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@rossmounce
rossmounce / trythis
Created Feb 11, 2014
Content Negotiation, example of Internal Server Error
View trythis
curl -g --location --header 'Accept: application/x-bibtex' "http://dx.doi.org/10.1651/0278-0372(2005)025[0159:GR]2.0.CO;2" > test.txt
RETURNS
<h1>Internal Server Error</h1>
(I've encountered about 91 DOIs that appear to give this error)
View gist:9f514d330ac2092200c7
I know I'm doing all types of wrong here:
Source HTML file here: http://mdpi.com/1420-3049/19/4/5150/htm
I want the text for the dc.source:
Molecules 2014, Vol. 19, Pages 5150-5162
Am using beautiful soup, so probably best to do it in that BUT it should also be regex-able. I can do this in bash no problem!
@rossmounce
rossmounce / reply1.txt
Last active Aug 29, 2015
Reply to Rod Page (having technical problems posting this at PeerJ PrePrints)
View reply1.txt
Thanks for your feedback Rod. I really value it.
I don't pretend to have all the answers. All of the academic content discovery
services are fairly murky about how they actually index things,
as I'm sure you know (Google Scholar perhaps being the most open-ish about how it does things?).
> how comparable are PLoS and Zootaxa from the perspective of search engines?
I am not a search engine. I am a human researcher. Whether a paper is
published in Nature, Science, PLOS ONE or Zootaxa, it is the same to me -
View sample.csv
We can make this file beautiful and searchable if this error is corrected: It looks like row 2 should actually have 34 columns, instead of 6. in line 1.
img1,Actinokineospora_fastidiosa,Amycolatopsis_alba_DSM_44262,Amycolatopsis_albidoflavus,Amycolatopsis_azurea,Amycolatopsis_balhimycina,Amycolatopsis_benzoatilytica,Amycolatopsis_coloradensis,Amycolatopsis_decaplanina_DSM_44594,Amycolatopsis_echigonensis,Amycolatopsis_kentuckyensis,Amycolatopsis_keratiniphila,Amycolatopsis_keratiniphila_subsp._nogabecina,Amycolatopsis_lexingtonensis,Amycolatopsis_lurida,Amycolatopsis_marina,Amycolatopsis_mediterranei,Amycolatopsis_methanolica_239,Amycolatopsis_nigrescens_CSC17Ta-90,Amycolatopsis_orientalis,Amycolatopsis_palatopharyngis,Amycolatopsis_plumensis,Amycolatopsis_regifaucium,Amycolatopsis_rifamycinica,Amycolatopsis_rubida,Amycolatopsis_saalfeldensis,Amycolatopsis_sacchari,Amycolatopsis_sp.,Amycolatopsis_sulphurea,Amycolatopsis_taiwanensis,Amycolatopsis_thermoflava_N1165,Amycolatopsis_tolypomycina,Amycolatopsis_vancoresmycina,Prauserella_rugosa
img2,Antarctobacter_heliothermus,Donghicola_eburneus,Jannaschia_helgolandensis,Ketogulonicigenium_vulgare,Loktanella_salsila
@rossmounce
rossmounce / data_err.csv
Created May 23, 2015
csvclean data.csv ; 70 errors logged to data_err.csv 13666 rows were joined/reduced to 6628 rows after eliminating expected internal line breaks.
View data_err.csv
line_number msg _id _full_text occurrenceID catalogNumber scientificName scientificNameAuthorship typeStatus locality country waterBody expedition recordedBy collectionCode kingdom phylum class order family genus subgenus specificEpithet infraspecificEpithet higherClassification taxonRank stateProvince continent island islandGroup higherGeography habitat decimalLongitude decimalLatitude geodeticDatum georeferenceProtocol maxError verbatimLongitude verbatimLatitude minimumElevationInMeters maximumElevationInMeters minimumDepthInMeters maximumDepthInMeters recordNumber individualCount lifeStage sex preparations identifiedBy dateIdentified identificationQualifier eventTime day month year earliestEonOrLowestEonothem latestEonOrHighestEonothem earliestEraOrLowestErathem latestEraOrHighestErathem earliestPeriodOrLowestSystem latestPeriodOrHighestSystem earliestEpochOrLowestSeries latestEpochOrHighestSeries earliestAgeOrLowestStage latestAgeOrHighestStage lowestBiostratigraphicZone highestBiostratigraphicZone group
@rossmounce
rossmounce / rsbl-suppdata
Created Jun 19, 2015
All supplementary data files for Biology Letters papers (Royal Society)
View rsbl-suppdata
http://rsbl.royalsocietypublishing.org/content/suppl/2008/12/08/2.1.101.DC1/rsbl20050379supp1.avi
http://rsbl.royalsocietypublishing.org/content/suppl/2008/12/08/2.1.101.DC1/rsbl20050379supp2.avi
http://rsbl.royalsocietypublishing.org/content/suppl/2008/12/08/2.1.113.DC1/rsbl20050374supp.pdf
http://rsbl.royalsocietypublishing.org/content/suppl/2008/12/08/2.1.116.DC1/rsbl20050406supp.pdf
http://rsbl.royalsocietypublishing.org/content/suppl/2008/12/08/2.1.125.DC1/rsbl20050378supp1.pdf
http://rsbl.royalsocietypublishing.org/content/suppl/2008/12/08/2.1.128.DC1/rsbl20050386supp.pdf
http://rsbl.royalsocietypublishing.org/content/suppl/2008/12/08/2.1.131.DC1/rsbl20050388supp.pdf
http://rsbl.royalsocietypublishing.org/content/suppl/2008/12/08/2.1.140.DC1/rsbl20050390supp.pdf
http://rsbl.royalsocietypublishing.org/content/suppl/2008/12/08/2.1.148.DC1/rsbl20050397supp.pdf
http://rsbl.royalsocietypublishing.org/content/suppl/2008/12/08/2.1.152.DC1/rsbl20050401supp.pdf
@rossmounce
rossmounce / asciitrees.tre
Last active Aug 29, 2015
example data for STK2 bug report
View asciitrees.tre
(((((EU379932:195.0,EU840722:135.0)NT1.25:86.0,EU840723:301.0)NT1.17:131.0,(NC_000853:251.0,NC_000918:364.0)NT1.15:106.0)NT1.5:12.0,(NC_009525:223.0,NC_004307:333.0)NT1.19:158.0)NT1.2:10.0,((NC_010571:441.0,(((Desulfo:295.0,((((ES:140.0,U32697:164.0)NT1.28:63.0,NC_OO2516:165.0)NT1.22:24.0,(NC_002929:183.0,NC_002946:185.0)NT1.26:55.0)NT1.21:78.0,(NC_009667:186.0,NC_002696:194.0)NT1.23:105.0)NT1.14:56.0)NT1.10:21.0,(NC_001218:279.0,NC_002967:302.0)NT1.16:107.0)NT1.8:8.0,((AEO15924:189.0,NC_003228:191.0)NT1.27:187.0,NC_OO2932:343.0)NT1.12:55.0)NT1.6:11.0,NC_005027:497.0)NT1.3:6.0,((NC_006576:348.0,(AJ307978:124.0,AJ307974:167.0)NT1.24:205.0)NT1.7:12.0,(NC_000912:484.0,((M94261:260.0,NC_010376:320.0)NT1.13:33.0,((Lactoba:157.0,NC_009785:181.0)NT1.20:21.0,NC_00964:152.0)NT1.18:91.0)NT1.11:22.0)NT1.9:32.0)NT1.4:11.0)NT1.1:9.0)NT1.60;
(((AACO7677:305.0,AAD36645:324.0)NT1.5:25.0,DU723069:293.0)NT1.2:11.0,(BAD79413:350.0,((ABY33776:363.0,(((((AAGO7791:238.0,(NP_285794:178.0,ABROO457:214.0)NT1.22:53.0)NT1.20:37.0,(AAW8
View error log
Apache Maven 3.0.5
Maven home: /usr/share/maven
Java version: 1.7.0_79, vendor: Oracle Corporation
Java home: /usr/lib/jvm/java-7-openjdk-amd64/jre
Default locale: en_GB, platform encoding: UTF-8
OS name: "linux", version: "3.19.0-25-generic", arch: "amd64", family: "unix"
[INFO] Error stacktraces are turned on.
[DEBUG] Reading global settings from /usr/share/maven/conf/settings.xml
[DEBUG] Reading user settings from /home/ross/.m2/settings.xml
[DEBUG] Using local repository at /home/ross/.m2/repository
@rossmounce
rossmounce / table.tsv
Last active Aug 29, 2015
Larger batch 2015-08-21
View table.tsv
We can make this file beautiful and searchable if this error is corrected: It looks like row 2 should actually have 1 column, instead of 6. in line 1.
FileName TipsInFile EmptyTips ExactMatchEGIDs SpacesInParentheses noEGID
02565-0-001 16 7 9 0 7
025668-0-000 12 2 7 3 2
025668-0-001 12 2 0 0 12
02567-0-000 21 21 0 0 21
025700-0-000 0 0 0 0 0
025718-0-000 30 7 18 5 8
025742-0-001 26 1 23 1 1
02576-0-000 21 0 0 0 21
02576-0-001 17 1 13 3 1
@rossmounce
rossmounce / log.log
Created Aug 21, 2015
mvn clean install (of latest code from pmr github)
View log.log
Apache Maven 3.0.5
Maven home: /usr/share/maven
Java version: 1.7.0_79, vendor: Oracle Corporation
Java home: /usr/lib/jvm/java-7-openjdk-amd64/jre
Default locale: en_GB, platform encoding: UTF-8
OS name: "linux", version: "3.19.0-26-generic", arch: "amd64", family: "unix"
[INFO] Error stacktraces are turned on.
[DEBUG] Reading global settings from /usr/share/maven/conf/settings.xml
[DEBUG] Reading user settings from /home/ross/.m2/settings.xml
[DEBUG] Using local repository at /home/ross/.m2/repository
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