Ross Mounce rossmounce
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rossmounce
/ trythis
Created
February 11, 2014 17:24
Content Negotiation, example of Internal Server Error
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| 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) |
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| 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
/ reply1.txt
Last active
August 29, 2015 14:12
Reply to Rod Page (having technical problems posting this at PeerJ PrePrints)
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| 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 - |
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.
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| 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
/ data_err.csv
Created
May 23, 2015 15:09
csvclean data.csv ; 70 errors logged to data_err.csv 13666 rows were joined/reduced to 6628 rows after eliminating expected internal line breaks.
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| 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
/ rsbl-suppdata
Created
June 19, 2015 14:40
All supplementary data files for Biology Letters papers (Royal Society)
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| 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 |
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| (((((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 |
rossmounce
/ error log
Created
August 18, 2015 12:14
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| 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 |
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.
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| 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
/ log.log
Created
August 21, 2015 21:32
mvn clean install (of latest code from pmr github)
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| 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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