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project:bioosm:start [2018/06/07 23:21] – [K cemu to je] sumie-dhproject:bioosm:start [2018/07/15 14:35] – Added links to wikipedia; plaintext log sachy
Line 97: Line 97:
  
 ==== parse_tellico.sh ==== ==== parse_tellico.sh ====
-<code bash>+<code bash parse_tellico.sh>
 #!/bin/bash #!/bin/bash
 # Parse Tellico database to BioOSM index.htm # Parse Tellico database to BioOSM index.htm
Line 103: Line 103:
 # Print result to stdout # Print result to stdout
 # #
-# Generate minis in simg folder 
 # find ./ -type f -exec mogrify -verbose -layers Dispose -resize 128\>x128\> -quality 100% {} + # find ./ -type f -exec mogrify -verbose -layers Dispose -resize 128\>x128\> -quality 100% {} +
 # #
 +# // vectorLayer.removeFeatures(atol)
 +# // map.removeLayer(vectorLayer)
 # #
 # #
Line 112: Line 113:
 #   ./det/ID.htm details of each and every entry #   ./det/ID.htm details of each and every entry
 # #
 +
 +ICON_animalia="animalia.png"
 +ICON_bacteria="bacteria.png"
 +ICON_fungi="fungi.png"
 +ICON_chromista="chromista.png"
 +ICON_plantae="plantae.svg"
 +ICON_plostenkoid="plostenkoid.png"
 +ICON_protista="protista.png"
 +ICON_biohazard="biohazard.svg"
 +
 +# Return icon by Regnum
 +function geticon () {
 + case "$1" in
 + "Animalia")
 + echo "$ICON_animalia";;
 + "Bacteria")
 + echo "$ICON_bacteria";;
 + "Fungi")
 + echo "$ICON_fungi";;
 + "Chromista")
 + echo "$ICON_chromista";;
 + "Plantae")
 + echo "$ICON_plantae";;
 + "Protista")
 + echo "$ICON_protista";;
 + *)
 + echo "$ICON_biohazard";;
 + esac
 +}
 +
  
 rm -rfv "./det/*" rm -rfv "./det/*"
Line 128: Line 159:
 echo '<head>' echo '<head>'
 echo ' <meta http-equiv="Content-Type" content="text/html; charset=utf-8">' echo ' <meta http-equiv="Content-Type" content="text/html; charset=utf-8">'
-echo ' <title>BioOSM</title>'+echo ' <title>brmlab - BioOSM</title>'
 echo ' <link rel="stylesheet" href="./style.css" type="text/css">' echo ' <link rel="stylesheet" href="./style.css" type="text/css">'
 +echo ' <link rel="favicon" href="./'$ICON_biohazard'">'
 echo ' <script src="./OpenLayers.js"></script>' echo ' <script src="./OpenLayers.js"></script>'
 echo '</head>' echo '</head>'
  
 echo "<body>" echo "<body>"
- echo "<h1 id='title'>BioOSM - armis biologica in tuis vicinia</h1>"+ echo "<div style='position:absolute;top:0;right:0;margin:1em'><b><a href='./plainlog.htm'>Plaintext log</a></b></div>" 
 + echo "<h1 id='title'>BioOSM - arma biologica in tuis vicinia</h1>"
  
  # Generate select  # Generate select
Line 189: Line 222:
 ox="" # Old X ox="" # Old X
 oy="" # Old Y oy="" # Old Y
 +datelog="" # Entries sorted by date for plaintext log
 +
  
 while IFS='' read -r radek || [[ -n "$radek" ]]; do while IFS='' read -r radek || [[ -n "$radek" ]]; do
Line 197: Line 232:
  kdex=$(echo "$kde" | grep -oPe '[0-9]{2}\.[0-9]{1,10}$')  kdex=$(echo "$kde" | grep -oPe '[0-9]{2}\.[0-9]{1,10}$')
  kdey=$(echo "$kde" | grep -oPe '^[0-9]{2}\.[0-9]{1,10}')  kdey=$(echo "$kde" | grep -oPe '^[0-9]{2}\.[0-9]{1,10}')
- kdy=$(echo "$radek" | grep -oe ' <taken-date>.*</taken-date> ' | sed -E 's/( )*<(\/)?taken-date>( )*//g')+ kdy=$(echo "$radek" | grep -oe ' <taken-date>.*</taken-date> ' | sed -E 's/( )*<(\/)?taken-date>( )*//g' | sed -E 's/([0-9]+)\.([0-9]+)\.([0-9]{4})/\3-\2-\1/g' | sed -E 's/-([0-9])-/-0\1-/g' | sed -E 's/-([0-9])$/-0\1/g')
  skop_typ=$(echo "$radek" | grep -oe ' <new-field-1>.*</new-field-1> ' | sed -E 's/( )*<(\/)?new-field-1>( )*//g')  skop_typ=$(echo "$radek" | grep -oe ' <new-field-1>.*</new-field-1> ' | sed -E 's/( )*<(\/)?new-field-1>( )*//g')
  skop=$(echo "$radek" | grep -oe ' <microscope>.*</microscope> ' | sed -E 's/( )*<(\/)?microscope>( )*//g')  skop=$(echo "$radek" | grep -oe ' <microscope>.*</microscope> ' | sed -E 's/( )*<(\/)?microscope>( )*//g')
Line 235: Line 270:
  detpg="$detpg</head><body>"  detpg="$detpg</head><body>"
  detpg="$detpg<table class='dettbl'><tr>"  detpg="$detpg<table class='dettbl'><tr>"
- detpg="$detpg<td><h1>$co</h1>"+ detpg="$detpg<td><h1>$co (<a href='https://en.wikipedia.org/wiki/$co' target='_blank'>wiki</a>)</h1>"
  if [[ "$imp" != "" ]]; then  if [[ "$imp" != "" ]]; then
- detpg="$detpg<b>Imperium:</b> $imp<br>"+ detpg="$detpg<b>Imperium:</b> <a href='https://en.wikipedia.org/wiki/$imp' target='_blank'>$imp</a><br>"
  fi  fi
  if [[ "$reg" != "" ]]; then  if [[ "$reg" != "" ]]; then
- detpg="$detpg<b>Regnum:</b> $reg<br>"+ detpg="$detpg<b>Regnum:</b> <a href='https://en.wikipedia.org/wiki/$reg' target='_blank'>$reg</a><br>"
  fi  fi
  if [[ "$phy" != "" ]]; then  if [[ "$phy" != "" ]]; then
- detpg="$detpg<b>Phylum:</b> $phy<br>"+ detpg="$detpg<b>Phylum:</b> <a href='https://en.wikipedia.org/wiki/$phy' target='_blank'>$phy</a><br>"
  fi  fi
  if [[ "$cla" != "" ]]; then  if [[ "$cla" != "" ]]; then
- detpg="$detpg<b>Classis:</b> $cla<br>"+ detpg="$detpg<b>Classis:</b> <a href='https://en.wikipedia.org/wiki/$cla' target='_blank'>$cla</a><br>"
  fi  fi
  if [[ "$ord" != "" ]]; then  if [[ "$ord" != "" ]]; then
- detpg="$detpg<b>Ordo:</b> $ord<br>"+ detpg="$detpg<b>Ordo:</b> <a href='https://en.wikipedia.org/wiki/$ord' target='_blank'>$ord</a><br>"
  fi  fi
  if [[ "$fam" != "" ]]; then  if [[ "$fam" != "" ]]; then
- detpg="$detpg<b>Familia:</b> $fam<br>"+ detpg="$detpg<b>Familia:</b> <a href='https://en.wikipedia.org/wiki/$fam' target='_blank'>$fam</a><br>"
  fi  fi
  if [[ "$gen" != "" ]]; then  if [[ "$gen" != "" ]]; then
- detpg="$detpg<b>Genus:</b> $gen<br>"+ detpg="$detpg<b>Genus:</b> <a href='https://en.wikipedia.org/wiki/$gen' target='_blank'>$gen</a><br>"
  fi  fi
  if [[ "$spe" != "" ]]; then  if [[ "$spe" != "" ]]; then
Line 285: Line 320:
  detpg="$detpg<b>Video:</b> <a href=\"$vid\" target=\"_blank\">$vid</a><br>"  detpg="$detpg<b>Video:</b> <a href=\"$vid\" target=\"_blank\">$vid</a><br>"
  fi  fi
- detpg="$detpg</td><td>"+ detpg="$detpg</td><td style='min-width:66%'>"
  if [[ "$obr" != "" ]]; then  if [[ "$obr" != "" ]]; then
  detpg="$detpg<a href=\"../img/$obr\"><img src=\"../img/$obr\" alt=\"$co\" class='detimg'></a>"  detpg="$detpg<a href=\"../img/$obr\"><img src=\"../img/$obr\" alt=\"$co\" class='detimg'></a>"
Line 299: Line 334:
  detpg="$detpg</body></html>"  detpg="$detpg</body></html>"
  echo "$detpg" > "./det/$detid.htm"  echo "$detpg" > "./det/$detid.htm"
 +
 + # Plain log of entries
 + datelog="$datelog $kdy $kde <a href='./det/$detid.htm' target='_blank'>$co</a><br>\n"
  
  # Pokracujem v hadovi  # Pokracujem v hadovi
Line 310: Line 348:
  fi  fi
  spoj="$spoj<td>$co<br>$kdy</td>"  spoj="$spoj<td>$co<br>$kdy</td>"
 + spoj="$spoj<!-- $reg -->" # Metadata
  spoj="$spoj</tr>"  spoj="$spoj</tr>"
  ox="$kdex"  ox="$kdex"
Line 320: Line 359:
  # Predchozi pozice jen 1 zaznam?  # Predchozi pozice jen 1 zaznam?
  if [[ "$sam" != "" ]]; then  if [[ "$sam" != "" ]]; then
- echo "var n$i = new OpenLayers.Feature.Vector(new OpenLayers.Geometry.Point($ox,$oy).transform(epsg4326,projectTo),{description:'"$sam"'},{externalGraphic:'./$3',graphicHeight:24,graphicWidth:24,graphicXOffset:-12,graphicYOffset:-12});"+ samicon=$(geticon $(echo "$sam" | grep -oPe "<b>Regnum:</b> <[^>]*>[a-zA-Z0-9]*" | grep -oPe "[a-zA-Z0-9]*$")) 
 + # >&2 echo "$samicon" 
 + 
 + echo "var n$i = new OpenLayers.Feature.Vector(new OpenLayers.Geometry.Point($ox,$oy).transform(epsg4326,projectTo),{description:'"$sam"'},{externalGraphic:'./$samicon',graphicHeight:24,graphicWidth:24,graphicXOffset:-12,graphicYOffset:-12});"
  echo "$2.addFeatures(n$i);"  echo "$2.addFeatures(n$i);"
  spoj=""  spoj=""
Line 327: Line 369:
  # Predchozi pozice vic zaznamu?  # Predchozi pozice vic zaznamu?
  if [[ "$spoj" != "" ]]; then  if [[ "$spoj" != "" ]]; then
- echo "var n$i = new OpenLayers.Feature.Vector(new OpenLayers.Geometry.Point($ox,$oy).transform(epsg4326,projectTo),{description:'<table class=\"hadtbl\">"$spoj"</table>'},{externalGraphic:'./$3',graphicHeight:24,graphicWidth:24,graphicXOffset:-12,graphicYOffset:-12});"+ muchicons=$(echo "$spoj" | grep -oPe "<!-- [a-zA-Z0-9]* -->" | grep -oPe "[a-zA-Z0-9]*" | sort | uniq | wc -l) 
 + #>&2 echo "*** $muchicons" 
 + if [[ "$muchicons" == "1" ]]; then 
 + spojicon=$(geticon $(echo "$spoj" | grep -oPe "<!-- [a-zA-Z0-9]* -->" | grep -oPe "[a-zA-Z0-9]*" | sort | uniq)) 
 + #>&2 echo "*** $spojicon" 
 + else 
 + spojicon="$ICON_biohazard" 
 + fi 
 + echo "var n$i = new OpenLayers.Feature.Vector(new OpenLayers.Geometry.Point($ox,$oy).transform(epsg4326,projectTo),{description:'<table class=\"hadtbl\">"$spoj"</table>'},{externalGraphic:'./$spojicon',graphicHeight:24,graphicWidth:24,graphicXOffset:-12,graphicYOffset:-12});"
     echo "$2.addFeatures(n$i);"     echo "$2.addFeatures(n$i);"
  spoj=""  spoj=""
Line 341: Line 391:
  fi  fi
  spoj="$spoj<td>$co<br>$kdy</td>"  spoj="$spoj<td>$co<br>$kdy</td>"
 + spoj="$spoj<!-- $reg -->" # Metadata pyco
  spoj="$spoj</tr>"  spoj="$spoj</tr>"
  
  sam="<a href=\"./det/$detid.htm\" target=\"_blank\"><img src=\"./simg/$obr\" alt=\"$co\" class=\"buttimg\"></a>"  sam="<a href=\"./det/$detid.htm\" target=\"_blank\"><img src=\"./simg/$obr\" alt=\"$co\" class=\"buttimg\"></a>"
- sam="$sam<br><span class=\"butttext\"><b>Qualis:</b> $co<br>"+ sam="$sam<br><span class=\"butttext\">" 
 + sam="$sam<b>Qualis:</b> <a href=\"https://en.wikipedia.org/wiki/$co\" target=\"_blank\">$co</a><br>"
  if [[ "$imp" != "" ]]; then  if [[ "$imp" != "" ]]; then
- sam="$sam<b>Imperium:</b> $imp<br>"+ sam="$sam<b>Imperium:</b> <a href=\"https://en.wikipedia.org/wiki/$imp\" target=\"_blank\">$imp</a><br>"
  fi  fi
  if [[ "$reg" != "" ]]; then  if [[ "$reg" != "" ]]; then
- sam="$sam<b>Regnum:</b> $reg<br>"+ sam="$sam<b>Regnum:</b> <a href=\"https://en.wikipedia.org/wiki/$reg\" target=\"_blank\">$reg</a><br>"
  fi  fi
  if [[ "$phy" != "" ]]; then  if [[ "$phy" != "" ]]; then
- sam="$sam<b>Phylum:</b> $phy<br>"+ sam="$sam<b>Phylum:</b> <a href=\"https://en.wikipedia.org/wiki/$phy\" target=\"_blank\">$phy</a><br>"
  fi  fi
  if [[ "$cla" != "" ]]; then  if [[ "$cla" != "" ]]; then
- sam="$sam<b>Classis:</b> $cla<br>"+ sam="$sam<b>Classis:</b> <a href=\"https://en.wikipedia.org/wiki/$cla\" target=\"_blank\">$cla</a><br>"
  fi  fi
  if [[ "$ord" != "" ]]; then  if [[ "$ord" != "" ]]; then
- sam="$sam<b>Ordo:</b> $ord<br>"+ sam="$sam<b>Ordo:</b> <a href=\"https://en.wikipedia.org/wiki/$ord\" target=\"_blank\">$ord</a><br>"
  fi  fi
  if [[ "$fam" != "" ]]; then  if [[ "$fam" != "" ]]; then
- sam="$sam<b>Familia:</b> $fam<br>"+ sam="$sam<b>Familia:</b> <a href=\"https://en.wikipedia.org/wiki/$fam\" target=\"_blank\">$fam</a><br>"
  fi  fi
  if [[ "$gen" != "" ]]; then  if [[ "$gen" != "" ]]; then
- sam="$sam<b>Genus:</b> $gen<br>"+ sam="$sam<b>Genus:</b> <a href=\"https://en.wikipedia.org/wiki/$gen\" target=\"_blank\">$gen</a><br>"
  fi  fi
  if [[ "$spe" != "" ]]; then  if [[ "$spe" != "" ]]; then
Line 393: Line 445:
  sam="$sam</span>"  sam="$sam</span>"
  
- #>&2 echo "$sam" 
  >&2 echo "$co $obs"  >&2 echo "$co $obs"
  
Line 410: Line 461:
 # Do not forget to print last line when WHILE ends! # Do not forget to print last line when WHILE ends!
 if [[ "$sam" = "" ]]; then if [[ "$sam" = "" ]]; then
 + muchicons=$(echo "$spoj" | grep -oPe "<!-- [a-zA-Z0-9]* -->" | grep -oPe "[a-zA-Z0-9]*" | sort | uniq | wc -l)
 + if [[ "$muchicons" == "1" ]]; then
 + samicon=$(geticon $(echo "$spoj" | grep -oPe "<!-- [a-zA-Z0-9]* -->" | grep -oPe "[a-zA-Z0-9]*" | sort | uniq))
 + else
 + samicon="$ICON_biohazard"
 + fi
  sam="<table style=\"hadtbl\">$spoj</table>"  sam="<table style=\"hadtbl\">$spoj</table>"
 +else
 + samicon=$(geticon $(echo "$sam" | grep -oPe "<b>Regnum:</b> [a-zA-Z0-9]*" | grep -oPe "[a-zA-Z0-9]*$"))
 fi fi
-echo "var n$i = new OpenLayers.Feature.Vector(new OpenLayers.Geometry.Point($kdex,$kdey).transform(epsg4326,projectTo),{description:'"$sam"'},{externalGraphic:'./$3',graphicHeight:24,graphicWidth:24,graphicXOffset:-12,graphicYOffset:-12});"+echo "var n$i = new OpenLayers.Feature.Vector(new OpenLayers.Geometry.Point($kdex,$kdey).transform(epsg4326,projectTo),{description:'"$sam"'},{externalGraphic:'./$samicon',graphicHeight:24,graphicWidth:24,graphicXOffset:-12,graphicYOffset:-12});"
 echo "$2.addFeatures(n$i);" echo "$2.addFeatures(n$i);"
  
Line 418: Line 477:
  
 echo "var ALL = new OpenLayers.Layer.Vector('Overlay',{attribution:'<a href=\"http://brmlab.cz\">Brmlab</a>'});" echo "var ALL = new OpenLayers.Layer.Vector('Overlay',{attribution:'<a href=\"http://brmlab.cz\">Brmlab</a>'});"
-spagety "$praseTC" "ALL" "biohazard.svg"+spagety "$praseTC" "ALL" "$ICON_biohazard"
 echo "map.addLayer(ALL);" echo "map.addLayer(ALL);"
 +
 +# Create plaintext log JUST AFTER "spagety ALL"
 +dateloghtm="<html><head>"
 +dateloghtm="$dateloghtm<meta http-equiv='Content-Type' content='text/html; charset=utf-8'>"
 +dateloghtm="$dateloghtm<link rel='stylesheet' href='./style.css' type='text/css'>"
 +dateloghtm="$dateloghtm<title>Brmlab - BioOSM plaintext log</title>"
 +dateloghtm="$dateloghtm</head><body>"
 +datelogsort=$(echo -e "$datelog" | sort -r | uniq)
 +dateloghtm="$dateloghtm $datelogsort"
 +dateloghtm="$dateloghtm</body></html>"
 +echo "$dateloghtm" > "./plainlog.htm"
  
 echo "var laycon = [vectorLayer,ALL];" # Layer controls JS array echo "var laycon = [vectorLayer,ALL];" # Layer controls JS array
Line 425: Line 495:
  echo "var $spag = new OpenLayers.Layer.Vector('Overlay',{attribution:'<a href=\"http://brmlab.cz\">Brmlab</a>'});"  echo "var $spag = new OpenLayers.Layer.Vector('Overlay',{attribution:'<a href=\"http://brmlab.cz\">Brmlab</a>'});"
  spg=$(echo "$praseTC" | grep "<new-field-4>$spag</new-field-4>")  spg=$(echo "$praseTC" | grep "<new-field-4>$spag</new-field-4>")
- case "$spag" in + icon=$(geticon "$spag")
- "Animalia") +
- icon="animalia.png";; +
- "Bacteria") +
- icon="bacteria.png";; +
- "Fungi") +
- icon="fungi.png";; +
- "Chromista") +
- icon="chromista.png";; +
- "Plantae") +
- icon="plantae.svg";; +
- "Protista") +
- icon="protista.png";; +
- *) +
- icon="biohazard.svg";; +
- esac +
  spagety "$spg" "$spag" "$icon"  spagety "$spg" "$spag" "$icon"
  echo "laycon.push($spag);"  echo "laycon.push($spag);"
Line 449: Line 503:
 spg=$(echo "$praseTC" | grep "<phylum>Platyhelminthes</phylum>") spg=$(echo "$praseTC" | grep "<phylum>Platyhelminthes</phylum>")
 echo "var Platyhelminthes = new OpenLayers.Layer.Vector('Overlay',{attribution:'<a href=\"http://brmlab.cz\">Brmlab</a>'});" echo "var Platyhelminthes = new OpenLayers.Layer.Vector('Overlay',{attribution:'<a href=\"http://brmlab.cz\">Brmlab</a>'});"
-spagety "$spg" "Platyhelminthes" "plostenkoid.png"+spagety "$spg" "Platyhelminthes" "$ICON_plostenkoid"
 echo "laycon.push(Platyhelminthes)" echo "laycon.push(Platyhelminthes)"
  
project/bioosm/start.txt · Last modified: 2023/09/21 12:15 by sachy