ami search

From Andy Jackson:

I'm trying to understand the data flow of ami-search @Peter Murray-Rust -- am I right in thinking it goes:
Scan text and generate snippets XML per item.
Read snippets XML and generate frequencies/counts XML etc. per item.
Read per-item XML data and generate top-level/summary XML or CSV (latter for co-occurrence data).
Generate HTML versions of XML and CSV for use.
In particular, am I right in thinking that all the outputs are generated from the snippets?

ami-search processes a CProject and iterates over each CTree.

• It creates scholarly.html. Probaly from ` "pseudo-make" where it skips

Running ami search for the "country dictionary"

Tester: Ambreen Hamadani

ami search tool was used to test the country dictionary

1. getpapers was used to create a directory of 1000 papers (including full texts wherever available) getpapers -q "viral epidemics" -o countr_dict -f v_epid/log.txt -x -p -k 1000

2. This directory was used to run ami search using country dictionary ami -p countr_dict search --dictionary country

3. After a successful run, HTML Documents were created that classified the papers on the basis of the _country _while citing the frequency of each country. eg:

ISSUES:

• ami search doesn't work directly unless the directory (cProject Directory) is specified before the search --dictionary eg The command ami search --dictionary country -p countr_dict1 throws the following error

================================
-v to see generic values

Specific values (AMISearchTool)
================================
created COMMAND: word(frequencies)xpath:@count>20~w.stopwords:pmcstop.txt_stopwords.txt search(country) search(-p) search(countr_dict1)
0    [main] DEBUG org.contentmine.ami.tools.AbstractAMISearchTool  - old style search command); to be changed
0 [main] DEBUG org.contentmine.ami.tools.AbstractAMISearchTool  - old style search command); to be changed
>ERROR: requires cProject

The correct command, in this case, is: ami -p countr_dict1 search --dictionary country