GSA-pipeline/TextpressoSystemGlobals.pm at master · kyook/GSA-pipeline · GitHub

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package TextpressoSystemGlobals;

# Package provides global constants for all
# build related matters of Textpresso.
#
# (c) 2005-8 Hans-Michael Muller, Caltech, Pasadena.

use strict;
require Exporter;
our @ISA = qw(Exporter);
our @EXPORT = qw(SY_ROOT SY_SUBROOTS SY_ANNOTATION_TYPE SY_ANNOTATION_SUBTYPE SY_ANNOTATION_SUBTYPE_INSTANCES SY_ANNOTATION_FIELDS SY_PASSTHROUGH_FIELDS SY_SOURCE_FIELDS SY_BIB_NAME SY_BIB_FIELDS SY_BIB_SEPARATOR SY_INDEX_TYPE SY_INDEX_SUBTYPE SY_INDEX_SUBTYPE_INSTANCES SY_INDEX_FIELDS SY_ONTOLOGY SY_SUPPLEMENTALS SY_MAX_NGRAM_SIZE SY_PREPROCESSING_TAGS SY_MARKUP_EXCEPTIONS);

use constant SY_ROOT => '/usr/local/textpresso/celegans/Data/';

use constant SY_SUBROOTS => { annotations => 'annotations/',
			      includes => 'includes/',
			      excludes => 'excludes/',
			      indices => 'indices/',
			      ontology => 'ontology/',
			      supplementals => 'supplementals/',
			      processedfiles => 'processedfiles/',
			      etc => 'etc/'};

use constant SY_ANNOTATION_FIELDS => { abstract => 'abstract/',
				       body => 'body/',
				       title => 'title/',
					   introduction => 'introduction/',
					   materials => 'materials/',
					   results => 'results/',
					   discussion => 'discussion/',
					   conclusion => 'conclusion/',
					   acknowledgments => 'acknowledgments/',
					   references => 'references/'
					   };

use constant SY_ANNOTATION_TYPE => { grammatical => 'grammatical/',
				     semantic => 'semantic/'};

use constant SY_ANNOTATION_SUBTYPE_INSTANCES => 'semantic';

use constant SY_ANNOTATION_SUBTYPE => { categories => 'categories/',
					attributes => 'attributes/'};

use constant SY_PASSTHROUGH_FIELDS =>  { author => 'author/',
					 accession => 'accession/',
					 citation => 'citation/',
					 journal => 'journal/',
					 type => 'type/',
					 year => 'year/'};

use constant SY_BIB_NAME => 'bib-all/';

use constant SY_BIB_FIELDS => { abstract => 'abstract/',
				author => 'author/',
				accession => 'accession/',
				citation => 'citation/',
				journal => 'journal/',
				title => 'title/',
				type => 'type/',
				year => 'year/'};

use constant SY_BIB_SEPARATOR => '_#';

use constant SY_SOURCE_FIELDS => { abstract => 'abstract/',
				   author => 'author/',
				   accession => 'accession/',
				   body => 'body/',
				   citation => 'citation/',
				   journal => 'journal/',
				   title => 'title/',
				   type => 'type/',
				   year => 'year/',
					   introduction => 'introduction/',
					   materials => 'materials/',
					   results => 'results/',
					   discussion => 'discussion/',
					   conclusion => 'conclusion/',
					   acknowledgments => 'acknowledgments/',
					   references => 'references/' };

use constant SY_INDEX_FIELDS => { abstract => 'abstract/',
				  author => 'author/',
				  accession => 'accession/',
				  body => 'body/',
				  journal => 'journal/',
				  title => 'title/',
				  type => 'type/',
				  year => 'year/',
					   introduction => 'introduction/',
					   materials => 'materials/',
					   results => 'results/',
					   discussion => 'discussion/',
					   conclusion => 'conclusion/',
					   acknowledgments => 'acknowledgments/',
					   references => 'references/'
				  };

use constant SY_INDEX_TYPE => { grammatical => 'grammatical/',
				semantic => 'semantic/',
				keyword => 'keyword/'};

use constant SY_INDEX_SUBTYPE_INSTANCES => 'semantic';

use constant SY_INDEX_SUBTYPE => { categories => 'categories/',
				   attributes => 'attributes/'};

use constant SY_ONTOLOGY => { definitions => 'definitions/',
			      compact_lexica => 'compact_lexica',
			      lexica => 'lexica/'};

use constant SY_SUPPLEMENTALS => { endnote => 'endnote/',
				   keyword => 'keyword/',
				   onlinetext => 'onlinetext/',
				   relatedarticle => 'relatedarticle/',
				   svm => 'svm/',
				   synonyms => 'synonyms/'};

use constant SY_SUPPLEMENTALS_DOCS => 'endnote onlinetext relatedarticle';

use constant SY_SUPPLEMENTALS_CONT => 'keyword';

use constant SY_PREPROCESSING_TAGS => ['WSD', 'HTML_ITALICS'];

use constant SY_MARKUP_EXCEPTIONS => ['gene_dmelanogaster'];

use constant SY_MAX_NGRAM_SIZE => 15;

1;