Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

PMC2803133/search.country.count.xml is empty, although PMC2803133/search.country.snippets.xml` has entries #32

Open
vinitamehlawat opened this issue Feb 16, 2019 · 1 comment
Assignees
Labels
bug Something isn't working documentation document possible bugs mustfix bug must be fixed

Comments

@vinitamehlawat
Copy link
Collaborator

using getpapers i run command "getpapers -q osanctum -x -k 100 " After that i run ami-search cooccur
i get 100 papers of osanctum ,when i open my osanctum projet i found soo many folders having their unique PMC ids. and one cooccur folder.I click on PMC1397864 which is present in tigr2ess/osanctum,i found a result folder and so many files having different extensions .I notice one thing in every file like when i open this search.country.count.xml no content is there .I just want to ask is this software error or i am doing something wrong that i got every .count file is empty.

@petermr petermr changed the title empty_xml results/search/country/count.xml is empty Feb 16, 2019
@petermr petermr changed the title results/search/country/count.xml is empty PMC2803133/search.country.count.xml is empty, although PMC2803133/search.country.snippets.xml` has entries Feb 16, 2019
@petermr
Copy link
Owner

petermr commented Feb 16, 2019

Thanks.
This is all part of the learning process.
I will rewrite the question/issue. We should always try to post just the essential details, including full filenames and snippets of code and data. Here's a revised version:

I have changed the title to be more specific and accurate:

PMC2803133/search.country.count.xml is empty, although 
   PMC2803133/search.country.snippets.xml has entries

This is more precise and lets us find the error more easily.

Narrative:

After running ami20190212a on the standard osanctum corpus the *.count.xml files contain no counts even though the corresponding *.snippets.xml has several entries:

in search.country.snippets.xml:

<?xml version="1.0" encoding="UTF-8"?>
<snippetsTree>
 <snippets file="/Users/pm286/workspace/tigr2ess/osanctum/PMC2803133/results/search/country/results.xml">
  <result pre="and Nutrition 0912-0009 1880-5086 the Society for Free Radical Research" exact="Japan" post="Kyoto, Japan pmcid: 2803133 jcbn09-52 doi: 10.3164/jcbn.09-52 : Original"/>
  <result pre="0912-0009 1880-5086 the Society for Free Radical Research Japan Kyoto," exact="Japan" post="pmcid: 2803133 jcbn09-52 doi: 10.3164/jcbn.09-52 : Original Article Antioxidant"/>
  <result pre="therapeutic in averting several diseases in various Asian countries including" exact="India" post="and Thailand. OS is a small herb, native to"/>
  <result pre="of Rangsit University, which is under The National Council of" exact="Thailand" post="for Animal Care. The rats were housed in a"/>
  <result pre="Acknowledgment This project was supported by the grant from The" exact="Thailand" post="Research Fund, Thailand (RMU 5080016). References References 1 Freedman"/>
  <result pre="was supported by the grant from The Thailand Research Fund," exact="Thailand" post="(RMU 5080016). References References 1 Freedman J.E. High-fat diets"/>
 </snippets>
</snippetsTree>

but in search.country.count.xml

<?xml version="1.0" encoding="UTF-8"?>
<results title="frequencies"/>

@petermr petermr self-assigned this Feb 16, 2019
@petermr petermr added bug Something isn't working documentation document possible bugs mustfix bug must be fixed labels Feb 16, 2019
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
bug Something isn't working documentation document possible bugs mustfix bug must be fixed
Projects
None yet
Development

No branches or pull requests

2 participants