CoNLLStreamExtractor / CoNLL2RDF produces unreadable ttl with SRL-Args

[glaserL]

Resolving trailing SRL annotations in conll sometimes produces exceptions due to unreadable TMP nodes.

the CoNLL2RDF.java class (in conll2ttl func) produces temporary nodes "TMP_SRL{ID}" that are fixed later on. However, if they can't be fixed, unusable ttl gets putout as "_TMP_SRL_2" for example isn't a valid node name.

A potential (hacky?) fix I found is to change "_TMP_SRL" to ":_TMP_SRL" at the following two places:

conll-rdf/src/org/acoli/conll/rdf/CoNLL2RDF.java

Lines 90 to 94 in 82b9dc4

	if(col2field.get(col2field.size()-1).toLowerCase().matches(".*args")) {
	for(int i = 0; i<predicates.size(); i++) {
	sentence=sentence.replaceAll("_TMP_"+col2field.get(col2field.size()-1).replaceFirst("[\\-_]*[Aa][rR][gG][sS]$","_"+i),predicates.get(i));
	}
	}

conll-rdf/src/org/acoli/conll/rdf/CoNLL2RDF.java

Lines 145 to 148 in 82b9dc4

	argTriples.add(
	"_TMP_"+col2field.get(col2field.size()-1).replaceFirst("[\\-_]*[Aa][rR][gG][sS]$","_"+(i+1-col2field.size()))+
	" conll:"+field[i].trim()+
	" "+URI);

This makes them acceptable node identifiers so one could fix them later in sparql queries?

Here a (somewhat) minimal example where this happens, I couldn't find a fix for the annotation so I can't sensibly minimize it. The call was
cat broken.conll | ./run.sh CoNLLStreamExtractor http://example.com ID WORD FEATS HEAD EDGE SRL SRL-ARGs

1	Although	_	6	mark	_	_	_	ARGM-ADV
2	data	_	6	nsubj	_	_	_	ARGM-ADV
3	in	_	2	prep	_	_	_	ARGM-ADV
4	this	_	5	det	_	_	_	ARGM-ADV
5	project	_	3	pobj	_	_	_	ARGM-ADV
6	are	_	24	advcl	_	_	_	ARGM-ADV
7	de	_	8	dep	_	ARG0	ARGM-MNR	ARGM-ADV
8	-	_	9	dep	-	V	_	ARGM-ADV
9	identified	_	12	amod	identified	_	V	ARGM-ADV
10	,	_	12	punct	_	_	_	_
11	certain	_	12	amod	_	_	_	_
12	information	_	24	nsubjpass	_	_	_	_
13	such	_	14	amod	_	_	_	_
14	as	_	12	prep	_	_	_	_
15	the	_	16	det	_	_	_	_
16	number	_	14	pobj	_	_	_	_
17	of	_	16	prep	_	_	_	_
18	ED	_	19	compound	_	_	_	_
19	visits	_	17	pobj	_	_	_	_
20	by	_	19	prep	_	_	_	_
21	zip	_	22	compound	_	_	_	_
22	code	_	20	pobj	_	_	_	_
23	were	_	24	auxpass	_	_	_	_
24	considered	_	0	ROOT	considered	_	_	V
25	proprietary	_	26	amod	_	_	_	ARG1
26	information	_	24	oprd	_	_	_	ARG1
27	by	_	26	prep	_	_	_	ARG0
28	some	_	30	det	_	_	_	ARG0
29	health	_	30	compound	_	_	_	ARG0
30	systems	_	27	pobj	_	_	_	ARG0
31	.	_	24	punct	_	_	_	_

And full error:

18:41:58 INFO  CoNLLStreamExtractor :: synopsis: CoNLLStreamExtractor baseURI FIELD1[.. FIELDn] [-u SPARQL_UPDATE1..m] [-s SPARQL_SELECT]
	baseURI       CoNLL base URI, cf. CoNLL2RDF
	FIELDi        CoNLL field label, cf. CoNLL2RDF
	SPARQL_UPDATE SPARQL UPDATE (DELETE/INSERT) query, either literally or its location (file/uri)
	              can be followed by an optional integer in {}-parentheses = number of repetitions
	              The SPARQL_UPDATE parameter is DEPRECATED - please use CoNLLRDFUpdater instead!
	SPARQL_SELECT SPARQL SELECT statement to produce TSV output
	reads CoNLL from stdin, splits sentences, creates CoNLL RDF, applies SPARQL queries
18:41:58 INFO  CoNLLStreamExtractor :: running CoNLLStreamExtractor
18:41:58 INFO  CoNLLStreamExtractor :: 	baseURI:       http://example.com
18:41:58 INFO  CoNLLStreamExtractor :: 	CoNLL columns: [ID, WORD, FEATS, HEAD, EDGE, SRL, SRL-ARGs]
18:41:58 INFO  CoNLLStreamExtractor :: 	SPARQL update: []
18:41:58 INFO  CoNLLStreamExtractor :: 	SPARQL select: null
18:41:58 INFO  CoNLLStreamExtractor :: read SPARQL ..
18:41:58 INFO  CoNLLStreamExtractor :: .. ok
18:41:58 INFO  CoNLLStreamExtractor :: process input ..
18:41:59 ERROR riot                 :: [line: 46, col: 1 ] Out of place: [UNDERSCORE]
org.apache.jena.riot.RiotException: [line: 46, col: 1 ] Out of place: [UNDERSCORE]
	at org.apache.jena.riot.system.ErrorHandlerFactory$ErrorHandlerStd.fatal(ErrorHandlerFactory.java:147)
	at org.apache.jena.riot.lang.LangEngine.raiseException(LangEngine.java:148)
	at org.apache.jena.riot.lang.LangEngine.exceptionDirect(LangEngine.java:143)
	at org.apache.jena.riot.lang.LangEngine.exception(LangEngine.java:137)
	at org.apache.jena.riot.lang.LangTurtleBase.triplesSameSubject(LangTurtleBase.java:239)
	at org.apache.jena.riot.lang.LangTurtle.oneTopLevelElement(LangTurtle.java:46)
	at org.apache.jena.riot.lang.LangTurtleBase.runParser(LangTurtleBase.java:91)
	at org.apache.jena.riot.lang.LangBase.parse(LangBase.java:41)
	at org.apache.jena.riot.RDFParserRegistry$ReaderRIOTLang.read(RDFParserRegistry.java:206)
	at org.apache.jena.riot.RDFParser.read(RDFParser.java:338)
	at org.apache.jena.riot.RDFParser.parseNotUri(RDFParser.java:324)
	at org.apache.jena.riot.RDFParser.parse(RDFParser.java:273)
	at org.apache.jena.riot.RDFParserBuilder.parse(RDFParserBuilder.java:498)
	at org.apache.jena.riot.RDFDataMgr.parseFromReader(RDFDataMgr.java:880)
	at org.apache.jena.riot.RDFDataMgr.read(RDFDataMgr.java:298)
	at org.apache.jena.riot.RDFDataMgr.read(RDFDataMgr.java:283)
	at org.apache.jena.riot.adapters.RDFReaderRIOT.read(RDFReaderRIOT.java:62)
	at org.apache.jena.rdf.model.impl.ModelCom.read(ModelCom.java:298)
	at org.acoli.conll.rdf.Format2RDF.conll2model(Format2RDF.java:235)
	at org.acoli.conll.rdf.CoNLL2RDF.conll2model(CoNLL2RDF.java:39)
	at org.acoli.conll.rdf.CoNLLStreamExtractor.processSentenceStream(CoNLLStreamExtractor.java:139)
	at org.acoli.conll.rdf.CoNLLStreamExtractor.main(CoNLLStreamExtractor.java:405)
18:41:59 INFO  Format2RDF           :: while processing the following input:
<code>
PREFIX nif: <http://persistence.uni-leipzig.org/nlp2rdf/ontologies/nif-core#>
PREFIX conll: <http://ufal.mff.cuni.cz/conll2009-st/task-description.html#>
PREFIX x: <http://purl.org/acoli/conll-rdf/xml#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX terms: <http://purl.org/acoli/open-ie/>
PREFIX powla: <http://purl.org/powla/powla.owl#>
PREFIX : <http://example.com>
:s1_0 a nif:Sentence.
:s1_1 a nif:Word; conll:ID "1"; conll:WORD "Although"; conll:HEAD :s1_6; conll:EDGE "mark"; nif:nextWord :s1_2.
:s1_2 a nif:Word; conll:ID "2"; conll:WORD "data"; conll:HEAD :s1_6; conll:EDGE "nsubj"; nif:nextWord :s1_3.
:s1_3 a nif:Word; conll:ID "3"; conll:WORD "in"; conll:HEAD :s1_2; conll:EDGE "prep"; nif:nextWord :s1_4.
:s1_4 a nif:Word; conll:ID "4"; conll:WORD "this"; conll:HEAD :s1_5; conll:EDGE "det"; nif:nextWord :s1_5.
:s1_5 a nif:Word; conll:ID "5"; conll:WORD "project"; conll:HEAD :s1_3; conll:EDGE "pobj"; nif:nextWord :s1_6.
:s1_6 a nif:Word; conll:ID "6"; conll:WORD "are"; conll:HEAD :s1_24; conll:EDGE "advcl"; nif:nextWord :s1_7.
:s1_7 a nif:Word; conll:ID "7"; conll:WORD "de"; conll:HEAD :s1_8; conll:EDGE "dep"; nif:nextWord :s1_8.
:s1_8 a nif:Word; conll:ID "8"; conll:HEAD :s1_9; conll:EDGE "dep"; nif:nextWord :s1_9.
:s1_9 a nif:Word; conll:ID "9"; conll:WORD "identified"; conll:HEAD :s1_12; conll:EDGE "amod"; conll:SRL "identified"; nif:nextWord :s1_10.
:s1_10 a nif:Word; conll:ID "10"; conll:WORD ","; conll:HEAD :s1_12; conll:EDGE "punct"; nif:nextWord :s1_11.
:s1_11 a nif:Word; conll:ID "11"; conll:WORD "certain"; conll:HEAD :s1_12; conll:EDGE "amod"; nif:nextWord :s1_12.
:s1_12 a nif:Word; conll:ID "12"; conll:WORD "information"; conll:HEAD :s1_24; conll:EDGE "nsubjpass"; nif:nextWord :s1_13.
:s1_13 a nif:Word; conll:ID "13"; conll:WORD "such"; conll:HEAD :s1_14; conll:EDGE "amod"; nif:nextWord :s1_14.
:s1_14 a nif:Word; conll:ID "14"; conll:WORD "as"; conll:HEAD :s1_12; conll:EDGE "prep"; nif:nextWord :s1_15.
:s1_15 a nif:Word; conll:ID "15"; conll:WORD "the"; conll:HEAD :s1_16; conll:EDGE "det"; nif:nextWord :s1_16.
:s1_16 a nif:Word; conll:ID "16"; conll:WORD "number"; conll:HEAD :s1_14; conll:EDGE "pobj"; nif:nextWord :s1_17.
:s1_17 a nif:Word; conll:ID "17"; conll:WORD "of"; conll:HEAD :s1_16; conll:EDGE "prep"; nif:nextWord :s1_18.
:s1_18 a nif:Word; conll:ID "18"; conll:WORD "ED"; conll:HEAD :s1_19; conll:EDGE "compound"; nif:nextWord :s1_19.
:s1_19 a nif:Word; conll:ID "19"; conll:WORD "visits"; conll:HEAD :s1_17; conll:EDGE "pobj"; nif:nextWord :s1_20.
:s1_20 a nif:Word; conll:ID "20"; conll:WORD "by"; conll:HEAD :s1_19; conll:EDGE "prep"; nif:nextWord :s1_21.
:s1_21 a nif:Word; conll:ID "21"; conll:WORD "zip"; conll:HEAD :s1_22; conll:EDGE "compound"; nif:nextWord :s1_22.
:s1_22 a nif:Word; conll:ID "22"; conll:WORD "code"; conll:HEAD :s1_20; conll:EDGE "pobj"; nif:nextWord :s1_23.
:s1_23 a nif:Word; conll:ID "23"; conll:WORD "were"; conll:HEAD :s1_24; conll:EDGE "auxpass"; nif:nextWord :s1_24.
:s1_24 a nif:Word; conll:ID "24"; conll:WORD "considered"; conll:HEAD :s1_0; conll:EDGE "ROOT"; conll:SRL "considered"; nif:nextWord :s1_25.
:s1_25 a nif:Word; conll:ID "25"; conll:WORD "proprietary"; conll:HEAD :s1_26; conll:EDGE "amod"; nif:nextWord :s1_26.
:s1_26 a nif:Word; conll:ID "26"; conll:WORD "information"; conll:HEAD :s1_24; conll:EDGE "oprd"; nif:nextWord :s1_27.
:s1_27 a nif:Word; conll:ID "27"; conll:WORD "by"; conll:HEAD :s1_26; conll:EDGE "prep"; nif:nextWord :s1_28.
:s1_28 a nif:Word; conll:ID "28"; conll:WORD "some"; conll:HEAD :s1_30; conll:EDGE "det"; nif:nextWord :s1_29.
:s1_29 a nif:Word; conll:ID "29"; conll:WORD "health"; conll:HEAD :s1_30; conll:EDGE "compound"; nif:nextWord :s1_30.
:s1_30 a nif:Word; conll:ID "30"; conll:WORD "systems"; conll:HEAD :s1_27; conll:EDGE "pobj"; nif:nextWord :s1_31.
:s1_31 a nif:Word; conll:ID "31"; conll:WORD "."; conll:HEAD :s1_24; conll:EDGE "punct".
:s1_9 conll:ARG0 :s1_7.
:s1_9 conll:V :s1_8.
:s1_24 conll:ARGM-MNR :s1_7.
:s1_24 conll:V :s1_9.
_TMP_SRL_2 conll:ARG0 :s1_27.
_TMP_SRL_2 conll:ARG0 :s1_28.
_TMP_SRL_2 conll:ARG0 :s1_29.
_TMP_SRL_2 conll:ARG0 :s1_30.
_TMP_SRL_2 conll:ARG1 :s1_25.
_TMP_SRL_2 conll:ARG1 :s1_26.
_TMP_SRL_2 conll:ARGM-ADV :s1_1.
_TMP_SRL_2 conll:ARGM-ADV :s1_2.
_TMP_SRL_2 conll:ARGM-ADV :s1_3.
_TMP_SRL_2 conll:ARGM-ADV :s1_4.
_TMP_SRL_2 conll:ARGM-ADV :s1_5.
_TMP_SRL_2 conll:ARGM-ADV :s1_6.
_TMP_SRL_2 conll:ARGM-ADV :s1_7.
_TMP_SRL_2 conll:ARGM-ADV :s1_8.
_TMP_SRL_2 conll:ARGM-ADV :s1_9.
_TMP_SRL_2 conll:V :s1_24.

</code>