TypeError: list indices must be integers, not str with xmltodict:

Question

I have got this XML file:

<?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>
...

I have tried to parse the above file in the following way:

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())
        tools_section = doc['toolbox']['section']['@name']
        print tools_section

However, I have got the following error:

Traceback (most recent call last):
  File "importTools2Galaxy.py", line 15, in <module>
    tools_section = doc['toolbox']['section']['@name']
TypeError: list indices must be integers, not str

What did I do wrong?

Answer 1

This is because doc['toolbox']['section'] returns a list of sections so you need to iterate over each section to get @name value. You may want check if @name is in given section. For that you may want to use .get instead of ['@name']

with open('tests/shed_tool_conf.xml') as fd:
        doc = xmltodict.parse(fd.read())
        for section in doc['toolbox']['section']:
            tools_section = section.get('@name')
        print tools_section