_41486873_r 0 -
chr15 41673708 41673857 CCDS10097.1_cds_0_0_chr15_41673709_f 0 +
chr15 41679161 41679250 CCDS10098.1_cds_0_0_chr15_41679162_r 0 -
chr15 41826029 41826196 CCDS10101.1_cds_0_0_chr15_41826030_f 0 +
chr16 142908 143003 CCDS10397.1_cds_0_0_chr16_142909_f 0 +
chr16 179963 180135 CCDS10401.1_cds_0_0_chr16_179964_r 0 -
chr16 244413 244681 CCDS10402.1_cds_0_0_chr16_244414_f 0 +
chr16 259268 259383 CCDS10403.1_cds_0_0_chr16_259269_r 0 -
chr18 23786114 23786321 CCDS11891.1_cds_0_0_chr18_23786115_r 0 -
chr18 59406881 59407046 CCDS11985.1_cds_0_0_chr18_59406882_f 0 +
chr18 59455932 59456337 CCDS11986.1_cds_0_0_chr18_59455933_r 0 -
chr18 59600586 59600754 CCDS11988.1_cds_0_0_chr18_59600587_f 0 +
chr19 59068595 59069564 CCDS12866.1_cds_0_0_chr19_59068596_f 0 +
chr19 59236026 59236146 CCDS12872.1_cds_0_0_chr19_59236027_r 0 -
chr19 59297998 59298008 CCDS12877.1_cds_0_0_chr19_59297999_f 0 +
chr19 59302168 59302288 CCDS12878.1_cds_0_0_chr19_59302169_r 0 -
chr2 118288583 118288668 CCDS2120.1_cds_0_0_chr2_118288584_f 0 +
chr2 118394148 118394202 CCDS2121.1_cds_0_0_chr2_118394149_r 0 -
chr2 220190202 220190242 CCDS2441.1_cds_0_0_chr2_220190203_f 0 +
chr2 220229609 220230869 CCDS2443.1_cds_0_0_chr2_220229610_r 0 -
chr20 33330413 33330423 CCDS13249.1_cds_0_0_chr20_33330414_r 0 -
chr20 33513606 33513792 CCDS13255.1_cds_0_0_chr20_33513607_f 0 +
chr20 33579500 33579527 CCDS13256.1_cds_0_0_chr20_33579501_r 0 -
chr20 33593260 33593348 CCDS13257.1_cds_0_0_chr20_33593261_f 0 +
chr21 32707032 32707192 CCDS13614.1_cds_0_0_chr21_32707033_f 0 +
chr21 32869641 32870022 CCDS13615.1_cds_0_0_chr21_32869642_r 0 -
chr21 33321040 33322012 CCDS13620.1_cds_0_0_chr21_33321041_f 0 +
chr21 33744994 33745040 CCDS13625.1_cds_0_0_chr21_33744995_r 0 -
chr22 30120223 30120265 CCDS13897.1_cds_0_0_chr22_30120224_f 0 +
chr22 30160419 30160661 CCDS13898.1_cds_0_0_chr22_30160420_r 0 -
chr22 30665273 30665360 CCDS13901.1_cds_0_0_chr22_30665274_f 0 +
chr22 30939054 30939266 CCDS13903.1_cds_0_0_chr22_30939055_r 0 -
chr5 131424298 131424460 CCDS4149.1_cds_0_0_chr5_131424299_f 0 +
chr5 131556601 131556672 CCDS4151.1_cds_0_0_chr5_131556602_r 0 -
chr5 131621326 131621419 CCDS4152.1_cds_0_0_chr5_131621327_f 0 +
chr5 131847541 131847666 CCDS4155.1_cds_0_0_chr5_131847542_r 0 -
chr6 108299600 108299744 CCDS5061.1_cds_0_0_chr6_108299601_r 0 -
chr6 108594662 108594687 CCDS5063.1_cds_0_0_chr6_108594663_f 0 +
chr6 108640045 108640151 CCDS5064.1_cds_0_0_chr6_108640046_r 0 -
chr6 108722976 108723115 CCDS5067.1_cds_0_0_chr6_108722977_f 0 +
chr7 113660517 113660685 CCDS5760.1_cds_0_0_chr7_113660518_f 0 +
chr7 116512159 116512389 CCDS5771.1_cds_0_0_chr7_116512160_r 0 -
chr7 116714099 116714152 CCDS5773.1_cds_0_0_chr7_116714100_f 0 +
chr7 116945541 116945787 CCDS5774.1_cds_0_0_chr7_116945542_r 0 -
chr8 118881131 118881317 CCDS6324.1_cds_0_0_chr8_118881132_r 0 -
chr9 128764156 128764189 CCDS6914.1_cds_0_0_chr9_128764157_f 0 +
chr9 128787519 128789136 CCDS6915.1_cds_0_0_chr9_128787520_r 0 -
chr9 128882427 128882523 CCDS6917.1_cds_0_0_chr9_128882428_f 0 +
chr9 128937229 128937445 CCDS6919.1_cds_0_0_chr9_128937230_r 0 -
chrX 122745047 122745924 CCDS14606.1_cds_0_0_chrX_122745048_f 0 +
chrX 152648964 152649196 CCDS14733.1_cds_0_0_chrX_152648965_r 0 -
chrX 152691446 152691471 CCDS14735.1_cds_0_0_chrX_152691447_f 0 +
chrX 152694029 152694263 CCDS14736.1_cds_0_0_chrX_152694030_r 0 -
@@ -0,0 +1 @@
chr5 131424298 131424460 CCDS4149.1_cds_0_0_chr5_131424299_f 0 +
@@ -4,7 +4,7 @@

class ShedLineTestCase(CliTestCase):

def test_valid_repo(self):
def test_valid_repos(self):
with self._isolate_repo("single_tool"):
self._check_exit_code(["shed_lint"])
with self._isolate_repo("multi_repos_nested"):
@@ -15,3 +15,10 @@ def test_valid_repo(self):
self._check_exit_code(["shed_lint"])
with self._isolate_repo("workflow_1"):
self._check_exit_code(["shed_lint"])

def test_invalid_repos(self):
# And now
with self._isolate_repo("bad_readme_rst"):
self._check_exit_code(["shed_lint"], exit_code=1)
with self._isolate_repo("bad_readme_md"):
self._check_exit_code(["shed_lint"], exit_code=1)

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