Commands dump from project 16h-c03. 2016-08-17 23:33 UTC+2 larsw@debian:~/public_html/cm-repo$ mkdir data larsw@debian:~/public_html/cm-repo$ cd data/ larsw@debian:~/public_html/cm-repo/data$ mkdir "0" larsw@debian:~/public_html/cm-repo/data$ cd 0/ larsw@debian:~/public_html/cm-repo/data/0$ cd ../../ larsw@debian:~/public_html/cm-repo$ mkdir commands larsw@debian:~/public_html/cm-repo$ cd commands/ larsw@debian:~/public_html/cm-repo/commands$ nano 16h-c.txt 2016-08-18 02:32 UTC+2 larsw@debian:~$ cd public_html/cm-repo/data/0/ larsw@debian:~/public_html/cm-repo/data/0$ getpapers --api eupmc -q Pinus -n info: Searching using eupmc API info: Running in no-execute mode, so nothing will be downloaded info: Found 3951 open access results larsw@debian:~/public_html/cm-repo/data/0$ getpapers --api eupmc -q Pinus -o . -k 200 -x info: Searching using eupmc API info: Found 3951 open access results info: Limiting to 200 hits Retrieving results [==============================] 100% (eta 0.0s) info: Done collecting results 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 "PMC4967841" was not Open Access (therefore no XML) warn: Article with pmcid "PMC4114966" was not Open Access (therefore no XML) info: Got XML URLs for 198 out of 200 results info: Downloading fulltext XML files Downloading files [==============================] 100% (198/198) [11.0s elapsed, eta 0.0] info: All downloads succeeded! larsw@debian:~/public_html/cm-repo/data/0$ ls -l | grep -c ^d 200 larsw@debian:~/public_html/cm-repo/data/0$ getpapers --api eupmc -q Abies -n info: Searching using eupmc API info: Running in no-execute mode, so nothing will be downloaded info: Found 1715 open access results larsw@debian:~/public_html/cm-repo/data/0$ getpapers --api eupmc -q Abies -o . -k 200 -x info: Searching using eupmc API info: Found 1715 open access results info: Limiting to 200 hits Retrieving results [==============================] 100% (eta 0.0s) info: Done collecting results 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 "PMC4963410" was not Open Access (therefore no XML) info: Got XML URLs for 199 out of 200 results info: Downloading fulltext XML files Downloading files [==============================] 100% (199/199) [11.3s elapsed, eta 0.0] info: All downloads succeeded! larsw@debian:~/public_html/cm-repo/data/0$ rm -r ./* larsw@debian:~/public_html/cm-repo/data/0$ getpapers --api eupmc -q 'Abies OR Pinus OR Picea' -n info: Searching using eupmc API info: Running in no-execute mode, so nothing will be downloaded info: Found 1366009 open access results larsw@debian:~/public_html/cm-repo/data/0$ getpapers --api eupmc -q 'Abies OR Pinus OR Picea' -o . -k 250 -x info: Searching using eupmc API info: Found 1366009 open access results info: Limiting to 250 hits Retrieving results [==============================] 100% (eta 0.0s) info: Done collecting results 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 "PMC4963410" was not Open Access (therefore no XML) info: Got XML URLs for 249 out of 250 results info: Downloading fulltext XML files Downloading files [==============================] 100% (249/249) [13.3s elapsed, eta 0.0] info: All downloads succeeded! larsw@debian:~/public_html/cm-repo/data/0$ norma --project . -i fulltext.xml -o scholarly.html --transform nlm2html .....UNKNOWN: sec-meta: Taxon classificationAnimaliaColeopteraCurculionidae UNKNOWN: sec-meta: Taxon classificationAnimaliaColeopteraCurculionidae UNKNOWN: sec-meta: Taxon classificationAnimaliaColeopteraCurculionidae UNKNOWN: sec-meta: Taxon classificationAnimaliaColeopteraCurculionidae UNKNOWN: sec-meta: Taxon classificationAnimaliaColeopteraCurculionidae UNKNOWN: sec-meta: Taxon classificationAnimaliaColeopteraCurculionidae UNKNOWN: sec-meta: Taxon classificationAnimaliaColeopteraCurculionidae UNKNOWN: sec-meta: Taxon classificationAnimaliaColeopteraCurculionidae UNKNOWN: sec-meta: Taxon classificationAnimaliaColeopteraCurculionidae UNKNOWN: sec-meta: Taxon classificationAnimaliaColeopteraCurculionidae UNKNOWN: sec-meta: Taxon classificationAnimaliaColeopteraCurculionidae UNKNOWN: sec-meta: Taxon classificationAnimaliaColeopteraCurculionidae UNKNOWN: sec-meta: Taxon classificationAnimaliaColeopteraCurculionidae UNKNOWN: sec-meta: Taxon classificationAnimaliaColeopteraCurculionidae UNKNOWN: sec-meta: Taxon classificationAnimaliaColeopteraCurculionidae UNKNOWN: sec-meta: Taxon classificationAnimaliaColeopteraCurculionidae UNKNOWN: sec-meta: Taxon classificationAnimaliaColeopteraCurculionidae UNKNOWN: sec-meta: Taxon classificationAnimaliaColeopteraCurculionidae UNKNOWN: sec-meta: Taxon classificationAnimaliaColeopteraCurculionidae UNKNOWN: sec-meta: Taxon classificationAnimaliaColeopteraCurculionidae UNKNOWN: sec-meta: Taxon classificationAnimaliaColeopteraCurculionidae UNKNOWN: sec-meta: Taxon classificationAnimaliaColeopteraCurculionidae UNKNOWN: sec-meta: Taxon classificationAnimaliaColeopteraCurculionidae UNKNOWN: sec-meta: Taxon classificationAnimaliaColeopteraCurculionidae UNKNOWN: sec-meta: Taxon classificationAnimaliaColeopteraCurculionidae UNKNOWN: sec-meta: Taxon classificationAnimaliaColeopteraCurculionidae UNKNOWN: page-range: 24–26 UNKNOWN: page-range: 48 UNKNOWN: page-range: 50 ..UNKNOWN: sec-meta: Taxon classificationAnimaliaColeopteraBostrichidae UNKNOWN: sec-meta: Taxon classificationAnimaliaColeopteraBostrichidae UNKNOWN: sec-meta: Taxon classificationAnimaliaColeopteraBostrichidae UNKNOWN: sec-meta: Taxon classificationAnimaliaColeopteraBostrichidae UNKNOWN: sec-meta: Taxon classificationAnimaliaColeopteraBostrichidae UNKNOWN: sec-meta: Taxon classificationAnimaliaColeopteraBostrichidae UNKNOWN: sec-meta: Taxon classificationAnimaliaColeopteraBostrichidae UNKNOWN: sec-meta: Taxon classificationAnimaliaColeopteraBostrichidae UNKNOWN: sec-meta: Taxon classificationAnimaliaColeopteraBostrichidae UNKNOWN: sec-meta: Taxon classificationAnimaliaColeopteraBostrichidae UNKNOWN: volume-series: sezione 1 UNKNOWN: volume-series: 2 UNKNOWN: overline: STAR UNKNOWN: overline: STAR UNKNOWN: overline: STAR UNKNOWN: overline: STAR UNKNOWN: overline: STAR UNKNOWN: overline: STAR UNKNOWN: overline: STAR UNKNOWN: overline: STAR UNKNOWN: overline: STAR UNKNOWN: overline: STAR UNKNOWN: overline: STAR ..UNKNOWN: sec-meta: Taxon classificationAnimaliaJulidaJulidae UNKNOWN: sec-meta: Taxon classificationAnimaliaJulidaJulidae UNKNOWN: sec-meta: Taxon classificationAnimaliaJulidaJulidae UNKNOWN: sec-meta: Taxon classificationAnimaliaJulidaJulidae UNKNOWN: sec-meta: Taxon classificationAnimaliaJulidaNemasomatidae UNKNOWN: sec-meta: Taxon classificationAnimaliaChordeumatidaDiplomaragnidae UNKNOWN: sec-meta: Taxon classificationAnimaliaChordeumatidaDiplomaragnidae UNKNOWN: sec-meta: Taxon classificationAnimaliaChordeumatidaDiplomaragnidae UNKNOWN: sec-meta: Taxon classificationAnimaliaChordeumatidaDiplomaragnidae UNKNOWN: sec-meta: Taxon classificationAnimaliaChordeumatidaDiplomaragnidae UNKNOWN: sec-meta: Taxon classificationAnimaliaChordeumatidaAnthroleucosomatidae UNKNOWN: sec-meta: Taxon classificationAnimaliaChordeumatidaAnthroleucosomatidae UNKNOWN: sec-meta: Taxon classificationAnimaliaChordeumatidaAltajellidae UNKNOWN: sec-meta: Taxon classificationAnimaliaPolydesmidaPolydesmidae UNKNOWN: sec-meta: Taxon classificationAnimaliaPolydesmidaPolydesmidae ..UNKNOWN: sec-meta: Taxon classificationPlantaeApialesApiaceae .UNKNOWN: textual-form: PLOSS = Stock-PC30 − Stock-P UNKNOWN: textual-form: Stock-PC30 = CPc × BDc × 30 ÷ 10 UNKNOWN: textual-form: Stock-P = Stock-PO + Stock-PAC30 UNKNOWN: textual-form: Stock-PO = CPo × BDo × Do ÷ 10 UNKNOWN: textual-form: Stock-PAC30 = (CPA × BDA × DA + CPC × BDC × (30 − DA)) ÷ 10 .UNKNOWN: mmultiscripts: Δ13 UNKNOWN: mprescripts: UNKNOWN: none: .UNKNOWN: page-range: 219–243, 245–258 ....UNKNOWN: nlm-citation: SaleemMNazirMAliMSHussainHLeeYSRiazNAntimicrobial natural products: an update on future antibiotic drug candidatesNat Prod Rep20102723825420111803 UNKNOWN: nlm-citation: RiosJLRecioMCMedicinal plants and antimicrobial activityJ Ethnopharmacol2005100808415964727 UNKNOWN: nlm-citation: DominMAHighly virulent pathogens-a post antibiotic eraBr J Theatre Nurs?1998814189677888 UNKNOWN: nlm-citation: CowanMMPlant products as antimicrobial agentsClin Microbiol Rev19991256458210515903 UNKNOWN: nlm-citation: Hames-KocabasEEYesil-SeliktasOIsletenMVardar-SukanFAntimicrobial activity of pine bark extract and assesment of potential application in cooked red meatGida200833123127 UNKNOWN: nlm-citation: HosseinzadehHKhooeiARKhashayarmaneshZMotamed-ShariatyVAntiurolithiatic activity of Pinus eldarica medw: fruits aqueous extract in ratsUrol J2010723223721170851 UNKNOWN: nlm-citation: Fallah HuseiniHMehrzadiSGhaznaviHTajallizadehkhoobYFakhrzadehHEffects of Pinus eldarica Medw. Nut extract on blood glucose and cholesterol levels in hypercholesterolemic alloxan-induced diabetic ratsJ Med Plant201316874 UNKNOWN: nlm-citation: BolandghamatSMoghimiAIranshahiMEffects of ethanolic extract of pine needles (Pinus eldarica Medw.) on reserpine-induced depression-like behavior in male Wistar ratsPharmacogn Mag2011724825321969797 UNKNOWN: nlm-citation: ZolfaghariBIravaniSEssential oil constituents of the bark of Pinus pinaster from IranJ Essent Oil Bear Pl201215348351 UNKNOWN: nlm-citation: LeeJHYangHYLeeHSHongSKChemical composition and antimicrobial activity of essential oil from cones of Pinus koraiensisJ Microbiol Biotechnol20081849750218388468 UNKNOWN: nlm-citation: VigoECepedaAGualilloOPerez-FernandezRIn vitro anti-inflammatory activity of Pinus sylvestris and Plantago lanceolata extracts: effect on inducible NOS, COX-1, COX-2 and their products in J774A.1 murine macrophagesJ Pharm Pharmacol20055738339115807995 UNKNOWN: nlm-citation: TorrasMACFauraCASchonlauFRohdewaldPAntimicrobial activity of Pycnogenol®Phytother Res20051964764816161029 UNKNOWN: nlm-citation: LodhiaMHBhattKRThakerVSAntibacterial activity of essential oils from palmarosa, evening primrose, lavender and tuberoseIndian J Pharm Sci20097113413620336210 UNKNOWN: nlm-citation: GolshaniZDawoodiVAnti-Pseudomonal activity of leaf extracts of Myrtaceae plants against B-lactamase-producing strainsZahedan J Res Med Sci2014163337 UNKNOWN: nlm-citation: IravaniSZolfaghariBPhytochemical analysis of Pinus eldarica barkRes Pharm Sci2014924325025657795 UNKNOWN: nlm-citation: ZellaguiAGherrafNLadjelSHameurlaineSChemical composition and antibacterial activity of the essential oils from Launaea resedifolia LOrg Med Chem Lett201222422373506 UNKNOWN: nlm-citation: AronsonNESandersJWMoranKAIn harm's way: infections in deployed American military forcesClin Infect Dis2006431045105116983619 UNKNOWN: nlm-citation: KoehnkeAFriedrichREAntibiotic Discovery in the age of structural biology - a comprehensive overview with special reference to development of drugs for the treatment of Pseudomonas aeruginosa infectionIn Vivo20152916116725792642 UNKNOWN: nlm-citation: PotronAPoirelLNordmannPEmerging broad-spectrum resistance in Pseudomonas aeruginosa and Acinetobacter baumannii: Mechanisms and epidemiologyInt J Antimicrob Agents20152456858525857949 UNKNOWN: nlm-citation: Abi-AyadMAbi-AyadFZLazzouniHARebiahiSAAntibacterial activity of Pinus halepensis essential oil from Algeria(Tlemcen)J Nat Prod Plant Resour201113336 UNKNOWN: nlm-citation: AhnJGruIUMustaphaAEffects of plant extracts on microbial growth, color change, and lipid oxidation in cooked beefFood Microbiol20072471416943089 UNKNOWN: nlm-citation: HammerKACarsonCFRileyTVAntimicrobial activity of essential oils and other plant extractsJ Appl Microbiol19998698599010438227 UNKNOWN: nlm-citation: ApetreiCLTuchilusCAprotosoaieACOpreaAMalterudKEMironAChemical, antioxidant and antimicrobial investigations of Pinus cembra L. bark and needlesMolecules2011167773778822143542 UNKNOWN: nlm-citation: IravaniSZolfaghariBGreen synthesis of silver nanoparticles using Pinus eldarica bark extractBiomed Res Int 20132013ID 639725 UNKNOWN: nlm-citation: LiYYFengJZhangXLCuiYYPine bark extracts: nutraceutical, pharmacological, and toxicological evaluationJ Pharmacol Exp Ther201535391625597308 UNKNOWN: nlm-citation: KotanRKordaliSCakirAScreening of antibacterial activities of twenty-one oxygenated monoterpenesZ Naturforsch C20076250751317913064 UNKNOWN: nlm-citation: Rivas da SilvaACLopesPMBarros de AzevedoMMCostaDCAlvianoCSAlvianoDSBiological activities of alpha-pinene and beta-pinene enantiomersMolecules2012176305631622634841 UNKNOWN: nlm-citation: TrombettaDCastelliFSarpietroMGVenutiVCristaniMDanieleCMechanisms of antibacterial action of three monoterpenesAntimicrob Agents Chemother2005492474247815917549 UNKNOWN: nlm-citation: DolaraPCorteBGhelardiniCPuglieseAMCerbaiEMenichettiSLocal anaesthetic, antibacterial and antifungal properties of sesquiterpenes from myrrhPlanta Med20006635635810865454 UNKNOWN: nlm-citation: InoueYShiraishiAHadaTHiroseKHamashimaHShimadaJThe antibacterial effects of terpene alcohols on Staphylococcus aureus and their mode of actionFEMS Microbiol Lett200423732533115321680 UNKNOWN: nlm-citation: FengSZengWLuoFZhaoJYangZSunQAntibacterial activity of organic acids in aqueous extracts from pine needles (Pinus massoniana Lamb)Food Sci Biotechnol2010193541 UNKNOWN: nlm-citation: PoliteoOSkocibusicMMaravicARuscicMMilosMChemical composition and antimicrobial activity of the essential oil of endemic Dalmatian black pine (Pinus nigra ssp. dalmatica)Chem Biodivers2011854054721404437 UNKNOWN: nlm-citation: Nasrollahzadeh-SabetMTabaei-AghdaeiSImaniAInvestigate the antibacterial effect of black pine essence (Pinus nigra) against the bacteria E. coli, Staphylococcus aureus and Enterococcus faecalis in three province of Ardabil, Gilan and TehranEurop J Zoologic Res201327681 UNKNOWN: nlm-citation: SakagamiHYoshiharaMFujimakiMWadaCKomatsuNNakashimaHEffect of pine seed shell extract on microbial and viral infectionIn Vivo1992613161627738 UNKNOWN: nlm-citation: ZulqarnainRahimAAhmadKUllahFUllahHNishanUIn vitro antibacterial activity of selected medicinal plants from lower HimalayasPak J Pharm Sci20152858158725730791 UNKNOWN: nlm-citation: Oh-HaraTSakagamiHFKawazoeYFKaiyaTFKomatsuNFOhsawaNFAntimicrobial spectrum of lignin-related pine cone extracts of Pinus parviflora Sieb. et ZuccIn Vivo199047122129479 UNKNOWN: nlm-citation: SonibareOOOlakunleKChemical composition and antibacterial activity of the essential oil of Pinus caribaea from NigeriaAfr J Biotechnol2008724622464 .UNKNOWN: sec-meta: Taxon classificationAnimaliaColeopteraAnthribidae UNKNOWN: sec-meta: Taxon classificationAnimaliaColeopteraAnthribidae UNKNOWN: sec-meta: Taxon classificationAnimaliaColeopteraAnthribidae UNKNOWN: sec-meta: Taxon classificationAnimaliaColeopteraNemonychidae UNKNOWN: sec-meta: Taxon classificationAnimaliaColeopteraBrentidae UNKNOWN: sec-meta: Taxon classificationAnimaliaColeopteraBrachyceridae UNKNOWN: sec-meta: Taxon classificationAnimaliaColeopteraCurculionidae UNKNOWN: sec-meta: Taxon classificationAnimaliaColeopteraCurculionidae UNKNOWN: sec-meta: Taxon classificationAnimaliaColeopteraCurculionidae UNKNOWN: sec-meta: Taxon classificationAnimaliaColeopteraCurculionidae UNKNOWN: sec-meta: Taxon classificationAnimaliaColeopteraCurculionidae UNKNOWN: sec-meta: Taxon classificationAnimaliaColeopteraCurculionidae UNKNOWN: sec-meta: Taxon classificationAnimaliaColeopteraCurculionidae UNKNOWN: sec-meta: Taxon classificationAnimaliaColeopteraCurculionidae UNKNOWN: sec-meta: Taxon classificationAnimaliaColeopteraCurculionidae UNKNOWN: sec-meta: Taxon classificationAnimaliaColeopteraCurculionidae UNKNOWN: sec-meta: Taxon classificationAnimaliaColeopteraCurculionidae UNKNOWN: sec-meta: Taxon classificationAnimaliaColeopteraCurculionidae UNKNOWN: sec-meta: Taxon classificationAnimaliaColeopteraCurculionidae UNKNOWN: sec-meta: Taxon classificationAnimaliaColeopteraCurculionidae UNKNOWN: sec-meta: Taxon classificationAnimaliaColeopteraCurculionidae UNKNOWN: sec-meta: Taxon classificationAnimaliaColeopteraCurculionidae UNKNOWN: sec-meta: Taxon classificationAnimaliaColeopteraCurculionidae UNKNOWN: sec-meta: Taxon classificationAnimaliaColeopteraCurculionidae UNKNOWN: sec-meta: Taxon classificationAnimaliaColeopteraCurculionidae UNKNOWN: sec-meta: Taxon classificationAnimaliaColeopteraCurculionidae UNKNOWN: sec-meta: Taxon classificationAnimaliaColeopteraCurculionidae UNKNOWN: sec-meta: Taxon classificationAnimaliaColeopteraCurculionidae UNKNOWN: sec-meta: Taxon classificationAnimaliaColeopteraCurculionidae UNKNOWN: sec-meta: Taxon classificationAnimaliaColeopteraCurculionidae UNKNOWN: sec-meta: Taxon classificationAnimaliaColeopteraCurculionidae UNKNOWN: sec-meta: Taxon classificationAnimaliaColeopteraCurculionidae .UNKNOWN: alt-text: Table ...UNKNOWN: sec-meta: Taxon classificationAnimaliaColeopteraGyrinidae UNKNOWN: sec-meta: Taxon classificationAnimaliaColeopteraGyrinidae UNKNOWN: sec-meta: Taxon classificationAnimaliaColeopteraGyrinidae UNKNOWN: sec-meta: Taxon classificationAnimaliaColeopteraHaliplidae UNKNOWN: sec-meta: Taxon classificationAnimaliaColeopteraDytiscidae UNKNOWN: sec-meta: Taxon classificationAnimaliaColeopteraDytiscidae UNKNOWN: sec-meta: Taxon classificationAnimaliaColeopteraDytiscidae UNKNOWN: sec-meta: Taxon classificationAnimaliaColeopteraDytiscidae UNKNOWN: sec-meta: Taxon classificationAnimaliaColeopteraDytiscidae UNKNOWN: sec-meta: Taxon classificationAnimaliaColeopteraDytiscidae UNKNOWN: sec-meta: Taxon classificationAnimaliaColeopteraDytiscidae UNKNOWN: sec-meta: Taxon classificationAnimaliaColeopteraDytiscidae UNKNOWN: sec-meta: Taxon classificationAnimaliaColeopteraDytiscidae UNKNOWN: sec-meta: Taxon classificationAnimaliaColeopteraDytiscidae UNKNOWN: sec-meta: Taxon classificationAnimaliaColeopteraDytiscidae UNKNOWN: sec-meta: Taxon classificationAnimaliaColeopteraDytiscidae UNKNOWN: sec-meta: Taxon classificationAnimaliaColeopteraDytiscidae UNKNOWN: sec-meta: Taxon classificationAnimaliaColeopteraDytiscidae UNKNOWN: sec-meta: Taxon classificationAnimaliaColeopteraDytiscidae UNKNOWN: sec-meta: Taxon classificationAnimaliaColeopteraDytiscidae UNKNOWN: sec-meta: Taxon classificationAnimaliaColeopteraDytiscidae UNKNOWN: sec-meta: Taxon classificationAnimaliaColeopteraDytiscidae UNKNOWN: sec-meta: Taxon classificationAnimaliaColeopteraDytiscidae UNKNOWN: sec-meta: Taxon classificationAnimaliaColeopteraDytiscidae UNKNOWN: sec-meta: Taxon classificationAnimaliaColeopteraDytiscidae UNKNOWN: sec-meta: Taxon classificationAnimaliaColeopteraDytiscidae UNKNOWN: sec-meta: Taxon classificationAnimaliaColeopteraDytiscidae UNKNOWN: sec-meta: Taxon classificationAnimaliaColeopteraDytiscidae UNKNOWN: sec-meta: Taxon classificationAnimaliaColeopteraDytiscidae UNKNOWN: sec-meta: Taxon classificationAnimaliaColeopteraDytiscidae UNKNOWN: sec-meta: Taxon classificationAnimaliaColeopteraDytiscidae UNKNOWN: alt-text: Table ..!UNKNOWN: array: LSClarge single copySSCsmall single copyIRinverted repeatMLmaximum likelihood larsw@debian:~/public_html/cm-repo/data/0$ ami2-species --project . -i scholarly.html --sp.species --sp.type genus .......................... larsw@debian:~/public_html/cm-repo/data/0$ ami2-species --project . -i scholarly.html --sp.species --sp.type binomial .......................... larsw@debian:~/public_html/cm-repo/data/0$ ami2-species --project . -i scholarly.html --sp.species --sp.type genussp .......................... larsw@debian:~/public_html/cm-repo/data/0$ ami2-gene --project . -i scholarly.html --g.gene --g.type human .......................... larsw@debian:~/public_html/cm-repo/data/0ami2-word --project . --w.words wordFrequencies --w.stopwords ~/public_html/cm-repo/Interview_task/stopwords.txt 0 [main] WARN org.xmlcml.ami2.wordutil.WordSetWrapper - Cannot read stopword stream: /home/larsw/public_html/cm-repo/Interview_task/stopwords.txt .........................47526 [main] WARN org.xmlcml.ami2.plugins.word.WordCollectionFactory - No scholarlyHtml or PDFTXT: ./PMC4963410 !47526 [main] WARN org.xmlcml.ami2.plugins.word.WordCollectionFactory - no words found to extract !47719 [main] WARN org.xmlcml.ami2.plugins.word.WordCollectionFactory - No scholarlyHtml or PDFTXT: ./target !47719 [main] WARN org.xmlcml.ami2.plugins.word.WordCollectionFactory - no words found to extract !.47720 [main] WARN org.xmlcml.ami2.plugins.word.WordCollectionFactory - No scholarlyHtml or PDFTXT: ./ursus !47720 [main] WARN org.xmlcml.ami2.plugins.word.WordCollectionFactory - no words found to extract ! larsw@debian:~/public_html/cm-repo/data/0$ 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 .........................36389 [main] WARN org.xmlcml.ami2.plugins.word.WordCollectionFactory - No scholarlyHtml or PDFTXT: ./PMC4963410 !36389 [main] WARN org.xmlcml.ami2.plugins.word.WordCollectionFactory - no words found to extract !36548 [main] WARN org.xmlcml.ami2.plugins.word.WordCollectionFactory - No scholarlyHtml or PDFTXT: ./target !36548 [main] WARN org.xmlcml.ami2.plugins.word.WordCollectionFactory - no words found to extract !.36549 [main] WARN org.xmlcml.ami2.plugins.word.WordCollectionFactory - No scholarlyHtml or PDFTXT: ./ursus !36549 [main] WARN org.xmlcml.ami2.plugins.word.WordCollectionFactory - no words found to extract larsw@debian:~/public_html/cm-repo/data/0$ ami2-sequence --project . --filter file\(\*\*/results.xml\) -o sequencesfiles.xml ......................... larsw@debian:~/public_html/cm-repo/data/0$ ls -l | grep -c ^d 250 larsw@debian:~/public_html/cm-repo/data/0$ find */results/species/genus/results.xml | wc -l 170 larsw@debian:~/public_html/cm-repo/data/0$ find */results/species/genussp/results.xml | wc -l 68 larsw@debian:~/public_html/cm-repo/data/0$ find */results/species/binomial/results.xml | wc -l 244 larsw@debian:~/public_html/cm-repo/data/0$ find */results/gene/human/results.xml | wc -l 54 larsw@debian:~/public_html/cm-repo/data/0$ find */results/word/frequencies/results.xml | wc -l 249 2016-08-21 03:44 UTC+2 larsw@debian:~/public_html/cm-repo$ node js/jsonMaker_0.js -p data/0/ -o data -f data.json -v debug 76: [DEBUG] data/0/ data data.json DEBUG 132: [INFO ] Saving output to ./data/data.json 136: [INFO ] Saving output succeeded! larsw@debian:~/public_html/cm-repo$ node js/jsonMaker_0.js -p data/0/ -o data -f data.json -v debug 77: [INFO ] Parsing CTree project in folder: data/0/ 78: [INFO ] Outputting to folder: data 79: [INFO ] Outputting to file: data.json 178: [INFO ] Saving output to ./data/data.json 180: [INFO ] Saving output succeeded!