http://git-wip-us.apache.org/repos/asf/tika/blob/38916f89/tika-parser-modules/tika-parser-scientific-module/src/test/resources/test-documents/Zamora2010.dif ---------------------------------------------------------------------- diff --git a/tika-parser-modules/tika-parser-scientific-module/src/test/resources/test-documents/Zamora2010.dif b/tika-parser-modules/tika-parser-scientific-module/src/test/resources/test-documents/Zamora2010.dif new file mode 100644 index 0000000..76c8757 --- /dev/null +++ b/tika-parser-modules/tika-parser-scientific-module/src/test/resources/test-documents/Zamora2010.dif @@ -0,0 +1,169 @@ +<?xml version="1.0" encoding="UTF-8"?> + <DIF xmlns="http://gcmd.gsfc.nasa.gov/Aboutus/xml/dif/"; xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"; xsi:schemaLocation="http://gcmd.gsfc.nasa.gov/Aboutus/xml/dif/ http://gcmd.gsfc.nasa.gov/Aboutus/xml/dif/dif_v9.8.4.xsd";> + <Entry_ID>00794186-48f9-11e3-9dcb-00c0f03d5b7c</Entry_ID> + <Entry_Title>Zamora 2010 Using Sediment Geochemistry, Particle Size Distribution and Remote Sensing to Study Provenance in the Kronebreen/Kongsvegen Glaciers, West Spitsbergen, Svalbard</Entry_Title> + + <Parameters> + <Category>EARTH SCIENCE</Category> + <Topic>PALEOCLIMATE</Topic> + <Term>OCEAN/LAKE RECORDS</Term> + <Variable_Level_1>SEDIMENTS</Variable_Level_1> + </Parameters> + <Parameters> + <Category>EARTH SCIENCE</Category> + <Topic>PALEOCLIMATE</Topic> + <Term>OCEAN/LAKE RECORDS</Term> + <Variable_Level_1>VARVE DEPOSITS</Variable_Level_1> + </Parameters> + <Parameters> + <Category>EARTH SCIENCE</Category> + <Topic>TERRESTRIAL HYDROSPHERE</Topic> + <Term>GLACIERS/ICE SHEETS</Term> + <Variable_Level_1>GLACIER MASS BALANCE/ICE SHEET MASS BALANCE</Variable_Level_1> + </Parameters> + <Parameters> + <Category>EARTH SCIENCE</Category> + <Topic>LAND SURFACE</Topic> + <Term>LAND TEMPERATURE</Term> + <Variable_Level_1>LAND SURFACE TEMPERATURE</Variable_Level_1> + </Parameters> + <Parameters> + <Category>EARTH SCIENCE</Category> + <Topic>LAND SURFACE</Topic> + <Term>EROSION/SEDIMENTATION</Term> + <Variable_Level_1>SEDIMENTS</Variable_Level_1> + </Parameters> + <Parameters> + <Category>EARTH SCIENCE</Category> + <Topic>OCEANS</Topic> + <Term>MARINE SEDIMENTS</Term> + <Variable_Level_1>TURBIDITY</Variable_Level_1> + </Parameters> + <Parameters> + <Category>EARTH SCIENCE</Category> + <Topic>LAND SURFACE</Topic> + <Term>EROSION/SEDIMENTATION</Term> + <Variable_Level_1>SEDIMENT TRANSPORT</Variable_Level_1> + </Parameters> + <Parameters> + <Category>EARTH SCIENCE</Category> + <Topic>CRYOSPHERE</Topic> + <Term>GLACIERS/ICE SHEETS</Term> + <Variable_Level_1>GLACIER MASS BALANCE/ICE SHEET MASS BALANCE</Variable_Level_1> + </Parameters> + <Parameters> + <Category>EARTH SCIENCE</Category> + <Topic>TERRESTRIAL HYDROSPHERE</Topic> + <Term>GLACIERS/ICE SHEETS</Term> + <Variable_Level_1>GLACIERS</Variable_Level_1> + </Parameters> + <Parameters> + <Category>EARTH SCIENCE</Category> + <Topic>PALEOCLIMATE</Topic> + <Term>LAND RECORDS</Term> + <Variable_Level_1>SEDIMENTS</Variable_Level_1> + </Parameters> + <Parameters> + <Category>EARTH SCIENCE</Category> + <Topic>LAND SURFACE</Topic> + <Term>EROSION/SEDIMENTATION</Term> + <Variable_Level_1>SEDIMENTATION</Variable_Level_1> + </Parameters> + <Parameters> + <Category>EARTH SCIENCE</Category> + <Topic>OCEANS</Topic> + <Term>OCEAN TEMPERATURE</Term> + <Variable_Level_1>WATER TEMPERATURE</Variable_Level_1> + </Parameters> + <Parameters> + <Category>EARTH SCIENCE</Category> + <Topic>PALEOCLIMATE</Topic> + <Term>OCEAN/LAKE RECORDS</Term> + <Variable_Level_1>LAKE LEVELS</Variable_Level_1> + </Parameters> + <Parameters> + <Category>EARTH SCIENCE</Category> + <Topic>OCEANS</Topic> + <Term>MARINE SEDIMENTS</Term> + <Variable_Level_1>SEDIMENT TRANSPORT</Variable_Level_1> + </Parameters> + <Parameters> + <Category>EARTH SCIENCE</Category> + <Topic>LAND SURFACE</Topic> + <Term>EROSION/SEDIMENTATION</Term> + <Variable_Level_1>DEGRADATION</Variable_Level_1> + </Parameters> + <Parameters> + <Category>EARTH SCIENCE</Category> + <Topic>CRYOSPHERE</Topic> + <Term>FROZEN GROUND</Term> + <Variable_Level_1>SOIL TEMPERATURE</Variable_Level_1> + </Parameters> + <Parameters> + <Category>EARTH SCIENCE</Category> + <Topic>CRYOSPHERE</Topic> + <Term>GLACIERS/ICE SHEETS</Term> + <Variable_Level_1>GLACIERS</Variable_Level_1> + </Parameters> + <Parameters> + <Category>EARTH SCIENCE</Category> + <Topic>CRYOSPHERE</Topic> + <Term>FROZEN GROUND</Term> + <Variable_Level_1>PERIGLACIAL PROCESSES</Variable_Level_1> + </Parameters> + <Parameters> + <Category>EARTH SCIENCE</Category> + <Topic>LAND SURFACE</Topic> + <Term>EROSION/SEDIMENTATION</Term> + <Variable_Level_1>ENTRAINMENT</Variable_Level_1> + </Parameters> + <Parameters> + <Category>EARTH SCIENCE</Category> + <Topic>LAND SURFACE</Topic> + <Term>EROSION/SEDIMENTATION</Term> + <Variable_Level_1>SUSPENDED SOLIDS</Variable_Level_1> + </Parameters> + + + <Spatial_Coverage> + <Southernmost_Latitude>78.833</Southernmost_Latitude> + <Northernmost_Latitude>79.016</Northernmost_Latitude> + <Westernmost_Longitude>11.64</Westernmost_Longitude> + <Easternmost_Longitude>13.34</Easternmost_Longitude> + </Spatial_Coverage> + + <Data_Center> + <Data_Center_Name> + <Short_Name>ACADIS</Short_Name> + <Long_Name>Advanced Cooperative Arctic Data and Information Service</Long_Name> + </Data_Center_Name> + <Data_Center_URL>http://www.aoncadis.org/</Data_Center_URL> + <Personnel> + <Role>DATA CENTER CONTACT</Role> + <First_Name>ACADIS</First_Name> + <Last_Name>User Services</Last_Name> + <Contact_Address> + <Address>NCAR/CISL</Address> + <Address>P.O. Box 3000</Address> + <City>Boulder</City> + <Province_or_State>CO</Province_or_State> + <Postal_Code>80307</Postal_Code> + <Country>USA</Country> + </Contact_Address> + </Personnel> + </Data_Center> + <Summary> + <Abstract>Abstract: Sediment provenance at the Kronerbreen/Kongsvegen glaciers in Spitsbergen can be used to understand the effects that climate change can have on the sedimentation in fjords, and streams at northern latitudes. These sediments are directly related to glacial processes and reflect the conditions under which they formed. Such conditions are sensitive to global climate change, which is amplified in northern latitudes, creating a unique environment for climate change research. Quantitative provenance studies have never been carried out in the Kongsfjorden before, and can provide data for a better understanding of glacial processes and dynamics, and changes in erosional conditions. Particularly, sedimentation rates and sediment grain size distribution can help unravel the glacial history of the area. This study will focus on analyzing the grain size distribution of the material being deposited by the mentioned glaciers and finding the source rock of these sed iments. Fine sediment was transported by streams and upflows identified in the field, and fed by the glaciers melting ice. On the other hand, coarser material ranging from cobble to boulder size was deposited by ice, moraines, and alluvial processes. Sediment and rock samples were collected during the months of July and August 2009, along the terminus of the glacier, and in the surrounding areas, respectively. Grain size analysis was performed on the samples using a Malvern Mastersizer with the resulting in different groups showing a change in particle size and sorting depending on the location along the glacier. This analysis is important as mineral composition and transportation is influenced by grain size. Electron microprobe studies were carried out on sediment grains to obtain a rough compositional profile of the sediments, and a first-order mineralogical make-up. The microprobe results provided us with information about composition of some of the minerals present, based on the content of Fe, Ca, K and Al derived from the erosion of the local lithologies. Chemical composition can distinguish sediments derived from different sources, and may ultimately be compared with representative rock samples taken from the moraines. Due to the limited accessibility to some areas, many geological units in the Kongsfjorden area have not been mapped or studied, limiting the possible comparisons with contributing material to the fjordâs seafloor. Remote sensing techniques were used to map lithologies in previously unmapped regions using ENVI®, and ASTER satellite imagery. A GER 3700 radiospectrometer was used to collect spectral properties of the rock samples. These properties were compared to the outcrops in the satellite imagery giving us an idea of the bedrock composition of the area. The results of our research can be compared with future studies in order to obtain information, regarding responses in the glacier dynamics and processes, related to climate change.</A bstract> + </Summary> + <Related_URL> + <URL_Content_Type> + <Type>GET DATA</Type> + </URL_Content_Type> + <URL>http://www.aoncadis.org/dataset/id/00794186-48f9-11e3-9dcb-00c0f03d5b7c.html</URL> + <Description>Data Center top-level access page for this resource</Description> + </Related_URL> + + <Metadata_Name>ACADIS IDN DIF</Metadata_Name> + <Metadata_Version>9.8.4</Metadata_Version> + <Last_DIF_Revision_Date>2015-02-05</Last_DIF_Revision_Date> + </DIF>
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codeListValue="dataset" codeSpace="005">dataset</gmd:MD_ScopeCode> + </gmd:hierarchyLevel> + + <gmd:contact> + <gmd:CI_ResponsibleParty> + <gmd:organisationName> + <gco:CharacterString>UCAR/NCAR - CISL - ACADIS</gco:CharacterString> + </gmd:organisationName> + <gmd:role> + <gmd:CI_RoleCode codeList="http://www.isotc211.org/2005/resources/Codelist/gmxCodelists.xml#CI_RoleCode"; codeListValue="resourceProvider">resourceProvider</gmd:CI_RoleCode> + </gmd:role> + </gmd:CI_ResponsibleParty> + </gmd:contact> + + <gmd:dateStamp> + <gco:DateTime>2013-12-16T13:26:08Z</gco:DateTime> + </gmd:dateStamp> + + <gmd:metadataStandardName> + <gco:CharacterString>ISO 19115 Geographic information - Metadata</gco:CharacterString> + </gmd:metadataStandardName> + + <gmd:metadataStandardVersion> + <gco:CharacterString>ISO 19115:2003(E)</gco:CharacterString> + </gmd:metadataStandardVersion> + + <gmd:dataSetURI> + <gco:CharacterString>https://www.aoncadis.org/dataset/id/4c1a919d-6690-11e3-9147-00c0f03d5b7c.iso19139</gco:CharacterString> + </gmd:dataSetURI> + + <gmd:identificationInfo> + <gmd:MD_DataIdentification> + <gmd:citation> + <gmd:CI_Citation> + <gmd:title> + <gco:CharacterString>Barrow Atqasuk ARCSS Plant</gco:CharacterString> + </gmd:title> + <gmd:date> + <gmd:CI_Date> + <gmd:date> + <gco:Date>2013-12-16</gco:Date> + </gmd:date> + <gmd:dateType> + <gmd:CI_DateTypeCode codeList="http://www.isotc211.org/2005/resources/Codelist/gmxCodelists.xml#CI_DateTypeCode"; codeListValue="creation">creation</gmd:CI_DateTypeCode> + </gmd:dateType> + </gmd:CI_Date> + </gmd:date> + <gmd:date> + <gmd:CI_Date> + <gmd:date> + <gco:Date>2015-03-11</gco:Date> + </gmd:date> + <gmd:dateType> + <gmd:CI_DateTypeCode codeList="http://www.isotc211.org/2005/resources/Codelist/gmxCodelists.xml#CI_DateTypeCode"; codeListValue="modified">modified</gmd:CI_DateTypeCode> + </gmd:dateType> + </gmd:CI_Date> + </gmd:date> + <gmd:citedResponsibleParty> + <gmd:CI_ResponsibleParty> + <gmd:individualName> + <gco:CharacterString>Robert Hollister</gco:CharacterString> + </gmd:individualName> + <gmd:contactInfo> + <gmd:CI_Contact> + <gmd:address> + <gmd:CI_Address> + <gmd:electronicMailAddress> + <gco:CharacterString>[email protected]</gco:CharacterString> + </gmd:electronicMailAddress> + </gmd:CI_Address> + </gmd:address> + </gmd:CI_Contact> + </gmd:contactInfo> + <gmd:role> + <gmd:CI_RoleCode codeList="http://www.isotc211.org/2005/resources/Codelist/gmxCodelists.xml#CI_RoleCode"; codeListValue="pointOfContact">pointOfContact</gmd:CI_RoleCode> + </gmd:role> + </gmd:CI_ResponsibleParty> + </gmd:citedResponsibleParty> + <gmd:citedResponsibleParty> + <gmd:CI_ResponsibleParty> + <gmd:individualName> + <gco:CharacterString>Robert Hollister</gco:CharacterString> + </gmd:individualName> + <gmd:role> + <gmd:CI_RoleCode codeList="http://www.isotc211.org/2005/resources/Codelist/gmxCodelists.xml#CI_RoleCode"; codeListValue="author">author</gmd:CI_RoleCode> + </gmd:role> + </gmd:CI_ResponsibleParty> + </gmd:citedResponsibleParty> + </gmd:CI_Citation> + </gmd:citation> + <gmd:abstract> + <gco:CharacterString>These files contain data representing the periodic plant measures of species within each plot in a text tab delimited format. The data presented are seasonal growth of graminoids (length of leaf and length of inflorescence) and seasonal flowering of all species (number of inflorescences in flower within a plot), collected weekly during the summers of 2012-20XX for a subset of 30 grid plots at two sites (Barrow ARCSS grid and Atqasuk ARCSS grid).</gco:CharacterString> + </gmd:abstract> + <gmd:status> + <gmd:MD_ProgressCode codeList="http://www.isotc211.org/2005/resources/Codelist/gmxCodelists.xml#MD_ProgressCode"; codeListValue="onGoing" codeSpace="004">onGoing</gmd:MD_ProgressCode> + </gmd:status> + <gmd:pointOfContact> + <gmd:CI_ResponsibleParty> + <gmd:individualName> + <gco:CharacterString>Robert Hollister</gco:CharacterString> + </gmd:individualName> + <gmd:contactInfo> + <gmd:CI_Contact> + <gmd:address> + <gmd:CI_Address> + <gmd:electronicMailAddress> + <gco:CharacterString>[email protected]</gco:CharacterString> + </gmd:electronicMailAddress> + </gmd:CI_Address> + </gmd:address> + </gmd:CI_Contact> + </gmd:contactInfo> + <gmd:role> + <gmd:CI_RoleCode codeList="http://www.isotc211.org/2005/resources/Codelist/gmxCodelists.xml#CI_RoleCode"; codeListValue="pointOfContact">pointOfContact</gmd:CI_RoleCode> + </gmd:role> + </gmd:CI_ResponsibleParty> + </gmd:pointOfContact> + <gmd:resourceFormat> + <gmd:MD_Format> + <gmd:name> + <gco:CharacterString>Other ASCII</gco:CharacterString> + </gmd:name> + <gmd:version gco:nilReason="unknown"/> + </gmd:MD_Format> + </gmd:resourceFormat> + <gmd:descriptiveKeywords> + <gmd:MD_Keywords> + <gmd:keyword> + <gco:CharacterString>EARTH SCIENCE > BIOSPHERE > TERRESTRIAL ECOSYSTEMS > ALPINE/TUNDRA</gco:CharacterString> + </gmd:keyword> + <gmd:type> + <gmd:MD_KeywordTypeCode codeList="http://www.isotc211.org/2005/resources/Codelist/gmxCodelists.xml#MD_KeywordTypeCode"; codeListValue="theme">theme</gmd:MD_KeywordTypeCode> + </gmd:type> + <gmd:thesaurusName> + <gmd:CI_Citation> + <gmd:title> + <gco:CharacterString>NASA/GCMD Earth Science Keywords</gco:CharacterString> + </gmd:title> + <gmd:alternateTitle> + <gco:CharacterString>Science and Services Keywords</gco:CharacterString> + </gmd:alternateTitle> + <gmd:date> + <gmd:CI_Date> + <gmd:date> + <gco:Date>2014-05-21</gco:Date> + </gmd:date> + <gmd:dateType> + <gmd:CI_DateTypeCode codeList="http://www.isotc211.org/2005/resources/Codelist/gmxCodelists.xml#CI_DateTypeCode"; codeListValue="revision">revision</gmd:CI_DateTypeCode> + </gmd:dateType> + </gmd:CI_Date> + </gmd:date> + <gmd:collectiveTitle> + <gco:CharacterString>Olsen, L.M., G. Major, K. Shein, J. Scialdone, S. Ritz, T. Stevens, M. Morahan, A. Aleman, R. Vogel, S. Leicester, H. Weir, M. Meaux, S. Grebas, C.Solomon, M. Holland, T. Northcutt, R. A. Restrepo, R. Bilodeau, 2013. NASA/Global Change Master Directory (GCMD) Earth Science Keywords. 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Major, K. Shein, J. Scialdone, S. Ritz, T. Stevens, M. Morahan, A. Aleman, R. Vogel, S. Leicester, H. Weir, M. Meaux, S. Grebas, C.Solomon, M. Holland, T. Northcutt, R. A. Restrepo, R. Bilodeau, 2013. NASA/Global Change Master Directory (GCMD) Earth Science Keywords. 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Major, K. Shein, J. Scialdone, S. Ritz, T. Stevens, M. Morahan, A. Aleman, R. Vogel, S. Leicester, H. Weir, M. Meaux, S. Grebas, C.Solomon, M. Holland, T. Northcutt, R. A. Restrepo, R. Bilodeau, 2013. NASA/Global Change Master Directory (GCMD) Earth Science Keywords. 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Use Constraints: No Use Constraints.</gco:CharacterString> + </gmd:otherConstraints> + </gmd:MD_LegalConstraints> + </gmd:resourceConstraints> + <gmd:language> + <gco:CharacterString>eng</gco:CharacterString> + </gmd:language> + <gmd:topicCategory> + <gmd:MD_TopicCategoryCode>biota</gmd:MD_TopicCategoryCode> + </gmd:topicCategory> + <gmd:extent> + <gmd:EX_Extent> + <gmd:geographicElement> + <gmd:EX_GeographicDescription> + <gmd:geographicIdentifier> + <gmd:MD_Identifier> + <gmd:authority> + <gmd:CI_Citation> + <gmd:title> + <gco:CharacterString>NASA/GCMD Earth Science Keywords</gco:CharacterString> + </gmd:title> + <gmd:alternateTitle> + <gco:CharacterString>Locations</gco:CharacterString> + </gmd:alternateTitle> + <gmd:date> + <gmd:CI_Date> + <gmd:date> + <gco:Date>2014-08-28</gco:Date> + </gmd:date> + <gmd:dateType> + <gmd:CI_DateTypeCode codeList="http://www.isotc211.org/2005/resources/Codelist/gmxCodelists.xml#CI_DateTypeCode"; codeListValue="revision">revision</gmd:CI_DateTypeCode> + </gmd:dateType> + </gmd:CI_Date> + </gmd:date> + <gmd:collectiveTitle> + <gco:CharacterString>Olsen, L.M., G. Major, K. Shein, J. Scialdone, S. Ritz, T. Stevens, M. Morahan, A. Aleman, R. Vogel, S. Leicester, H. Weir, M. Meaux, S. Grebas, C.Solomon, M. Holland, T. Northcutt, R. A. Restrepo, R. Bilodeau, 2013. NASA/Global Change Master Directory (GCMD) Earth Science Keywords. 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<gml:beginPosition>2012-08-07T00:00:00</gml:beginPosition> + <gml:endPosition>2013-08-04T00:00:00</gml:endPosition> + </gml:TimePeriod> + </gmd:extent> + </gmd:EX_TemporalExtent> + </gmd:temporalElement> + </gmd:EX_Extent> + </gmd:extent> + </gmd:MD_DataIdentification> + </gmd:identificationInfo> + + <gmd:distributionInfo> + <gmd:MD_Distribution> + <gmd:distributionFormat> + <gmd:MD_Format> + <gmd:name> + <gco:CharacterString>Other ASCII</gco:CharacterString> + </gmd:name> + <gmd:version gco:nilReason="unknown"/> + </gmd:MD_Format> + </gmd:distributionFormat> + <gmd:distributor> + <gmd:MD_Distributor> + <gmd:distributorContact> + <gmd:CI_ResponsibleParty> + <gmd:organisationName> + <gco:CharacterString>UCAR/NCAR - CISL - ACADIS</gco:CharacterString> + </gmd:organisationName> + <gmd:role> + <gmd:CI_RoleCode codeList="http://www.isotc211.org/2005/resources/Codelist/gmxCodelists.xml#CI_RoleCode"; codeListValue="resourceProvider">resourceProvider</gmd:CI_RoleCode> + </gmd:role> + </gmd:CI_ResponsibleParty> + </gmd:distributorContact> + </gmd:MD_Distributor> + </gmd:distributor> + <gmd:transferOptions> + <gmd:MD_DigitalTransferOptions> + <gmd:onLine> + <gmd:CI_OnlineResource> + <gmd:linkage> + <gmd:URL>https://www.aoncadis.org/dataset/id/4c1a919d-6690-11e3-9147-00c0f03d5b7c.html</gmd:URL> + </gmd:linkage> + <gmd:protocol> + <gco:CharacterString>https</gco:CharacterString> + </gmd:protocol> + <gmd:applicationProfile> + <gco:CharacterString>browser</gco:CharacterString> + </gmd:applicationProfile> + <gmd:name> + <gco:CharacterString>Barrow Atqasuk ARCSS Plant</gco:CharacterString> + </gmd:name> + <gmd:description> + <gco:CharacterString>Metadata Link</gco:CharacterString> + </gmd:description> + <gmd:function> + <gmd:CI_OnLineFunctionCode codeList="http://www.isotc211.org/2005/resources/Codelist/gmxCodelists.xml#CI_OnLineFunctionCode"; codeListValue="download">download</gmd:CI_OnLineFunctionCode> + </gmd:function> + </gmd:CI_OnlineResource> + </gmd:onLine> + </gmd:MD_DigitalTransferOptions> + </gmd:transferOptions> + </gmd:MD_Distribution> + </gmd:distributionInfo> + +</gmd:MD_Metadata> http://git-wip-us.apache.org/repos/asf/tika/blob/38916f89/tika-parser-modules/tika-parser-scientific-module/src/test/resources/test-documents/sresa1b_ncar_ccsm3_0_run1_200001.nc ---------------------------------------------------------------------- diff --git a/tika-parser-modules/tika-parser-scientific-module/src/test/resources/test-documents/sresa1b_ncar_ccsm3_0_run1_200001.nc b/tika-parser-modules/tika-parser-scientific-module/src/test/resources/test-documents/sresa1b_ncar_ccsm3_0_run1_200001.nc new file mode 100644 index 0000000..dc9da6d Binary files /dev/null and b/tika-parser-modules/tika-parser-scientific-module/src/test/resources/test-documents/sresa1b_ncar_ccsm3_0_run1_200001.nc differ http://git-wip-us.apache.org/repos/asf/tika/blob/38916f89/tika-parser-modules/tika-parser-scientific-module/src/test/resources/test-documents/test.hdf ---------------------------------------------------------------------- diff --git a/tika-parser-modules/tika-parser-scientific-module/src/test/resources/test-documents/test.hdf b/tika-parser-modules/tika-parser-scientific-module/src/test/resources/test-documents/test.hdf new file mode 100644 index 0000000..a9a1d24 Binary files /dev/null and b/tika-parser-modules/tika-parser-scientific-module/src/test/resources/test-documents/test.hdf differ http://git-wip-us.apache.org/repos/asf/tika/blob/38916f89/tika-parser-modules/tika-parser-scientific-module/src/test/resources/test-documents/test.he5 ---------------------------------------------------------------------- diff --git a/tika-parser-modules/tika-parser-scientific-module/src/test/resources/test-documents/test.he5 b/tika-parser-modules/tika-parser-scientific-module/src/test/resources/test-documents/test.he5 new file mode 100644 index 0000000..decd552 Binary files /dev/null and b/tika-parser-modules/tika-parser-scientific-module/src/test/resources/test-documents/test.he5 differ http://git-wip-us.apache.org/repos/asf/tika/blob/38916f89/tika-parser-modules/tika-parser-scientific-module/src/test/resources/test-documents/testISATab_BII-I-1/a_bii-s-2_metabolite profiling_NMR spectroscopy.txt ---------------------------------------------------------------------- diff --git a/tika-parser-modules/tika-parser-scientific-module/src/test/resources/test-documents/testISATab_BII-I-1/a_bii-s-2_metabolite profiling_NMR spectroscopy.txt b/tika-parser-modules/tika-parser-scientific-module/src/test/resources/test-documents/testISATab_BII-I-1/a_bii-s-2_metabolite profiling_NMR spectroscopy.txt new file mode 100644 index 0000000..f7fc146 --- /dev/null +++ b/tika-parser-modules/tika-parser-scientific-module/src/test/resources/test-documents/testISATab_BII-I-1/a_bii-s-2_metabolite profiling_NMR spectroscopy.txt @@ -0,0 +1,51 @@ +"Sample Name" "Protocol REF" "Extract Name" "Protocol REF" "Labeled Extract Name" "Label" "Term Source REF" "Term Accession Number" "Protocol REF" "Parameter Value[instrument]" "Parameter Value[NMR Probe]" "Parameter Value[number of acquisition]" "Parameter Value[magnetic field strength]" "Unit" "Term Source REF" "Term Accession Number" "Acquisition Parameter Data File" "Protocol REF" "NMR Assay Name" "Free Induction Decay Data File" "Protocol REF" "Normalization Name" "Protocol REF" "Data Transformation Name" "Derived Spectral Data File" "Metabolite Assignment File" +"" "extraction" "" "labeling" "" "" "" "" "NMR spectroscopy" "" "" "" "" "" "" "" "" "nmr assay" "" "" "data normalization" "" "data transformation" "" "" "" +"" "extraction" "" "labeling" "" "" "" "" "NMR spectroscopy" "" "" "" "" "" "" "" "" "nmr assay" "" "" "data normalization" "" "data transformation" "" "" "" +"" "extraction" "" "labeling" "" "" "" "" "NMR spectroscopy" "" "" "" "" "" "" "" "" "nmr assay" "" "" "data normalization" "" "data transformation" "" "" "" +"" "extraction" "" "labeling" "" "" "" "" "NMR spectroscopy" "" "" "" "" "" "" "" "" "nmr assay" "" "" "data normalization" "" "data transformation" "" "" "" +"" "extraction" "" "labeling" "" "" "" "" "NMR spectroscopy" "" "" "" "" "" "" "" "" "nmr assay" "" "" "data normalization" "" "data transformation" "" "" "" +"" "extraction" "" "labeling" "" "" "" "" "NMR spectroscopy" "" "" "" "" "" "" "" "" "nmr assay" "" "" "data normalization" "" "data transformation" "" "" "" +"" "extraction" "" "labeling" "" "" "" "" "NMR spectroscopy" "" "" "" "" "" "" "" "" "nmr assay" "" "" "data normalization" "" "data transformation" "" "" "" +"" "extraction" "" "labeling" "" "" "" "" "NMR spectroscopy" "" "" "" "" "" "" "" "" "nmr assay" "" "" "data normalization" "" "data transformation" "" "" "" +"" "extraction" "" "labeling" "" "" "" "" "NMR spectroscopy" "" "" "" "" "" "" "" "" "nmr assay" "" "" "data normalization" "" "data transformation" "" "" "" +"" "extraction" "" "labeling" "" "" "" "" "NMR spectroscopy" "" "" "" "" "" "" "" "" "nmr assay" "" "" "data normalization" "" "data transformation" "" "" "" +"" "extraction" "" "labeling" "" "" "" "" "NMR spectroscopy" "" "" "" "" "" "" "" "" "nmr assay" "" "" "data normalization" "" "data transformation" "" "" "" +"" "extraction" "" "labeling" "" "" "" "" "NMR spectroscopy" "" "" "" "" "" "" "" "" "nmr assay" "" "" "data normalization" "" "data transformation" "" "" "" +"" "extraction" "" "labeling" "" "" "" "" "NMR spectroscopy" "" "" "" "" "" "" "" "" "nmr assay" "" "" "data normalization" "" "data transformation" "" "" "" +"" "extraction" "" "labeling" "" "" "" "" "NMR spectroscopy" "" "" "" "" "" "" "" "" "nmr assay" "" "" "data normalization" "" "data transformation" "" "" "" +"" "extraction" "" "labeling" "" "" "" "" "NMR spectroscopy" "" "" "" "" "" "" "" "" "nmr assay" "" "" "data normalization" "" "data transformation" "" "" "" +"" "extraction" "" "labeling" "" "" "" "" "NMR spectroscopy" "" "" "" "" "" "" "" "" "nmr assay" "" "" "data normalization" "" "data transformation" "" "" "" +"" "extraction" "" "labeling" "" "" "" "" "NMR spectroscopy" "" "" "" "" "" "" "" "" "nmr assay" "" "" "data normalization" "" "data transformation" "" "" "" +"" "extraction" "" "labeling" "" "" "" "" "NMR spectroscopy" "" "" "" "" "" "" "" "" "nmr assay" "" "" "data normalization" "" "data transformation" "" "" "" +"" "extraction" "" "labeling" "" "" "" "" "NMR spectroscopy" "" "" "" "" "" "" "" "" "nmr assay" "" "" "data normalization" "" "data transformation" "" "" "" +"" "extraction" "" "labeling" "" "" "" "" "NMR spectroscopy" "" "" "" "" "" "" "" "" "nmr assay" "" "" "data normalization" "" "data transformation" "" "" "" +"" "extraction" "" "labeling" "" "" "" "" "NMR spectroscopy" "" "" "" "" "" "" "" "" "nmr assay" "" "" "data normalization" "" "data transformation" "" "" "" +"" "extraction" "" "labeling" "" "" "" "" "NMR spectroscopy" "" "" "" "" "" "" "" "" "nmr assay" "" "" "data normalization" "" "data transformation" "" "" "" +"" "extraction" "" "labeling" "" "" "" "" "NMR spectroscopy" "" "" "" "" "" "" "" "" "nmr assay" "" "" "data normalization" "" "data transformation" "" "" "" +"" "extraction" "" "labeling" "" "" "" "" "NMR spectroscopy" "" "" "" "" "" "" "" "" "nmr assay" "" "" "data normalization" "" "data transformation" "" "" "" +"" "extraction" "" "labeling" "" "" "" "" "NMR spectroscopy" "" "" "" "" "" "" "" "" "nmr assay" "" "" "data normalization" "" "data transformation" "" "" "" +"" "extraction" "" "labeling" "" "" "" "" "NMR spectroscopy" "" "" "" "" "" "" "" "" "nmr assay" "" "" "data normalization" "" "data transformation" "" "" "" +"" "extraction" "" "labeling" "" "" "" "" "NMR spectroscopy" "" "" "" "" "" "" "" "" "nmr assay" "" "" "data normalization" "" "data transformation" "" "" "" +"" "extraction" "" "labeling" "" "" "" "" "NMR spectroscopy" "" "" "" "" "" "" "" "" "nmr assay" "" "" "data normalization" "" "data transformation" "" "" "" +"" "extraction" "" "labeling" "" "" "" "" "NMR spectroscopy" "" "" "" "" "" "" "" "" "nmr assay" "" "" "data normalization" "" "data transformation" "" "" "" +"" "extraction" "" "labeling" "" "" "" "" "NMR spectroscopy" "" "" "" "" "" "" "" "" "nmr assay" "" "" "data normalization" "" "data transformation" "" "" "" +"" "extraction" "" "labeling" "" "" "" "" "NMR spectroscopy" "" "" "" "" "" "" "" "" "nmr assay" "" "" "data normalization" "" "data transformation" "" "" "" +"" "extraction" "" "labeling" "" "" "" "" "NMR spectroscopy" "" "" "" "" "" "" "" "" "nmr assay" "" "" "data normalization" "" "data transformation" "" "" "" +"" "extraction" "" "labeling" "" "" "" "" "NMR spectroscopy" "" "" "" "" "" "" "" "" "nmr assay" "" "" "data normalization" "" "data transformation" "" "" "" +"" "extraction" "" "labeling" "" "" "" "" "NMR spectroscopy" "" "" "" "" "" "" "" "" "nmr assay" "" "" "data normalization" "" "data transformation" "" "" "" +"" "extraction" "" "labeling" "" "" "" "" "NMR spectroscopy" "" "" "" "" "" "" "" "" "nmr assay" "" "" "data normalization" "" "data transformation" "" "" "" +"" "extraction" "" "labeling" "" "" "" "" "NMR spectroscopy" "" "" "" "" "" "" "" "" "nmr assay" "" "" "data normalization" "" "data transformation" "" "" "" +"" "extraction" "" "labeling" "" "" "" "" "NMR spectroscopy" "" "" "" "" "" "" "" "" "nmr assay" "" "" "data normalization" "" "data transformation" "" "" "" +"" "extraction" "" "labeling" "" "" "" "" "NMR spectroscopy" "" "" "" "" "" "" "" "" "nmr assay" "" "" "data normalization" "" "data transformation" "" "" "" +"" "extraction" "" "labeling" "" "" "" "" "NMR spectroscopy" "" "" "" "" "" "" "" "" "nmr assay" "" "" "data normalization" "" "data transformation" "" "" "" +"" "extraction" "" "labeling" "" "" "" "" "NMR spectroscopy" "" "" "" "" "" "" "" "" "nmr assay" "" "" "data normalization" "" "data transformation" "" "" "" +"" "extraction" "" "labeling" "" "" "" "" "NMR spectroscopy" "" "" "" "" "" "" "" "" "nmr assay" "" "" "data normalization" "" "data transformation" "" "" "" +"" "extraction" "" "labeling" "" "" "" "" "NMR spectroscopy" "" "" "" "" "" "" "" "" "nmr assay" "" "" "data normalization" "" "data transformation" "" "" "" +"" "extraction" "" "labeling" "" "" "" "" "NMR spectroscopy" "" "" "" "" "" "" "" "" "nmr assay" "" "" "data normalization" "" "data transformation" "" "" "" +"" "extraction" "" "labeling" "" "" "" "" "NMR spectroscopy" "" "" "" "" "" "" "" "" "nmr assay" "" "" "data normalization" "" "data transformation" "" "" "" +"" "extraction" "" "labeling" "" "" "" "" "NMR spectroscopy" "" "" "" "" "" "" "" "" "nmr assay" "" "" "data normalization" "" "data transformation" "" "" "" +"" "extraction" "" "labeling" "" "" "" "" "NMR spectroscopy" "" "" "" "" "" "" "" "" "nmr assay" "" "" "data normalization" "" "data transformation" "" "" "" +"" "extraction" "" "labeling" "" "" "" "" "NMR spectroscopy" "" "" "" "" "" "" "" "" "nmr assay" "" "" "data normalization" "" "data transformation" "" "" "" +"" "extraction" "" "labeling" "" "" "" "" "NMR spectroscopy" "" "" "" "" "" "" "" "" "nmr assay" "" "" "data normalization" "" "data transformation" "" "" "" +"" "extraction" "" "labeling" "" "" "" "" "NMR spectroscopy" "" "" "" "" "" "" "" "" "nmr assay" "" "" "data normalization" "" "data transformation" "" "" "" +"" "extraction" "" "labeling" "" "" "" "" "NMR spectroscopy" "" "" "" "" "" "" "" "" "nmr assay" "" "" "data normalization" "" "data transformation" "" "" "" http://git-wip-us.apache.org/repos/asf/tika/blob/38916f89/tika-parser-modules/tika-parser-scientific-module/src/test/resources/test-documents/testISATab_BII-I-1/a_metabolome.txt ---------------------------------------------------------------------- diff --git a/tika-parser-modules/tika-parser-scientific-module/src/test/resources/test-documents/testISATab_BII-I-1/a_metabolome.txt b/tika-parser-modules/tika-parser-scientific-module/src/test/resources/test-documents/testISATab_BII-I-1/a_metabolome.txt new file mode 100644 index 0000000..0207dfb --- /dev/null +++ b/tika-parser-modules/tika-parser-scientific-module/src/test/resources/test-documents/testISATab_BII-I-1/a_metabolome.txt @@ -0,0 +1,112 @@ +"Sample Name" "Material Type" "Term Source REF" "Term Accession Number" "Protocol REF" "Parameter Value[standard volume]" "Unit" "Term Source REF" "Term Accession Number" "Parameter Value[sample volume]" "Unit" "Term Source REF" "Term Accession Number" "Extract Name" "MS Assay Name" "Raw Spectral Data File" "Factor Value[limiting nutrient]" "Term Source REF" "Term Accession Number" "Factor Value[rate]" "Unit" "Term Source REF" "Term Accession Number" +"C-0.1-aliquot1" "internal" "EHDAA" "http://purl.obolibrary.org/obo/EHDAA_7477"; "metabolite extraction" "4" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101"; "200" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101"; "S-0.2-aliquot8" "JIC36_Sulphate_0.20_Internal_1_3" "JIC36_Sulphate_0.20_Internal_1_3.txt" "carbon" "EFO" "http://purl.obolibrary.org/obo/CHEBI_27594"; "0.1" "l/hour" "" "" +"S-0.07-aliquot5" "external" "EHDAA" "http://purl.obolibrary.org/obo/EHDAA_8260"; "metabolite extraction" "20" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101"; "1000" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101"; "S-0.07-aliquot5" "JIC82_Sulphate_0.07_External_1_1" "JIC82_Sulphate_0.07_External_1_1.txt" "sulphur" "" "" "0.07" "l/hr" "" "" +"S-0.07-aliquot6" "external" "EHDAA" "http://purl.obolibrary.org/obo/EHDAA_8260"; "metabolite extraction" "20" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101"; "1000" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101"; "S-0.07-aliquot6" "JIC83_Sulphate_0.07_External_2_1" "sample-data" "sulphur" "" "" "0.07" "l/hr" "" "" +"S-0.07-aliquot7" "external" "EHDAA" "http://purl.obolibrary.org/obo/EHDAA_8260"; "metabolite extraction" "20" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101"; "1000" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101"; "S-0.07-aliquot7" "JIC84_Sulphate_0.07_External_3_1" "ISAtab" "sulphur" "" "" "0.07" "l/hr" "" "" +"S-0.07-aliquot5" "external" "EHDAA" "http://purl.obolibrary.org/obo/EHDAA_8260"; "metabolite extraction" "20" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101"; "1000" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101"; "S-0.07-aliquot5" "JIC82_Sulphate_0.07_External_1_2" "Presentation Images" "sulphur" "" "" "0.07" "l/hr" "" "" +"S-0.07-aliquot5" "external" "EHDAA" "http://purl.obolibrary.org/obo/EHDAA_8260"; "metabolite extraction" "20" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101"; "1000" "microliter" "UO" "http://purl.obolibrary.org/obo/UO_0000101"; "S-0.07-aliquot5" "JIC82_Sulphate_0.07_External_1_3" "Presentations" "sulphur" "" "" "0.07" 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