contentmine / ami Goto Github PK

Apache Maven 3.3.3 (7994120775791599e205a5524ec3e0dfe41d4a06; 2015-04-22T12:57:37+01:00)
Maven home: /usr/share/maven-bin-3.3
Java version: 1.8.0_51, vendor: Oracle Corporation
Java home: /opt/oracle-jdk-bin-1.8.0.51/jre
Default locale: en_GB, platform encoding: UTF-8
OS name: "linux", version: "4.0.5-gentoo", arch: "amd64", family: "unix"

Failed tests:   testIdentifier(org.xmlcml.ami2.TutorialTest): results assertion failure: starts with: <results title="bio.ena"><result pre="an usher protein family domain (PFA" exact="M00577" post=") and/or flanking chaperone (PF00345, PF02753 or C" xpath="/*[local-name()='html'][1]/*[local-name()='body'][1]/*[local-name()='div'][1]/*[local-name()='div'][6]/*[local-name()='div'][1]/*[local-name()='p
  testGeneDictionary(org.xmlcml.ami2.plugins.gene.GeneArgProcessorTest): results assertion failure: starts with: <results title="hgnc" />

$ getpapers -V
0.4.14

$ norma --version
norma(0.3.1)
norma(0.3.1)

$ ami2-regex --version
regex(null)
regex(null)

# (from the 0.2.24 .deb release)

$ mkdir tmp
$ getpapers -q PMCID:PMC4833924 -x -o tmp
$ norma -p . -i fulltext.xml -o scholarly.html --transform nlm2html

<compoundRegex title="jrc">
  <regex fields="jrc">NM[-]?\d\d\d</regex>
</compoundRegex>

$ ami2-regex --project tmp --context 25 25 -i scholarly.html --r.regex regex.xml
$ more tmp/PMC4833924/results/regex/jrc/results.xml | wc -l
94

$ ami2-regex --project tmp --context 0 0 -i scholarly.html --r.regex regex.xml
$ more tmp/PMC4833924/results/regex/jrc/results.xml | wc -l
115

$ ami2-regex --project tmp --context 256721 256721 -i scholarly.html --r.regex regex.xml
$ more tmp/PMC4833924/results/regex/jrc/results.xml | wc -l
50 # note that there's text wrapping happening here too

euclid
svg
html
imageanalysis
pdf2svg
svg2xml

<?xml version="1.0" encoding="UTF-8"?>
<results title="human">
 <result pre="Tgfb3, Cdk1 and Ccna2 with known functions in cell growth and proliferation, and " 
    exact="P53"
    post=", Tnfsf10 and Prkar2b genes in regulation of cell death, see Supplement"
    xpath="/html[1]/body[1]/div[2]/div[3]/div[12]/p[1]"
    dictionary="hgnc"
    dictionaryCheck="false"
    name="human"/>
 <result pre="R as previously described 58. Goose glyceraldehyde-3-phosphate dehydrogenase gene ( "
    exact="GAPDH"
    post=") gene was used as an internal control. The primer sequences of the genes were listed in &lt;a href=&quot;#"
    name="human"/>
</results>

[ERROR] Failed to execute goal on project ami2: Could not resolve dependencies for project org.xml-cml:ami2:jar:0.3.0: Failed to collect dependencies for [org.xml-cml:norma:jar:0.3.0 (compile), org.xml-cml:diagramanalyzer:jar:0.1-SNAPSHOT (compile), org.apache.lucene:lucene-core:jar:4.10.3 (compile), org.apache.lucene:lucene-analyzers-common:jar:4.10.3 (compile), com.google.guava:guava:jar:18.0 (compile), junit:junit:jar:4.11 (test), blogspot.software-and-algorithms:stern-library:jar:0.1 (compile), org.vafer:jdeb:jar:1.3 (provided), com.jayway.jsonpath:json-path:jar:2.0.0 (compile), com.univocity:univocity-parsers:jar:1.5.6 (compile)]: Failed to read artifact descriptor for org.xml-cml:norma:jar:0.3.0: Could not transfer artifact org.xml-cml:norma:pom:0.3.0 from/to ebi-repo (http://www.ebi.ac.uk/intact/maven/nexus/content/repositories/ebi-repo/): Failed to transfer file: http://www.ebi.ac.uk/intact/maven/nexus/content/repositories/ebi-repo/org/xml-cml/norma/0.3.0/norma-0.3.0.pom. Return code is: 500 , ReasonPhrase:Internal Server Error. -> [Help 1]

$ getpapers -V
0.4.14

$ norma --version
norma(0.3.1)
norma(0.3.1)

$ ami2-regex --version
regex(null)
regex(null)

# (from the 0.2.24 .deb release)

$ mkdir tmp
$ getpapers -q PMCID:PMC4833924 -x -o tmp
$ norma -p . -i fulltext.xml -o scholarly.html --transform nlm2html
$ ami2-regex --project tmp --context 25 25 -i scholarly.html --r.regex regex.xml

<compoundRegex title="jrc">
  <regex fields="jrc">NM[-]?\d\d\d</regex>
</compoundRegex>

<?xml version="1.0" encoding="UTF-8"?>
<results title="jrc">
 <result pre=" 7 April 2016). Since Ag " name0="jrc" value0="NM-300" post="K was provided as dispers" xpath="/html[1]/body[1]/div[2]/div[5]/p[3]"/>
 <result pre="ispersant alone, i.e. Ag " name0="jrc" value0="NM-300" post="K DIS, was assessed (NM-x" xpath="/html[1]/body[1]/div[2]/div[5]/p[3]"/>
...
 <result pre="as. The dispersant of Ag " name0="jrc" value0="NM-300" post="K alone (that does not co" xpath="/html[1]/body[1]/div[2]/div[5]/p[3]"/>
 <result pre="e’ in the BCOP assay; Ag " name0="jrc" value0="NM-300" post="K DIS was assessed as ‘no"/>
</results>

1225 [main] DEBUG org.xmlcml.ami2.plugins.regex.RegexComponent  - Unusual fieldList: [food, supply] in dinosaurfood; found: <regex weight="1.0" fields="food supply">(.{0,50})(([Ff]ood)\s(supply))\s+(.{0,50})</regex>
11409 [main] ERROR org.xmlcml.ami2.plugins.MatcherResult  - groupList (5; [t. Nevertheless, we are aware that parental care, , food supply, food, supply, and the allocation of available energy to growth a]) does not match fieldList (2;[food, supply])

1164 [main] DEBUG org.xmlcml.ami2.plugins.regex.RegexComponent  - Unusual fieldList: [food, supply] in dinosaurfood; found: <regex weight="1.0" fields="food supply">(.{0,50})([Ff]ood)\s(supply)\s+(.{0,50})</regex>
10386 [main] ERROR org.xmlcml.ami2.plugins.MatcherResult  - groupList (4; [t. Nevertheless, we are aware that parental care, , food, supply, and the allocation of available energy to growth a]) does not match fieldList (2;[food, supply])

1211 [main] DEBUG org.xmlcml.ami2.plugins.regex.RegexComponent  - Unusual fieldList: [foodsupply, food, supply] in dinosaurfood; found: <regex weight="1.0" fields="foodsupply food supply">(.{0,50})(([Ff]ood)\s(supply))\s+(.{0,50})</regex>
11297 [main] ERROR org.xmlcml.ami2.plugins.MatcherResult  - groupList (5; [t. Nevertheless, we are aware that parental care, , food supply, food, supply, and the allocation of available energy to growth a]) does not match fieldList (3;[foodsupply, food, supply])

1222 [main] DEBUG org.xmlcml.ami2.plugins.regex.RegexComponent  - Unusual fieldList: [foodsupply, food, supply] in dinosaurfood; found: <regex weight="1.0" fields="foodsupply food supply">(.{0,0})(([Ff]ood)\s(supply))\s+(.{0,0})</regex>
8086 [main] ERROR org.xmlcml.ami2.plugins.MatcherResult  - groupList (5; [, food supply, food, supply, ]) does not match fieldList (3;[foodsupply, food, supply])

[ERROR] /home/travis/build/ContentMine/ami-plugin/src/main/java/org/xmlcml/ami2/plugins/phylotree/PhyloTreeArgProcessor.java:[80,17] cannot find symbol
  symbol:   method CORE_LOG()
  location: class org.xmlcml.ami2.plugins.phylotree.PhyloTreeArgProcessor
[ERROR] /home/travis/build/ContentMine/ami-plugin/src/main/java/org/xmlcml/ami2/plugins/phylotree/PhyloTreeArgProcessor.java:[130,27] cannot find symbol
  symbol:   method CORE_LOG()
  location: class org.xmlcml.ami2.plugins.phylotree.PhyloTreeArgProcessor
[ERROR] /home/travis/build/ContentMine/ami-plugin/src/main/java/org/xmlcml/ami2/plugins/ResultsAnalysis.java:[249,31] cannot find symbol
  symbol:   method setColumnHeadingList(java.util.List<org.xmlcml.cmine.util.CellRenderer>)
  location: variable dataTablesTool of type org.xmlcml.cmine.util.DataTablesTool
[ERROR] /home/travis/build/ContentMine/ami-plugin/src/main/java/org/xmlcml/ami2/plugins/CommandProcessor.java:[147,41] cannot find symbol
  symbol:   variable columnHeadingList
  location: variable dataTablesTool of type org.xmlcml.cmine.util.DataTablesTool
[ERROR] /home/travis/build/ContentMine/ami-plugin/src/main/java/org/xmlcml/ami2/plugins/CommandProcessor.java:[149,56] cannot find symbol
  symbol:   variable columnHeadingList
  location: variable dataTablesTool of type org.xmlcml.cmine.util.DataTablesTool

<results title="binomial">
 <result pre="ntimicrobial activity (assessed on " exact="Vibrio harveyi" match="Vibrio harveyi" post=" cultures) was limited in both H an" name="binomial"/>
 <result pre="ia genus Vibrio, including; " exact="V. harveyi" match="Vibrio harveyi" post=" [ 14], V. mediterranei [ 7]" name="binomial"/>
 <result pre="ncluding; V. harveyi [ 14], " exact="V. mediterranei" match="Vibrio mediterranei" post=" [ 7], V. owensii [ 15] and " name="binomial"/>
 <result pre=" 14], V. mediterranei [ 7], " exact="V. owensii" match="Vibrio owensii" post=" [ 15] and V. coralliilyticus&lt;/i" name="binomial"/>
 <result pre=" [ 7], V. owensii [ 15] and " exact="V. coralliilyticus" match="Vibrio coralliilyticus" post=" [ 10]. Furthermore, Piskorska, Smi" name="binomial"/>
 <result pre="Smith [ 7], reports an increase in " exact="V. mediterranei" match="Vibrio mediterranei" post=" in the mucus of WS-affected Ech" name="binomial"/>
 <result pre="ei in the mucus of WS-affected " exact="Echinopora lamellosa" match="Echinopora lamellosa" post=", compared to healthy samples. Howe" name="binomial"/>
 <result pre="iated with healthy and WS-affected " exact="E. lamellosa" match="Echinopora lamellosa" post=", an approach that can lead to phyl" name="binomial"/>
 <result pre="ve a dominant presence in diseased " exact="A. muricata" match="A. muricata" post=" samples in a study screening the m" name="binomial"/>
 <result pre="Sweet and Bythell [ 18] also found " exact="V. harveyi" match="Vibrio harveyi" post=" to increase in diseased samples, b" name="binomial"/>
 <result pre=" healthy samples does not rule out " exact="V. harveyi" match="Vibrio harveyi" post=" as a primary causal agent in WS, a" name="binomial"/>
 <result pre="ated from WS-affected specimens of " exact="Acropora muricata" match="Acropora muricata" post=" and shown to be able to ingest the" name="binomial"/>
 <result pre="te community associated with WS in " exact="E. lamellosa" match="Echinopora lamellosa" post=" and their roles in disease aetiolo" name="binomial"/>
 <result pre="iated with healthy and WS-affected " exact="E. lamellosa" match="Echinopora lamellosa" post=" in aquaria, using culture-independ" name="binomial"/>
 <result pre="ciliate communities of WS-affected " exact="E. lamellosa" match="Echinopora lamellosa" post=" was analysed to determine the effi" name="binomial"/>
 <result pre="ealthy and White Syndrome-affected " exact="Echinopora lamellosa" match="Echinopora lamellosa" post=" fragments (donated by the Horniman" name="binomial"/>
 <result pre="mining the causal agent/s of WS in " exact="Echinopora lamellosa" match="Echinopora lamellosa" post=" through a process of elimination. " name="binomial"/>
 <result pre="WSU) and treated WS-affected (WST) " exact="E. lamellosa" match="Echinopora lamellosa" post=" samples, n = 3 H, n = 3 ST, n = 3 " name="binomial"/>
 <result pre="apparently healthy and WS-affected " exact="E. lamellosa" match="Echinopora lamellosa" post=" samples. Each tissue sample was tr" name="binomial"/>
 <result pre="Pure cultures of " exact="Vibrio harveyi" match="Vibrio harveyi" post=", a bacterial species heavily consi" name="binomial"/>
 <result pre="viously housed WS-affected corals. " exact="V. harveyi" match="Vibrio harveyi" post=" was isolated using thiosulfate-cit" name="binomial"/>
 <result pre="triplicate control for uninhibited " exact="V. harveyi" match="Vibrio harveyi" post=" growth (97.5 μl Mueller Hinton Bro" name="binomial"/>
 <result pre=" Mueller Hinton Broth + 97.5 μl of " exact="V. harveyi" match="Vibrio harveyi" post=" culture), a triplicate control for" name="binomial"/>
 <result pre=" MHB + 5 μl 100% ethanol + 97.5 μl " exact="V. harveyi" match="Vibrio harveyi" post=" culture) and a triplicate of each " name="binomial"/>
 <result pre=" + 5 μl coral extract + 97.5 μl of " exact="V. harveyi" match="Vibrio harveyi" post="). Using 5 μl coral extract in a 20" name="binomial"/>
 <result pre="tely equal, bacterial abundance in " exact="E. lamellosa" match="Echinopora lamellosa" post=" samples was compared across all sa" name="binomial"/>
 <result pre="nstead to determine differences in " exact="Vibrio harveyi" match="Vibrio harveyi" post=" growth inhibition between coral sa" name="binomial"/>
 <result pre="drome (WS) and treated WS-affected " exact="Echinopora lamellosa" match="Echinopora lamellosa" post=" samples (based on DGGE band matchi" name="binomial"/>
 <result pre=" to their association with healthy " exact="E. lamellosa" match="Echinopora lamellosa" post=" samples, these bacteria were consi" name="binomial"/>
 <result pre="ated White Syndrome-affected (WST) " exact="Echinopora lamellosa" match="Echinopora lamellosa" post=" samples. Error bars represent SE. " name="binomial"/>
 <result pre="ies in all white syndrome-affected " exact="E. lamellosa" match="Echinopora lamellosa" post=" samples (treated and untreated), w" name="binomial"/>
 <result pre="3). Ciliates C1 (97% similarity to " exact="Cohnilembus verminus" match="Cohnilembus verminus" post=") and C3 (99% similarity to Pseu" name="binomial"/>
 <result pre="ound to be most closely related to " exact="Philaster digitformis" match="Philaster digitformis" post=" Morph 3 ( Fig. 6), a ciliate isola" name="binomial"/>
 <result pre="4 is proposed to be a new morph of " exact="P. digitformis" match="Philaster digitformis" post=", designated as Morph 4. Morph 4 di" name="binomial"/>
 <result pre="445 bases. C2 (98% similarity with " exact="Loxophyllum rostratum" match="Loxophyllum rostratum" post=") is only represented in two WSU an" name="binomial"/>
 <result pre="el [ 40] with an opalinid protist; " exact="Opalina ranarum" match="Opalina ranarum" post=" (AF141970) as the outgroup, as use" name="binomial"/>
 <result pre="samples of the scleractinian coral " exact="Echinopora lamellosa" match="Echinopora lamellosa" post=", whilst also determining WS-associ" name="binomial"/>
 <result pre="6S rRNA) diversity associated with " exact="E. lamellosa" match="Echinopora lamellosa" post=" was found to increase between heal" name="binomial"/>
 <result pre=" being absent in healthy samples). " exact="Tenacibaculum maritimum" match="Tenacibaculum maritimum" post=" has previously been shown to be as" name="binomial"/>
 <result pre="iofilm on the coral surface [ 43]. " exact="T. maritimum" match="Tenacibaculum maritimum" post=" has also been shown to be responsi" name="binomial"/>
 <result pre="and tumour-affected soft tissue in " exact="Echinopora lamellosa" match="Echinopora lamellosa" post=", which often subsequently became a" name="binomial"/>
 <result pre="ecently been associated with WS in " exact="Acropora cervicornis" match="Acropora cervicornis" post=" [ 46]. Interestingly, the ribotype" name="binomial"/>
 <result pre="usly been found in associated with " exact="Oculina patagonica" match="Oculina patagonica" post=", from which isolates showed antimi" name="binomial"/>
 <result pre="action against the coral pathogens " exact="Vibrio shiloi" match="Vibrio shiloi" post=", V. coralliilyticus and " name="binomial"/>
 <result pre="al pathogens Vibrio shiloi, " exact="V. coralliilyticus" match="Vibrio coralliilyticus" post=" and Thalassomonas loyana [ " name="binomial"/>
 <result pre="/i&gt;, V. coralliilyticus and " exact="Thalassomonas loyana" match="Thalassomonas loyana" post=" [ 22]. It could therefore be expec" name="binomial"/>
 <result pre="owever, was found to be present in " exact="E. lamellosa" match="Echinopora lamellosa" post=" samples treated with the antibioti" name="binomial"/>
 <result pre=", previously proposed WS pathogen) " exact="Vibrio harveyi" match="Vibrio harveyi" post=". This could suggest that antimicro" name="binomial"/>
 <result pre="althy and diseased specimens, with " exact="E. lamellosa" match="Echinopora lamellosa" post=" appearing to have a naturally very" name="binomial"/>
 <result pre="ted antimicrobial capacity against " exact="Vibrio harveyi" match="Vibrio harveyi" post=". This could suggest that not all c" name="binomial"/>
 <result pre="ggest that not all corals, such as " exact="Echinopora lamellosa" match="Echinopora lamellosa" post=", possess such antimicrobial qualit" name="binomial"/>
 <result pre=" [ 60– 62] and it is possible that " exact="E. lamellosa" match="Echinopora lamellosa" post=" features antimicrobial properties " name="binomial"/>
 <result pre="perties that do not select against " exact="Vibrio harveyi" match="Vibrio harveyi" post=". To understand the overall antimic" name="binomial"/>
 <result pre="robial capacity and selectivity of " exact="E. lamellosa" match="Echinopora lamellosa" post=" (and other species), future antimi" name="binomial"/>
 <result pre="iliates were identified in healthy " exact="E. lamellosa" match="Echinopora lamellosa" post=" samples, thus making this the firs" name="binomial"/>
 <result pre="iates with WS in the plating coral " exact="E. lamellosa" match="Echinopora lamellosa" post=". A Philaster sp was also fo" name="binomial"/>
 <result pre="e of another Philaster sp ( " exact="P. lucinda" match="Philaster lucinda" post=") in WBD and WS [ 46, 63]. It was o" name="binomial"/>
 <result pre="ued. This promotes the theory that " exact="P. lucinda" match="Philaster lucinda" post=" is a secondary agent in WBD, which" name="binomial"/>
 <result pre="ate being found in all WS-affected " exact="E. lamellosa" match="Echinopora lamellosa" post=" samples in the present study. C" name="binomial"/>
 <result pre="es between healthy and WS-affected " exact="E. lamellosa" match="Echinopora lamellosa" post=". Given its association with the fo" name="binomial"/>
 <result pre="n formation and tissue necrosis in " exact="Echinopora lamellosa" match="Echinopora lamellosa" post=". Since this bacterium has not been" name="binomial"/>
</results>

<compoundRegex title="jrc">
    <regex fields="jrc">NM[-]?\d\d\d[K]?</regex>
</compoundRegex>

    {
      "pre": " OECD reference material ",
      "name0": "jrc",
      "value0": "NM-300",
      "post": "K; nano-AgB 5–50 nm) on t",
      "pmc": "PMC3841577"
    },

running: word([frequencies])[{xpath:@count>20}, {w.stopwords:pmcstop.txt stopwords.txt}]
WS: XXXXX  .............................!!.................................................................................!!...............................!!.................................................................................................Exception in thread "main" java.lang.OutOfMemoryError: GC overhead limit exceeded
    at nu.xom.ParentNode.checkCapacity(Unknown Source)
    at nu.xom.ParentNode.fastInsertChild(Unknown Source)
    at nu.xom.NonVerifyingHandler.startElement(Unknown Source)
    at org.apache.xerces.parsers.AbstractSAXParser.startElement(Unknown Source)
    at org.apache.xerces.impl.XMLNamespaceBinder.handleStartElement(Unknown Source)
    at org.apache.xerces.impl.XMLNamespaceBinder.startElement(Unknown Source)
    at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanStartElement(Unknown Source)
    at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$FragmentContentDispatcher.dispatch(Unknown Source)
    at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source)
    at org.apache.xerces.parsers.DTDConfiguration.parse(Unknown Source)
    at org.apache.xerces.parsers.DTDConfiguration.parse(Unknown Source)
    at org.apache.xerces.parsers.XMLParser.parse(Unknown Source)
    at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source)
    at nu.xom.Builder.build(Unknown Source)
    at nu.xom.Builder.build(Unknown Source)
    at org.xmlcml.xml.XMLUtil.parseXML(XMLUtil.java:366)
    at org.xmlcml.html.HtmlFactory.parseToXHTML(HtmlFactory.java:701)
    at org.xmlcml.html.HtmlFactory.parse(HtmlFactory.java:646)
    at org.xmlcml.html.HtmlFactory.parse(HtmlFactory.java:623)
    at org.xmlcml.cmine.args.DefaultArgProcessor.getScholarlyHtmlElement(DefaultArgProcessor.java:1176)
    at org.xmlcml.cmine.files.CTree.ensureScholarlyHtmlElement(CTree.java:947)
    at org.xmlcml.cmine.args.DefaultArgProcessor.extractPSectionElements(DefaultArgProcessor.java:1159)
    at org.xmlcml.ami2.plugins.AMIArgProcessor.ensureSectionElements(AMIArgProcessor.java:191)
    at org.xmlcml.ami2.plugins.AMIArgProcessor.runRunMethodsOnChosenArgOptions(AMIArgProcessor.java:162)
    at org.xmlcml.cmine.args.DefaultArgProcessor.runAndOutput(DefaultArgProcessor.java:1100)
    at org.xmlcml.ami2.plugins.word.WordPluginOption.run(WordPluginOption.java:46)
    at org.xmlcml.ami2.plugins.CommandProcessor.runCommands(CommandProcessor.java:86)
    at org.xmlcml.ami2.plugins.CommandProcessor.processCommands(CommandProcessor.java:60)
    at org.xmlcml.ami2.plugins.CommandProcessor.main(CommandProcessor.java:176)
cmine XXXXX  3597,93s user 13,90s system 403% cpu 14:54,94 total

tom@pisces newstack % ami-plugin/target/appassembler/bin/ami2-species --project ./zika -i scholarly.html --sp.species --context 35 --sp.type binomial genus 
java.lang.RuntimeException: invoke runExtractSpecies fails
        at org.xmlcml.cmine.args.DefaultArgProcessor.instantiateAndRunMethod(DefaultArgProcessor.java:873)
        at org.xmlcml.cmine.args.DefaultArgProcessor.runMethodsOfType(DefaultArgProcessor.java:768)
        at org.xmlcml.cmine.args.DefaultArgProcessor.runRunMethodsOnChosenArgOptions(DefaultArgProcessor.java:749)
        at org.xmlcml.ami2.plugins.AMIArgProcessor.runRunMethodsOnChosenArgOptions(AMIArgProcessor.java:176)
        at org.xmlcml.cmine.args.DefaultArgProcessor.runAndOutput(DefaultArgProcessor.java:929)
        at org.xmlcml.ami2.plugins.species.SpeciesPlugin.main(SpeciesPlugin.java:36)
Caused by: java.lang.reflect.InvocationTargetException
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:497)
        at org.xmlcml.cmine.args.DefaultArgProcessor.instantiateAndRunMethod(DefaultArgProcessor.java:871)
        ... 5 more
Caused by: java.lang.NullPointerException
        at org.xmlcml.ami2.dictionary.DefaultAMIDictionary.contains(DefaultAMIDictionary.java:112)
        at org.xmlcml.ami2.plugins.AMISearcher.markFalsePositives(AMISearcher.java:380)
        at org.xmlcml.ami2.plugins.AMISearcher.search(AMISearcher.java:284)
        at org.xmlcml.ami2.plugins.AMIArgProcessor.searchSectionElements(AMIArgProcessor.java:298)
        at org.xmlcml.ami2.plugins.species.SpeciesArgProcessor.runExtractSpecies(SpeciesArgProcessor.java:57)
        ... 10 more
java.lang.RuntimeException: invoke runExtractSpecies fails
        at org.xmlcml.cmine.args.DefaultArgProcessor.instantiateAndRunMethod(DefaultArgProcessor.java:873)
        at org.xmlcml.cmine.args.DefaultArgProcessor.runMethodsOfType(DefaultArgProcessor.java:768)
        at org.xmlcml.cmine.args.DefaultArgProcessor.runRunMethodsOnChosenArgOptions(DefaultArgProcessor.java:749)
        at org.xmlcml.ami2.plugins.AMIArgProcessor.runRunMethodsOnChosenArgOptions(AMIArgProcessor.java:176)
        at org.xmlcml.cmine.args.DefaultArgProcessor.runAndOutput(DefaultArgProcessor.java:929)
        at org.xmlcml.ami2.plugins.species.SpeciesPlugin.main(SpeciesPlugin.java:36)
Caused by: java.lang.reflect.InvocationTargetException
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:497)
        at org.xmlcml.cmine.args.DefaultArgProcessor.instantiateAndRunMethod(DefaultArgProcessor.java:871)
        ... 5 more
Caused by: java.lang.NullPointerException
        at org.xmlcml.ami2.dictionary.DefaultAMIDictionary.contains(DefaultAMIDictionary.java:112)
        at org.xmlcml.ami2.plugins.AMISearcher.markFalsePositives(AMISearcher.java:380)
        at org.xmlcml.ami2.plugins.AMISearcher.search(AMISearcher.java:284)
        at org.xmlcml.ami2.plugins.AMIArgProcessor.searchSectionElements(AMIArgProcessor.java:298)
        at org.xmlcml.ami2.plugins.species.SpeciesArgProcessor.runExtractSpecies(SpeciesArgProcessor.java:57)
        ... 10 more
java.lang.RuntimeException: invoke runExtractSpecies fails
        at org.xmlcml.cmine.args.DefaultArgProcessor.instantiateAndRunMethod(DefaultArgProcessor.java:873)
        at org.xmlcml.cmine.args.DefaultArgProcessor.runMethodsOfType(DefaultArgProcessor.java:768)
        at org.xmlcml.cmine.args.DefaultArgProcessor.runRunMethodsOnChosenArgOptions(DefaultArgProcessor.java:749)
        at org.xmlcml.ami2.plugins.AMIArgProcessor.runRunMethodsOnChosenArgOptions(AMIArgProcessor.java:176)
        at org.xmlcml.cmine.args.DefaultArgProcessor.runAndOutput(DefaultArgProcessor.java:929)
        at org.xmlcml.ami2.plugins.species.SpeciesPlugin.main(SpeciesPlugin.java:36)
Caused by: java.lang.reflect.InvocationTargetException
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:497)
        at org.xmlcml.cmine.args.DefaultArgProcessor.instantiateAndRunMethod(DefaultArgProcessor.java:871)
        ... 5 more
Caused by: java.lang.NullPointerException
        at org.xmlcml.ami2.dictionary.DefaultAMIDictionary.contains(DefaultAMIDictionary.java:112)
        at org.xmlcml.ami2.plugins.AMISearcher.markFalsePositives(AMISearcher.java:380)
        at org.xmlcml.ami2.plugins.AMISearcher.search(AMISearcher.java:284)
        at org.xmlcml.ami2.plugins.AMIArgProcessor.searchSectionElements(AMIArgProcessor.java:298)
        at org.xmlcml.ami2.plugins.species.SpeciesArgProcessor.runExtractSpecies(SpeciesArgProcessor.java:57)
        ... 10 more