BioOSM je mapa vyskytu mikroorganismu (ras, bakterii, plostenek, …) a do budoucna i dalsich prirodnin (mineralu, …).
Podklad jsou OSM, ktere maji API OpenLayers jez umoznuje pridavat do mapy vlastni body, vrstvy…
Jednotliva pozorovani jsou v databazi Tellico. Udelal jsem script parse_tellico.sh, ktery z .tc databaze (je to vlastne ZIP s XML uvnitr) vyparsuje jednotlive polozky a vygeneruje HTML soubor s mapou a podadresar “det” s HTML strankami s detaily jednotlivych pozorovani. Vygeneruje se taky JSON s vyparsovanymi polozkami, ktery lze z webu projektu stahnout.
Pro nadsence je vygenerovany taky prehled prispevku plainlog.htm serazeny dle data pridani do databaze.
Pokud chcete vedet co je noveho, odebirejte projektovou RSS
Obrazky v plnem rozliseni jsou v podadresari “img”, nahledy v “simg”. Videa jsou nahrana na YT a misto nahledu maji generickou ikonu.
Pozorovani ktera se v mape zobrazi lze filtrovat dle prislusnosti k radu (bakterie, zvirata, rostliny,…) az po prislusnost k jednotlivym druhum.
Az se mi ho podari nekam nahrat tak nekde bude. Nebo mozna nejaky webxicht…
praseTC=$(unzip -p "$1" tellico.xml | tr -d '\n' | sed -e $'s/<entry id="/\\\n<entry id="/g' -e $'s/<\/entry>/<\/entry>\\\n/g' | grep -Pe '^<entry id="' | grep "<strcit-do-mapy>yep</strcit-do-mapy>" | sed -E 's/(^.*)(<locality>.*<\/locality>)(.*$)/\2\1\3/' | sort)
Nazvy vrstev musi byt v JS poli kvuli ovladacimu API (skryti/zobrazeni)
var laycon = [vectorLayer,ALL]; ... laycon.push(vrstva);
var controls = { selector: new OpenLayers.Control.SelectFeature(laycon,{onSelect: createPopup, onUnselect: destroyPopup}) }; map.addControl(controls['selector']); controls['selector'].activate();
function kinchange() { kinsel=document.getElementById('kin'); kinopt=kinsel.options[kinsel.selectedIndex].text; for (var i = map.layers.length - 1; i >= 1; i--) { map.removeLayer(map.layers[i]); } map.addLayer(window[kinopt]) }
OpenLayers.Layer.Vector('Overlay',{attribution:'<a href="http://brmlab.cz">Brmlab</a>'});
OSM maji defaultne copyright nesmyslne odsazeny od spodniho okraje mapy, CSS zmena na nejaky rozumny offset:
.olControlAttribution { bottom:0.5em; }
#!/bin/bash # Parse Tellico database to BioOSM index.htm # $1 = tellico .tc file # Print result to /json/*.json # # Creates: # (to stdout) HTML file with the map and static entries # ./det/ID.htm details of each and every entry # ./bioosm.json JSON of all entries # ./bioosm.rss updated RSS feed # ./plainlog.htm sorted entries for easy human/alg # rm -rfv "./det/*" mkdir -p "./det" ICON_animalia="animalia.png" ICON_bacteria="bacteria.png" ICON_fungi="fungi.png" ICON_chromista="chromista.png" ICON_plantae="plantae.svg" ICON_plostenkoid="plostenkoid.png" ICON_protista="protista.png" ICON_biohazard="biohazard.svg" json="" geojson="" rss=$'<?xml version="1.0" encoding="UTF-8" ?>\n' rss+=$'<rss version="2.0">\n' rss+=$'<channel>\n' rss+=$'<title>Brmlab BioOSM RSS feed</title>\n' rss+=$'<description>New entries in the BioOSM database</description>\n' rss+=$'<link>https://bioosm.s0c4.net</link>\n' rss+=$'<lastBuildDate></lastBuildDate>\n' rss+=$'<pubDate></pubDate>\n' rss+=$'<ttl>86400</ttl>\n' # paticka (co, rok, odkaz) function obioosm () { r="<div id='obioosm'><p>Welcome to BioOSM! This site is owned and maintained by members of the <a href='https://brmlab.cz' target='_blank'>hackerspace brmlab</a>. See our wiki page for further <a href='https://brmlab.cz/project/bioosm/start' target='_blank'>details</a><br>License: <a href='https://creativecommons.org/licenses/by-nc-nd/4.0/' target='_blank'>CC BY-NC-ND</a>. In case you have any questions, suggestions, please let us know at bioosm<span id='zavinacvmejlu'></span>s0c4.net.</p><p>To cite any material (including images) in your publication, please use following format: <br><i>Plskova K, Sacha M, brmlab. BioOSM" if [[ "$1" != "" ]]; then r+=" - $1" fi r+=". " if [[ "$2" != "" ]]; then r+="$2. " else r+="2023. " fi if [[ "$3" != "" ]]; then r+="$3" else r+="https://bioosm.s0c4.net" fi r+="</i></p></div>" echo "$r" } # 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 } function safehtml () { echo "$1" | sed -e 's/#/%23/g' -e "s/'/\'/g" -e 's/"/\"/g' -e 's/</\</g' -e 's/>/\>/g' -e 's/^[ ]*//g' -e 's/[ ]*$//g' } function getgeo () { #g=$(echo "$1 $2" | gdallocationinfo -wgs84 ./geo/eusr5000_600dpi_cesko_8b_geo.tif | grep -v 255 | grep -oPe '[0-9]+$') g=$(echo "$1 $2" | gdallocationinfo -wgs84 ./geo/eusr5000_600dpi_cesko_8b_geo.tif | grep -v 255 | grep -oE '[0-9]+$') case "$g" in "1") echo "Fluvial deposits, sediments";; "128") echo "Weathering residues of different rocks, loess";; "130") echo "Volcanic rocks";; "133") echo "Igneous and metamorphic rocks, Palaeozoic sedimentary rocks, loess";; "143") echo "Loess, igneous and metamorphic rocks";; "144") echo "Loess, Cretaceous sandstone and marl";; "147") echo "Igneous, metamorphic and Palaeozoic sedimentary rocks, loess";; "148") echo "Igneous and metamorphic rocks, loess";; "149") echo "Igneous and metamorphic rocks, Palaeozoic sedimentary rocks, loess";; # asi fakt stejny jako 133 omg "150") echo "Igneous and metamorphic rocks, palaeozoic sedimentary rocks";; "153") echo "Sandy and loamy loess, Tertiary sediments, fluvial deposits";; "205") echo "Cretaceous and Tertiary flysch, marl, sandstone, limestone";; *) echo "";; esac } i=1 # GLOBAL increment must persist multiple spagety() calls; incremented to infinity # Core function generating entries matching selection criteria (ie Kingdom) # !!! BEZ ODSAZENI !!! # $1 = list of entries # $2 = layer name = JSON filename without suffix # $3 = icon of the points function spagety () { bylo="" # Minula pozice sam="" # HTML samostatneho zaznamu osam="" # predchozi $sam spoj="" # HTML had z popisu stejnych pozic ospoj="" # Predchozi $spoj ox="" # Old X oy="" # Old Y datelog="" # Entries sorted by date for plaintext log json="var data='{\"version\":\"$(date --rfc-3339=seconds)\",\"fund\":\"$2\",\"arma\":[" geojson='{"type":"FeatureCollection","version":"BIOOSM_' geojson+="$(date --rfc-3339=seconds)" geojson+='","features":[' while IFS='' read -r radek || [[ -n "$radek" ]]; do if [[ "$radek" = "" ]]; then continue; fi entryid=$(echo "$radek" | sed -E 's/^.*<entry id="([0-9]+)">.*$/\1/g;t;d') co=$(echo "$radek" | sed -E 's/^.*<title>(.*)<\/title>.*$/\1/g;t;d') co=$(safehtml "$co") obr=$(echo "$radek" | sed -E 's/^.*<image>(.*)<\/image>.*$/\1/g;t;d' | sed -E 's/^.*\///g') kde=$(echo "$radek" | sed -E 's/^.*<locality>(.*)<\/locality>.*$/\1/g;t;d') kde=$(safehtml "$kde") kdex=$(echo "$kde" | sed -E 's/^[0-9]+\.[0-9]+[, ]*//g;t;d') # keep second part kdey=$(echo "$kde" | sed -E 's/[, ]*[0-9]+\.[0-9]+$//g;t;d') # keep first part kdy=$(echo "$radek" | sed -E 's/^.*<taken-date>(.*)<\/taken-date>.*$/\1/g;t;d' | 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])$/-0\1/g') kdy=$(safehtml "$kdy") skop_typ=$(echo "$radek" | sed -E 's/^.*<new-field-1>(.*)<\/new-field-1>.*$/\1/g;t;d') skop_typ=$(safehtml "$skop_typ") skop=$(echo "$radek" | sed -E 's/^.*<microscope>(.*)<\/microscope>.*$/\1/g;t;d') skop=$(safehtml "$skop") imp=$(echo "$radek" | sed -E 's/^.*<new-field-3>(.*)<\/new-field-3>.*$/\1/g;t;d') imp=$(safehtml "$imp") reg=$(echo "$radek" | sed -E 's/^.*<new-field-4>(.*)<\/new-field-4>.*$/\1/g;t;d') reg=$(safehtml "$reg") phy=$(echo "$radek" | sed -E 's/^.*<phylum>(.*)<\/phylum>.*$/\1/g;t;d') phy=$(safehtml "$phy") cla=$(echo "$radek" | sed -E 's/^.*<class>(.*)<\/class>.*$/\1/g;t;d') cla=$(safehtml "$cla") ord=$(echo "$radek" | sed -E 's/^.*<order>(.*)<\/order>.*$/\1/g;t;d') ord=$(safehtml "$ord") fam=$(echo "$radek" | sed -E 's/^.*<family>(.*)<\/family>.*$/\1/g;t;d') fam=$(safehtml "$fam") gen=$(echo "$radek" | sed -E 's/^.*<genus>(.*)<\/genus>.*$/\1/g;t;d') gen=$(safehtml "$gen") spe=$(echo "$radek" | sed -E 's/^.*<species>(.*)<\/species>.*$/\1/g;t;d') spe=$(safehtml "$spe") loc=$(echo "$radek" | sed -E 's/^.*<locality---plaintext>(.*)<\/locality---plaintext>.*$/\1/g;t;d') loc=$(safehtml "$loc") des=$(echo "$radek" | sed -E 's/^.*<description>(.*)<\/description>.*$/\1/g;t;d') des=$(safehtml "$des") vid=$(echo "$radek" | sed -E 's/^.*<videolink>(.*)<\/videolink>.*$/\1/g;t;d') vid=$(safehtml "$vid") bio=$(echo "$radek" | sed -E 's/^.*<biotope>(.*)<\/biotope>.*$/\1/g;t;d') bio=$(safehtml "$bio") eng=$(echo "$radek" | sed -E 's/^.*<enlargement>(.*)<\/enlargement>.*$/\1/g;t;d') eng=$(safehtml "$eng") obs=$(echo "$radek" | sed -E 's/^.*<observer>(.*)<\/observer>.*$/\1/g;t;d') obs=$(safehtml "$obs") lnk=$(echo "$radek" | sed -E 's/^.*<localitylink>(.*)<\/localitylink>.*$/\1/g;t;d') lnk=$(safehtml "$lnk") har=$(echo "$radek" | sed -E 's/^.*<harvesting-method>(.*)<\/harvesting-method>.*$/\1/g;t;d') den=$(echo "$radek" | sed -E 's/^.*<population-density>(.*)<\/population-density>.*$/\1/g;t;d') dur=$(echo "$radek" | sed -E 's/^.*<min>(.*)<\/min>.*$/\1/g;t;d') lor=$(echo "$radek" | sed -E 's/^.*<locality-reference>(.*)<\/locality-reference>.*$/\1/g;t;d') lrl=$(echo "$radek" | sed -E 's/^.*<locality-reference---link>(.*)<\/locality-reference---link>.*$/\1/g;t;d') lov=$(echo "$radek" | sed -E 's/^.*<locality---vobrazek>(.*)<\/locality---vobrazek>.*$/\1/g;t;d' | sed -E 's/^.*\///g') lov=$(safehtml "$lov") cls=$(echo "$radek" | sed -E 's/^.*<cluster>([0-9]*)<\/cluster>.*$/\1/g;t;d') mpi=$(echo "$radek" | grep -oe ' <mainpic>yep</mainpic> ') elv=$(echo "$kdex $kdey" | gdallocationinfo -wgs84 ./elev/cesko_big.tiff | grep "Value" | grep -oe '[0-9]+$') geo=$(getgeo "$kdex" "$kdey") gra=$(echo "$radek" | sed -E 's/^.*<grant>(.*)<\/grant>.*$/\1/g;t;d') tem=$(echo "$radek" | sed -E 's/^.*<temperature>(.*)<\/temperature>.*$/\1/g;t;d') cnd=$(echo "$radek" | sed -E 's/^.*<conductivity>(.*)<\/conductivity>.*$/\1/g;t;d') ph=$(echo "$radek" | sed -E 's/^.*<ph>(.*)<\/ph>.*$/\1/g;t;d') kar=$(echo "$radek" | sed -E 's/^.*<karyotype>(.*)<\/karyotype>.*$/\1/g;t;d') lid=$(echo "$radek" | sed -E 's/^.*<localityid>(.*)<\/localityid>.*$/\1/g;t;d') #>&2 echo "$co - $har - $den - $dur - $lor - $lrl - $lov - $elv" #continue; detid=$(echo "brmlab$co$obr$kde$kdy" | md5sum | grep -oe '[a-zA-Z0-9]*') if [[ "$kdex" = "" ]]; then >&2 echo -e "\033[31m $lid KDEX '$kde' '$co' \033[0m" >&2 echo -e "\033[31m $lid RADEK '$radek' \033[0m" continue; fi zkurvenetellico=$(echo "$obr" | grep -oe '\.[a-zA-Z]*$') odkurvenyobr=$(echo "$obr" | sed -e 's/%23/#/g') #if [[ "$zkurvenetellico" = ".jpeg" ]]; then if [[ ! -f "./img/$odkurvenyobr" ]]; then if [[ "$gen" != "negative" ]]; then >&2 echo -e "\033[31m $lid OBR $odkurvenyobr $co\033[0m" continue; fi fi obr=$(safehtml "$obr") if [[ "$spe" = "sp." ]]; then wikisp="https://en.wikipedia.org/wiki/$gen" else wikisp="https://en.wikipedia.org/wiki/$gen $spe" fi povr="" povs="" pov="" if [[ "$phy" = "Platyhelminthes" ]]; then povr=$(cat "./povodi_r.json" | ./povodi.py "$kdey" "$kdex") #povrf=$(echo "$povr" | grep -oPe '^[^ ]*' | tr 'e' 'E') povrf=$(echo "$povr" | sed -e 's/ .*$//g' | tr 'e' 'E') povrn=$(echo "$povr" | sed -e 's/^[^ ]* //g') povs=$(cat "./povodi_s.json" | ./povodi.py "$kdey" "$kdex") #povsf=$(echo "$povs" | grep -oPe '^[^ ]*' | tr 'e' 'E') povsf=$(echo "$povs" | sed -e 's/ .*$//g' | tr 'e' 'E') povsn=$(echo "$povs" | sed -e 's/^[^ ]* //g') if (( $(echo "$povsf < $povrf" | bc -l) )) ; then pov="$povsn - $povrn" else pov="$povrn" fi fi if [[ "$cls" = "" ]]; then cls=0 fi if [[ "$mpi" = "" ]]; then mpi="" else mpi="y" fi Tjson="{" Tjson+=" \"title\":\"$co\"," # qualis Tjson+=" \"imperium\":\"$imp\"," Tjson+=" \"regnum\":\"$reg\"," Tjson+=" \"phylum\":\"$phy\"," Tjson+=" \"classis\":\"$cla\"," Tjson+=" \"ordo\":\"$ord\"," Tjson+=" \"familia\":\"$fam\"," Tjson+=" \"genus\":\"$gen\"," Tjson+=" \"specie\":\"$spe\"," Tjson+=" \"locality\":\"$kde\"," # locus Tjson+=" \"x\":\"$kdex\"," Tjson+=" \"y\":\"$kdey\"," Tjson+=" \"locplain\":\"$loc\"," Tjson+=" \"description\":\"$des\"," # depictio Tjson+=" \"takendate\":\"$kdy\"," # quando Tjson+=" \"obr\":\"$obr\"," Tjson+=" \"micro\":\"$skop\"," Tjson+=" \"microtyp\":\"$skop_typ\"," Tjson+=" \"videolink\":\"$vid\"," # vid Tjson+=" \"biotope\":\"$bio\"," # bio Tjson+=" \"enlargement\":\"$eng\"," # amp Tjson+=" \"observer\":\"$obs\"," # spec Tjson+=" \"detid\":\"$detid\"," Tjson+=" \"harvestingmethod\":\"$har\"," # har Tjson+=" \"populationdensity\":\"$den\"," # den Tjson+=" \"min\":\"$dur\"," # dur Tjson+=" \"localityreference\":\"$lor\"," # lor Tjson+=" \"localityreferencelink\":\"$lrl\"," #lrl Tjson+=" \"localityvobrazek\":\"$lov\"," # lov Tjson+=" \"localitylink\":\"$lnk\"," # lnk Tjson+=" \"cluster\":$cls," # cls Tjson+=" \"mainpic\":\"$mpi\"," # mpi Tjson+=" \"pov\":\"$pov\"," Tjson+=" \"elv\":\"$elv\"," Tjson+=" \"geo\":\"$geo\"," Tjson+=" \"temperature\":\"$tem\"," # tem Tjson+=" \"conductivity\":\"$cnd\"," # cnd Tjson+=" \"ph\":\"$ph\"," Tjson+=" \"karyotype\":\"$kar\"" # kar # Last without ',' Tjson+="}" json+="$Tjson," geojson+='{"type":"Feature","geometry":{"type":"point","coordinates":[' geojson+="$kdex,$kdey" geojson+=']},"properties":' geojson+="$Tjson}," rss+=$'<item>\n' rss+=$' <title>'"$co"$'</title>\n' rss+=$' <description>'"$des"$'</description>\n' rss+=$' <link>http://brmlab.s0c4.net/bioosm/det/'"$detid"$'.htm</link>\n' rss+=$' <guid isPermaLink="false">'"$detid"$'</guid>\n' rss+=$' <pubDate>'"$kdy"$'</pubDate>\n' rss+=$'</item>\n' # Generate detail page detid=$(echo "brmlab$co$obr$kde$kdy" | md5sum | grep -oe '[a-zA-Z0-9]*') detpg="<html><head>" detpg+="<meta http-equiv='Content-Type' content='text/html; charset=utf-8'>" detpg+="<link rel='stylesheet' href='../style.css' type='text/css'>" detpg+="<title>Brmlab - BioOSM $co $kde</title>" detpg+="<meta property='og:title' content='BioOSM - $co $kde'>" detpg+="<meta property='og:description' content='$obs found $co and took an image and additional notes.'>" detpg+="<meta property='og:image' content='https://brmlab.s0c4.net/bioosm/img/$obr'>" detpg+="<meta property='og:url' content='https://brmlab.s0c4.net/bioosm/det/$detid.htm'>" detpg+="<meta name='twitter:card' content='summary_large_image'>" detpg+="<meta name='og:type' content='website'>" detpg+="<meta property='og:site_name' content='BioOSM - creatures around us'>" detpg+="<meta name='twitter:image:alt' content='Image of $co'>" detpg+="</head>" if [[ "$cls" != "0" ]]; then detpg+="<script src='../bioosmdet.js'></script>" detpg+="<script>getJSONarma($cls)</script>" fi detpg+="<body>" detpg+="<table class='dettbl'><tr>" detpg+="<h1>$co (<a href='$wikisp' target='_blank'>wiki</a>)</h1>" detpg+="<td style='width:33%;vertical-align:top'>" if [[ "$imp" != "" ]]; then detpg+="<b>Domain:</b> <a href='https://en.wikipedia.org/wiki/$imp' target='_blank'>$imp</a><br>" fi if [[ "$reg" != "" ]]; then detpg+="<b>Kingdom:</b> <a href='https://en.wikipedia.org/wiki/$reg' target='_blank'>$reg</a><br>" fi if [[ "$phy" != "" ]]; then detpg+="<b>Phylum:</b> <a href='https://en.wikipedia.org/wiki/$phy' target='_blank'>$phy</a><br>" fi if [[ "$cla" != "" ]]; then detpg+="<b>Class:</b> <a href='https://en.wikipedia.org/wiki/$cla' target='_blank'>$cla</a><br>" fi if [[ "$ord" != "" ]]; then detpg+="<b>Order:</b> <a href='https://en.wikipedia.org/wiki/$ord' target='_blank'>$ord</a><br>" fi if [[ "$fam" != "" ]]; then detpg+="<b>Family:</b> <a href='https://en.wikipedia.org/wiki/$fam' target='_blank'>$fam</a><br>" fi if [[ "$gen" != "" ]]; then detpg+="<b>Genus:</b> <a href='https://en.wikipedia.org/wiki/$gen' target='_blank'>$gen</a><br>" fi if [[ "$spe" != "" ]]; then detpg+="<b>Species:</b> <a href='$wikisp' target='_blank'>$spe</a><br>" fi if [[ "$kar" != "" ]]; then detpg+="<b>Karyotype:</b> $kar<br>" fi detpg+="<br>" if [[ "$kdy" != "" ]]; then detpg+="<b>Date:</b> $kdy<br>" fi if [[ "$lnk" != "" ]]; then loc="<a href=\"$lnk\" target=\"_blank\">$loc</a>" # Yes, escaped " fi detpg+="<b>Place:</b> $kde ($loc)<br>" if [[ "$elv" != "" ]]; then detpg+="<b>Elevation:</b> $elv m<br>" fi if [[ "$obs" != "" ]]; then detpg+="<b>Observer:</b> $obs<br>" fi if [[ "$bio" != "" ]]; then detpg+="<b>Biotope:</b> $bio<br>" fi if [[ "$pov" != "" ]]; then detpg+="<b>River:</b> $pov<br>" fi if [[ "$geo" != "" ]]; then detpg+="<b>Bedrock:</b> $geo<br>" fi if [[ "$tem" != "" ]]; then detpg+="<b>Temperature:</b> $tem °C<br>" fi if [[ "$cnd" != "" ]]; then detpg+="<b>Conductivity:</b> $cnd mSv<br>" fi if [[ "$ph" != "" ]]; then detpg+="<b>pH:</b> $ph<br>" fi detpg+="<span id='microscopeval'>" if [[ "$skop" != "" ]]; then detpg+="<b>Microscope:</b> $skop ($skop_typ)<br>" fi detpg+="</span>" detpg+="<span id='ampval'>" if [[ "$eng" != "" ]]; then detpg+="<b>Amplification:</b> $eng<br>" fi detpg+="</span>" if [[ "$vid" != "" ]]; then detpg+="<b>Video:</b> <a href=\"$vid\" target=\"_blank\">$vid</a><br>" fi if [[ "$har" != "" ]]; then detpg+="<b>Collecting method:</b> $har<br>" fi if [[ "$den" != "" ]]; then detpg+="<b>Individuals found:</b> $den<br>" fi if [[ "$dur" != "" ]]; then detpg+="<b>Duration on stage:</b> $dur<br>" fi if [[ "$lrl" != "" ]]; then detpg+="<b>Locality reference:</b> <a href=\"$lrl\" target=\"_blank\">$lor</a><br>" elif [[ "$lor" != "" ]]; then detpg+="<b>Locality reference:</b> $lor<br>" fi detpg+="<span id='descval'>" if [[ "$des" != "" ]]; then detpg+="<b>Description:</b> $des<br>" fi detpg+="</span>" detpg+="<br><b>More on <a href=\"../\">BioOSM map</a></b><br>" detpg+="<br>" lhx=$(echo "$kdex-0.022" | bc) lhy=$(echo "$kdey-0.010" | bc) pdx=$(echo "$kdex+0.022" | bc) pdy=$(echo "$kdey+0.010" | bc) detpg+="<iframe id='minimapa' src='https://www.openstreetmap.org/export/embed.html?bbox=$lhx%2C$lhy%2C$pdx%2C$pdy&layer=mapnik&marker=$kdey%2C$kdex'></iframe>" detpg+="</td><td style='min-width:66%;vertical-align:top'>" if [[ "$obr" != "" ]]; then detpg+="<div id='maximatura'><a href=\"../img/$obr\"><img src=\"../img/$obr\" alt=\"$co\" class='detimg'></a></div>" detpg+="<div id='miniatury'></div>" else if [[ "$vid" != "" ]]; then detyt=$(echo "$vid" | sed -e 's/youtube.com\/watch?v=/youtube.com\/embed\//g') detpg+="<iframe class='detvid' src='$detyt' frameborder='0' allow='encrypted-media' allowfullscreen></iframe>" else if [[ "$gen" == "negative" ]]; then detpg+="<img src=\"../negative.png\" alt=\"Negative observation\" class='detimg'>" else detpg+="<img src=\"../$3\" alt=\"video\" class='detimg'>" fi fi fi if [[ "$lov" != "" ]]; then detpg+="<img class=\"detimg\" src=\"../lokality/$lov\" alt=\"Locality photo\"><br>" fi detpg+="</td></tr></table>" detpg+=$(obioosm "$co" "$quando" "https://brmlab.s0c4.net/bioosm/det/$detid.htm") detpg+="</body><script>document.getElementById('zavinacvmejlu').innerHTML='@'</script></html>" echo "$detpg" > "./det/$detid.htm" # Plain log of entries datelog+="$kdy $kde <a href='./det/$detid.htm' target='_blank'>$co</a><br>\n" >&2 echo -e "\033[32m$lid $co $obs\033[0m" ox="$kdex" oy="$kdey" i=$(($i+1)) done <<< $(echo "$1") # Zere parametr spaget, nikoli $1 scriptu !!! echo -e "$json{}]}" | sed -e "s/^var data='//g" > "./jsonrss/$2.json" # echo -e "$json{}]}'" echo -e "$geojson{}]}" > "./jsonrss/geo_$2.geojson" rss+=$'</channel>\n' rss+=$'</rss>\n' echo "$rss" > "./jsonrss/$2.rss" } # KONEC FCE SPAGETY # Sorted unique Kingdoms (to be passed as selection criteria) #kingdoms=$(unzip -p "$1" tellico.xml | grep -oe '<new-field-4>.*</new-field-4>' | sed -E 's/( )*<(\/)?new-field-4>( )*//g' | sort | uniq) kingdoms=$(unzip -p "$1" tellico.xml | sed -E 's/^.*<new-field-4>(.*)<\/new-field-4>.*$/\1/g;t;d' | sort | uniq) echo '<!DOCTYPE html>' echo '<html>' echo '<head>' echo ' <meta http-equiv="Content-Type" content="text/html; charset=utf-8">' echo ' <title>brmlab - BioOSM</title>' echo ' <link rel="stylesheet" href="./style.css" type="text/css">' echo ' <link rel="favicon" href="./'$ICON_biohazard'">' echo ' <script src="./OpenLayers.js"></script>' echo '</head>' echo '<body>' # Generate select echo "<div id='plainlog'><b><a href='./bioosm.rss'>RSS feed</a><br><a href='./plainlog.htm'>Quick news log</a></b></div>" #echo "<h1 id='title'>BioOSM - arma biologica in tuis vicinia</h1>" echo "<h1 id='title'>BioOSM - creatures around us</h1>" ksel="<select id='reg' onChange='genphy()'>" ksel="$ksel<option value='ALL' selected>ALL</option>" while IFS='' read -r king || [[ -n "$king" ]]; do ksel="$ksel<option value='"$king"'>$king</option>" done <<< $(echo "$kingdoms") ksel="$ksel</select>" echo "Kingdom: $ksel " echo "Phylum: <select id='phy' onChange='gencla()'><option>ALL</option></select> " echo "Class: <select id='cla' onChange='genord()'><option>ALL</option></select> " echo "Order: <select id='ord' onChange='genfam()'><option>ALL</option></select> " echo "Family: <select id='fam' onChange='gengen()'><option>ALL</option></select> " echo "Genus: <select id='gen' onChange='genspe()'><option>ALL</option></select>" echo "Species: <select id='spe' onChange='armageddon()'><option>ALL</option></select>" echo "<br><input type='button' value='Platyhelminthes' onClick='plostenkoidy()'>" echo "<label><input type='checkbox' id='studchecker' onChange='studdrv()'>Springs</label>" #echo "<input type='button' value='Bugs' onClick='buggy()'>" echo "<form style='display:inline;margin-left:5em'><input type='text' length=10 id='srch'><input type='submit' value='🔍' onClick='limit();return false;'></form>" echo "<br><br><div id='map' class='smallmap'></div>" echo $(obioosm "" "" "") echo "</body>" echo "<script>" echo 'document.getElementById("zavinacvmejlu").innerHTML="@";' echo 'map = new OpenLayers.Map("map");' echo 'map.addLayer(new OpenLayers.Layer.OSM());' echo 'epsg4326 = new OpenLayers.Projection("EPSG:4326"); //WGS 1984 projection' echo 'projectTo = map.getProjectionObject(); //The map projection (Spherical Mercator)' echo 'var lonLat = new OpenLayers.LonLat(15.478, 49.817).transform(epsg4326, projectTo);' echo 'var zoom=8;' echo 'map.setCenter (lonLat, zoom);' echo 'var vectorLayer = new OpenLayers.Layer.Vector("Overlay",{attribution:"<a href=\"http://brmlab.cz\">Brmlab</a>"});' echo '// Define markers as "features" of the vector layer:' echo 'var atol = new OpenLayers.Feature.Vector(' echo ' new OpenLayers.Geometry.Point(14.41876, 50.10554).transform(epsg4326, projectTo),' echo ' {description:"Atomovy atol Brmkini"} ,' echo ' {externalGraphic: "./biohazard.svg", graphicHeight:8, graphicWidth:8, graphicXOffset:-4, graphicYOffset:-4},' echo ');' echo 'vectorLayer.addFeatures(atol);' # Sem prijdou dalsi staticke ficury echo "map.addLayer(vectorLayer);" # Parse Tellico file to get list of entries granty=$(unzip -p "$1" tellico.xml | grep "<grant>" | sed -E 's/( )*<(\/)?grant>( )*//g' | sed -E 's/_additional$//g' | sort -u | grep -v "^none$") #praseTC=$(unzip -p "$1" tellico.xml | tr -d '\n' | sed -e $'s/<entry id="/\\\n<entry id="/g' -e $'s/<\/entry>/<\/entry>\\\n/g' | grep -Pe '^<entry id="' | grep "<strcit-do-mapy>yep</strcit-do-mapy>" | sed -E 's/(^.*)(<locality>.*<\/locality>)(.*$)/\2\1\3/' | sort) #praseTC=$(unzip -p "$1" tellico.xml | tr -d '\n' | sed -e $'s/<entry id="/\\\n<entry id="/g' -e $'s/<\/entry>/<\/entry>\\\n/g' | grep -Pe '^<entry id="' | sed -E 's/(^.*)(<locality>.*<\/locality>)(.*$)/\2\1\3/' | sort) praseTC=$(unzip -p "$1" tellico.xml | tr -d '\n' | sed -e $'s/<entry id="/\\\n<entry id="/g' -e $'s/<\/entry>/<\/entry>\\\n/g' | grep -E '^<entry id="' | sed -E 's/(^.*)(<locality>.*<\/locality>)(.*$)/\2\1\3/' | sort) velkyvepr=$(echo "$praseTC" | grep "<strcit-do-mapy>yep</strcit-do-mapy>") spagety "$velkyvepr" "bioosm" "$ICON_biohazard" # VSECHNO i non-public - zakomentuj predchozi "spagety" a odkomunetuj tohle + exit #spagety "$praseTC" "celytraktor" "$ICON_biohazard" # vsechno i non-public #exit while IFS='' read -r grnt || [[ -n "$grnt" ]]; do # 'nope' pokud to ma byt jen na grantstrance ale ne ve velkem bioosm #vepr=$(echo "$praseTC" | grep -Pe "<strcit-do-mapy>(yep)|(negative)|(nope)</strcit-do-mapy>" | grep -Pe "<grant>$grnt(_additional)?</grant>") vepr=$(echo "$praseTC" | grep -E "<strcit-do-mapy>(yep)|(negative)|(nope)</strcit-do-mapy>" | grep -E "<grant>$grnt(_additional)?</grant>") spagety "$vepr" "$grnt" "$ICON_biohazard" done <<< $(echo "$granty") #echo -e "$json{}]}" echo '</script>' echo '<script src="./bioosm.js"></script>' # Must be after JSON echo "</html>" # Create plaintext log dateloghtm="<html><head>" dateloghtm+="<meta http-equiv='Content-Type' content='text/html; charset=utf-8'>" dateloghtm+="<link rel='stylesheet' href='./style.css' type='text/css'>" dateloghtm+="<title>Brmlab - BioOSM plaintext log</title>" dateloghtm+="</head><body>" datelogsort=$(echo -e "$datelog" | sort -r | uniq) dateloghtm+="$datelogsort" dateloghtm+="</body></html>" echo "$dateloghtm" > "./plainlog.htm"
window.blob=JSON.parse('{}'); window.arma=null; // // MAIN LOAD START HERE // https://web.archive.org/web/20200502112446/http://dev.openlayers.org/releases/OpenLayers-2.13.1/doc/apidocs/files/OpenLayers-js.html // // function getJSONbioosm() { url="./bioosm.json"; var request; if(window.XMLHttpRequest) request=new XMLHttpRequest(); else request=new ActiveXObject("Microsoft.XMLHTTP"); request.onreadystatechange=function() { if(request.readyState==4) { window.blob=JSON.parse(request.responseText); window.arma=blob.arma; // Display ONLY platyhelminthes if reguired pus=document.URL.match(/platyhelminthes=understone/); if(pus) plostenkoidy(); else // Else initial load armageddon() } } request.open("GET",url,true); request.send(); } wat=document.URL.match(/(index.htm)|(bioosm\/$)/); if(wat) getJSONbioosm(); var stud=JSON.parse('{}'); var vectorLayerDynamic = new OpenLayers.Layer.Vector('Overlay',{attribution:'<a href="http://brmlab.cz">Brmlab</a>'}); var vectorLayerPonygon = new OpenLayers.Layer.Vector('Overlay',{attribution:'<a href="http://brmlab.cz">Brmlab</a>'}); map.addLayer(vectorLayerPonygon); map.addLayer(vectorLayerDynamic); //map.setLayerZIndex(vectorLayerDynamic,999); //map.raiseLayer(vectorLayerDynamic,map.layers.length); var studlay = new OpenLayers.Layer.Vector("Overlay",{attribution:"<a href=\"http://brmlab.cz\">Brmlab</a>"}); // studanky map.addLayer(studlay); var regsel=document.getElementById("reg") var physel=document.getElementById("phy") var clasel=document.getElementById("cla") var ordsel=document.getElementById("ord") var famsel=document.getElementById("fam") var gensel=document.getElementById("gen") var spesel=document.getElementById("spe") var ICON_animalia="animalia.png" var ICON_bacteria="bacteria.png" var ICON_fungi="fungi.png" var ICON_chromista="chromista.png" var ICON_plantae="plantae.svg" var ICON_plostenkoid="plostenkoid.png" var ICON_protista="protista.png" var ICON_biohazard="biohazard.svg" var ICON_studanka="studanka.png" var ICON_negative="negative.png" function getJSONcsop21() { url="./CSOP_122123.json"; var request; if(window.XMLHttpRequest) request=new XMLHttpRequest(); else request=new ActiveXObject("Microsoft.XMLHTTP"); request.onreadystatechange=function() { if(request.readyState==4) { window.blob=JSON.parse(request.responseText); window.arma=blob.arma; armageddon() } } request.open("GET",url,true); request.send(); } function getJSONcsop22() { url="./CSOP_122210.json"; var request; if(window.XMLHttpRequest) request=new XMLHttpRequest(); else request=new ActiveXObject("Microsoft.XMLHTTP"); request.onreadystatechange=function() { if(request.readyState==4) { window.blob=JSON.parse(request.responseText); window.arma=blob.arma; armageddon() } } request.open("GET",url,true); request.send(); } function getJSONexfissgtig() { url="./none_exfiss_gtig.json"; var request; if(window.XMLHttpRequest) request=new XMLHttpRequest(); else request=new ActiveXObject("Microsoft.XMLHTTP"); request.onreadystatechange=function() { if(request.readyState==4) { window.blob=JSON.parse(request.responseText); window.arma=blob.arma; armageddon() } } request.open("GET",url,true); request.send(); } function getJSONempb22() { url="./EPMB2022.json"; // jo preklep kurva var request; if(window.XMLHttpRequest) request=new XMLHttpRequest(); else request=new ActiveXObject("Microsoft.XMLHTTP"); request.onreadystatechange=function() { if(request.readyState==4) { window.blob=JSON.parse(request.responseText); window.arma=blob.arma; armageddon() } } request.open("GET",url,true); request.send(); } function getJSONparas() { url="./parasitology.json"; // jo preklep kurva var request; if(window.XMLHttpRequest) request=new XMLHttpRequest(); else request=new ActiveXObject("Microsoft.XMLHTTP"); request.onreadystatechange=function() { if(request.readyState==4) { window.blob=JSON.parse(request.responseText); window.arma=blob.arma; armageddon() } } request.open("GET",url,true); request.send(); } function getJSONstud() { url="./stud.json"; var request; if(window.XMLHttpRequest) request=new XMLHttpRequest(); else request=new ActiveXObject("Microsoft.XMLHTTP"); request.onreadystatechange=function() { if(request.readyState==4) { stud=JSON.parse(request.responseText); studdraw(stud); } } request.open("GET",url,true); request.send(); } function studdraw(sj) { studlay.destroyFeatures(); sjs=stud.std; s=[]; for(i=0;i<sjs.length;i++) { s[i] = new OpenLayers.Feature.Vector(new OpenLayers.Geometry.Point(sjs[i].lon,sjs[i].lat).transform(epsg4326,projectTo),{'description':"<table class=\"hadtbl\">"+sjs[i].name+"</table>"},{'externalGraphic':ICON_studanka,'graphicHeight':24,'graphicWidth':24,'graphicXOffset':-12,'graphicYOffset':-12}); studlay.addFeatures(s[i]); } } function studdrv() { box=document.getElementById("studchecker"); if(box.checked) getJSONstud(); else studlay.destroyFeatures(); } // Return icon by Regnum function geticon (a,i) { if(a[i].genus=="negative") return ICON_negative; var p=true; var r="" if(document.getElementById("reg").value!="ALL") { r=document.getElementById("reg").value p=false; } else { r=a[i].regnum for(var e=i;e>=0 && a[e].locality==a[i].locality;e--) { if(a[e].phylum!="Platyhelminthes") p=false; if(a[e].regnum!=a[i].regnum) { r="ALL"; break; } } } switch (r) { case "Animalia": { if(p) return ICON_plostenkoid; return ICON_animalia; } case "Bacteria": return ICON_bacteria; case "Fungi": return ICON_fungi; case "Chromista": return ICON_chromista; case "Plantae": return ICON_plantae; case "Protista": return ICON_protista; default: return ICON_biohazard } } function genphy() { physel.innerHTML="<option>ALL</option>" clasel.innerHTML="<option>ALL</option>" ordsel.innerHTML="<option>ALL</option>" famsel.innerHTML="<option>ALL</option>" gensel.innerHTML="<option>ALL</option>" spesel.innerHTML="<option>ALL</option>" var phyarr=[] for (var i=0;i<window.arma.length-1;i++) { if(regsel.value==window.arma[i].regnum && window.arma[i].phynum!="") phyarr.push(window.arma[i].phylum) } phyarr.sort() for (var i=0;i<phyarr.length;i++) { if(i==0) { physel.innerHTML+="<option>"+phyarr[0]+"</option>" continue } if(phyarr[i]!=phyarr[i-1]) physel.innerHTML+="<option>"+phyarr[i]+"</option>" } armageddon() // Populate the map with monsters... } function gencla() { clasel.innerHTML="<option>ALL</option>" ordsel.innerHTML="<option>ALL</option>" famsel.innerHTML="<option>ALL</option>" gensel.innerHTML="<option>ALL</option>" spesel.innerHTML="<option>ALL</option>" var claarr=[] for (var i=0;i<window.arma.length-1;i++) { if(physel.value==window.arma[i].phylum && window.arma.classis!="") claarr.push(window.arma[i].classis) } claarr.sort() for (var i=0;i<claarr.length;i++) { if(i==0) { clasel.innerHTML+="<option>"+claarr[0]+"</option>" continue } if(claarr[i]!=claarr[i-1]) clasel.innerHTML+="<option>"+claarr[i]+"</option>" } armageddon() // Populate the map with monsters... } function genord() { ordsel.innerHTML="<option>ALL</option>" famsel.innerHTML="<option>ALL</option>" gensel.innerHTML="<option>ALL</option>" spesel.innerHTML="<option>ALL</option>" var ordarr=[] for (var i=0;i<window.arma.length-1;i++) { if(clasel.value==window.arma[i].classis && window.arma[i].ordo!="") ordarr.push(window.arma[i].ordo) } ordarr.sort() for (var i=0;i<ordarr.length;i++) { if(i==0) { ordsel.innerHTML+="<option>"+ordarr[0]+"</option>" continue } if(ordarr[i]!=ordarr[i-1]) ordsel.innerHTML+="<option>"+ordarr[i]+"</option>" } armageddon() // Populate the map with monsters... } function genfam() { famsel.innerHTML="<option>ALL</option>" gensel.innerHTML="<option>ALL</option>" spesel.innerHTML="<option>ALL</option>" var famarr=[] for (var i=0;i<window.arma.length-1;i++) { if(ordsel.value==window.arma[i].ordo && window.arma[i].familia!="") famarr.push(window.arma[i].familia) } famarr.sort() for (var i=0;i<famarr.length;i++) { if(i==0) { famsel.innerHTML+="<option>"+famarr[0]+"</option>" continue } if(famarr[i]!=famarr[i-1]) famsel.innerHTML+="<option>"+famarr[i]+"</option>" } armageddon() // Populate the map with monsters... } function gengen() { gensel.innerHTML="<option>ALL</option>" spesel.innerHTML="<option>ALL</option>" var genarr=[] for (var i=0;i<window.arma.length-1;i++) { if(famsel.value==window.arma[i].familia && window.arma[i].genus!="") genarr.push(window.arma[i].genus) } genarr.sort() for (var i=0;i<genarr.length;i++) { if(i==0) { gensel.innerHTML+="<option>"+genarr[0]+"</option>" continue } if(genarr[i]!=genarr[i-1]) gensel.innerHTML+="<option>"+genarr[i]+"</option>" } //genspe() // ...and here we go armageddon() // Populate the map with monsters... } function genspe() { spesel.innerHTML="<option>ALL</option>" var spearr=[] for (var i=0;i<window.arma.length-1;i++) { if(gensel.value==window.arma[i].genus && window.arma[i].specie!="") spearr.push(window.arma[i].specie) } spearr.sort() for (var i=0;i<spearr.length;i++) { if(i==0) { spesel.innerHTML+="<option>"+spearr[0]+"</option>" continue } if(spearr[i]!=spearr[i-1]) spesel.innerHTML+="<option>"+spearr[i]+"</option>" } armageddon() // Populate the map with monsters... } function armageddon() { var speval=document.getElementById("spe").value var genval=document.getElementById("gen").value var famval=document.getElementById("fam").value var ordval=document.getElementById("ord").value var claval=document.getElementById("cla").value var phyval=document.getElementById("phy").value var regval=document.getElementById("reg").value var a=[] if(speval!="ALL") { for(var i=0;i<window.arma.length-1;i++) if(window.arma[i].specie==speval && window.arma[i].genus==genval) // Check genus because of unknown "sp." a.push(window.arma[i]) } else if(genval!="ALL") { for(var i=0;i<window.arma.length-1;i++) if(window.arma[i].genus==genval) a.push(window.arma[i]) } else if(famval!="ALL") { for(var i=0;i<window.arma.length-1;i++) if(window.arma[i].familia==famval) a.push(window.arma[i]) } else if(ordval!="ALL") { for(var i=0;i<window.arma.length-1;i++) if(window.arma[i].ordo==ordval) a.push(window.arma[i]) } else if(claval!="ALL") { for(var i=0;i<window.arma.length-1;i++) if(window.arma[i].classis==claval) a.push(window.arma[i]) } else if(phyval!="ALL") { for(var i=0;i<window.arma.length-1;i++) if(window.arma[i].phylum==phyval) a.push(window.arma[i]) } else if(regval!="ALL") { for(var i=0;i<window.arma.length-1;i++) if(window.arma[i].regnum==regval) a.push(window.arma[i]) } else // Regnum: ALL { for(var i=0;i<window.arma.length-1;i++) a.push(window.arma[i]) } icongeddon(a) } function buggy() { var p=[] for(var i=0;i<window.arma.length-1;i++) { if(window.arma[i].regnum==""|| window.arma[i].phylum==""|| window.arma[i].classis==""|| window.arma[i].ordo==""|| window.arma[i].familia==""|| window.arma[i].genus=="") p.push(window.arma[i]) } icongeddon(p) } function plostenkoidy() { var p=[] for(var i=0;i<window.arma.length-1;i++) { if(window.arma[i].phylum=="Platyhelminthes") p.push(window.arma[i]) } icongeddon(p) } function icongeddon(a) { //alert(a.length) // #thingies to show in the map' while(map.popups.length) map.removePopup(map.popups[0]) vectorLayerDynamic.destroyFeatures() var bylo="" // Minula pozice var sam="" // HTML samostatneho zaznamu var osam="" // predchozi $sam var spoj="" // HTML had z popisu stejnych pozic var ospoj="" // Predchozi spoj var ox="" // Old X var oy="" // Old Y var datelog="" // Entries sorted by date for plaintext log var i=0 // Iterator over a[] (needed after FOR) var n=[] // New points in the layer var muchicons=0 // How much Regnum's? var samicon=ICON_biohazard // Icon var spojicon=ICON_biohazard // Icon for(;i<a.length;i++) // -1 fix for last empty entry { if(a[i].cluster!=0&&a[i].mainpic!="y") // show only in gallery, without icon in map continue; // Pokracujem v hadovi if(a[i].locality == bylo) { sam=""; spoj+="<tr><td>" spoj+='<a href="./det/'+a[i].detid+'.htm" target="_blank">' if(a[i].obr != "") spoj+='<img src="./simg/'+a[i].obr+'" class="hadimg"></a></td>' else spoj+='<img src=./"'+ICON_biohazard+'" class="hadimg"></a></td>' spoj+="<td>"+a[i].title+"<br>"+a[i].takendate+"</td>" spoj+="</tr>" ox=a[i].x oy=a[i].y continue; } switch(a[i].specie) { case "sp.": { wikisp="https://en.wikipedia.org/wiki/"+a[i].genus break; } case "negative": case "": { wikisp="https://en.wikipedia.org/wiki/Null_result" break; } default: { wikisp="https://en.wikipedia.org/wiki/"+a[i].genus+" "+a[i].specie break; } } // Bud prvni zaznam, nebo zmena pozice // Predchozi pozice jen 1 zaznam? if(sam != "") { samicon=geticon(a,i-1) 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}); vectorLayerDynamic.addFeatures(n[i]); spoj="" sam="" } // ELSE vytvori prazdny radek // Predchozi pozice vic zaznamu? if(spoj!="") { spojicon=geticon(a,i-1) 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}); vectorLayerDynamic.addFeatures(n[i]); spoj="" sam="" } bylo=a[i].locality spoj='<tr><td><a href="./det/'+a[i].detid+'.htm" target="_blank">' if(a[i].obr != "") spoj+='<img src="./simg/'+a[i].obr+'" class="hadimg"></a></td>' else spoj+='<img src="./'+geticon(a,i)+'" class="hadimg"</a></td>' spoj+='<td>'+a[i].title+'<br>'+a[i].takendate+'</td>' spoj+="</tr>" sam='<a href="./det/'+a[i].detid+'.htm" target="_blank"><img src="'+(a[i].genus=='negative'?ICON_negative:'./simg/'+a[i].obr)+'" alt="'+a[i].title+'" class="buttimg"></a>' sam+='<br><span class="butttext">' sam+='<a href="'+wikisp+'" target="_blank">'+(a[i].title=="negative"?"Negative observation":a[i].title)+'</a><br>' if(a[i].imperium != "") sam+='<b>Domain:</b> <a href="https://en.wikipedia.org/wiki/'+a[i].imperium+'" target="_blank">'+a[i].imperium+'</a><br>' if(a[i].regnum != "") sam+='<b>Kingdom:</b> <a href="https://en.wikipedia.org/wiki/'+a[i].regnum+'" target="_blank">'+a[i].regnum+'</a><br>' if(a[i].phylum != "") sam+='<b>Phylum:</b> <a href="https://en.wikipedia.org/wiki/'+a[i].phylum+'" target="_blank">'+a[i].phylum+'</a><br>' if(a[i].classis != "") sam+='<b>Class:</b> <a href="https://en.wikipedia.org/wiki/'+a[i].classis+'" target="_blank">'+a[i].classis+'</a><br>' if(a[i].ordo != "") sam+='<b>Order:</b> <a href="https://en.wikipedia.org/wiki/'+a[i].ordo+'" target="_blank">'+a[i].ordo+'</a><br>' if(a[i].familia != "") sam+='<b>Family:</b> <a href="https://en.wikipedia.org/wiki/'+a[i].familia+'" target="_blank">'+a[i].familia+'</a><br>' if(a[i].genus != "" && a[i].genus!="negative") sam+='<b>Genus:</b> <a href="https://en.wikipedia.org/wiki/'+a[i].genus+'" target="_blank">'+a[i].genus+'</a><br>' if(a[i].specie != "") sam+='<b>Species:</b> <a href="'+wikisp+'" target="_blank">'+a[i].specie+'</a><br>' if(a[i].biotope != "") sam+="<b>Biotope:</b> "+a[i].biotope+"<br>" if(a[i].pov != "") sam+="<b>River:</b> "+a[i].pov+"<br>" if(a[i].temperature != "") sam+="<b>Temperature:</b> "+a[i].temperature+" °C<br>" if(a[i].pov != "") sam+="<b>Conductivity:</b> "+a[i].conductivity+" mSv<br>" if(a[i].pov != "") sam+="<b>pH:</b> "+a[i].ph+"<br>" if(a[i].takendate != "") sam+="<b>Date:</b> "+a[i].takendate+"<br>" sam+="<b>Location:</b> "+a[i].locality+" ("+a[i].locplain+")<br>" if(a[i].observer != "") sam+="<b>Spectator:</b> "+a[i].observer+"<br>" if(a[i].micro != "") sam+="<b>Microscope:</b> "+a[i].micro+" ("+a[i].microtyp+")<br>" if(a[i].enlargement != "") sam+="<b>Amplification:</b> "+a[i].enlargement+"<br>" /* if [[ "$des" != "" ]]; then # sam="$sam<b>Depictio:</b> $des<br>" # fi */ //if(a[i].videolink != "") // sam+='<b>Video:</b> <a href="'+a[i].videolink+'" target="_blank">'+a[i].videolink+'</a><br>' sam+="</span>" ox=a[i].x oy=a[i].y } // Konec prochazeni a[] // Do not forget to print last line when FOR ends! samicon=geticon(a,i-1) if(sam == "") sam='<table style="hadtbl">'+spoj+'</table>' n[i]=new OpenLayers.Feature.Vector(new OpenLayers.Geometry.Point(a[i-1].x,a[i-1].y).transform(epsg4326,projectTo),{description:"'"+sam+"'"},{externalGraphic:samicon,graphicHeight:24,graphicWidth:24,graphicXOffset:-12,graphicYOffset:-12}); vectorLayerDynamic.addFeatures(n[i]); } // Konec armageddonu //var laycon = [vectorLayer,vectorLayerPonygon,vectorLayerDynamic,studlay]; var laycon = [vectorLayer,vectorLayerDynamic,studlay]; var controls = {selector: new OpenLayers.Control.SelectFeature(laycon, { onSelect: createPopup, onUnselect: destroyPopup })}; map.addControl(controls['selector']); controls['selector'].activate(); function createPopup(feature) { feature.popup = new OpenLayers.Popup.FramedCloud('pop', feature.geometry.getBounds().getCenterLonLat(), null, '<div class="markerContent">'+feature.attributes.description+'</div>', null, false, // Close button? function() { controls['selector'].unselectAll(); } ); //feature.popup.closeOnMove = true; map.addPopup(feature.popup); } function destroyPopup(feature) { feature.popup.destroy(); feature.popup = null; } // Vyhledavani function limit() { srch=document.getElementById("srch").value.toLowerCase(); var p=[] for(var i=0;i<window.arma.length-1;i++) { if(window.arma[i].title.toLowerCase().indexOf(srch)>=0|| window.arma[i].imperium.toLowerCase().indexOf(srch)>=0|| window.arma[i].regnum.toLowerCase().indexOf(srch)>=0|| window.arma[i].phylum.toLowerCase().indexOf(srch)>=0|| window.arma[i].classis.toLowerCase().indexOf(srch)>=0|| window.arma[i].ordo.toLowerCase().indexOf(srch)>=0|| window.arma[i].familia.toLowerCase().indexOf(srch)>=0|| //window.arma[i].genus.toLowerCase().indexOf(srch)>=0|| // v "qualis" //window.arma[i].observerie.toLowerCase().indexOf(srch)>=0|| window.arma[i].locplain.toLowerCase().indexOf(srch)>=0|| window.arma[i].description.toLowerCase().indexOf(srch)>=0|| window.arma[i].takendate.toLowerCase().indexOf(srch)>=0|| window.arma[i].micro.toLowerCase().indexOf(srch)>=0|| window.arma[i].microtyp.toLowerCase().indexOf(srch)>=0|| window.arma[i].biotope.toLowerCase().indexOf(srch)>=0|| window.arma[i].pov.toLowerCase().indexOf(srch)>=0) p.push(arma[i]) } icongeddon(p) } // ====== GEOJSON ====== var metageo=JSON.parse("{}"); var geje=[]; var gejbarva=""; function placegeo(coor,gejbarva) { var geja=new Array; epsg4326 = new OpenLayers.Projection("EPSG:4326"); //WGS 1984 projection projectTo = map.getProjectionObject(); for(i=0;i<coor.length;i++) { geja.push(new OpenLayers.Geometry.Point(coor[i][0],coor[i][1]).transform(epsg4326, projectTo)) } /* "default" namespaces work for Layers, not Features var lajna=new OpenLayers.StyleMap({ "default": new OpenLayers.Style({ //strokeColor: "#FF0000", strokeColor: gejbarva, strokeOpacity: 1, strokeWidth: 5, pointRadius: 6, }), "select": new OpenLayers.Style({ //strokeColor: "#0000FF", strokeColor: gejbarva, strokeOpacity: 1, strokeWidth: 5, pointRadius: 6, }) }); */ var lajna={ // Feature without the namespaces strokeColor: gejbarva, strokeOpacity: 1, strokeWidth: 5, pointRadius: 6, }; gejs=new OpenLayers.Geometry.LineString(geja); vectorLayerPonygon.addFeatures([new OpenLayers.Feature.Vector(gejs,{},lajna)]); } function getsld(url,s,g) { var request; if(window.XMLHttpRequest) request=new XMLHttpRequest(); else request=new ActiveXObject("Microsoft.XMLHTTP"); request.overrideMimeType("text/plain"); request.onreadystatechange=function() { if(request.readyState==4) { tmpc=request.responseText; tmpc=tmpc.match(/SvgParameter name="stroke">#[0-9a-fA-F]*<\/se:SvgParameter/)[0].match(/#[0-9a-fA-F]*/)[0]; getgeo(url,g,tmpc); //console.log(tmpc); } } request.open("GET",url+s,true); request.send(); } function getgeo(url,g,c) { var request; if(window.XMLHttpRequest) request=new XMLHttpRequest(); else request=new ActiveXObject("Microsoft.XMLHTTP"); request.overrideMimeType("application/geo+json"); request.onreadystatechange=function() { if(request.readyState==4) { tmpg=JSON.parse(request.responseText); for(var e=0;e<tmpg.features.length;e++) { if(typeof tmpg.features[e].properties === 'undefined') // || tmpg.features[e].properties.osm_type!="way") continue; for(var i=0;i<tmpg.features[e].geometry.coordinates.length;i++) { for(var j=0;j<tmpg.features[e].geometry.coordinates[i].length;j++) { if(tmpg.features[e].geometry.coordinates[i][j].length<2) continue; //console.log(tmpg.features[e].properties.osm_type+" "+tmpg.features[e].geometry.coordinates[i][j].length); placegeo(tmpg.features[e].geometry.coordinates[i][j],c); } } } } } request.open("GET",url+g,true); request.send(); } // ENTRY POINT // parametr je ./ adresar ve kterem je metadata.json S LOMITKEM NA KONCI function drawgeojson(url) { var request; if(window.XMLHttpRequest) request=new XMLHttpRequest(); else request=new ActiveXObject("Microsoft.XMLHTTP"); request.onreadystatechange=function() { if(request.readyState==4) { window.metageo=JSON.parse(request.responseText); for(var i=0;i<metageo.layers.length;i++) { //console.log(metageo.layers[i].geojson); getsld(url,metageo.layers[i].sld,metageo.layers[i].geojson) } } } request.open("GET",url+"metadata.json",true); request.send(); }
To be able to better plan routes for collecting planarians, the knowledge of locations of springs seems to be important. So BioOSM can show them! Below is a script to get the locations from OSM XMLs obtainable from http://osm.kyblsoft.cz/archiv/.
#!/bin/bash # generate BioOSM compatible "springs" # Usage: studanky.sh osmdump.xml # # Download OSM file to be passed as $1 # wget "http://osm.kyblsoft.cz/archiv/czech_republic-2019-11-03.osm.gz" # gzip -kd ./czech_republic-2019-11-03.osm.gz # # Pozor ^^ sezere spoustu rameti # osm=$(cat "$1" | sed -e 's/<node/\'$'\a<node/g' -e 's/<\/node>/<\/node\'$'\a/g' -e 's/<way/\'$'\a<way/g' -e 's/<\/way>/<\/way>\'$'\a/g' -e 's/<relation/\'$'\a<relation/g' -e 's/<\/relation>/<\/relation>\'$'\a/g' | tr -d '\n' | tr '\a' '\n' | grep 'v="spring"' | grep 'k="natural"') json='{"version":"'$(date --rfc-3339=seconds)'","std":[' while IFS='' read -r spr || [[ -n "$spr" ]]; do n=$(echo "$spr" | grep -oPe 'k="name" v="[^"]*"' | sed -e 's/k="name" v="//g' -e 's/"$//g') lat=$(echo "$spr" | grep -oPe ' lat="[^"]*"' | sed -e 's/ lat="//g' -e 's/"$//g') lon=$(echo "$spr" | grep -oPe ' lon="[^"]*"' | sed -e 's/ lon="//g' -e 's/"$//g') if [ "$lat" = "" ] || [ "$lon" = "" ]; then continue; # <way> a tak fi if [[ "$n" = "" ]]; then n="inkognito" >&2 echo -e "\033[34m $lat $lon \033[0m"; fi json+="{" json+=" \"name\":\"$n\"," json+=" \"lon\":\"$lon\"," json+=" \"lat\":\"$lat\"" json+="}," >&2 echo -e "\033[32m $n $lat $lon\033[0m" done <<< $(echo "$osm") echo "$json{}]}"
#!/bin/bash T=$(mktemp) unzip -p "$1" tellico.xml | tr -d '\n' | sed -e $'s/<entry id="/\\\n<entry id="/g' -e $'s/<\/entry>/<\/entry>\\\n/g' > "$T" hf=$(cat "$T" | grep -Pe '^<entry id="' | grep '<hasflatworms>yep</hasflatworms>') # nejvyssi dosazene ID mid=$(cat "$T" | grep -Pe '^<entry id="' | grep -oe ' <localityid>.*</localityid> ' | grep -oPe '[0-9]+' | sort | tail -n 1) mid=$(($mid+1)) function ll() { while IFS='' read -r r || [[ -n "$r" ]]; do t=$(echo "$r" | grep -oe ' <taken-date>.*</taken-date> ' | sed -E 's/( )*<(\/)?taken-date>( )*//g' | sed -E 's/([0-9]+)\.([0-9]+)\.([0-9]{4})/\3-\2-\1/g' | sed -E 's/-([0-9])-/-0\1-/g' | sed -E 's/-([0-9])$/-0\1/g') l=$(echo "$r" | grep -oe '<locality>.*</locality>' | grep -oPe '[0-9]+\.[0-9]+[, ]*[0-9]+\.[0-9]+') echo "$t@$l" done <<< $(echo "$1") } srt=$(ll "$hf" | sort -u) uid=$mid while IFS='' read -r r || [[ -n "$r" ]]; do l=$(echo "$r" | grep -oPe '@.*$' | tr -d '@') lid=$(cat "$T" | grep " <locality>$l</locality> " | grep -oe ' <localityid>.*</localityid> ' | grep -oPe '[0-9]+') if [[ "$lid" = "" ]]; then sedexp="s/( <locality>$l<\/locality> .*<hasflatworms>yep<\/hasflatworms> )/ \\1 <localityid>$uid<\/localityid> /g" #echo "$sedexp" sed -E "$sedexp" -i "$T" uid=$(($uid+1)) fi done <<< $(echo "$srt") D=$(mktemp -d) cp -f "$T" "$D/tellico.xml" zip -j "./micro_new.tc" "$D/tellico.xml" rm -rfv "$T" rm -rfv "$D"
