Commands dump from project 16i-c05. 2016-09-10 01:32 UTC+2 larsw@debian:~/public_html/cm-repo$ mkdir data/1 larsw@debian:~/public_html/cm-repo$ cd data/1/ larsw@debian:~/public_html/cm-repo/data/1$ getpapers -q ABSTRACT:zika ABSTRACT:dengue ABSTRACT:spondweni -n info: Searching using eupmc API info: Running in no-execute mode, so nothing will be downloaded info: Found 139 open access results larsw@debian:~/public_html/cm-repo/data/1$ getpapers -q 'ABSTRACT:zika OR ABSTRACT:dengue OR ABSTRACT:spondweni' -n info: Searching using eupmc API info: Running in no-execute mode, so nothing will be downloaded info: Found 1373157 open access results larsw@debian:~/public_html/cm-repo/data/1$ getpapers -q 'ABSTRACT:zika OR ABSTRACT:dengue OR ABSTRACT:spondweni' -k 500 -x info: Searching using eupmc API error: No output directory given. You must provide the --outdir argument. larsw@debian:~/public_html/cm-repo/data/1$ getpapers -q 'ABSTRACT:zika OR ABSTRACT:dengue OR ABSTRACT:spondweni' -k 500 -x -o . info: Searching using eupmc API info: Found 1373157 open access results info: Limiting to 500 hits Retrieving results [==============================] 100% (eta 0.0s) info: Done collecting results info: Duplicate records found: 497 unique results identified info: Saving result metadata info: Full EUPMC result metadata written to eupmc_results.json info: Individual EUPMC result metadata records written info: Extracting fulltext HTML URL list (may not be available for all articles) info: Fulltext HTML URL list written to eupmc_fulltext_html_urls.txt warn: Article with pmcid "PMC4993616" was not Open Access (therefore no XML) warn: Article with pmcid "PMC4995799" was not Open Access (therefore no XML) warn: Article with pmcid "PMC4943480" was not Open Access (therefore no XML) info: Got XML URLs for 494 out of 497 results info: Downloading fulltext XML files Downloading files [==============================] 100% (494/494) [8.7s elapsed, eta 0.0] info: All downloads succeeded! larsw@debian:~/public_html/cm-repo/data/1$ norma --project . -i fulltext.xml -o scholarly.html --transform nlm2html ....UNKNOWN: isbn: 9241542098 UNKNOWN: isbn: 978-92-9022-387-0 ....UNKNOWN: alt-text: Table ......UNKNOWN: page-range: 3–11, 76–9 .UNKNOWN: isbn: 978-953-51-0050-8 ....UNKNOWN: issn-l: 1043-3155 .UNKNOWN: prefix: St .....UNKNOWN: preformat: ircigvsnrd 301 fvegmsggtw vdvvlehggc vtvmaqdkpt vdielvtttv snmaevrsyc yeasisdmas 361 dsrcptqgea yldkqsdtqy vckrtlvdrg wgngcglfgk gslvtcakfa cskkmtgksi 421 qpenleyrim lsvhgsqhsg mivndtghet denrakveit pnspraeatl ggfgslgldc 481 eprtgldfsd lyyltmnnkh wlvhkewfhd iplpwhagad tgtphwnnke alvefkdaha 541 krqtvvvlgs qegavhtala galeaemdga kgrlssghlk crlkmdklrl kgvsyslcta 601 aftftkipae tlhgtvtvev qyagtdgpck vpaqmavdmq tltpvgrlit anpviteste 661 nskmmleldp pfgdsyivig vgekkithhw hrsgsti ............UNKNOWN: alt-text: Image 1 ...UNKNOWN: array: BIVABioimpedance vector analysisBMIBody mass indexECFExtracellular fluidICFIntracellular fluid ..!...UNKNOWN: array: EXPO 2015Universal Exhibition 2015MBDsMosquito-borne diseasesDENVDengue virusCHIKVChikungunya virusWNVWest Nile virusCDCCentre for Disease ControlBGBiogents UNKNOWN: array: DENVDengue virusWHOWorld Health OrganizationGLMGeneralized linear modelLRMLogistic regression modelIRInfection ratesVIVector index .UNKNOWN: prefix: de UNKNOWN: prefix: van UNKNOWN: prefix: de UNKNOWN: prefix: du .UNKNOWN: alt-text: Table 2 UNKNOWN: alt-text: Table 3 UNKNOWN: alt-text: Image 1 .XREF .UNKNOWN: prefix: Prof. UNKNOWN: prefix: Dr. UNKNOWN: prefix: Dr. UNKNOWN: prefix: Dr. UNKNOWN: prefix: Dr. UNKNOWN: prefix: Dr. UNKNOWN: prefix: Dr. .!! larsw@debian:~/public_html/cm-repo/data/1$ ami2-species --project . -i scholarly.html --sp.species --sp.type genus .................................................. larsw@debian:~/public_html/cm-repo/data/1$ ami2-species --project . -i scholarly.html --sp.species --sp.type binomial .................................................. larsw@debian:~/public_html/cm-repo/data/1$ ami2-word --project . --w.words wordFrequencies --w.stopwords stopwords.txt 0 [main] DEBUG org.xmlcml.ami2.wordutil.WordSetWrapper - symbol expands to: /org/xmlcml/ami2/wordutil/stopwords.txt ..........................................47854 [main] WARN org.xmlcml.ami2.plugins.word.WordCollectionFactory - No scholarlyHtml or PDFTXT: ./PMC4943480 !47855 [main] WARN org.xmlcml.ami2.plugins.word.WordCollectionFactory - no words found to extract !........54406 [main] WARN org.xmlcml.ami2.plugins.word.WordCollectionFactory - No scholarlyHtml or PDFTXT: ./PMC4993616 !54406 [main] WARN org.xmlcml.ami2.plugins.word.WordCollectionFactory - no words found to extract !54476 [main] WARN org.xmlcml.ami2.plugins.word.WordCollectionFactory - No scholarlyHtml or PDFTXT: ./PMC4995799 !54476 [main] WARN org.xmlcml.ami2.plugins.word.WordCollectionFactory - no words found to extract !54477 [main] WARN org.xmlcml.ami2.plugins.word.WordCollectionFactory - No scholarlyHtml or PDFTXT: ./target !54477 [main] WARN org.xmlcml.ami2.plugins.word.WordCollectionFactory - no words found to extract ! larsw@debian:~/public_html/cm-repo/data/1$ ami2-sequence --project . --filter file\(\*\*/results.xml\) -o sequencesfiles.xml .................................................. larsw@debian:~/public_html/cm-repo/data/1$ node ~/public_html/ctj/ctj.js -p . -o . -c genus,binomial 116: [INFO ] Parsing CProject in folder: . 117: [INFO ] Result will be saved in folder: . 118: [INFO ] AMI results of types: genus, binomial will be saved. [==============================] Parsing directory 497/497: PMC4995799 (eta 0.0s) 248: [INFO ] Saving output... 256: [INFO ] Saving output succeeded! larsw@debian:~/public_html/cm-repo/data/1$ cd ../../ larsw@debian:~/public_html/cm-repo$ node js/c05-words.js larsw@debian:~/public_html/cm-repo$ node js/c05.js