Created
August 3, 2015 02:44
-
-
Save mictadlo/05d09b7a5c2161864bfe to your computer and use it in GitHub Desktop.
TypeError: string indices must be integers with XMLtoDict
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Traceback (most recent call last): | |
File "importTools2Galaxy.py", line 12, in <module> | |
tool_section_name = section['@name'] | |
TypeError: string indices must be integers |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
<?xml version="1.0"?> | |
<toolbox tool_path="/galaxy/main/shed_tools"> | |
<section id="snpeff" name="snpEff" version=""> | |
<tool file="toolshed.g2.bx.psu.edu/repos/pcingola/snpeff/c052639fa666/snpeff/snpEff_2_1a/snpEff_2_1a/galaxy/snpSift_filter.xml" guid="toolshed.g2.bx.psu.edu/repos/pcingola/snpeff/snpSift_filter/1.0"> | |
<tool_shed>toolshed.g2.bx.psu.edu</tool_shed> | |
<repository_name>snpeff</repository_name> | |
<repository_owner>pcingola</repository_owner> | |
<installed_changeset_revision>c052639fa666</installed_changeset_revision> | |
<id>toolshed.g2.bx.psu.edu/repos/pcingola/snpeff/snpSift_filter/1.0</id> | |
<version>1.0</version> | |
</tool> | |
<tool file="toolshed.g2.bx.psu.edu/repos/pcingola/snpeff/c052639fa666/snpeff/snpEff_2_1a/snpEff_2_1a/galaxy/snpEff.xml" guid="toolshed.g2.bx.psu.edu/repos/pcingola/snpeff/snpEff/1.0"> | |
<tool_shed>toolshed.g2.bx.psu.edu</tool_shed> | |
<repository_name>snpeff</repository_name> | |
<repository_owner>pcingola</repository_owner> | |
<installed_changeset_revision>c052639fa666</installed_changeset_revision> | |
<id>toolshed.g2.bx.psu.edu/repos/pcingola/snpeff/snpEff/1.0</id> | |
<version>1.0</version> | |
</tool> | |
<tool file="toolshed.g2.bx.psu.edu/repos/gregory-minevich/check_snpeff_candidates/22c8c4f8d11c/check_snpeff_candidates/checkSnpEffCandidates.xml" guid="toolshed.g2.bx.psu.edu/repos/gregory-minevich/check_snpeff_candidates/check_snpeff_candidates/1.0.0"> | |
<tool_shed>toolshed.g2.bx.psu.edu</tool_shed> | |
<repository_name>check_snpeff_candidates</repository_name> | |
<repository_owner>gregory-minevich</repository_owner> | |
<installed_changeset_revision>22c8c4f8d11c</installed_changeset_revision> | |
<id>toolshed.g2.bx.psu.edu/repos/gregory-minevich/check_snpeff_candidates/check_snpeff_candidates/1.0.0</id> | |
<version>1.0.0</version> | |
</tool> | |
</section> | |
</toolbox> |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
import xmltodict | |
# wget -c https://raw.githubusercontent.com/galaxyproject/usegalaxy-playbook/c55aa042825fe02ef4a02d958eb811adba8ea45f/files/galaxy/usegalaxy.org/var/shed_tool_conf.xml | |
if __name__ == '__main__': | |
with open('tests/shed_tool_conf.xml') as fd: | |
doc = xmltodict.parse(fd.read()) | |
for section in doc['toolbox']['section']: | |
tool_section_name = section['@name'] | |
print "1", tool_section_name | |
for tool in section['tool']: | |
print tool | |
print "2", tool['tool_shed'] | |
print "3", tool['repository_owner'] | |
print tool['@file'] |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment