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BioOSM

Biologicke zbrane ve vasem okoli
bioosm.jpg
founder: sachy
depends on:
interested: sumie-dh
software license: CC-BY-SA
hardware license: N/A

~~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

  1. ziskani tellico.xml
  2. radkovani dle polozek
  3. pouze verejne (strcit-do-mapy = yep)
  4. preneseni lokality na zacatek radku s informacemi o polozce
  5. 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
#
# find ./ -type f -exec mogrify -verbose -layers Dispose -resize 128\>x128\> -quality 100% {} +
#
# <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&amp;layer=mapnik&amp;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 "$1" | sed -e "s/'/\&#39;/g" -e 's/"/\&#34;/g' -e 's/</\&lt;/g' -e 's/>/\&gt;/g' -e 's/^[ ]*//g' -e 's/[ ]*$//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>Harvesting:</b> $vid<br>"
		fi
		if [[ "$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&amp;layer=mapnik&amp;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='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 vectorLayerDynamic = new OpenLayers.Layer.Vector('Overlay',{attribution:'<a href="http://brmlab.cz">Brmlab</a>'});
map.addLayer(vectorLayerDynamic);
 
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"
 
// 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];
 
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()

Taxonomie dle rodoveho jmena

Script bere jako jediny parametr rodove jmeno a z wikipedie vyparsuje zbytek taxonomie.

tax.sh
#!/bin/bash
 
wat=$(wget -q -O - "https://en.wikipedia.org/wiki/Template:Taxonomy/$1" 2>/dev/null | tr -d '\n' | sed -e $'s/<\/tr>/<\/tr>\\n/g' | grep "<tr>" | sed -e 's/<[^>]*>//g' | grep -o -e "^[a-zA-Z]*:[a-zA-Z]*")
 
echo $(echo "$wat" | grep "Domain:")
echo $(echo "$wat" | grep "Kingdom:")
echo $(echo "$wat" | grep "Phylum:")
echo $(echo "$wat" | grep "Class:")
echo $(echo "$wat" | grep "Order:")
echo $(echo "$wat" | grep "Family:")
echo $(echo "$wat" | grep "Genus:")
project/bioosm/start.1567157056.txt.gz · Last modified: 2019/08/30 09:24 by sachy