Revision 6cc19306
Added by Jim Regetz over 12 years ago
- ID 6cc19306e6fe6474eb824a4559c53b952f5b10ac
| shared/extra/organisms-content-migration.sh | ||
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# Full sequence of (bash) commands used to transform the original |
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# organisms@jupiter home directory structure to the new layers@atlas |
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# home directory structure. This was done after first rsyncing the |
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# entire ~organisms home directory from jupiter onto atlas at |
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# /home/organisms, and creating a new 'layers' user with home directory |
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# /home/layers. |
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# |
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# Jim Regetz |
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# NCEAS |
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# Created on 23-Feb-2012 |
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export ORGANISMS="/home/organisms" |
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export LAYERS="/home/layers" |
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#======================================================================= |
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# set up some directories |
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#======================================================================= |
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# create master home for all datasets |
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mkdir $LAYERS/data |
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mkdir $LAYERS/data/climate |
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mkdir $LAYERS/data/terrain |
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mkdir $LAYERS/data/land-cover |
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# create (temporary) home for associated readmes, documentation, etc |
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mkdir $LAYERS/documentation |
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mkdir $LAYERS/documentation/climate |
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mkdir $LAYERS/documentation/terrain |
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mkdir $LAYERS/documentation/land-cover |
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# create (temporary) home for processing code |
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mkdir $LAYERS/code |
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mkdir $LAYERS/code/climate |
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mkdir $LAYERS/code/terrain |
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mkdir $LAYERS/code/land-cover |
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# create (temporary) home for other cruft that i'm not quite ready to delete |
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mkdir $LAYERS/cruft |
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# create (temporary?) home for everything else |
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mkdir $LAYERS/experimental |
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mkdir $LAYERS/experimental/terrain |
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mkdir $LAYERS/experimental/land-cover |
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#======================================================================= |
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# carry out file migration, reorganization, and cleanup |
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#======================================================================= |
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#========# |
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# Marine # |
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#========# |
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# easy one ... just delete, as we're retaining this work on the original |
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# server |
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rm -rf Marine/ |
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#=====# |
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# DEM # |
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#=====# |
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# |
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# SRTM 1km |
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# |
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# migrate original rar file |
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mkdir $LAYERS/data/terrain/dem-cgiar-srtm-1km-ascii |
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mv $ORGANISMS/DEM/SRTM_1km_ASCII.rar $LAYERS/data/terrain/dem-cgiar-srtm-1km-ascii/srtm_1km_ascii.rar |
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# migrate clipped/reprojected bil |
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mv $ORGANISMS/Oregon_SRTM $LAYERS/data/terrain/dem-cgiar-srtm-1km-OR/ |
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# |
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# CGIAR SRTM 90m |
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# |
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# SRTM 90m zips |
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mv $ORGANISMS/DEM/cgiarSrtm/archive $LAYERS/data/terrain/dem-cgiar-srtm-90m-zips |
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# SRTM 90m tiles and processed descendents |
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# first flatten out SRTM 90m directories |
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mv $ORGANISMS/DEM/cgiarSrtm/SRTM_90m_ASCII_4_1/Tiles_Resampled/Mosaiced \ |
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$ORGANISMS/DEM/cgiarSrtm/SRTM_90m_ASCII_4_1_Resampled_Mosaiced |
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mv $ORGANISMS/DEM/cgiarSrtm/SRTM_90m_ASCII_4_1/Tiles_Resampled \ |
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$ORGANISMS/DEM/cgiarSrtm/SRTM_90m_ASCII_4_1_Resampled |
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# now migrate to ~layers |
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mv $ORGANISMS/DEM/cgiarSrtm/SRTM_90m_ASCII_4_1 \ |
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$LAYERS/data/terrain/dem-cgiar-srtm-90m-asc |
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mv $ORGANISMS/DEM/cgiarSrtm/SRTM_90m_ASCII_4_1_Resampled \ |
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$LAYERS/data/terrain/dem-cgiar-srtm-90m-asc-resamp |
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mv $ORGANISMS/DEM/cgiarSrtm/SRTM_90m_ASCII_4_1_Resampled_Mosaiced \ |
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$LAYERS/data/terrain/dem-cgiar-srtm-90m-asc-resamp-mosaic |
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# SRTM 90m tile index (zipped) |
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mkdir $LAYERS/data/terrain/dem-cgiar-srtm-90m-index-zip |
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mv $ORGANISMS/DEM/cgiarSrtm/srtm-tile-index_v4.1_shp.zip \ |
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$LAYERS/data/terrain/dem-cgiar-srtm-90m-index-zip/ |
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# SRTM 90m tile index (unzipped) |
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mv $ORGANISMS/DEM/cgiarSrtm/index \ |
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$LAYERS/data/terrain/dem-cgiar-srtm-90m-index |
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# move readme to deal with later |
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mv $ORGANISMS/DEM/cgiarSrtm/README.txt $LAYERS/documentation/terrain/cgiar-srtm-90m-readme.txt |
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# remove now-empty directory |
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rmdir $ORGANISMS/DEM/cgiarSrtm |
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# |
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# ASTER GDEM2 |
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# |
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# remove gdal-generated metadata files |
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rm $ORGANISMS/DEM/asterGdem2/*.aux.xml |
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rm $ORGANISMS/DEM/asterGdem2/90m_NoPixelOffset/*.aux.xml |
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rm $ORGANISMS/DEM/asterGdem2/90m_NoPixelOffset/Mosaiced/N59to60/*.aux.xml |
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# first flatten out directories |
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mv $ORGANISMS/DEM/asterGdem2/90m_NoPixelOffset/Mosaiced/N59to60 \ |
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$ORGANISMS/DEM/asterGdem2-90m_NoPixelOffset-Mosaiced-N59to60 |
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mv $ORGANISMS/DEM/asterGdem2/90m_NoPixelOffset/Mosaiced \ |
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$ORGANISMS/DEM/asterGdem2-90m_NoPixelOffset-Mosaiced |
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mv $ORGANISMS/DEM/asterGdem2/90m_NoPixelOffset \ |
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$ORGANISMS/DEM/asterGdem2-90m_NoPixelOffset |
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# now migrate to ~layers |
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mv $ORGANISMS/DEM/asterGdem2 \ |
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$LAYERS/data/terrain/dem-aster-gdem2-30m-orig |
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mv $ORGANISMS/DEM/asterGdem2-90m_NoPixelOffset \ |
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$LAYERS/data/terrain/dem-aster-gdem2-90m-resamp |
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mv $ORGANISMS/DEM/asterGdem2-90m_NoPixelOffset-Mosaiced \ |
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$LAYERS/data/terrain/dem-aster-gdem2-90m-resamp-mosaic-N60to83 |
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mv $ORGANISMS/DEM/asterGdem2-90m_NoPixelOffset-Mosaiced-N59to60 \ |
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$LAYERS/data/terrain/dem-aster-gdem2-90m-resamp-mosaic-N59to60 |
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# |
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# ASTER GDEM1 |
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# |
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#TODO |
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# |
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# CDED |
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# |
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# remove duplicate files (confirmed by diffing) |
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rm $ORGANISMS/DEM/CanadaDED/084b\ \(1\).zip |
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rm $ORGANISMS/DEM/CanadaDED/Monday/114p\ \(1\).zip |
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rm $ORGANISMS/DEM/CanadaDED/mosaicMostCanadaDem.sh |
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rm $ORGANISMS/DEM/CanadaDED/Monday/mergeCanada104105.{tif,aux,rrd}
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# migrate zips |
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mkdir $LAYERS/data/terrain/dem-cded-zip |
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mv -i $ORGANISMS/DEM/CanadaDED/0*.zip \ |
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$LAYERS/data/terrain/dem-cded-zip/ |
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mv -i $ORGANISMS/DEM/CanadaDED/Monday/1*.zip \ |
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$LAYERS/data/terrain/dem-cded-zip/ |
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# migrate documentation |
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mv -i $ORGANISMS/DEM/CanadaDED/CanadaDEDTechRefManual.pdf \ |
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$LAYERS/documentation/terrain/cded-TechRefManual.pdf |
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# migrate some stuff to experimental, for now... |
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mkdir $LAYERS/experimental/terrain/dem-cded |
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# ... vrt files, what the heck |
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mv -i $ORGANISMS/DEM/CanadaDED/*demFile.vrt \ |
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$LAYERS/experimental/terrain/dem-cded/ |
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# ... misc scripts and log files |
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mv -i $ORGANISMS/DEM/CanadaDED/in*DemFile.txt \ |
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$LAYERS/experimental/terrain/dem-cded/ |
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mv -i $ORGANISMS/DEM/CanadaDED/unzipFiles.sh \ |
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$LAYERS/experimental/terrain/dem-cded/unzipFiles_0.sh |
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mv -i $ORGANISMS/DEM/CanadaDED/Monday/unzipFiles.sh \ |
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$LAYERS/experimental/terrain/dem-cded/unzipFiles_1.sh |
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mv -i $ORGANISMS/DEM/CanadaDED/{.,/Monday}/*.sh \
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$LAYERS/experimental/terrain/dem-cded/ |
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mv -i $ORGANISMS/DEM/CanadaDED/*.log \ |
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$LAYERS/experimental/terrain/dem-cded/ |
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mv -i $ORGANISMS/DEM/CanadaDED/moscomps \ |
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$LAYERS/experimental/terrain/dem-cded/ |
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mv -i $ORGANISMS/DEM/CanadaDED/Monday/filesToMosaic \ |
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$LAYERS/experimental/terrain/dem-cded/ |
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mv -i $ORGANISMS/DEM/CanadaDED/Monday/*Log \ |
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$LAYERS/experimental/terrain/dem-cded/ |
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# remove extracted data (no plans to use it), after determining that these are |
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# the set of files matching globs "*.dem" or "*_fgdc_*.{xml,html}"
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# # ---- bash code ---# |
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# # list out all files contained in the zips |
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# cd $LAYERS/data/terrain/dem-cded-zip && ls \ |
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# | xargs -I+ sh -c 'unzip -l + | grep -e " 200[7-9]-"' \ |
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# | awk '{print $4}' > /home/layers/cded-extracts.txt
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# # ----- R code -----# |
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# # read in the extracted file names |
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# extracts <- scan("/home/layers/cded-extracts.txt", what="")
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# # read in all CDED files stored in the organisms home dir |
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# files <- list.files(path=c("/home/organisms/DEM/CanadaDED",
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# "/home/organisms/DEM/CanadaDED/Monday")) |
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# # note that all zip contents had been extracted (...based on filename) |
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# all(extracts %in% files) |
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# ## [1] TRUE |
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# # isolate files *not* extracted from the zips |
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# others <- setdiff(files, extracts) |
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# # show that all extracted filenames match one of two patterns |
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# all(grepl("dem$", extracts) | grepl("_fgdc_", extracts))
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# ## [1] TRUE |
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# # and show that no other files match these |
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# any(grepl("dem$", others) | grepl("_fgdc_", others))
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# ## [1] FALSE |
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# # ------------------# |
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rm $ORGANISMS/DEM/CanadaDED/*.dem |
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rm $ORGANISMS/DEM/CanadaDED/*_fgdc_*.{xml,html}
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rm $ORGANISMS/DEM/CanadaDED/Monday/*.dem |
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rm $ORGANISMS/DEM/CanadaDED/Monday/*_fgdc_*.{xml,html}
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# now remove items of uncertain origin |
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rm $ORGANISMS/DEM/CanadaDED/*.dem.aux.xml |
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rm $ORGANISMS/DEM/CanadaDED/Monday/*.dem.aux.xml |
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rm $ORGANISMS/DEM/CanadaDED/*dem?.{aux,rrd}
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rm $ORGANISMS/DEM/CanadaDED/Monday/*dem?.{aux,rrd}
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rm $ORGANISMS/DEM/CanadaDED/*demFile.{aux,rrd,vrt.aux,tif.aux.xml,tif,vrt.rrd}
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rm $ORGANISMS/DEM/CanadaDED/CDEMPlySRTMDf.aux |
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rm -r $ORGANISMS/DEM/CanadaDED/cdemplysrtmdf |
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rm -r $ORGANISMS/DEM/CanadaDED/info |
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# what the hell, remove other generated tifs because I really can't account for |
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# the details of their creation... |
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rm $ORGANISMS/DEM/CanadaDED/CanadaDemMos*.{tif,rrd,aux,aux.xml,tif.xml,img,vat.dbf}
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rm $ORGANISMS/DEM/CanadaDED/mergeCanada104105.{tif,aux,rrd}
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# remove now-empty directories |
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rmdir $ORGANISMS/DEM/CanadaDED/Monday |
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rmdir $ORGANISMS/DEM/CanadaDED |
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# |
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# FUSED DEM |
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# |
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# remove gdal-generated metadata files |
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rm $ORGANISMS/DEM/GlobalProduct/*.aux.xml |
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# migrate to ~layers |
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mv $ORGANISMS/DEM/GlobalProduct $LAYERS/data/terrain/dem-fused |
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# |
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# GTOPO30 |
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# |
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# remove gdal-generated metadata file |
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rm $ORGANISMS/DEM/usgsGTOPO30/e020n90/*.aux.xml |
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# now migrate to ~layers |
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mv $ORGANISMS/DEM/usgsGTOPO30 $LAYERS/data/terrain/dem-usgs-gtopo30 |
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# |
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# GMTED2010 |
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# |
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# remove gdal-generated metadata files |
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rm $ORGANISMS/GMTED2010/*.aux.xml |
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# remove ArcMap(?) schema lock file |
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rm $ORGANISMS/GMTED2010/GMTED2010_Spatial_Metadata/GMTED2010_Spatial_Metadata.shp.IGSKMNCNWK00726.6284.8844.sr.lock |
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# migrate original (I think) downloaded data (OR only) |
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mkdir $LAYERS/data/terrain/dem-gmted2010-mea300-OR-tiles |
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mv $ORGANISMS/GMTED2010/30N150W_20101117_gmted_mea300.tif \ |
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$LAYERS/data/terrain/dem-gmted2010-mea300-OR-tiles/ |
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mv $ORGANISMS/GMTED2010/30N120W_20101117_gmted_mea300.tif \ |
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$LAYERS/data/terrain/dem-gmted2010-mea300-OR-tiles/ |
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# migrate merged OR tiles (i think) |
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mkdir $LAYERS/data/terrain/dem-gmted2010-mea300-OR-mosaic |
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mv $ORGANISMS/GMTED2010/OR_Coverage.tif \ |
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$LAYERS/data/terrain/dem-gmted2010-mea300-OR-mosaic/ |
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# migrate OR clipped/reprojected data |
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mkdir $LAYERS/data/terrain/dem-gmted2010-mea300-OR-clip-proj-sinu-tif |
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mv $ORGANISMS/GMTED2010/OR_ClippedToMODIS_InSinu.tif \ |
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$LAYERS/data/terrain/dem-gmted2010-mea300-OR-clip-proj-sinu-tif/ |
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mkdir $LAYERS/data/terrain/dem-gmted2010-mea300-OR-clip-proj-sinu-bil |
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mv $ORGANISMS/GMTED2010/OR_ClippedToMODIS_InSinu.{prj,hdr,bil} \
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$LAYERS/data/terrain/dem-gmted2010-mea300-OR-clip-proj-sinu-bil/ |
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# migrate shapefile |
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mv $ORGANISMS/GMTED2010/GMTED2010_Spatial_Metadata \ |
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$LAYERS/data/terrain/dem-gmted2010-spatial-metadata |
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# migrate documentation |
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mv $ORGANISMS/GMTED2010/of2011-1073.pdf $LAYERS/documentation/terrain/gmted2010-report.pdf |
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mv $ORGANISMS/GMTED2010/ReadMe $LAYERS/documentation/terrain/gmted2010-readme.txt |
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# remove now-empty directory |
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rmdir $ORGANISMS/GMTED2010 |
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# |
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# Nunokawa content |
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# |
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# TODO: deal with data |
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$ORGANISMS/DEM/Yuni/Data/aster2/aster2_*_82N.tif # Int16 59N-82N GDEM2 elevation |
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$ORGANISMS/DEM/Yuni/Data/aster2/aster2_*_below.tif # Int16 59N-60N GDEM2 elevation |
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$ORGANISMS/DEM/Yuni/Data/aster2/aster2_*_above.tif # Int16 60N-61N GDEM2 elevation |
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$ORGANISMS/DEM/Yuni/Data/aster2/aster2_*_straddle.tif # Int16 59N-61N GDEM2 elevation (GDEM2 above, GDEM2 below) |
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$ORGANISMS/DEM/Yuni/Data/aster2/aster2_*_straddle_a.tif # Flt32 59N-61N GDEM2-based aspect |
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$ORGANISMS/DEM/Yuni/Data/aster2/aster2_*_straddle_s.tif # Flt32 59N-61N GDEM2-based slope |
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$ORGANISMS/DEM/Yuni/Data/aster2/aster2_*_below_blendgau.tif # Flt32 59N-60N GDEM2/SRTM blended elevation |
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$ORGANISMS/DEM/Yuni/Data/aster2/fused_*_straddle.tif # Int16 59N-61N GDEM2/SRTM unblended elevation (GDEM2 above, SRTM below) |
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$ORGANISMS/DEM/Yuni/Data/aster2/fused_*_straddle_a.tif # Flt32 59N-61N unblended-based aspect |
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$ORGANISMS/DEM/Yuni/Data/aster2/fused_*_straddle_s.tif # Flt32 59N-61N unblended-based aspect |
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$ORGANISMS/DEM/Yuni/Data/aster2/fused_*_blendgau.tif # Int16 59N-61N GDEM2/SRTM blended elevation (GDEM2 above, blended below) |
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$ORGANISMS/DEM/Yuni/Data/aster2/fused_*_blendgau_a.tif # Flt32 59N-61N blend-based aspect |
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$ORGANISMS/DEM/Yuni/Data/aster2/fused_*_blendgau_s.tif # Flt32 59N-61N blend-based aspect |
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$ORGANISMS/DEM/Yuni/Data/srtm/srtm_*_below.tif # Int16 59N-60N SRTM elevation |
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$ORGANISMS/DEM/Yuni/Data/srtm/srtm_*_below_a.tif # Flt32 59N-60N SRTM-based aspect |
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$ORGANISMS/DEM/Yuni/Data/srtm/srtm_*_below_below_s.tif # Flt32 59N-60N SRTM-based slope |
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$ORGANISMS/DEM/Yuni/Data/aster2/aster.vrt # VRT - GDEM2 from ~59N-82N (with 1/2-pixel offset) |
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$ORGANISMS/DEM/Yuni/Data/srtm/srtm.vrt # VRT - SRTM from ~55N-60N (with 1/2-pixel offset) |
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$ORGANISMS/DEM/Yuni/Data/GTOPO30/*.dem # 59N-~82N GTOPO30 elevation clipped |
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# remove duplicate file |
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rm $ORGANISMS/DEM/Yuni/Data/aster2/fused_w180w141 |
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# remove redundant backup files (but leaving some others) |
|
| 309 |
rm $ORGANISMS/DEM/Yuni/scripts/toAnalyzeData/aspect.r~ |
|
| 310 |
rm $ORGANISMS/DEM/Yuni/scripts/toAnalyzeData/check.r~ |
|
| 311 |
rm $ORGANISMS/DEM/Yuni/scripts/toAnalyzeData/meanElv.r~ |
|
| 312 |
rm $ORGANISMS/DEM/Yuni/scripts/toAnalyzeData/meanElv_onlyN59.r~ |
|
| 313 |
rm $ORGANISMS/DEM/Yuni/scripts/toAnalyzeData/ |
|
| 314 |
rm $ORGANISMS/DEM/Yuni/scripts/toProduceData/assembling.r~ |
|
| 315 |
rm $ORGANISMS/DEM/Yuni/scripts/toProduceData/gaussian.r~ |
|
| 316 |
rm $ORGANISMS/DEM/Yuni/scripts/toProduceData/mkVrt_Tiff.r~ |
|
| 317 |
rm $ORGANISMS/DEM/Yuni/scripts/toProduceData/slope_aspect.r~ |
|
| 318 |
# migrate scripts files |
|
| 319 |
mv $ORGANISMS/DEM/Yuni/scripts \ |
|
| 320 |
$LAYERS/code/terrain/nunokawa-scripts |
|
| 321 |
# migrate documents |
|
| 322 |
mv -i $ORGANISMS/DEM/Yuni/documents \ |
|
| 323 |
$LAYERS/documentation/terrain/nunokawa-documents |
|
| 324 |
mv -i $ORGANISMS/DEM/Yuni/missing_gdem2_tiles.txt \ |
|
| 325 |
$LAYERS/documentation/terrain/nunokawa-documents/ |
|
| 326 |
mv -i $ORGANISMS/DEM/Yuni/metadata.txt \ |
|
| 327 |
$LAYERS/documentation/terrain/nunokawa-documents/ |
|
| 328 |
|
|
| 329 |
# |
|
| 330 |
# Remaining DEM content |
|
| 331 |
# |
|
| 332 |
|
|
| 333 |
mv $ORGANISMS/DEM/DEM_ProcessingScripts $LAYERS/code/terrain/ |
|
| 334 |
mv $ORGANISMS/DEM/ReadMeInProgress.txt $LAYERS/documentation/terrain/misc-partial-readme.txt |
|
| 335 |
|
|
| 336 |
|
|
| 337 |
rm $ORGANISMS/DEM/checklog |
|
| 338 |
mv $ORGANISMS/DEM/checkBadAsterGDEMFiles.sh $LAYERS/cruft/ |
|
| 339 |
mv $ORGANISMS/DEM/CheckGDEMLog.txt $LAYERS/cruft/ |
|
| 340 |
|
|
| 341 |
|
|
| 342 |
#=========# |
|
| 343 |
# CLIMATE # |
|
| 344 |
#=========# |
|
| 345 |
|
|
| 346 |
# |
|
| 347 |
# CRU |
|
| 348 |
# |
|
| 349 |
|
|
| 350 |
# migrate original gz data from CRU (or so it appears...) |
|
| 351 |
mkdir $LAYERS/data/climate/cru-ts-3.0-1901-2006-gzip |
|
| 352 |
mv $ORGANISMS/CRU_TS_3.0/*.gz $LAYERS/data/climate/cru-ts-3.0-1901-2006-gzip/ |
|
| 353 |
# I confirmed that the gunzipped files are identical to the gz contents (by |
|
| 354 |
# gunzipping to /tmp and then diffing):w |
|
| 355 |
# ...so let's delete the uncompressed versions |
|
| 356 |
rm $ORGANISMS/CRU_TS_3.0/cru_ts_3_00.1901.2006.pre.nc |
|
| 357 |
rm $ORGANISMS/CRU_TS_3.0/cru_ts_3_00.1901.2006.tmn.nc |
|
| 358 |
rm $ORGANISMS/CRU_TS_3.0/cru_ts_3_00.1901.2006.tmp.nc |
|
| 359 |
rm $ORGANISMS/CRU_TS_3.0/cru_ts_3_00.1901.2006.tmx.nc |
|
| 360 |
# migrate extracted ASCII grid files |
|
| 361 |
mv $ORGANISMS/CRU_TS_3.0/PRE $LAYERS/data/climate/cru-ts-3.0-1967-2006-asc-pre |
|
| 362 |
mv $ORGANISMS/CRU_TS_3.0/TMN $LAYERS/data/climate/cru-ts-3.0-1967-2006-asc-tmn |
|
| 363 |
mv $ORGANISMS/CRU_TS_3.0/TMP $LAYERS/data/climate/cru-ts-3.0-1967-2006-asc-tmp |
|
| 364 |
mv $ORGANISMS/CRU_TS_3.0/TMX $LAYERS/data/climate/cru-ts-3.0-1967-2006-asc-tmx |
|
| 365 |
# migrate R script for asc extraction |
|
| 366 |
mv -i $ORGANISMS/CRU_TS_3.0/R/cru_3.0_data_extract.r $LAYERS/code/climate/ |
|
| 367 |
# rename then migrate readmes |
|
| 368 |
rename 's/(Read_Me)/clim-cru-ts-3.0-\1/' $ORGANISMS/CRU_TS_3.0/Read_Me_*.txt |
|
| 369 |
mv $ORGANISMS/CRU_TS_3.0/*Read_Me_*.txt $LAYERS/documentation/climate/ |
|
| 370 |
# now remove empty directory structure |
|
| 371 |
find $ORGANISMS/CRU_TS_3.0 -depth -type d -exec rmdir {} \;
|
|
| 372 |
|
|
| 373 |
# |
|
| 374 |
# GSOD |
|
| 375 |
# |
|
| 376 |
|
|
| 377 |
# for now, just move the whole thing as-is |
|
| 378 |
mv $ORGANISMS/gsod $LAYERS/data/climate/gsod |
|
| 379 |
|
|
| 380 |
# |
|
| 381 |
# GHCN |
|
| 382 |
# |
|
| 383 |
|
|
| 384 |
# for now, just move the whole thing as-is |
|
| 385 |
mv $ORGANISMS/ghcn $LAYERS/data/climate/ghcn |
|
| 386 |
|
|
| 387 |
# |
|
| 388 |
# MODIS LST |
|
| 389 |
# |
|
| 390 |
|
|
| 391 |
# migrate MOD11A1 V4 daily 1km L3 LST (March 1-7, 2000) |
|
| 392 |
mv $ORGANISMS/MODIS\ LST/MOD11A1.004 $LAYERS/data/climate/MOD11A1.004-daily-1km-L3-LST/ |
|
| 393 |
# migrate MOD11A2 V4 8-day 1km L3 LST (March 5, 2000) |
|
| 394 |
mkdir $LAYERS/data/climate/MOD11A2.004-8day-1km-L3-LST |
|
| 395 |
mv $ORGANISMS/MODIS\ LST/2000.03.05 $LAYERS/data/climate/MOD11A2.004-8day-1km-L3-LST/ |
|
| 396 |
# also remove identical copies of the MOD11A2 data (confirmed by diffing) |
|
| 397 |
rm $ORGANISMS/Modis_2000.03.05/MOD11A2.A2000065.*.hdf |
|
| 398 |
rm $ORGANISMS/Modis_2000.03.05/MOD11A2.A2000065.*.hdf.xml |
|
| 399 |
rmdir $ORGANISMS/Modis_2000.03.05 |
|
| 400 |
# remove now-empty directory |
|
| 401 |
rmdir $ORGANISMS/MODIS\ LST |
|
| 402 |
|
|
| 403 |
# |
|
| 404 |
# MODIS LST -- Oregon |
|
| 405 |
# |
|
| 406 |
|
|
| 407 |
# migrate original MODIS OR hdfs (2001-2010?) |
|
| 408 |
mkdir $LAYERS/data/climate/MOD11A1.004-OR-orig |
|
| 409 |
mv $ORGANISMS/MODIS_LST_Oregon/MOD11A1.*.hdf \ |
|
| 410 |
$LAYERS/data/climate/MOD11A1.004-OR-orig/ |
|
| 411 |
mv $ORGANISMS/MODIS_LST_Oregon/MOD11A1.*.hdf.xml \ |
|
| 412 |
$LAYERS/data/climate/MOD11A1.004-OR-orig/ |
|
| 413 |
# migrate original MODIS OR hdfs (2000, not used) |
|
| 414 |
mkdir $LAYERS/data/climate/MOD11A1.004-OR-orig-2000 |
|
| 415 |
mv $ORGANISMS/MODIS_LST_Oregon/2000\ _WithheldFromAVG/MOD11A1.A2000*.hdf \ |
|
| 416 |
$LAYERS/data/climate/MOD11A1.004-OR-orig-2000/ |
|
| 417 |
mv $ORGANISMS/MODIS_LST_Oregon/2000\ _WithheldFromAVG/MOD11A1.A2000*.hdf.xml \ |
|
| 418 |
$LAYERS/data/climate/MOD11A1.004-OR-orig-2000/ |
|
| 419 |
# migrate ClearDayCov OR img extracts (2001-2010?) |
|
| 420 |
mkdir $LAYERS/data/climate/MOD11A1.004-OR-clearday-img |
|
| 421 |
mv $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/ClearDay_Original_IMG_Extracts/MOD11A1.*.img \ |
|
| 422 |
$LAYERS/data/climate/MOD11A1.004-OR-clearday-img/ |
|
| 423 |
mv $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/ClearDay_Original_IMG_Extracts/MOD11A1.*.img.aux.xml \ |
|
| 424 |
$LAYERS/data/climate/MOD11A1.004-OR-clearday-img/ |
|
| 425 |
# migrate ClearDayCov OR img extracts (2000, not used) |
|
| 426 |
mkdir $LAYERS/data/climate/MOD11A1.004-OR-clearday-img-2000 |
|
| 427 |
mv $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/ClearDay_Original_IMG_Extracts/2000_WithheldFromAVG/MOD11A1.A2000*.005_ClearDay.img \ |
|
| 428 |
$LAYERS/data/climate/MOD11A1.004-OR-clearday-img-2000/ |
|
| 429 |
mv $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/ClearDay_Original_IMG_Extracts/2000_WithheldFromAVG/MOD11A1.A2000*.005_ClearDay.img.aux.xml \ |
|
| 430 |
$LAYERS/data/climate/MOD11A1.004-OR-clearday-img-2000/ |
|
| 431 |
|
|
| 432 |
# migrate renamed ClearDayCov OR img extracts (2001-2010?) |
|
| 433 |
mkdir $LAYERS/data/climate/MOD11A1.004-OR-clearday-img-renamed |
|
| 434 |
mv $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/ClearDay_Original_IMG_Extracts/ByDate/*.img \ |
|
| 435 |
$LAYERS/data/climate/MOD11A1.004-OR-clearday-img-renamed/ |
|
| 436 |
# migrate renamed ClearDayCov OR img extracts (2000, not used) |
|
| 437 |
mkdir $LAYERS/data/climate/MOD11A1.004-OR-clearday-img-renamed-2000 |
|
| 438 |
mv $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/ClearDay_Original_IMG_Extracts/ByDate/2000_WithheldFromAVG/MOD11A1.A.2000.*.img \ |
|
| 439 |
$LAYERS/data/climate/MOD11A1.004-OR-clearday-img-renamed-2000/ |
|
| 440 |
|
|
| 441 |
# migrate renamed ClearDayCov OR img extracts with corrected pixels |
|
| 442 |
mkdir $LAYERS/data/climate/MOD11A1.004-OR-clearday-img-renamed-fixed |
|
| 443 |
mv $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/ClearDay_Original_IMG_Extracts/ByDate/BadPixelsCorrected_Tiles/*.img \ |
|
| 444 |
$LAYERS/data/climate/MOD11A1.004-OR-clearday-img-renamed-fixed/ |
|
| 445 |
mv $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/ClearDay_Original_IMG_Extracts/ByDate/BadPixelsCorrected_Tiles/*.img.aux.xml \ |
|
| 446 |
$LAYERS/data/climate/MOD11A1.004-OR-clearday-img-renamed-fixed/ |
|
| 447 |
|
|
| 448 |
# migrate ClearDayCov OR daily avg tiles |
|
| 449 |
mkdir $LAYERS/data/climate/MOD11A1.004-OR-clearday-dailyavg-tiles-img |
|
| 450 |
mv $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_DailyAvgs_Tiles/day*.img \ |
|
| 451 |
$LAYERS/data/climate/MOD11A1.004-OR-clearday-dailyavg-tiles-img/ |
|
| 452 |
mv $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_DailyAvgs_Tiles/day*.img.aux.xml \ |
|
| 453 |
$LAYERS/data/climate/MOD11A1.004-OR-clearday-dailyavg-tiles-img/ |
|
| 454 |
# migrate ClearDayCov OR daily avg mosaic imgs |
|
| 455 |
mkdir $LAYERS/data/climate/MOD11A1.004-OR-clearday-dailyavg-mosaics-img |
|
| 456 |
mv $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_DailyAvgs_Mosaics/Day*_Mosaic_DailyAvg_Scaled.img \ |
|
| 457 |
$LAYERS/data/climate/MOD11A1.004-OR-clearday-dailyavg-mosaics-img |
|
| 458 |
mv $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_DailyAvgs_Mosaics/Day*_Mosaic_DailyAvg_Scaled.img.aux.xml \ |
|
| 459 |
$LAYERS/data/climate/MOD11A1.004-OR-clearday-dailyavg-mosaics-img |
|
| 460 |
# migrate ClearDayCov OR daily avg mosaic bils |
|
| 461 |
mkdir $LAYERS/data/climate/MOD11A1.004-OR-clearday-dailyavg-mosaics-bil |
|
| 462 |
mv $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_DailyAvgs_Mosaics/Day*_Mosaic_DailyAvg_Scaled.prj \ |
|
| 463 |
$LAYERS/data/climate/MOD11A1.004-OR-clearday-dailyavg-mosaics-bil/ |
|
| 464 |
mv $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_DailyAvgs_Mosaics/Day*_Mosaic_DailyAvg_Scaled.bil \ |
|
| 465 |
$LAYERS/data/climate/MOD11A1.004-OR-clearday-dailyavg-mosaics-bil/ |
|
| 466 |
mv $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_DailyAvgs_Mosaics/Day*_Mosaic_DailyAvg_Scaled.bil.aux.xml \ |
|
| 467 |
$LAYERS/data/climate/MOD11A1.004-OR-clearday-dailyavg-mosaics-bil/ |
|
| 468 |
mv $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_DailyAvgs_Mosaics/Day*_Mosaic_DailyAvg_Scaled.hdr \ |
|
| 469 |
$LAYERS/data/climate/MOD11A1.004-OR-clearday-dailyavg-mosaics-bil/ |
|
| 470 |
|
|
| 471 |
# migrate ClearDayCov OR monthly avg tiles |
|
| 472 |
mkdir $LAYERS/data/climate/MOD11A1.004-OR-clearday-monthlyavg-tiles-img |
|
| 473 |
mv $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_MonthlyAvgs_Tiles/*_AVG_Scaled.img \ |
|
| 474 |
$LAYERS/data/climate/MOD11A1.004-OR-clearday-monthlyavg-tiles-img/ |
|
| 475 |
mv $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_MonthlyAvgs_Tiles/*_AVG_Scaled.img.aux.xml \ |
|
| 476 |
$LAYERS/data/climate/MOD11A1.004-OR-clearday-monthlyavg-tiles-img/ |
|
| 477 |
# migrate ClearDayCov OR monthly avg mosaic imgs |
|
| 478 |
mkdir $LAYERS/data/climate/MOD11A1.004-OR-clearday-monthlyavg-mosaics-img |
|
| 479 |
mv $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_MonthlyAvgs_Mosaics/*Mosaic_MonthlyAvg_Scaled.img \ |
|
| 480 |
$LAYERS/data/climate/MOD11A1.004-OR-clearday-monthlyavg-mosaics-img/ |
|
| 481 |
mv $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_MonthlyAvgs_Mosaics/*Mosaic_MonthlyAvg_Scaled.img.aux.xml \ |
|
| 482 |
$LAYERS/data/climate/MOD11A1.004-OR-clearday-monthlyavg-mosaics-img/ |
|
| 483 |
# migrate ClearDayCov OR monthly avg mosaic bils |
|
| 484 |
mkdir $LAYERS/data/climate/MOD11A1.004-OR-clearday-monthlyavg-mosaics-bil |
|
| 485 |
mv $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_MonthlyAvgs_Mosaics/*Mosaic_MonthlyAvg_Scaled.prj \ |
|
| 486 |
$LAYERS/data/climate/MOD11A1.004-OR-clearday-monthlyavg-mosaics-bil/ |
|
| 487 |
mv $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_MonthlyAvgs_Mosaics/*Mosaic_MonthlyAvg_Scaled.bil \ |
|
| 488 |
$LAYERS/data/climate/MOD11A1.004-OR-clearday-monthlyavg-mosaics-bil/ |
|
| 489 |
mv $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_MonthlyAvgs_Mosaics/*Mosaic_MonthlyAvg_Scaled.bil.aux.xml \ |
|
| 490 |
$LAYERS/data/climate/MOD11A1.004-OR-clearday-monthlyavg-mosaics-bil/ |
|
| 491 |
mv $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_MonthlyAvgs_Mosaics/*Mosaic_MonthlyAvg_Scaled.hdr \ |
|
| 492 |
$LAYERS/data/climate/MOD11A1.004-OR-clearday-monthlyavg-mosaics-bil/ |
|
| 493 |
|
|
| 494 |
# migrate *old* (wrong?) ClearDayCov OR daily avg tiles |
|
| 495 |
mkdir $LAYERS/data/climate/MOD11A1.004-OR-clearday-dailyavg-tiles-img-OLD |
|
| 496 |
mv $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/ClearDay_DailyAverage_Tiles_Old/Day_*_Average_Scaled_*.img \ |
|
| 497 |
$LAYERS/data/climate/MOD11A1.004-OR-clearday-dailyavg-tiles-img-OLD/ |
|
| 498 |
mv $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/ClearDay_DailyAverage_Tiles_Old/Day_*_Average_Scaled_*.img.aux.xml \ |
|
| 499 |
$LAYERS/data/climate/MOD11A1.004-OR-clearday-dailyavg-tiles-img-OLD/ |
|
| 500 |
# migrate *old* (wrong?) ClearDayCov OR daily avg mosaics |
|
| 501 |
mkdir $LAYERS/data/climate/MOD11A1.004-OR-clearday-dailyavg-mosaics-img-OLD |
|
| 502 |
mv $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/ClearDay_DailyAverage_Mosaic_Old/Day_*_ClearDay_Average.img \ |
|
| 503 |
$LAYERS/data/climate/MOD11A1.004-OR-clearday-dailyavg-mosaics-img-OLD/ |
|
| 504 |
mv $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/ClearDay_DailyAverage_Mosaic_Old/Day_*_ClearDay_Average.img.aux.xml \ |
|
| 505 |
$LAYERS/data/climate/MOD11A1.004-OR-clearday-dailyavg-mosaics-img-OLD/ |
|
| 506 |
|
|
| 507 |
# remove identical copies of (old) ClearDayCov daily avgs for tile h08v04 |
|
| 508 |
# *Note*: I first confirmed that these are duplicate copies: |
|
| 509 |
# for i in {1..366};
|
|
| 510 |
# do |
|
| 511 |
# diff -q $ORGANISMS/MODIS_LST_Oregon/DailyAvg1_old/Day_"$i"_Average_Scaled.img \ |
|
| 512 |
# $LAYERS/data/climate/MOD11A1.004-OR-clearday-dailyavg-tiles-img-OLD/Day_"$i"_Average_Scaled_h08v04.img |
|
| 513 |
# done |
|
| 514 |
rm $ORGANISMS/MODIS_LST_Oregon/DailyAvg1_old/Day_{1..366}_Average_Scaled.img
|
|
| 515 |
rm $ORGANISMS/MODIS_LST_Oregon/DailyAvg1_old/Day_{1..366}_Average_Scaled.img.aux.xml
|
|
| 516 |
# remove now-empty directory |
|
| 517 |
rmdir $ORGANISMS/MODIS_LST_Oregon/DailyAvg1_old |
|
| 518 |
|
|
| 519 |
# remove misc bil statistics (stx) files) |
|
| 520 |
rm $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_DailyAvgs_Mosaics/Day11_Mosaic_DailyAvg_Scaled.stx |
|
| 521 |
rm $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_DailyAvgs_Mosaics/Day1_Mosaic_DailyAvg_Scaled.stx |
|
| 522 |
rm $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_MonthlyAvgs_Mosaics/AprMosaic_MonthlyAvg_Scaled.stx |
|
| 523 |
|
|
| 524 |
# remove pyc file |
|
| 525 |
rm $ORGANISMS/MODIS_LST_Oregon/GDAL_Extract_ClearDay_from_HDF_Files.pyc |
|
| 526 |
|
|
| 527 |
# move and (if needed) rename documentation files |
|
| 528 |
mv -i $ORGANISMS/MODIS_LST_Oregon/1\ ReadMe\ First.txt \ |
|
| 529 |
$LAYERS/documentation/climate/clim-MOD11A1.004-OR-orig-readme.txt |
|
| 530 |
mv -i $ORGANISMS/MODIS_LST_Oregon/MODIS_Oregon_ProcessingInfo.doc \ |
|
| 531 |
$LAYERS/documentation/climate/ |
|
| 532 |
mv -i $ORGANISMS/MODIS_LST_Oregon/2000\ _WithheldFromAVG/ReadMe \ |
|
| 533 |
$LAYERS/documentation/climate/clim-MOD11A1.004-OR-orig-2000-readme.txt |
|
| 534 |
mv -i $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/1\ ReadMe\ First.txt \ |
|
| 535 |
$LAYERS/documentation/climate/clim-MOD11A1.004-OR-clearday-readme.txt |
|
| 536 |
mv -i $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/ClearDay_Original_IMG_Extracts/ByDate/BadPixelsCorrected_Tiles/1\ ReadMe\ First \ |
|
| 537 |
$LAYERS/documentation/climate/clim-MOD11A1.004-OR-clearday-img-renamed-fixed-readme.txt |
|
| 538 |
|
|
| 539 |
# move scripts |
|
| 540 |
mkdir $LAYERS/code/climate/modis-lst-oregon |
|
| 541 |
mv -i $ORGANISMS/MODIS_LST_Oregon/GDAL_Extract_ClearDay_from_HDF_Files.py \ |
|
| 542 |
$LAYERS/code/climate/modis-lst-oregon/ |
|
| 543 |
mv -i $ORGANISMS/MODIS_LST_Oregon/QCTagCheck \ |
|
| 544 |
$LAYERS/code/climate/modis-lst-oregon/QCTagCheck.py |
|
| 545 |
mv -i $ORGANISMS/MODIS_LST_Oregon/ConvertMODIStobil.py \ |
|
| 546 |
$LAYERS/code/climate/modis-lst-oregon/ |
|
| 547 |
mv -i $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_DailyAvgs_Tiles/DayAVGCalcs_h08v04TIles.r \ |
|
| 548 |
$LAYERS/code/climate/modis-lst-oregon/ |
|
| 549 |
mv -i $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_DailyAvgs_Tiles/DayAVGCalcs_h09v04TIles.r \ |
|
| 550 |
$LAYERS/code/climate/modis-lst-oregon/ |
|
| 551 |
mv -i $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_DailyAvgs_Mosaics/LST_Mosaicing_DailyAvgs.r \ |
|
| 552 |
$LAYERS/code/climate/modis-lst-oregon/ |
|
| 553 |
mv -i $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_MonthlyAvgs_Mosaics/LST_Mosaicing_MonthlyAvgs.R \ |
|
| 554 |
$LAYERS/code/climate/modis-lst-oregon/ |
|
| 555 |
mv -i $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_MonthlyAvgs_Mosaics/Conversion_hdf_to_img.py \ |
|
| 556 |
$LAYERS/code/climate/modis-lst-oregon/ |
|
| 557 |
mv -i $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/ClearDay_Original_IMG_Extracts/ByDate/BadPixelsCorrected_Tiles/h09v04Tiles_BadPixelCorrection.r \ |
|
| 558 |
$LAYERS/code/climate/modis-lst-oregon/ |
|
| 559 |
mv -i $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/ClearDay_Original_IMG_Extracts/ByDate/BadPixelsCorrected_Tiles/h08v04Tiles_BadPixelCorrection.r \ |
|
| 560 |
$LAYERS/code/climate/modis-lst-oregon/ |
|
| 561 |
mv -i $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/ClearDay_Original_IMG_Extracts/Convert\ MODIS\ Day\ of\ Year\ to\ Date\ File\ Name.py \ |
|
| 562 |
$LAYERS/code/climate/modis-lst-oregon/ |
|
| 563 |
mv -i $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_MonthlyAvgs_Tiles/MonthlyAvgCalcs_h08v04Tiles.r \ |
|
| 564 |
$LAYERS/code/climate/modis-lst-oregon/ |
|
| 565 |
mv -i $ORGANISMS/MODIS_LST_Oregon/ClearDayGDAL/NewClearDay_MonthlyAvgs_Tiles/MonthlyAvgCalcs_h09v04Tiles.r \ |
|
| 566 |
$LAYERS/code/climate/modis-lst-oregon/ |
|
| 567 |
|
|
| 568 |
# move last few things... |
|
| 569 |
mv -i $ORGANISMS/MODIS_LST_Oregon/hdf.txt \ |
|
| 570 |
$LAYERS/cruft/clim-MOD11A1.004-OR-orig-hdf.txt |
|
| 571 |
mv -i $ORGANISMS/MODIS_LST_Oregon/SDS_PctFills.txt \ |
|
| 572 |
$LAYERS/cruft/clim-MOD11A1.004-OR-orig-SDS_PctFills.txt |
|
| 573 |
|
|
| 574 |
# remove all the now-empty directories... |
|
| 575 |
# tree $ORGANISMS/MODIS_LST_Oregon |
|
| 576 |
# /home/organisms/MODIS_LST_Oregon |
|
| 577 |
# . |
|
| 578 |
# ├── 2000 _WithheldFromAVG |
|
| 579 |
# └── ClearDayGDAL |
|
| 580 |
# ├── ClearDay_DailyAverage_Mosaic_Old |
|
| 581 |
# ├── ClearDay_DailyAverage_Tiles_Old |
|
| 582 |
# ├── ClearDay_Original_IMG_Extracts |
|
| 583 |
# │ ├── 2000_WithheldFromAVG |
|
| 584 |
# │ └── ByDate |
|
| 585 |
# │ ├── 2000_WithheldFromAVG |
|
| 586 |
# │ └── BadPixelsCorrected_Tiles |
|
| 587 |
# ├── NewClearDay_DailyAvgs_Mosaics |
|
| 588 |
# ├── NewClearDay_DailyAvgs_Tiles |
|
| 589 |
# ├── NewClearDay_MonthlyAvgs_Mosaics |
|
| 590 |
# └── NewClearDay_MonthlyAvgs_Tiles |
|
| 591 |
find $ORGANISMS/MODIS_LST_Oregon -depth -type d -exec rmdir {} \;
|
|
| 592 |
|
|
| 593 |
# last but not least, deal with top level R directory |
|
| 594 |
# ...move some (old? superceded?) scripts |
|
| 595 |
mv -i $ORGANISMS/R/ReClass Clear Day Rasters h08v04.r \ |
|
| 596 |
$LAYERS/code/climate/modis-lst-oregon/ |
|
| 597 |
mv -i $ORGANISMS/R/Calc Clear Day Daily Avg.r \ |
|
| 598 |
$LAYERS/code/climate/modis-lst-oregon/ |
|
| 599 |
mv -i $ORGANISMS/R/Mosaic Clear Day Average Grids.r \ |
|
| 600 |
$LAYERS/code/climate/modis-lst-oregon/ |
|
| 601 |
mv -i $ORGANISMS/R/Calc Clear Day Monthly Avg.r \ |
|
| 602 |
$LAYERS/code/climate/modis-lst-oregon/ |
|
| 603 |
# don't know how this was created, but it's clearly derived data... |
|
| 604 |
mv -i $ORGANISMS/R/Modis_LSTdaily_climatology $LAYERS/data/clim-modis-lstdaily |
|
| 605 |
# remove now-empty directory |
|
| 606 |
rmdir $ORGANISMS/R |
|
| 607 |
|
|
| 608 |
# |
|
| 609 |
# TRMM |
|
| 610 |
# |
|
| 611 |
|
|
| 612 |
# this was an *empty* directory! removing... |
|
| 613 |
rmdir $ORGANISMS/TRMM |
|
| 614 |
|
|
| 615 |
# |
|
| 616 |
# WorldClim |
|
| 617 |
# |
|
| 618 |
|
|
| 619 |
# migrate each one into its own directory |
|
| 620 |
mkdir $LAYERS/data/climate/worldclim-bio-30s-esri-zip |
|
| 621 |
mv $ORGANISMS/WorldClim/bio_30s_esri.zip $LAYERS/data/climate/worldclim-bio-30s-esri-zip/ |
|
| 622 |
mkdir $LAYERS/data/climate/worldclim-prec-30s-esri-zip |
|
| 623 |
mv $ORGANISMS/WorldClim/prec_30s_esri.zip $LAYERS/data/climate/worldclim-prec-30s-esri-zip/ |
|
| 624 |
mkdir $LAYERS/data/climate/worldclim-tmax-30s-esri-zip |
|
| 625 |
mv $ORGANISMS/WorldClim/tmax_30s_esri.zip $LAYERS/data/climate/worldclim-tmax-30s-esri-zip/ |
|
| 626 |
mkdir $LAYERS/data/climate/worldclim-tmean-30s-esri-zip |
|
| 627 |
mv $ORGANISMS/WorldClim/tmean_30s_esri.zip $LAYERS/data/climate/worldclim-tmean-30s-esri-zip/ |
|
| 628 |
mkdir $LAYERS/data/climate/worldclim-tmin-30s-esri-zip |
|
| 629 |
mv $ORGANISMS/WorldClim/tmin_30s_esri.zip $LAYERS/data/climate/worldclim-tmin-30s-esri-zip/ |
|
| 630 |
# remove now-empty directory |
|
| 631 |
rmdir $ORGANISMS/WorldClim |
|
| 632 |
|
|
| 633 |
|
|
| 634 |
#============# |
|
| 635 |
# LAND COVER # |
|
| 636 |
#============# |
|
| 637 |
|
|
| 638 |
# |
|
| 639 |
# GLCNMO |
|
| 640 |
# |
|
| 641 |
|
|
| 642 |
# for now, just move the whole thing as-is |
|
| 643 |
mv $ORGANISMS/GLCNMO $LAYERS/experimental/land-cover/ |
|
| 644 |
|
|
| 645 |
# |
|
| 646 |
# GlobCover |
|
| 647 |
# |
|
| 648 |
# migrate what seems like the original data (?) |
|
| 649 |
mkdir $LAYERS/data/land-cover/GlobCover-v2.2 |
|
| 650 |
mv -i $ORGANISMS/GlobCoverv2.2/GLOBCOVER_200412_200606_V2.2_Global_CLA* \ |
|
| 651 |
$LAYERS/data/land-cover/GlobCover-v2.2/ |
|
| 652 |
# migrate mysterious derivatives of the above |
|
| 653 |
mkdir $LAYERS/data/land-cover/GlobCover-v2.2-arcgis |
|
| 654 |
mv -i $ORGANISMS/GlobCoverv2.2/globcov22_beh $LAYERS/data/land-cover/GlobCover-v2.2-arcgis/ |
|
| 655 |
mv -i $ORGANISMS/GlobCoverv2.2/globcoverv22 $LAYERS/data/land-cover/GlobCover-v2.2-arcgis/ |
|
| 656 |
# migrate reference info to documentation area |
|
| 657 |
mv -i $ORGANISMS/GlobCoverv2.2/Globcover_* $LAYERS/documentation/land-cover/ |
|
| 658 |
# remove now-empty directory |
|
| 659 |
rmdir $ORGANISMS/GlobCoverv2.2 |
|
| 660 |
|
|
| 661 |
# |
|
| 662 |
# LandCover (whatever that is) |
|
| 663 |
# |
|
| 664 |
|
|
| 665 |
# remove gdal-generated metadata file |
|
| 666 |
rm $ORGANISMS/LandCover/Layer10_Clip1.tif.aux.xml |
|
| 667 |
# migrate original OR landcover tiles |
|
| 668 |
mkdir $LAYERS/data/land-cover/lc-OR-tiles |
|
| 669 |
mv $ORGANISMS/LandCover/Layer*_Clip[1-3].tif \ |
|
| 670 |
$LAYERS/data/land-cover/lc-OR-tiles/ |
|
| 671 |
# migrate OR landcover mosaics |
|
| 672 |
mkdir $LAYERS/data/land-cover/lc-OR-mosaic |
|
| 673 |
mv $ORGANISMS/LandCover/Layer*_Mosaic.tif \ |
|
| 674 |
$LAYERS/data/land-cover/lc-OR-mosaic/ |
|
| 675 |
# migrate OR clipped/reprojected landcover mosaics |
|
| 676 |
mkdir $LAYERS/data/land-cover/lc-OR-mosaic-clip-proj-sinu |
|
| 677 |
mv $ORGANISMS/LandCover/Layer*_ClippedToMODIS_Sinu.* \ |
|
| 678 |
$LAYERS/data/land-cover/lc-OR-mosaic-clip-proj-sinu/ |
|
| 679 |
# migrate OR multiband clipped/reprojected landcover mosaic |
|
| 680 |
mkdir $LAYERS/data/land-cover/lc-OR-mosaic-clip-proj-sinu-multiband |
|
| 681 |
mv $ORGANISMS/LandCover/Final_Multiband_SinuGrid.* \ |
|
| 682 |
$LAYERS/data/land-cover/lc-OR-mosaic-clip-proj-sinu-multiband/ |
|
| 683 |
# migrate documentation |
|
| 684 |
mv $ORGANISMS/LandCover/ReadMe $LAYERS/documentation/land-cover/landcover-ReadMe.txt |
|
| 685 |
mv $ORGANISMS/LandCover/LCT\ calculations.xlsx $LAYERS/documentation/land-cover/ |
|
| 686 |
mv $ORGANISMS/LandCover/landcover_method_v3.docx $LAYERS/documentation/land-cover/ |
|
| 687 |
# migrate scripts |
|
| 688 |
mv $ORGANISMS/LandCover/CheckForNoDataValues_LandCoverFiles.txt $LAYERS/code/land-cover/ |
|
| 689 |
# remove now-empty directory |
|
| 690 |
rmdir $ORGANISMS/LandCover |
|
| 691 |
|
|
| 692 |
# |
|
| 693 |
# Tree height |
|
| 694 |
# |
|
| 695 |
|
|
| 696 |
# migrate $ORGANISMS/Tree_height/Lefsky2010 |
|
| 697 |
mkdir $LAYERS/data/land-cover/treeheight-lefsky2010 |
|
| 698 |
mv $ORGANISMS/Tree_height/Lefsky2010/x2_080809_global.img \ |
|
| 699 |
$LAYERS/data/land-cover/treeheight-lefsky2010/ |
|
| 700 |
mv $ORGANISMS/Tree_height/Lefsky2010/p_080809_global.img* \ |
|
| 701 |
$LAYERS/data/land-cover/treeheight-lefsky2010/ |
|
| 702 |
# migrate associated publication do documentation area |
|
| 703 |
mv $ORGANISMS/Tree_height/Lefsky2010/Lefsky\ et\ al.\ 2010\ GeoRLett.pdf \ |
|
| 704 |
$LAYERS/documentation/land-cover/treeheight-Lefsky2010-GeoRLett.pdf |
|
| 705 |
# remove now-empty directory |
|
| 706 |
rmdir $ORGANISMS/Tree_height/Lefsky2010 |
|
| 707 |
|
|
| 708 |
# migrate $ORGANISMS/Tree_height/Simard2011 |
|
| 709 |
mkdir $LAYERS/data/land-cover/treeheight-simard2011 |
|
| 710 |
mv $ORGANISMS/Tree_height/Simard2011/Simard_Pinto_3DGlobalVeg_JGR.tif \ |
|
| 711 |
$LAYERS/data/land-cover/treeheight-simard2011/ |
|
| 712 |
# remove gdal-generated metadata file |
|
| 713 |
rm $ORGANISMS/Tree_height/Simard2011/Simard_Pinto_3DGlobalVeg_JGR.tif.aux.xml |
|
| 714 |
# migrate clipped/reprojected file (bil) |
|
| 715 |
mkdir $LAYERS/data/land-cover/treeheight-simard2011-OR-clip-proj-sinu-bil |
|
| 716 |
mv $ORGANISMS/Tree_height/Simard2011/GlobalCanopy_ClippedToMODIS_InSinu.* \ |
|
| 717 |
$LAYERS/data/land-cover/treeheight-simard2011-OR-clip-proj-sinu-bil/ |
|
| 718 |
# migrate documentation |
|
| 719 |
mv $ORGANISMS/Tree_height/Simard2011/SimardEtAl2011_GlobalTreeHeight_WithLIDAR.pdf \ |
|
| 720 |
$LAYERS/documentation/land-cover/treeheight-SimardEtAl_GlobalTreeHeight_WithLIDAR.pdf |
|
| 721 |
mv $ORGANISMS/Tree_height/Simard2011/ReadMe \ |
|
| 722 |
$LAYERS/documentation/land-cover/treeheight-ReadMe.txt |
|
| 723 |
# remove remaining files as per instructions from Natalie Robinson |
|
| 724 |
rm $ORGANISMS/Tree_height/Simard2011/Test_Clip.tif |
|
| 725 |
rm $ORGANISMS/Tree_height/Simard2011/GDALTranslate_test.* |
|
| 726 |
rm $ORGANISMS/Tree_height/Simard2011/GDALTranslate_DT_int16.* |
|
| 727 |
# remove now-empty directory |
|
| 728 |
rmdir $ORGANISMS/Tree_height/Simard2011 |
|
| 729 |
|
|
| 730 |
# lastely, remove now-empty Tree_height directory |
|
| 731 |
rmdir $ORGANISMS/Tree_height |
|
| 732 |
|
|
| 733 |
|
|
| 734 |
#=================# |
|
| 735 |
# Remaining stuff # |
|
| 736 |
#=================# |
|
| 737 |
|
|
| 738 |
# |
|
| 739 |
# top level directory |
|
| 740 |
# |
|
| 741 |
|
|
| 742 |
# move top level notes |
|
| 743 |
mv $ORGANISMS/Oregon_CaseStudy_FileProcessingInfo $LAYERS/documentation/ |
|
| 744 |
mv $ORGANISMS/ReProjection_To_MODIS $LAYERS/documentation/ |
|
| 745 |
mv $ORGANISMS/README.txt $LAYERS/documentation/organisms-homedir-readme.txt |
|
| 746 |
mv $ORGANISMS/CHANGES.txt $LAYERS/documentation/organisms-homedir-changes.txt |
|
| 747 |
# move old file extension summary |
|
| 748 |
mv -i $ORGANISMS/file-extension-summary.txt $LAYERS/cruft/ |
|
| 749 |
|
|
| 750 |
# |
|
| 751 |
# Desktop |
|
| 752 |
# |
|
| 753 |
|
|
| 754 |
# move MRT installer to cruft |
|
| 755 |
mv $ORGANISMS/Desktop/MRT_download_Linux $LAYERS/cruft/ |
|
| 756 |
# remove orphaned bil metadata file |
|
| 757 |
rm $ORGANISMS/Desktop/ASTER_Test.bil.aux.xml |
|
| 758 |
# remove empty Desktop dir |
|
| 759 |
rmdir $ORGANISMS/Desktop |
|
| 760 |
|
|
| 761 |
# |
|
| 762 |
# pyhdf |
|
| 763 |
# |
|
| 764 |
|
|
| 765 |
# move pyhdf package to cruft |
|
| 766 |
mv $ORGANISMS/pyhdf $LAYERS/cruft/ |
|
| 767 |
|
|
| 768 |
# |
|
| 769 |
# GIS/GDD |
|
| 770 |
# |
|
| 771 |
|
|
| 772 |
# confirmed that /tmean contains unzipped tmean, except there are additional |
|
| 773 |
# aux files presumably autogenerated by Arc -- I'm find with deleting them |
|
| 774 |
# # ---- bash code ---# |
|
| 775 |
# cd /tmp && unzip $ORGANISMS/GIS/GDD/tmean_30s_esri.zip |
|
| 776 |
# diff -qr /tmp/tmean /home/organisms/GIS/GDD/tmean_30s_esri/tmean/ |
|
| 777 |
# done |
|
| 778 |
# # ------------------# |
|
| 779 |
# delete the uncompressed tmean_30s_esri directory |
|
| 780 |
rm -r $ORGANISMS/GIS/GDD/tmean_30s_esri |
|
| 781 |
|
|
| 782 |
# confirmed that WorldClim zips are identical to what we already have elsewhere |
|
| 783 |
# # ---- bash code ---# |
|
| 784 |
# for var in {'prec','tmin','tmax','tmean','bio'}
|
|
| 785 |
# do |
|
| 786 |
# diff -s $ORGANISMS/GIS/GDD/"$var"_30s_esri.zip \ |
|
| 787 |
# $LAYERS/data/climate/worldclim-"$var"-30s-esri-zip/*.zip |
|
| 788 |
# done |
|
| 789 |
# done |
|
| 790 |
# # ------------------# |
|
| 791 |
# delete the duplicate worldclim zips |
|
| 792 |
rm $ORGANISMS/GIS/GDD/prec_30s_esri.zip |
|
| 793 |
rm $ORGANISMS/GIS/GDD/tmin_30s_esri.zip |
|
| 794 |
rm $ORGANISMS/GIS/GDD/tmax_30s_esri.zip |
|
| 795 |
rm $ORGANISMS/GIS/GDD/tmean_30s_esri.zip |
|
| 796 |
rm $ORGANISMS/GIS/GDD/bio_30s_esri.zip |
|
| 797 |
|
|
| 798 |
# confirmed that all MODIS files here are identical to (though in fact they are |
|
| 799 |
# only a subset of) what we already have elsewhere |
|
| 800 |
# # ---- bash code ---# |
|
| 801 |
# for dir in `ls $ORGANISMS/GIS/GDD/MOD11A1.004` |
|
| 802 |
# do |
|
| 803 |
# echo checking "$dir"... |
|
| 804 |
# ls $ORGANISMS/GIS/GDD/MOD11A1.004/"$dir" \ |
|
| 805 |
# | xargs -I+ \ |
|
| 806 |
# diff -q $ORGANISMS/GIS/GDD/MOD11A1.004/"$dir"/+ \ |
|
| 807 |
# $LAYERS/data/climate/MOD11A1.004-daily-1km-L3-LST/"$dir"/+ |
|
| 808 |
# done |
|
| 809 |
# # ------------------# |
|
| 810 |
# delete the duplicate MODIS data |
|
| 811 |
# note that the last 3 dirs were already empty... |
|
| 812 |
rm $ORGANISMS/GIS/GDD/MOD11A1.004/2000.03.01/MOD11A1.A2000*.{hdf,hdf.xml}
|
|
| 813 |
rmdir $ORGANISMS/GIS/GDD/MOD11A1.004/2000.03.01 |
|
| 814 |
rm $ORGANISMS/GIS/GDD/MOD11A1.004/2000.03.02/MOD11A1.A2000*.{hdf,hdf.xml}
|
|
| 815 |
rmdir $ORGANISMS/GIS/GDD/MOD11A1.004/2000.03.02 |
|
| 816 |
rm $ORGANISMS/GIS/GDD/MOD11A1.004/2000.03.03/MOD11A1.A2000*.{hdf,hdf.xml}
|
|
| 817 |
rmdir $ORGANISMS/GIS/GDD/MOD11A1.004/2000.03.03 |
|
| 818 |
rm $ORGANISMS/GIS/GDD/MOD11A1.004/2000.03.04/MOD11A1.A2000*.{hdf,hdf.xml}
|
|
| 819 |
rmdir $ORGANISMS/GIS/GDD/MOD11A1.004/2000.03.04 |
|
| 820 |
rmdir $ORGANISMS/GIS/GDD/MOD11A1.004/2000.03.05 |
|
| 821 |
rmdir $ORGANISMS/GIS/GDD/MOD11A1.004/2000.03.06 |
|
| 822 |
rmdir $ORGANISMS/GIS/GDD/MOD11A1.004/2000.03.07 |
|
| 823 |
rmdir $ORGANISMS/GIS/GDD/MOD11A1.004 |
|
| 824 |
|
|
| 825 |
# migrate remaining text (script?) file |
|
| 826 |
mv $ORGANISMS/GIS/GDD/map\ algebra.txt $LAYERS/code/climate/gdd-worldclim-tmean-map-algebra.txt |
|
| 827 |
# remove empty directory |
|
| 828 |
rmdir $ORGANISMS/GIS/GDD |
|
| 829 |
|
|
| 830 |
# |
|
| 831 |
# GIS/terrain |
|
| 832 |
# |
|
| 833 |
|
|
| 834 |
# remove empty test directory |
|
| 835 |
rmdir $ORGANISMS/GIS/terrain/test |
|
| 836 |
# for now just migrate everything else to experimental area |
|
| 837 |
mv $ORGANISMS/GIS/terrain $LAYERS/experimental/terrain/arcgis |
|
| 838 |
|
|
| 839 |
# remove empty directory |
|
| 840 |
rmdir $ORGANISMS/GIS |
|
| 841 |
|
|
| 842 |
# |
|
| 843 |
# Oregon |
|
| 844 |
# |
|
| 845 |
|
|
| 846 |
# TODO |
|
| 847 |
|
|
| 848 |
# |
|
| 849 |
# steph |
|
| 850 |
# |
|
| 851 |
|
|
| 852 |
# delete as per verbal instructions from Stephanie Pau |
|
| 853 |
rm -rf $ORGANISMS/steph |
|
| 854 |
|
|
| 855 |
# |
|
| 856 |
# topo |
|
| 857 |
# |
|
| 858 |
|
|
| 859 |
# for now just migrate to experimental area |
|
| 860 |
mv $ORGANISMS/topo $LAYERS/experimental/ |
|
| 861 |
|
|
| 862 |
# |
|
| 863 |
# temp_benoit |
|
| 864 |
# |
|
| 865 |
|
|
| 866 |
# for now just migrate to experimental area |
|
| 867 |
mv $ORGANISMS/temp_benoit $LAYERS/experimental/ |
|
| 868 |
|
|
| 869 |
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|
| 870 |
#======================================================================= |
|
| 871 |
# fix up permissions and ownership |
|
| 872 |
#======================================================================= |
|
| 873 |
|
|
| 874 |
chgrp -R layers $LAYERS/data |
|
| 875 |
find $LAYERS/data -type f -exec chmod 640 {} \;
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|
| 876 |
find $LAYERS/data -type d -exec chmod g-s {} \;
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|
| 877 |
find $LAYERS/data -type d -exec chmod 750 {} \;
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Also available in: Unified diff
added organisms->layers content migration 'script'