petermr
commented
5 years ago 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 entriesThis 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"/>
using
getpapersi 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.