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petermr / tigr2ess

Materials for TIGR2ESS workshop in Delhi Feb 2019 - joint UK(Cambridge) - India project on Food Security.
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"Test run of ami-search-new for the release of ami-jars - ami20190220. " #78

Closed ambarishK closed 5 years ago

ambarishK commented 5 years ago

Status of the test run is successful.

It is finding all searches and cooccurrences.

Snapshot

ambarish123@ubuntu:~$ ami-search-new -p rice/ --dictionary country gene

Generic values (AMISearchTool)
================================
basename            null
cproject            /home/ambarish123/rice
ctree               
cTreeList           10 trees [rice/PMC6024620, rice/PMC6024883, rice/PMC6031371
dryrun              false
excludeBase         null
excludeTrees        null
file types          []
forceMake           false
includeBase         null
includeTrees        null
log4j               
logfile             null
verbose             0

Specific values (AMISearchTool)
================================
dictionaryList       [country, gene]
dictionaryTop        null
dictionarySuffix     [xml]
ignorePlugins        []

cProject: rice

running: word; word([frequencies])[{xpath:@count>20}, {w.stopwords:pmcstop.txt stopwords.txt}]...
running: search; search([country])[]...
running: gene; gene([human])[]0    [main] DEBUG org.contentmine.ami.dictionary.gene.HGNCDictionary  - is /org/contentmine/ami/plugins/gene/hgnc/hgnc.xml
...
create data tables
rrrr
petermr commented 5 years ago

Thank you. Will close

On Fri, Feb 22, 2019 at 7:52 AM Ambarish Kumar notifications@github.com wrote:

Status of the test run is successful. It is finding all searches and cooccurrences. Snapshot

ambarish123@ubuntu:~$ ami-search-new -p rice/ --dictionary country gene

Generic values (AMISearchTool)

basename null cproject /home/ambarish123/rice ctree cTreeList 10 trees [rice/PMC6024620, rice/PMC6024883, rice/PMC6031371 dryrun false excludeBase null excludeTrees null file types [] forceMake false includeBase null includeTrees null log4j logfile null verbose 0

Specific values (AMISearchTool)

dictionaryList [country, gene] dictionaryTop null dictionarySuffix [xml] ignorePlugins []

cProject: rice

running: word; word([frequencies])[{xpath:@count>20}, {w.stopwords:pmcstop.txt stopwords.txt}]... running: search; search([country])[]... running: gene; gene([human])[]0 [main] DEBUG org.contentmine.ami.dictionary.gene.HGNCDictionary - is /org/contentmine/ami/plugins/gene/hgnc/hgnc.xml ... create data tables rrrr

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