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Table of Contents
BioOSM
~~META: status = active &relation firstimage = :project:bioosm:bioosm.jpg ~~
BioOSM je mapa vyskytu mikroorganismu (ras, bakterii, plostenek, …) a do budoucna i dalsich prirodnin (mineralu, …).
K cemu to je
- interaktivni mapa vhodna k zobrazovani vetsiho mnozstvi fotek, brmlabi wiki, sluzby typu phtagr a soup se zdaly nevhodne k publikaci tohoto typu obsahu, wiki by byla prilis obludna, na beznych sdilecich obrazkovych sluzbach se neda nic pohodlne dohledavat a davat tam biologicky smysluplne a prehledne popisky
- monitoring zivocichu a rostlin podle zajmu prispevovatelu
- snadne klikaci katalogovani nalezu skrze Tellico nevyzadujici coding skills
- TODO - jednoduche selekce zajmoveho okruhu subjektu [napr. podle rodu, biotopu, datumu] na mape
- procvicovani temne magie commandu grep, sed a regexpu
Jak to funguje
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.
Tellico sample database
Az se mi ho podari nekam nahrat tak nekde bude. Nebo mozna nejaky webxicht…
Kusy zdrojaku k nezapomenuti
Extrakce polozek z Tellico databaze
- ziskani tellico.xml
- radkovani dle polozek
- pouze verejne (strcit-do-mapy = yep)
- preneseni lokality na zacatek radku s informacemi o polozce
- seskupeni dle lokality
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)
Prepinani vrstev
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();
Prepnuti viditelnych vrstev
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]) }
Nastaveni brmlabu do paticky map
OpenLayers.Layer.Vector('Overlay',{attribution:'<a href="http://brmlab.cz">Brmlab</a>'});
Umisteni copyrightu
OSM maji defaultne copyright nesmyslne odsazeny od spodniho okraje mapy, CSS zmena na nejaky rozumny offset:
.olControlAttribution { bottom:0.5em; }
parse_tellico.sh
- parse_tellico.sh
#!/bin/bash # Parse Tellico database to BioOSM index.htm # $1 = tellico .tc file # Print result to stdout # # <iframe width="500" height="500" frameborder="0" scrolling="no" marginheight="0" marginwidth="0" src="https://www.openstreetmap.org/export/embed.html?bbox=14.978000%2C49.990000%2C15.022000%2C50.010000&layer=mapnik&marker=50.000000%2C15.000000"></iframe> # // vectorLayer.removeFeatures(atol) # // map.removeLayer(vectorLayer) # # # Creates: # (to stdout) HTML file with the map and static entries # ./det/ID.htm details of each and every entry # ./bioosm.json JSON of all entries # ./bioosm.rss updated RSS feed # ./plainlog.htm sorted entries for easy human/alg # rm -rfv "./det/*" mkdir -p "./det" ICON_animalia="animalia.png" ICON_bacteria="bacteria.png" ICON_fungi="fungi.png" ICON_chromista="chromista.png" ICON_plantae="plantae.svg" ICON_plostenkoid="plostenkoid.png" ICON_protista="protista.png" ICON_biohazard="biohazard.svg" json="" rss=$'<?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 on 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' # 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 "$1" | sed -e "s/'/\'/g" -e 's/"/\"/g' -e 's/</\</g' -e 's/>/\>/g' -e 's/^[ ]*//g' -e 's/[ ]*$//g' } 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 # $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)\",\"arma\":[" while IFS='' read -r radek || [[ -n "$radek" ]]; do co=$(echo "$radek" | grep -oe ' <title>.*</title> ' | sed -E 's/( )*<(\/)?title>( )*//g') co=$(safehtml "$co") obr=$(echo "$radek" | grep -oe ' <image>.*</image> ' | sed -E 's/( )*<(\/)?image>( )*//g' | grep -oPe '[^/]*$') obr=$(safehtml "$obr") kde=$(echo "$radek" | grep -oe '<locality>.*</locality>' | grep -oPe '[0-9]+\.[0-9]{1,10}[, ]*[0-9]+\.[0-9]{1,10}') kde=$(safehtml "$kde") kdex=$(echo "$kde" | grep -oPe '[0-9]+\.[0-9]{1,10}$') kdex=$(safehtml "$kdex") kdey=$(echo "$kde" | grep -oPe '^[0-9]+\.[0-9]{1,10}') kdey=$(safehtml "$kdey") kdy=$(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') kdy=$(safehtml "$kdy") skop_typ=$(echo "$radek" | grep -oe ' <new-field-1>.*</new-field-1> ' | sed -E 's/( )*<(\/)?new-field-1>( )*//g') skop_typ=$(safehtml "$skop_typ") skop=$(echo "$radek" | grep -oe ' <microscope>.*</microscope> ' | sed -E 's/( )*<(\/)?microscope>( )*//g') skop=$(safehtml "$skop") imp=$(echo "$radek" | grep -oe ' <new-field-3>.*</new-field-3> ' | sed -E 's/( )*<(\/)?new-field-3>( )*//g') imp=$(safehtml "$imp") reg=$(echo "$radek" | grep -oe ' <new-field-4>.*</new-field-4> ' | sed -E 's/( )*<(\/)?new-field-4>( )*//g') reg=$(safehtml "$reg") phy=$(echo "$radek" | grep -oe ' <phylum>.*</phylum> ' | sed -E 's/( )*<(\/)?phylum>( )*//g') phy=$(safehtml "$phy") cla=$(echo "$radek" | grep -oe ' <class>.*</class> ' | sed -E 's/( )*<(\/)?class>( )*//g') cla=$(safehtml "$cla") ord=$(echo "$radek" | grep -oe ' <order>.*</order> ' | sed -E 's/( )*<(\/)?order>( )*//g') ord=$(safehtml "$ord") fam=$(echo "$radek" | grep -oe ' <family>.*</family> ' | sed -E 's/( )*<(\/)?family>( )*//g') fam=$(safehtml "$fam") gen=$(echo "$radek" | grep -oe ' <genus>.*</genus> ' | sed -E 's/( )*<(\/)?genus( )*>//g') gen=$(safehtml "$gen") spe=$(echo "$radek" | grep -oe ' <species>.*</species> ' | sed -E 's/( )*<(\/)?species>( )*//g') spe=$(safehtml "$spe") loc=$(echo "$radek" | grep -oe ' <locality---plaintext>.*</locality---plaintext> ' | sed -E 's/( )*<(\/)?locality---plaintext>( )*//g') loc=$(safehtml "$loc") des=$(echo "$radek" | grep -oe ' <description>.*</description> ' | sed -E 's/( )*<(\/)?description>( )*//g') des=$(safehtml "$des") vid=$(echo "$radek" | grep -oe ' <videolink>.*</videolink> ' | sed -E 's/( )*<(\/)?videolink>( )*//g') vid=$(safehtml "$vid") bio=$(echo "$radek" | grep -oe ' <biotope>.*</biotope> ' | sed -E 's/( )*<(\/)?biotope>( )*//g') bio=$(safehtml "$bio") eng=$(echo "$radek" | grep -oe ' <enlargement>.*</enlargement> ' | sed -E 's/( )*<(\/)?enlargement>( )*//g') eng=$(safehtml "$eng") obs=$(echo "$radek" | grep -oe ' <observer>.*</observer> ' | sed -E 's/( )*<(\/)?observer>( )*//g') obs=$(safehtml "$obs") lnk=$(echo "$radek" | grep -oe ' <localitylink>.*</localitylink> ' | sed -E 's/( )*<(\/)?localitylink>( )*//g') lnk=$(safehtml "$lnk") har=$(echo "$radek" | grep -oe ' <harvesting-method>.*</harvesting-method> ' | sed -E 's/( )*<(\/)?harvesting-method>( )*//g') den=$(echo "$radek" | grep -oe ' <population-density>.*</population-density> ' | sed -E 's/( )*<(\/)?population-density>( )*//g') dur=$(echo "$radek" | grep -oe ' <min>.*</min> ' | sed -E 's/( )*<(\/)?min>( )*//g') lor=$(echo "$radek" | grep -oe ' <locality-reference>.*</locality-reference> ' | sed -E 's/( )*<(\/)?locality-reference>( )*//g') lrl=$(echo "$radek" | grep -oe ' <locality-reference---link>.*</locality-reference---link> ' | sed -E 's/( )*<(\/)?locality-reference---link>( )*//g') lov=$(echo "$radek" | grep -oe ' <locality---vobrazek>.*</locality---vobrazek> ' | sed -E 's/( )*<(\/)?locality---vobrazek>( )*//g' | grep -oPe '[^/]*$') # >&2 echo "$co - $har - $den - $dur - $lor - $lrl - $lov" detid=$(echo "brmlab$co$obr$kde$kdy" | md5sum | grep -oe '[a-zA-Z0-9]*') if [[ "$kdex" = "" ]]; then >&2 echo -e "\033[31m" $(echo "$radek" | grep -oe '<locality>.*</locality>') " $co\033[0m" continue; fi zkurvenetellico=$(echo "$obr" | grep -oe '\.[a-zA-Z]*$') if [[ "$zkurvenetellico" = ".jpeg" ]]; then >&2 echo -e "\033[31m$obr $co\033[0m" continue; fi if [[ "$spe" = "sp." ]]; then wikisp="https://en.wikipedia.org/wiki/$gen" else wikisp="https://en.wikipedia.org/wiki/$gen $spe" fi json+="{" json+=" \"qualis\":\"$co\"," json+=" \"imperium\":\"$imp\"," json+=" \"regnum\":\"$reg\"," json+=" \"phylum\":\"$phy\"," json+=" \"classis\":\"$cla\"," json+=" \"ordo\":\"$ord\"," json+=" \"familia\":\"$fam\"," json+=" \"genus\":\"$gen\"," json+=" \"specie\":\"$spe\"," json+=" \"locus\":\"$kde\"," json+=" \"x\":\"$kdex\"," json+=" \"y\":\"$kdey\"," json+=" \"locplain\":\"$loc\"," json+=" \"depictio\":\"$des\"," json+=" \"quando\":\"$kdy\"," json+=" \"obr\":\"$obr\"," json+=" \"micro\":\"$skop\"," json+=" \"microtyp\":\"$skop_typ\"," json+=" \"vid\":\"$vid\"," json+=" \"bio\":\"$bio\"," json+=" \"amp\":\"$eng\"," json+=" \"spec\":\"$obs\"," json+=" \"detid\":\"$detid\"," json+=" \"har\":\"$har\"," json+=" \"den\":\"$den\"," json+=" \"dur\":\"$dur\"," json+=" \"lor\":\"$lor\"," json+=" \"lrl\":\"$lrl\"," json+=" \"lov\":\"$lov\"," json+=" \"lnk\":\"$lnk\"" # Lastone without ',' json+="}," rss+=$'<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 $kde</title>" detpg+="</head><body>" detpg+="<table class='dettbl'><tr>" detpg+="<h1>$co (<a href='$wikisp' target='_blank'>wiki</a>)</h1>" detpg+="<td style='width:33%;vertical-align:top'>" if [[ "$imp" != "" ]]; then detpg+="<b>Imperium:</b> <a href='https://en.wikipedia.org/wiki/$imp' target='_blank'>$imp</a><br>" fi if [[ "$reg" != "" ]]; then detpg+="<b>Regnum:</b> <a href='https://en.wikipedia.org/wiki/$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 [[ "$cla" != "" ]]; then detpg+="<b>Classis:</b> <a href='https://en.wikipedia.org/wiki/$cla' target='_blank'>$cla</a><br>" fi if [[ "$ord" != "" ]]; then detpg+="<b>Ordo:</b> <a href='https://en.wikipedia.org/wiki/$ord' target='_blank'>$ord</a><br>" fi if [[ "$fam" != "" ]]; then detpg+="<b>Familia:</b> <a href='https://en.wikipedia.org/wiki/$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 [[ "$spe" != "" ]]; then detpg+="<b>Specie:</b> <a href='$wikisp' target='_blank'>$spe</a><br>" fi detpg+="<br>" if [[ "$kdy" != "" ]]; then detpg+="<b>Quando:</b> $kdy<br>" fi if [[ "$lnk" != "" ]]; then loc="<a href=\"$lnk\" target=\"_blank\">$loc</a>" # Yes, escaped " fi detpg+="<b>Locus:</b> $kde ($loc)<br>" if [[ "$obs" != "" ]]; then detpg+="<b>Spectator:</b> $obs<br>" fi if [[ "$bio" != "" ]]; then detpg+="<b>Biotope:</b> $bio<br>" fi if [[ "$skop" != "" ]]; then detpg+="<b>Microscopium:</b> $skop ($skop_typ)<br>" fi if [[ "$eng" != "" ]]; then detpg+="<b>Amplificatio:</b> $eng<br>" fi if [[ "$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> $lor<br>" fi if [[ "$des" != "" ]]; then detpg+="<b>Depictio:</b> $des<br>" fi detpg+="<br><b>More on <a href=\"../\">BioOSM map</a></b><br>" detpg+="<br>" lhx=$(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+="<a href=\"../img/$obr\"><img src=\"../img/$obr\" alt=\"$co\" class='detimg'></a>" else if [[ "$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 detpg+="<img src=\"../$3\" alt=\"video\" class='detimg'>" fi fi if [[ "$lov" != "" ]]; then detpg+="<img class=\"detimg\" src=\"../lokality/$lov\" alt=\"Locality photo\"><br>" fi detpg+="</td></tr></table>" detpg+="</body></html>" echo "$detpg" > "./det/$detid.htm" # Plain log of entries datelog+="$kdy $kde <a href='./det/$detid.htm' target='_blank'>$co</a><br>\n" >&2 echo -e "\033[32m$co $obs\033[0m" ox="$kdex" oy="$kdey" i=$(($i+1)) done <<< $(echo "$1") # Zere parametr spaget, nikoli $1 scriptu !!! echo "$json{}]}" | sed -e "s/^var data='//g" > "./bioosm.json" echo "$json{}]}'" rss+=$'</channel>\n' rss+=$'</rss>\n' echo "$rss" > "./bioosm.rss" } # KONEC FCE SPAGETY # Parse Tellico file to list of entries 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) # Sorted unique Kingdoms (to be passed as selection criteria) kingdoms=$(echo "$praseTC" | grep -oe ' <new-field-4>.*</new-field-4> ' | sed -E 's/( )*<(\/)?new-field-4>( )*//g' | 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="./'$ICON_biohazard'">' echo ' <script src="./OpenLayers.js"></script>' echo '</head>' echo '<body>' # Generate select echo "<div id='plainlog'><b><a href='./bioosm.rss'>RSS feed</a><br><a href='./plainlog.htm'>Quick news log</a></b></div>" echo "<h1 id='title'>BioOSM - arma biologica in tuis vicinia</h1>" ksel="<select id='reg' onChange='genphy()'>" ksel="$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 "Regnum: $ksel " echo "Phylum: <select id='phy' onChange='gencla()'><option>ALL</option></select> " echo "Classis: <select id='cla' onChange='genord()'><option>ALL</option></select> " echo "Ordo: <select id='ord' onChange='genfam()'><option>ALL</option></select> " echo "Familia: <select id='fam' onChange='gengen()'><option>ALL</option></select> " echo "Genus: <select id='gen' onChange='genspe()'><option>ALL</option></select>" echo "Specie: <select id='spe' onChange='armageddon()'><option>ALL</option></select>" echo "<br><input type='button' value='Platyhelminthes' onClick='plostenkoidy()'>" echo "<input type='checkbox' id='studchecker' onChange='studdrv()'> Springs" #echo "<input type='button' value='Bugs' onClick='buggy()'>" echo "<br><br><div id='map' class='smallmap'></div>" echo "<br><p>Welcome! You can download the <a href='./bioosm.json' target='_blank'>source data as JSON file</a><br>" echo "This site is owned by members of the <a href='https://brmlab.cz' target='_blank'>hackerspace brmlab</a>. See our wiki page for <a href='https://brmlab.cz/project/bioosm/start' target='_blank'>details and contact info</a><br>License: CC-BY-SA</p>" echo "</body>" echo "<script>" 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);" spagety "$praseTC" "ALL" "$ICON_biohazard" echo '</script>' echo '<script src="./bioosm.js"></script>' # Must be after JSON echo "</html>" # Create plaintext log dateloghtm="<html><head>" dateloghtm+="<meta http-equiv='Content-Type' content='text/html; charset=utf-8'>" dateloghtm+="<link rel='stylesheet' href='./style.css' type='text/css'>" dateloghtm+="<title>Brmlab - BioOSM plaintext log</title>" dateloghtm+="</head><body>" datelogsort=$(echo -e "$datelog" | sort -r | uniq) dateloghtm+="$datelogsort" dateloghtm+="</body></html>" echo "$dateloghtm" > "./plainlog.htm"
bioosm.js
- bioosm.js
var blob=JSON.parse(data) var arma=blob.arma var stud=JSON.parse('{}'); var vectorLayerDynamic = new OpenLayers.Layer.Vector('Overlay',{attribution:'<a href="http://brmlab.cz">Brmlab</a>'}); map.addLayer(vectorLayerDynamic); 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" 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) { var r="" if(document.getElementById("reg").value!="ALL") r=document.getElementById("reg").value else { r=a[i].regnum for(var e=i;e>=0 && a[e].locus==a[i].locus;e--) if(a[e].regnum!=a[i].regnum) { r="ALL"; break; } } switch (r) { case "Animalia": 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<arma.length-1;i++) { if(regsel.value==arma[i].regnum && arma[i].phynum!="") phyarr.push(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<arma.length-1;i++) { if(physel.value==arma[i].phylum && arma.classis!="") claarr.push(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<arma.length-1;i++) { if(clasel.value==arma[i].classis && arma[i].ordo!="") ordarr.push(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<arma.length-1;i++) { if(ordsel.value==arma[i].ordo && arma[i].familia!="") famarr.push(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<arma.length-1;i++) { if(famsel.value==arma[i].familia && arma[i].genus!="") genarr.push(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<arma.length-1;i++) { if(gensel.value==arma[i].genus && arma[i].specie!="") spearr.push(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<arma.length-1;i++) if(arma[i].specie==speval && arma[i].genus==genval) // Check genus because of unknown "sp." a.push(arma[i]) } else if(genval!="ALL") { for(var i=0;i<arma.length-1;i++) if(arma[i].genus==genval) a.push(arma[i]) } else if(famval!="ALL") { for(var i=0;i<arma.length-1;i++) if(arma[i].familia==famval) a.push(arma[i]) } else if(ordval!="ALL") { for(var i=0;i<arma.length-1;i++) if(arma[i].ordo==ordval) a.push(arma[i]) } else if(claval!="ALL") { for(var i=0;i<arma.length-1;i++) if(arma[i].classis==claval) a.push(arma[i]) } else if(phyval!="ALL") { for(var i=0;i<arma.length-1;i++) if(arma[i].phylum==phyval) a.push(arma[i]) } else if(regval!="ALL") { for(var i=0;i<arma.length-1;i++) if(arma[i].regnum==regval) a.push(arma[i]) } else // Regnum: ALL { for(var i=0;i<arma.length-1;i++) a.push(arma[i]) } icongeddon(a) } function buggy() { var p=[] for(var i=0;i<arma.length-1;i++) { if(arma[i].regnum==""|| arma[i].phylum==""|| arma[i].classis==""|| arma[i].ordo==""|| arma[i].familia==""|| arma[i].genus=="") p.push(arma[i]) } icongeddon(p) } function plostenkoidy() { var p=[] for(var i=0;i<arma.length-1;i++) { if(arma[i].phylum=="Platyhelminthes") p.push(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 { // Pokracujem v hadovi if(a[i].locus == 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].qualis+"<br>"+a[i].quando+"</td>" spoj+="</tr>" ox=a[i].x oy=a[i].y continue; } if(a[i].specie=="sp.") wikisp="https://en.wikipedia.org/wiki/"+a[i].genus else wikisp="https://en.wikipedia.org/wiki/"+a[i].genus+" "+a[i].specie // 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].locus 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].qualis+'<br>'+a[i].quando+'</td>' spoj+="</tr>" sam='<a href="./det/'+a[i].detid+'.htm" target="_blank"><img src="./simg/'+a[i].obr+'" alt="'+a[i].qualis+'" class="buttimg"></a>' sam+='<br><span class="butttext">' sam+='<b>Qualis:</b> <a href="'+wikisp+'" target="_blank">'+a[i].qualis+'</a><br>' if(a[i].imperium != "") sam+='<b>Imperium:</b> <a href="https://en.wikipedia.org/wiki/'+a[i].imperium+'" target="_blank">'+a[i].imperium+'</a><br>' if(a[i].regnum != "") sam+='<b>Regnum:</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>Classis:</b> <a href="https://en.wikipedia.org/wiki/'+a[i].classis+'" target="_blank">'+a[i].classis+'</a><br>' if(a[i].ordo != "") sam+='<b>Ordo:</b> <a href="https://en.wikipedia.org/wiki/'+a[i].ordo+'" target="_blank">'+a[i].ordo+'</a><br>' if(a[i].familia != "") sam+='<b>Familia:</b> <a href="https://en.wikipedia.org/wiki/'+a[i].familia+'" target="_blank">'+a[i].familia+'</a><br>' if(a[i].genus != "") 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>Specie:</b> <a href="'+wikisp+'" target="_blank">'+a[i].specie+'</a><br>' if(a[i].bio != "") sam+="<b>Biotope:</b> "+a[i].bio+"<br>" if(a[i].quando != "") sam+="<b>Quando:</b> "+a[i].quando+"<br>" sam+="<b>Locus:</b> "+a[i].locus+" ("+a[i].locplain+")<br>" if(a[i].spec != "") sam+="<b>Spectator:</b> "+a[i].spec+"<br>" if(a[i].micro != "") sam+="<b>Microscopium:</b> "+a[i].micro+" ("+a[i].microtyp+")<br>" if(a[i].amp != "") sam+="<b>Amplificatio:</b> "+a[i].amp+"<br>" /* if [[ "$des" != "" ]]; then # sam="$sam<b>Depictio:</b> $des<br>" # fi */ if(a[i].vid != "") sam+='<b>Video:</b> <a href="'+a[i].vid+'" target="_blank">'+a[i].vid+'</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,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; } // Run armageddon on initial load armageddon()
Springs
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/.
- studanky.sh
#!/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{}]}"