## lucegene.properties
## general/common configurations

## ******* REQUIRED full path setting *******
## this *should* be only place we have to set full path
## see also dbs/lucegene/*.properties  

## see instead WEB-INF/web.xml for relative path
# LUCEGENE_ROOT=/bio/biodb/flybase

# title of application and footer value to display
appTitle  = FlyBase Search

# admin email
adminEmail = flybase-help@flybase.net


# relative to LUCEGENE_ROOT or ARGOS_SERVICE_ROOT
# can use absolute paths here, or assume ARGOS_SERVICE_ROOT is set
DATA_ROOT=web/data/

INDEX_ROOT=indices/lucene

# library config/properties folder; relative to webapp base
CONF_ROOT=conf/

# default lib ?
LIB_NAME = 

# use only if not specified elsewhere
defaultlib = ugpxml

storefields=docid docclass title url

## ** ? make searchReturn type a lucegene.properties value **
## searchReturn.main = resultfile OR searchresults  (former eats memory; later may still be flaky, subject to timeouts)
##   .main requires javax.*.directory.SearchResults subclass objects for results pages
## default == DocumentList.get(i) returns LuceneSearchHit; NOT for searchReturn.main
## searchresults == DocumentList.get(i) returns SearchResults; 
## resultfile == LuceneSearchResultFile; .get(i) returns SearchResults; ( eats memory)
## for JSP only, see dosearch.jsp, dosearchlist.jsp, domultisearch.jsp,  javalib/lucyutils/Search.java

searchReturn = default
## use resultfile for demo? more tested
# searchReturn.main = searchresults
searchReturn.main = resultfile


# libraries to include on main page for searching.
# # automatically read from indices/lucene ? or use defined list only?
# libList = \
#   fbgn, Genes, \
#   fban, Annotations, \
#   fbrf, References, \
#   seqs, Sequences, \
#   gamexml, Game XML, \
#   go, Gene Ontology, \
#   docs, Web Documents

## better to get these titles from lib .properties 
title.anatomy=Anatomy
title.fbgn=Genes
title.fbal=Alleles
title.fban=Annotations
title.fbrf=References
title.fbab=Aberrations
title.fbtp=Transgenes
title.fbti=Insertions
title.fbpp=Polypeptides
title.fbtr=Transcripts
title.fbst=Stocks
title.seqs=Gene Sequences
title.webdocs=Web Documents
title.go=Gene Ontology
title.medline=Medline abstracts
title.ugpxml=Gene Summary XML
title.gnomap=Genome features

title.bindxml=BIND Prot. Inter.
title.blasttab=BLAST Results
title.geo=GEO Gene Express.
title.paperspdf=Papers (PDF)
title.uniprot=UniProt sequences

fieldlabel.contents=contents
fieldlabel.docid=ID
fieldlabel.docclass=Class
# field.label.xxx=

libskip.gamexml=1
libskip.gff_dmelhet=1
libskip.gnomap_dmelhet=1
libskip.libs=1
libskip.table=1
libskip.fbgns=1
libskip.fbgna=1
# what the heck is in table index?

## for search only?
searchskip.MAIN_CLA=1
searchskip.docclass=1
#searchskip.CLA=1
##searchskip.contents=1
searchskip.count=1
searchskip.field=1
searchskip.title=1
searchskip.uid=1
searchskip.url=1
searchskip.EOR=1
searchskip.modified=1
searchskip.lastModified=1

## not same as searchskip - this flag means dont parse field in QueryParser
QueryParser.skip = ListFilter

## load in all those field labels...
include.fieldlabel=acode-labels.properties

# report server is optional, if not defined, then the current server 
#  name is used. DO include the protocol (http, ftp, etc)
#reportServer = http://flybase.net/
# report port is also optional, if not defined, then the current server port is used.
#reportPort = 7072

# report extension is NOT optional, this must be set.  This 
#  defines what scripts, jsp, etc will handle the report pages.
reportExtension = /cgi-bin/fbidq.html?
## add optional
## batchURL = xxxx

docurl=http://flybase.net/cgi-bin/fbidq.html?
# docurl=http://flybase.net/cgi-bin/fbidq.html?
batchurl=/cgi-bin/fbidq.html?
batchproc=cgi-bin/fbidq.html
batch.forward=
# LUCEGENE_ROOT/cgi-bin...

resultspage = results.jsp
## for xslt to produce the result page tables
# resultxsl = conf/lucegene_result.xsl
# resultspage = resultxsl.jsp

gmapurl = /cgi-bin/gbrowse_fb/dmel?name=

## Fields that can be searched/displayed
## no good here; very lib specific.
# fieldList =\
#   all,  All Fields,   CEL, Cellular Location,     	\

# fields that user can sort on
# genes.sort=
# sortFields = SYM, NAM, CHR

# Fields to display when xml chosen on search result page.
# genes.display=
# displayFields = ID, SYM, NAM, CHR

# default search field (if one not chosen from list on web)
# defaultSearchField = all

searchfield = all
## if we have indexed all of data into one field; use that instead
## of multi-field searches -- can be slow, memory intensive 
## for complex queries w/ many fields
# searchallfield = contents
searchallfield = all

# batchFormats =\
#   text/html, Document Hypertext, \
#   text/plain, Document Text, \
#   text/csv, Spreadsheet commas, \
#   text/tsv, Spreadsheet tabbed, \
#   text/xml, Database XML, \
#   text/acode, Database acode, \
#   text/acode-pretty, Labelled acode,

batchformats = text/html, text/plain, text/csv, text/tsv, text/xml, text/acode

title.text/html=Document Hypertext
title.text/plain=Document Text
title.text/csv=Spreadsheet commas
title.text/tsv=Spreadsheet tabbed
title.text/xml=Database XML
title.text/acode=Database Acode

## --------------------------

# search page title -- leave to header.html or search.jsp
# searchtitle = <center><h1> FlyBase Search <small>(LuceGene)</small> </h1></center>

# results page title -- leave to header.html or search.jsp
# restitle = FlyBase Search Results

# see instead header.html, footer.html
# appFooter = <p align="right"><i>powered by LuceGene (www.gmod.org/lucegene)</i></p>

# see instead header.html, footer.html
# appHeader =\
# <center> <small>\
# <a href=/>FlyBase</a> \
# ..  <a href=/anatomy/>Anatomy</a> \
# ..  <a href=/blast/>BLAST</a> \
# ..  <a href=/genes/>Genes</a> \
# ..  <a href=/maps/>Maps</a> \
# ..  <a href=/refs/>References</a> \
# ..  <a href=/annot/>Seqs &amp; Annotations</a> \
# ..  <a href=/stocks/>Stocks</a> \
# <a href=/docs/>Help</a> \
# </small> </center> <hr>

# ---- Results page params ---- #
# header/footer for xml output (results are always
#  sent to the jsp pages as xml, which *should* be
#  transformed with an xsl template).
# xmlHeaderFooter = ArgosResults

# default format
format = html


# ---- handler stuff ---- 

## dgg here, adding some props
## visible urls previously hard coded
# index.html=/index.html
# ArgosIndexHandler=org.argos.handlers.ArgosIndexHandler

## the main page from ArgosIndexHandler
# indexJsp=searchform.jsp

# search.html=/search.html
# ArgosSearchHandler=org.argos.handlers.ArgosSearchHandler
# jsp page that will handle the search (for controller only?)
# searchJsp = search.html

# results.html=/results.html
#  jsp/html page that will handle the search results
#  The html value is 'virtual', trapped by controller to pass to .jsp
# searchResultsJsp = results.jsp
# searchResultsHtml = results.html
# ArgosSearchResultHandler=org.argos.handlers.ArgosSearchResultHandler

# The number of results (initially) to hold in memory.
#  if not defined, ArgosDefaults.NUM_DOCS_MEMORY is used. 
# numResultsMemory = 40

# The factor used to adjust the number of results held in memory.   
#  ArgosDefaults.NUM_RESULTS_MEMORY_MULTIPLIER is used.
# resultsMemoryMultiplier = 2

# The maximum number of results to hold in memory. 
#  defined, ArgosDefaults.MAX_RESULTS_MEMORY is used.
## dgg - rename ArgosDefaults.MAX_RESULTS_MEMORY
# maxResultsInMemory = 100

# xsl file to transform the xml output to HTML
# searchXslHtml = conf/searchReport.xsl

# xsl file to transform the xml output to pretty print xml
# searchXslPrettyXml = conf/searchReportXML.xsl

# searchXslText = conf/searchReportText.xsl

# number of results to show per page (by default)
# numberResultsPerPage = 20
pagesize = 15

# batch downloads/viewing
# max must be set while using external program to generate
# maxBatchDownload = 50