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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-cooccur for the new release of ami20190219b." #67

Closed ambarishK closed 5 years ago

ambarishK commented 5 years ago
Status of the test run of the ami-search-cooccur for the new release of the ami20190219b is not successful.
Error is of run time exception related of not finding metadata file (most probably generated from eupmc_results.json containing bibliographic information).
Failed to find all cooccurrences among specified search terms.
Run time log
ambarish123@ubuntu:~$ ami-search-cooccur ricenew/ country gene drugs
*******************************
WARNING: AMISearch is being replaced by AMISearchTool (ami-search-new)
*******************************

1    [main] DEBUG org.contentmine.ami.AMIProcessor  - project name: ricenew/ /home/ambarish123

running: word; word([frequencies])[{xpath:@count>20}, {w.stopwords:pmcstop.txt stopwords.txt}]...
running: search; search([country])[]...
running: gene; gene([human])[]47800 [main] DEBUG org.contentmine.ami.dictionary.gene.HGNCDictionary  - is /org/contentmine/ami/plugins/gene/hgnc/hgnc.xml
...
running: search; search([drugs])[]...
create data tables
Exception in thread "main" java.lang.RuntimeException: Null metadataByTreename
    at org.contentmine.cproject.util.DataTablesTool.setMetadataByTreename(DataTablesTool.java:501)
    at org.contentmine.ami.plugins.CommandProcessor.createDataTables(CommandProcessor.java:212)
    at org.contentmine.ami.AMIProcessor.runSearches(AMIProcessor.java:118)
    at org.contentmine.ami.AMIProcessor.runSearchesAndCooccurrence(AMIProcessor.java:193)
    at org.contentmine.ami.tools.AMISearch.runAMISearches(AMISearch.java:51)
    at org.contentmine.ami.tools.AMISearch.main(AMISearch.java:32)
petermr commented 5 years ago

The error message specifically says that you should no longer use

On Wed, Feb 20, 2019 at 6:49 AM Ambarish Kumar notifications@github.com wrote:

Status of the test run of the ami-search-cooccur for the new release of the ami20190219b is not successful.

That's because it has been superseded.

Error is of run time exception related of not finding metadata file (most

probably generated from eupmc_results.json containing bibliographic information). Failed to find all cooccurrences among specified search terms. Run time log

ambarish123@ubuntu:~$ ami-search-cooccur ricenew/ country gene drugs

WARNING: AMISearch is being replaced by AMISearchTool (ami-search-new)

^^^ Is this message unclear? If so I will strengthen it.

-- Peter Murray-Rust Reader Emeritus in Molecular Informatics Unilever Centre, Dept. Of Chemistry University of Cambridge CB2 1EW, UK +44-1223-763069