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project:bioosm:start [2018/08/27 22:55] – pridan taxonomator sachyproject:bioosm:start [2025/10/30 16:29] (current) – sachy
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 name=Biologicke zbrane ve vasem okoli| name=Biologicke zbrane ve vasem okoli|
 image= bioosm:bioosm.jpg?400 | image= bioosm:bioosm.jpg?400 |
-founder=[[user:sachy:start]]|+founder=[[user:sachy]]|
 interested=[[user:sumie-dh]]| interested=[[user:sumie-dh]]|
 sw=CC-BY-SA| sw=CC-BY-SA|
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 &relation firstimage = :project:bioosm:bioosm.jpg &relation firstimage = :project:bioosm:bioosm.jpg
 ~~ ~~
 +---- dataentry project ----
 +name: BioOSM
 +status: active
 +image: {{:project:bioosm:bioosm.jpg}}
 +----
  
-[[http://brmlab.s0c4.net/bioosm/|BioOSM]] je mapa vyskytu mikroorganismu (ras, bakterii, plostenek, ...) a do budoucna i dalsich prirodnin (mineralu, ...).+On hold - leaving Tellico, welcome Specify 6/7 
 + 
 +[[https://brmlab.s0c4.net/bioosm/|BioOSM]] je mapa vyskytu mikroorganismu (ras, bakterii, plostenek, ...) a do budoucna i dalsich prirodnin (mineralu, ...).
  
 ==== K cemu to je ==== ==== 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 +  * 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  +  * monitoring zivocichu a rostlin podle zajmu prispevovatelu  
-  *  snadne klikaci katalogovani nalezu skrze Tellico nevyzadujici coding skills +  * snadne klikaci katalogovani nalezu skrze Tellico nevyzadujici coding skills 
-  *  TODO - jednoduche selekce zajmoveho okruhu subjektu [napr. podle rodu, biotopu, datumu] na mape+  * TODO - jednoduche selekce zajmoveho okruhu subjektu [napr. podle rodu, biotopu, datumu] na mape
   * procvicovani temne magie commandu grep, sed a regexpu   * procvicovani temne magie commandu grep, sed a regexpu
  
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 Pro nadsence je vygenerovany taky prehled prispevku plainlog.htm serazeny dle data pridani do databaze. Pro nadsence je vygenerovany taky prehled prispevku plainlog.htm serazeny dle data pridani do databaze.
 +
 +Pokud chcete vedet co je noveho, odebirejte projektovou [[http://brmlab.s0c4.net/bioosm/bioosm.rss|RSS]]
  
 Obrazky v plnem rozliseni jsou v podadresari "img", nahledy v "simg". Videa jsou nahrana na YT a misto nahledu maji generickou ikonu. Obrazky v plnem rozliseni jsou v podadresari "img", nahledy v "simg". Videa jsou nahrana na YT a misto nahledu maji generickou ikonu.
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 # Parse Tellico database to BioOSM index.htm # Parse Tellico database to BioOSM index.htm
 # $1 = tellico .tc file # $1 = tellico .tc file
-# Print result to stdout+# $2 = "" terminal stderr (default) 
 +#    = "html" html marked stderr (for web bioosm)
 # #
-# find ./ -type f -exec mogrify -verbose -layers Dispose -resize 128\>x128\> -quality 100% {} ++# Print result to /jsonrss/*.json
 # #
 +# find ./ -type f -name '*.jpg' -newermt "2023-09-03" -exec mogrify -verbose -layers Dispose -resize 1600\>x1600\> -quality 90% {} +
 +# echo "14.7345 48.7145" | gdallocationinfo -wgs84 ./cesko_big.tiff
 +# gdal_translate -of GTiff -a_srs WGS84 -a_ullr 11.6863 50.9745 19.9876 48.3729 ./source.tif ./result.tif
 +# https://data.geus.dk/egdi/#baslay=baseMapGEUS&extent=3953440,2399890,4757540,2763830&layers=igme5000
 +
 +#bnds=new OpenLayers.Bounds(11.6863000,48.3729000 ,19.9876000,50.9745000);
 +#var geoimg = new OpenLayers.Layer.Image("geo","https://brmlab.s0c4.net/bioosm/eusr5000_600dpi_cesko.png", bnds,bnds.getSize(),{numZoomLevels: 20,isBaseLayer:false});
 +#map.addLayer(geoimg);
 +
 +
 +#
 +# <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) # // vectorLayer.removeFeatures(atol)
 # // map.removeLayer(vectorLayer) # // map.removeLayer(vectorLayer)
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 # #
 # Creates: # Creates:
-#   (to stdout) index.htm file with the map and static entries+#   (to stdout) HTML file with the map and static entries
 #   ./det/ID.htm details of each and every entry #   ./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/*" rm -rfv "./det/*"
Line 129: Line 156:
  
 json="" 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'
 +
 +errhtml="$2"
 +
 +# 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"
 +}
 +
 +# HTML fajl per project
 +function genhtml() {
 + o=$(obioosm "$1" "" "" | sed -e 's/\//\\\//g') # make "\/" from "/" so sed below is OK
 + h=$(cat "./__BIOVZOR__.htm" | sed -e "s/__BIOVZOR_TIT__/$1/g" | sed -e "s/__BIOVZOR_CPRT__/$o/g" | sed -e "s/__BIOVZOR_J__/$1/g")
 + echo "$h" > "./jsonrss/$1.htm"
 + echo "*** $1 done ***"
 +}
  
 # Return icon by Regnum # Return icon by Regnum
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 function safehtml () { 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'+ echo "$1" | sed -e 's/#/%23/g' -e "s/'/\&#39;/g" -e 's/"/\&#34;/g' -e 's/</\&lt;/g' -e 's/>/\&gt;/g' -e 's/^[ ]*//g' -e 's/[ ]*$//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
 } }
  
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 # !!! BEZ ODSAZENI !!! # !!! BEZ ODSAZENI !!!
 # $1 = list of entries # $1 = list of entries
-# $2 = layer name+# $2 = layer name = JSON filename without suffix
 # $3 = icon of the points # $3 = icon of the points
 function spagety () { function spagety () {
 +
 + if [[ "$errhtml" == "" ]]; then
 + >&2 echo "===== $2 ====="
 + else
 + >&2 echo "<h2>$2</h2>"
 + fi
  
  bylo="" # Minula pozice  bylo="" # Minula pozice
Line 170: Line 278:
  oy="" # Old Y  oy="" # Old Y
  datelog="" # Entries sorted by date for plaintext log  datelog="" # Entries sorted by date for plaintext log
- json="var data='{\"version\":\"$(date --rfc-3339=seconds)\",\"arma\":["+ json="var data='{\"version\":\"$(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 "$radek" ]]; do  while IFS='' read -r radek || [[ -n "$radek" ]]; do
- co=$(echo "$radek" | grep -oe ' <title>.*</title> ' | sed -E 's/( )*<(\/)?title>( )*//g')+ 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 "$co")  co=$(safehtml "$co")
- obr=$(echo "$radek" | grep -oe ' <image>.*</image> ' | sed -E 's/( )*<(\/)?image>( )*//g' | grep -oPe '[^/]*$') + obr=$(echo "$radek" | sed -E 's/^.*<image>(.*)<\/image>.*$/\1/g;t;d' | sed -E 's/^.*\///g') 
- obr=$(safehtml "$obr") + kde=$(echo "$radek" | sed -E 's/^.*<locality>(.*)<\/locality>.*$/\1/g;t;d')
- kde=$(echo "$radek" | grep -oe '<locality>.*</locality>' | grep -oPe '[0-9]{2}\.[0-9]{1,10}[, ]*[0-9]{2}\.[0-9]{1,10}')+
  kde=$(safehtml "$kde")  kde=$(safehtml "$kde")
- kdex=$(echo "$kde" | grep -oPe '[0-9]{2}\.[0-9]{1,10}$') + kdex=$(echo "$kde" | sed -E 's/^[0-9]+\.[0-9]+[, ]*//g;t;d') # keep second part 
- kdex=$(safehtml "$kdex") + kdey=$(echo "$kde" | sed -E 's/[, ]*[0-9]+\.[0-9]+$//g;t;d') # keep first part 
- kdey=$(echo "$kde" | grep -oPe '^[0-9]{2}\.[0-9]{1,10}') + 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')
- 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 "$kdy")  kdy=$(safehtml "$kdy")
- skop_typ=$(echo "$radek" | grep -oe ' <new-field-1>.*</new-field-1> ' | sed -E 's/( )*<(\/)?new-field-1>( )*//g')+ skop_typ=$(echo "$radek" | sed -E 's/^.*<new-field-1>(.*)<\/new-field-1>.*$/\1/g;t;d')
  skop_typ=$(safehtml "$skop_typ")  skop_typ=$(safehtml "$skop_typ")
- skop=$(echo "$radek" | grep -oe ' <microscope>.*</microscope> ' | sed -E 's/( )*<(\/)?microscope>( )*//g')+ skop=$(echo "$radek" | sed -E 's/^.*<microscope>(.*)<\/microscope>.*$/\1/g;t;d')
  skop=$(safehtml "$skop")  skop=$(safehtml "$skop")
- imp=$(echo "$radek" | grep -oe ' <new-field-3>.*</new-field-3> ' | sed -E 's/( )*<(\/)?new-field-3>( )*//g')+ imp=$(echo "$radek" | sed -E 's/^.*<new-field-3>(.*)<\/new-field-3>.*$/\1/g;t;d')
  imp=$(safehtml "$imp")  imp=$(safehtml "$imp")
- reg=$(echo "$radek" | grep -oe ' <new-field-4>.*</new-field-4> ' | sed -E 's/( )*<(\/)?new-field-4>( )*//g')+ reg=$(echo "$radek" | sed -E 's/^.*<new-field-4>(.*)<\/new-field-4>.*$/\1/g;t;d')
  reg=$(safehtml "$reg")  reg=$(safehtml "$reg")
- phy=$(echo "$radek" | grep -oe ' <phylum>.*</phylum> ' | sed -E 's/( )*<(\/)?phylum>( )*//g')+ phy=$(echo "$radek" | sed -E 's/^.*<phylum>(.*)<\/phylum>.*$/\1/g;t;d')
  phy=$(safehtml "$phy")  phy=$(safehtml "$phy")
- cla=$(echo "$radek" | grep -oe ' <class>.*</class> ' | sed -E 's/( )*<(\/)?class>( )*//g')+ cla=$(echo "$radek" | sed -E 's/^.*<class>(.*)<\/class>.*$/\1/g;t;d')
  cla=$(safehtml "$cla")  cla=$(safehtml "$cla")
- ord=$(echo "$radek" | grep -oe ' <order>.*</order> ' | sed -E 's/( )*<(\/)?order>( )*//g')+ ord=$(echo "$radek" | sed -E 's/^.*<order>(.*)<\/order>.*$/\1/g;t;d')
  ord=$(safehtml "$ord")  ord=$(safehtml "$ord")
- fam=$(echo "$radek" | grep -oe ' <family>.*</family> ' | sed -E 's/( )*<(\/)?family>( )*//g')+ fam=$(echo "$radek" | sed -E 's/^.*<family>(.*)<\/family>.*$/\1/g;t;d')
  fam=$(safehtml "$fam")  fam=$(safehtml "$fam")
- gen=$(echo "$radek" | grep -oe ' <genus>.*</genus> ' | sed -E 's/( )*<(\/)?genus( )*>//g')+ gen=$(echo "$radek" | sed -E 's/^.*<genus>(.*)<\/genus>.*$/\1/g;t;d')
  gen=$(safehtml "$gen")  gen=$(safehtml "$gen")
- spe=$(echo "$radek" | grep -oe ' <species>.*</species> ' | sed -E 's/( )*<(\/)?species>( )*//g')+ spe=$(echo "$radek" | sed -E 's/^.*<species>(.*)<\/species>.*$/\1/g;t;d')
  spe=$(safehtml "$spe")  spe=$(safehtml "$spe")
- loc=$(echo "$radek" | grep -oe ' <locality---plaintext>.*</locality---plaintext> ' | sed -E 's/( )*<(\/)?locality---plaintext>( )*//g')+ loc=$(echo "$radek" | sed -E 's/^.*<locality---plaintext>(.*)<\/locality---plaintext>.*$/\1/g;t;d')
  loc=$(safehtml "$loc")  loc=$(safehtml "$loc")
- des=$(echo "$radek" | grep -oe ' <description>.*</description> ' | sed -E 's/( )*<(\/)?description>( )*//g')+ des=$(echo "$radek" | sed -E 's/^.*<description>(.*)<\/description>.*$/\1/g;t;d')
  des=$(safehtml "$des")  des=$(safehtml "$des")
- vid=$(echo "$radek" | grep -oe ' <videolink>.*</videolink> ' | sed -E 's/( )*<(\/)?videolink>( )*//g')+ vid=$(echo "$radek" | sed -E 's/^.*<videolink>(.*)<\/videolink>.*$/\1/g;t;d')
  vid=$(safehtml "$vid")  vid=$(safehtml "$vid")
- bio=$(echo "$radek" | grep -oe ' <biotope>.*</biotope> ' | sed -E 's/( )*<(\/)?biotope>( )*//g')+ bio=$(echo "$radek" | sed -E 's/^.*<biotope>(.*)<\/biotope>.*$/\1/g;t;d')
  bio=$(safehtml "$bio")  bio=$(safehtml "$bio")
- eng=$(echo "$radek" | grep -oe ' <enlargement>.*</enlargement> ' | sed -E 's/( )*<(\/)?enlargement>( )*//g')+ eng=$(echo "$radek" | sed -E 's/^.*<enlargement>(.*)<\/enlargement>.*$/\1/g;t;d')
  eng=$(safehtml "$eng")  eng=$(safehtml "$eng")
- obs=$(echo "$radek" | grep -oe ' <observer>.*</observer> ' | sed -E 's/( )*<(\/)?observer>( )*//g')+ obs=$(echo "$radek" | sed -E 's/^.*<observer>(.*)<\/observer>.*$/\1/g;t;d')
  obs=$(safehtml "$obs")  obs=$(safehtml "$obs")
- lnk=$(echo "$radek" | grep -oe ' <localitylink>.*</localitylink> ' | sed -E 's/( )*<(\/)?localitylink>( )*//g')+ lnk=$(echo "$radek" | sed -E 's/^.*<localitylink>(.*)<\/localitylink>.*$/\1/g;t;d')
  lnk=$(safehtml "$lnk")  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>.*$/\1/g;t;d')
 +
 +# if [[ "$errhtml" == "" ]]; then
 +# >&2 echo "$co - $har - $den - $dur - $lor - $lrl - $lov - $elv"
 +# else
 +# >&2 echo "<span class='nok'>$co - $har - $den - $dur - $lor - $lrl - $lov - $elv</span><br>"
 +# fi
 +# continue;
 +
  detid=$(echo "brmlab$co$obr$kde$kdy" | md5sum | grep -oe '[a-zA-Z0-9]*')  detid=$(echo "brmlab$co$obr$kde$kdy" | md5sum | grep -oe '[a-zA-Z0-9]*')
  
  if [[ "$kdex" = "" ]]; then  if [[ "$kdex" = "" ]]; then
- >&2 echo $(echo "$radek" | grep -oe '<locality>.*</locality>') " $co" + if [[ "$errhtml" == "" ]]; then 
- continue;+ >&2 echo -e "\033[31m $lid KDEX '$kde' '$co' \033[0m" 
 + >&2 echo -e "\033[31m $lid RADEK '$radek' \033[0m" 
 + else 
 + >&2 echo "<span class='nok'>$lid KDEX '$kde' '$co'</span><br>" 
 + >&2 echo "<span class='nok'><pre>$radek</pre></span>" 
 + fi
  fi  fi
 +
  zkurvenetellico=$(echo "$obr" | grep -oe '\.[a-zA-Z]*$')  zkurvenetellico=$(echo "$obr" | grep -oe '\.[a-zA-Z]*$')
- if [[ "$zkurvenetellico" = ".jpeg" ]]; then + odkurvenyobr=$(echo "$obr" | sed -e 's/%23/#/g') 
- >&2 echo "$obr $co" + #if [[ "$zkurvenetellico" = ".jpeg" ]]; then 
- continue;+ if [[ ! -f "./img/$odkurvenyobr" ]]; then 
 + if [[ "$gen" != "negative" ]]; then 
 + if [[ "$errhtml" == "" ]]; then 
 + >&2 echo -e "\033[31m $lid OBR $odkurvenyobr $co\033[0m" 
 + else 
 + >&2 echo "<span class='nok'>$lid OBR $odkurvenyobr $co</span>" 
 + fi 
 + continue; 
 + fi
  fi  fi
 + obr=$(safehtml "$obr")
  
  if [[ "$spe" = "sp." ]]; then  if [[ "$spe" = "sp." ]]; then
Line 237: Line 390:
  fi  fi
  
- json="$json{" + povr="" 
- json="$json \"qualis\":\"$co\"," + povs="" 
- json="$json \"imperium\":\"$imp\"," + pov="" 
- json="$json \"regnum\":\"$reg\"," + if [[ "$phy" = "Platyhelminthes" ]]; then 
- json="$json \"phylum\":\"$phy\"," + povr=$(cat "./povodi_r.json" | ./povodi.py "$kdey" "$kdex") 
- json="$json \"classis\":\"$cla\"," + #povrf=$(echo "$povr" | grep -oPe '^[^ ]*' | tr 'e' 'E') 
- json="$json \"ordo\":\"$ord\"," + povrf=$(echo "$povr" | sed -e 's/ .*$//g' | tr 'e' 'E') 
- json="$json \"familia\":\"$fam\"," + povrn=$(echo "$povr" | sed -e 's/^[^ ]* //g') 
- json="$json \"genus\":\"$gen\"," + povs=$(cat "./povodi_s.json" | ./povodi.py "$kdey" "$kdex") 
- json="$json \"specie\":\"$spe\"," + #povsf=$(echo "$povs" | grep -oPe '^[^ ]*' | tr 'e' 'E') 
- json="$json \"locus\":\"$kde\"," + povsf=$(echo "$povs" | sed -e 's/ .*$//g' | tr 'e' 'E') 
- json="$json \"x\":\"$kdex\"," + povsn=$(echo "$povs" | sed -e 's/^[^ ]* //g') 
- json="$json \"y\":\"$kdey\"," + if (( $(echo "$povsf < $povrf" | bc -l) )) ; then 
- json="$json \"locplain\":\"$loc\"," + pov="$povsn - $povrn" 
- json="$json \"depictio\":\"$des\"," + else 
- json="$json \"quando\":\"$kdy\"," + pov="$povrn" 
- json="$json \"obr\":\"$obr\"," + fi 
- json="$json \"micro\":\"$skop\"," + fi 
- json="$json \"microtyp\":\"$skop_typ\"," + 
- json="$json \"vid\":\"$vid\"," + if [[ "$cls" = "" ]]; then 
- json="$json \"bio\":\"$bio\"," + cls=0 
- json="$json \"amp\":\"$eng\"," + fi 
- json="$json \"spec\":\"$obs\"," + 
- json="$json \"detid\":\"$detid\"," + if [[ "$mpi" = "" ]]; then 
- json="$json \"lnk\":\"$lnk\"" # Lastone without ',' + mpi="" 
- json="$json },"+ else 
 + mpi="y" 
 + fi 
 + 
 + Tjson="{" 
 + Tjson+=" \"title\":\"$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'
  
  
Line 268: Line 479:
  detid=$(echo "brmlab$co$obr$kde$kdy" | md5sum | grep -oe '[a-zA-Z0-9]*')  detid=$(echo "brmlab$co$obr$kde$kdy" | md5sum | grep -oe '[a-zA-Z0-9]*')
  detpg="<html><head>"  detpg="<html><head>"
- detpg="$detpg<meta http-equiv='Content-Type' content='text/html; charset=utf-8'>" + detpg+="<meta http-equiv='Content-Type' content='text/html; charset=utf-8'>" 
- detpg="$detpg<link rel='stylesheet' href='../style.css' type='text/css'>" + detpg+="<link rel='stylesheet' href='../style.css' type='text/css'>" 
- detpg="$detpg<title>Brmlab - BioOSM $co $kde</title>" + detpg+="<title>Brmlab - BioOSM $co $kde</title>" 
- detpg="$detpg</head><body>" + 
- detpg="$detpg<table class='dettbl'><tr>" + detpg+="<meta property='og:title' content='BioOSM - $co $kde'>" 
- detpg="$detpg<td><h1>$co (<a href='$wikisp' target='_blank'>wiki</a>)</h1>"+ 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  if [[ "$imp" != "" ]]; then
- detpg="$detpg<b>Imperium:</b> <a href='https://en.wikipedia.org/wiki/$imp' target='_blank'>$imp</a><br>"+ detpg+="<b>Domain:</b> <a href='https://en.wikipedia.org/wiki/$imp' target='_blank'>$imp</a><br>"
  fi  fi
  if [[ "$reg" != "" ]]; then  if [[ "$reg" != "" ]]; then
- detpg="$detpg<b>Regnum:</b> <a href='https://en.wikipedia.org/wiki/$reg' target='_blank'>$reg</a><br>"+ detpg+="<b>Kingdom:</b> <a href='https://en.wikipedia.org/wiki/$reg' target='_blank'>$reg</a><br>"
  fi  fi
  if [[ "$phy" != "" ]]; then  if [[ "$phy" != "" ]]; then
- detpg="$detpg<b>Phylum:</b> <a href='https://en.wikipedia.org/wiki/$phy' target='_blank'>$phy</a><br>"+ detpg+="<b>Phylum:</b> <a href='https://en.wikipedia.org/wiki/$phy' target='_blank'>$phy</a><br>"
  fi  fi
  if [[ "$cla" != "" ]]; then  if [[ "$cla" != "" ]]; then
- detpg="$detpg<b>Classis:</b> <a href='https://en.wikipedia.org/wiki/$cla' target='_blank'>$cla</a><br>"+ detpg+="<b>Class:</b> <a href='https://en.wikipedia.org/wiki/$cla' target='_blank'>$cla</a><br>"
  fi  fi
  if [[ "$ord" != "" ]]; then  if [[ "$ord" != "" ]]; then
- detpg="$detpg<b>Ordo:</b> <a href='https://en.wikipedia.org/wiki/$ord' target='_blank'>$ord</a><br>"+ detpg+="<b>Order:</b> <a href='https://en.wikipedia.org/wiki/$ord' target='_blank'>$ord</a><br>"
  fi  fi
  if [[ "$fam" != "" ]]; then  if [[ "$fam" != "" ]]; then
- detpg="$detpg<b>Familia:</b> <a href='https://en.wikipedia.org/wiki/$fam' target='_blank'>$fam</a><br>"+ detpg+="<b>Family:</b> <a href='https://en.wikipedia.org/wiki/$fam' target='_blank'>$fam</a><br>"
  fi  fi
  if [[ "$gen" != "" ]]; then  if [[ "$gen" != "" ]]; then
- detpg="$detpg<b>Genus:</b> <a href='https://en.wikipedia.org/wiki/$gen' target='_blank'>$gen</a><br>"+ detpg+="<b>Genus:</b> <a href='https://en.wikipedia.org/wiki/$gen' target='_blank'>$gen</a><br>"
  fi  fi
  if [[ "$spe" != "" ]]; then  if [[ "$spe" != "" ]]; then
- detpg="$detpg<b>Specie:</b> <a href='$wikisp' target='_blank'>$spe</a><br>"+ detpg+="<b>Species:</b> <a href='$wikisp' target='_blank'>$spe</a><br>"
  fi  fi
- detpg="$detpg<br>"+ if [[ "$kar" != "" ]]; then 
 + detpg+="<b>Karyotype:</b> $kar<br>" 
 + fi 
 + detpg+="<br>"
  if [[ "$kdy" != "" ]]; then  if [[ "$kdy" != "" ]]; then
- detpg="$detpg<b>Quando:</b> $kdy<br>"+ detpg+="<b>Date:</b> $kdy<br>"
  fi  fi
  if [[ "$lnk" != "" ]]; then  if [[ "$lnk" != "" ]]; then
  loc="<a href=\"$lnk\" target=\"_blank\">$loc</a>" # Yes, escaped "  loc="<a href=\"$lnk\" target=\"_blank\">$loc</a>" # Yes, escaped "
  fi  fi
- detpg="$detpg<b>Locus:</b> $kde ($loc)<br>"+ detpg+="<b>Place:</b> $kde ($loc)<br>" 
 + if [[ "$elv" != "" ]]; then 
 + detpg+="<b>Elevation:</b> $elv m<br>" 
 + fi 
  if [[ "$obs" != "" ]]; then  if [[ "$obs" != "" ]]; then
- detpg="$detpg<b>Spectator:</b> $obs<br>"+ detpg+="<b>Observer:</b> $obs<br>"
  fi  fi
  if [[ "$bio" != "" ]]; then  if [[ "$bio" != "" ]]; then
- detpg="$detpg<b>Biotope:</b> $bio<br>"+ 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> $ph<br>"
  fi  fi
- detpg="$detpg<br>"+ detpg+="<span id='microscopeval'>"
  if [[ "$skop" != "" ]]; then  if [[ "$skop" != "" ]]; then
- detpg="$detpg<b>Microscopium:</b> $skop ($skop_typ)<br>"+ detpg+="<b>Microscope:</b> $skop ($skop_typ)<br>"
  fi  fi
 + detpg+="</span>"
 + detpg+="<span id='ampval'>"
  if [[ "$eng" != "" ]]; then  if [[ "$eng" != "" ]]; then
- detpg="$detpg<b>Amplificatio:</b> $eng<br>" + detpg+="<b>Amplification:</b> $eng<br>"
- fi +
- detpg="$detpg<br>" +
- if [[ "$des" != "" ]]; then +
- detpg="$detpg<b>Depictio:</b> $des<br>"+
  fi  fi
 + detpg+="</span>"
  if [[ "$vid" != "" ]]; then  if [[ "$vid" != "" ]]; then
- detpg="$detpg<b>Video:</b> <a href=\"$vid\" target=\"_blank\">$vid</a><br>"+ detpg+="<b>Video:</b> <a href=\"$vid\" target=\"_blank\">$vid</a><br>"
  fi  fi
- detpg="$detpg</td><td style='min-width:66%'>"+ if [[ "$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$pdy&amp;layer=mapnik&amp;marker=$kdey%2C$kdex'></iframe>" 
 + detpg+="</td><td style='min-width:66%;vertical-align:top'>" 
  if [[ "$obr" != "" ]]; then  if [[ "$obr" != "" ]]; then
- detpg="$detpg<a href=\"../img/$obr\"><img src=\"../img/$obr\" alt=\"$co\" class='detimg'></a>"+ detpg+="<div id='maximatura'><a href=\"../img/$obr\"><img src=\"../img/$obr\" alt=\"$co\" class='detimg'></a></div>" 
 + detpg+="<div id='miniatury'></div>"
  else  else
  if [[ "$vid" != "" ]]; then  if [[ "$vid" != "" ]]; then
  detyt=$(echo "$vid" | sed -e 's/youtube.com\/watch?v=/youtube.com\/embed\//g')  detyt=$(echo "$vid" | sed -e 's/youtube.com\/watch?v=/youtube.com\/embed\//g')
- detpg="$detpg<iframe class='detvid' src='$detyt' frameborder='0' allow='encrypted-media' allowfullscreen></iframe>"+ detpg+="<iframe class='detvid' src='$detyt' frameborder='0' allow='encrypted-media' allowfullscreen></iframe>"
  else  else
- detpg="$detpg<img src=\"../$3\" alt=\"video\" class='detimg'>"+ if [[ "$gen" == "negative" ]]; then 
 + detpg+="<img src=\"../negative.png\" alt=\"Negative observation\" class='detimg'>" 
 + else 
 + detpg+="<img src=\"../$3\" alt=\"video\" class='detimg'>" 
 + fi
  fi  fi
  fi  fi
- detpg="$detpg</td></tr></table>" + if [[ "$lov" != "" ]]; then 
- detpg="$detpg</body></html>"+ 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/$detid.htm"  echo "$detpg" > "./det/$detid.htm"
  
  # Plain log of entries  # Plain log of entries
- datelog="$datelog $kdy $kde <a href='./det/$detid.htm' target='_blank'>$co</a><br>\n"+ datelog+="$kdy $kde <a href='./det/$detid.htm' target='_blank'>$co</a><br>\n"
  
- >&2 echo "$co $obs"+ if [[ "$errhtml" == "" ]]; then 
 + >&2 echo -e "\033[32m$lid $co $obs\033[0m" 
 + else 
 + >&2 echo "<span class='ok'>$lid $co $obs</span>" 
 + fi
  
  ox="$kdex"  ox="$kdex"
Line 352: Line 642:
  
  done <<< $(echo "$1") # Zere parametr spaget, nikoli $1 scriptu !!!  done <<< $(echo "$1") # Zere parametr spaget, nikoli $1 scriptu !!!
- echo "$json{}]}" | sed -e "s/^var data='//g" > "./bioosm.json" + echo -e "$json{}]}" | sed -e "s/^var data='//g" > "./jsonrss/$2.json" 
- echo "$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 } # 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) # 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)+#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 '<!DOCTYPE html>' 
-echo '<html>' +#echo '<html>' 
-echo '<head>' +#echo '<head>' 
-echo ' <meta http-equiv="Content-Type" content="text/html; charset=utf-8">' +#echo ' <meta http-equiv="Content-Type" content="text/html; charset=utf-8">' 
-echo ' <title>brmlab - BioOSM</title>' +#echo ' <title>brmlab - BioOSM</title>' 
-echo ' <link rel="stylesheet" href="./style.css" type="text/css">' +#echo ' <link rel="stylesheet" href="./style.css" type="text/css">' 
-echo ' <link rel="favicon" href="./'$ICON_biohazard'">' +#echo ' <link rel="favicon" href="./'$ICON_biohazard'">' 
-echo ' <script src="./OpenLayers.js"></script>' +#echo ' <script src="./OpenLayers.js"></script>' 
-echo '</head>' +#echo '</head>' 
-echo '<body>' +#echo '<body>' 
-# Generate select +## Generate select 
-echo "<div id='plainlog'><b><a href='./plainlog.htm'>Plaintext log</a></b></div>" +#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 - arma biologica in tuis vicinia</h1>" 
-ksel="<select id='reg' onChange='genphy()'>" +#echo "<h1 id='title'>BioOSM - creatures around us</h1>" 
-ksel="$ksel<option value='ALL' selected>ALL</option>" +# 
-while IFS='' read -r king || [[ -n "$king" ]]; do +#ksel="<select id='reg' onChange='genphy()'>" 
- ksel="$ksel<option value='"$king"'>$king</option>" +#ksel="$ksel<option value='ALL' selected>ALL</option>" 
-done <<< $(echo "$kingdoms") +#while IFS='' read -r king || [[ -n "$king" ]]; do 
-ksel="$ksel</select>" +# ksel="$ksel<option value='"$king"'>$king</option>" 
-echo "Regnum: $ksel "+#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='&#x1F50D;' 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);" 
 +#
  
-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>" +# Parse Tellico file to get list of entries 
-echo 'map = new OpenLayers.Map("map");' +granty=$(unzip -p "$1" tellico.xml | grep "<grant>" | sed -E 's/( )*<(\/)?grant>( )*//g' | sed -E 's/_additional$//g' | sort -u | grep -v "^none$") 
-echo 'map.addLayer(new OpenLayers.Layer.OSM());' +#praseTC=$(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) 
-echo 'epsg4326 =  new OpenLayers.Projection("EPSG:4326"); //WGS 1984 projection' +#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) 
-echo 'projectTo = map.getProjectionObject(); //The map projection (Spherical Mercator)' +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)
-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:'+velkyvepr=$(echo "$praseTC" | grep "<strcit-do-mapy>yep</strcit-do-mapy>") 
 +spagety "$velkyvepr" "bioosm" "$ICON_biohazard"
  
-echo 'var atol = new OpenLayers.Feature.Vector(' +# VSECHNO i non-public - zakomentuj predchozi "spagety" a odkomunetuj tohle + exit 
-echo ' new OpenLayers.Geometry.Point(14.41876, 50.10554).transform(epsg4326, projectTo),' +#spagety "$praseTC" "celytraktor" "$ICON_biohazard" # vsechno i non-public 
-echo ' {description:"Atomovy atol Brmkini"} ,' +#exit
-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"+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" 
 + genhtml "$grnt" 
 +done <<< $(echo "$granty")
  
-echo '</script>' +#if [[ "$errhtml" == "html" ]]; then 
-echo '<script src="./bioosm.js"></script>' # Must be after JSON + >&2 echo "*** DONE ***" 
-echo "</html>"+#fi 
 + 
 + 
 +##echo -e "$json{}]}" 
 +#echo '</script>' 
 +#echo '<script src="./bioosm.js"></script>' # Must be after JSON 
 +#echo "</html>"
  
 # Create plaintext log # Create plaintext log
 dateloghtm="<html><head>" dateloghtm="<html><head>"
-dateloghtm="$dateloghtm<meta http-equiv='Content-Type' content='text/html; charset=utf-8'>" +dateloghtm+="<meta http-equiv='Content-Type' content='text/html; charset=utf-8'>" 
-dateloghtm="$dateloghtm<link rel='stylesheet' href='./style.css' type='text/css'>" +dateloghtm+="<link rel='stylesheet' href='./style.css' type='text/css'>" 
-dateloghtm="$dateloghtm<title>Brmlab - BioOSM plaintext log</title>" +dateloghtm+="<title>Brmlab - BioOSM plaintext log</title>" 
-dateloghtm="$dateloghtm</head><body>"+dateloghtm+="</head><body>"
 datelogsort=$(echo -e "$datelog" | sort -r | uniq) datelogsort=$(echo -e "$datelog" | sort -r | uniq)
-dateloghtm="$dateloghtm $datelogsort" +dateloghtm+="$datelogsort" 
-dateloghtm="$dateloghtm</body></html>"+dateloghtm+="</body></html>"
 echo "$dateloghtm" > "./plainlog.htm" echo "$dateloghtm" > "./plainlog.htm"
 </code> </code>
Line 442: Line 767:
  
 <code javascript bioosm.js> <code javascript bioosm.js>
-var blob=JSON.parse(data) +window.blob=JSON.parse('{}'); 
-var arma=blob.arma+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/); 
 + console.log(pus); 
 + if(pus) 
 + plostenkoidy(); 
 + else 
 + // Else initial load 
 + armageddon() 
 + } 
 + } 
 + request.open("GET","./"+ubermaster+".json",true); // defined in html 
 + request.send(); 
 +} 
 + 
 +getJSONbioosm(); 
 + 
 +var stud=JSON.parse('{}');
  
 var vectorLayerDynamic = new OpenLayers.Layer.Vector('Overlay',{attribution:'<a href="http://brmlab.cz">Brmlab</a>'}); 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.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 regsel=document.getElementById("reg")
Line 464: Line 831:
 var ICON_protista="protista.png" var ICON_protista="protista.png"
 var ICON_biohazard="biohazard.svg" var ICON_biohazard="biohazard.svg"
 +var ICON_studanka="studanka.png"
 +var ICON_negative="negative.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 // Return icon by Regnum
 function geticon (a,i) function geticon (a,i)
 { {
 + if(a[i].genus=="negative")
 + return ICON_negative;
 +
 + var p=true;
  var r=""  var r=""
  if(document.getElementById("reg").value!="ALL")  if(document.getElementById("reg").value!="ALL")
 + {
  r=document.getElementById("reg").value  r=document.getElementById("reg").value
 + p=false;
 + }
  else  else
  {  {
  r=a[i].regnum  r=a[i].regnum
- for(var e=i;e>=0 && a[e].locus==a[i].locus;e--)+ 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)  if(a[e].regnum!=a[i].regnum)
  {  {
Line 480: Line 902:
  break;  break;
  }  }
 + }
  }  }
 +
  
  switch (r)  switch (r)
  {  {
  case "Animalia":  case "Animalia":
 + {
 + if(p)
 + return ICON_plostenkoid;
  return ICON_animalia;  return ICON_animalia;
 + }
  case "Bacteria":  case "Bacteria":
  return ICON_bacteria;  return ICON_bacteria;
Line 510: Line 938:
  
  var phyarr=[]  var phyarr=[]
- for (var i=0;i<arma.length-1;i++)+ for (var i=0;i<window.arma.length-1;i++)
  {  {
- if(regsel.value==arma[i].regnum && arma[i].phynum!="") + if(regsel.value==window.arma[i].regnum && window.arma[i].phynum!="") 
- phyarr.push(arma[i].phylum)+ phyarr.push(window.arma[i].phylum)
  }  }
  phyarr.sort()  phyarr.sort()
Line 537: Line 965:
  
  var claarr=[]  var claarr=[]
- for (var i=0;i<arma.length-1;i++)+ for (var i=0;i<window.arma.length-1;i++)
  {  {
- if(physel.value==arma[i].phylum && arma.classis!="") + if(physel.value==window.arma[i].phylum && window.arma.classis!="") 
- claarr.push(arma[i].classis)+ claarr.push(window.arma[i].classis)
  }  }
  claarr.sort()  claarr.sort()
Line 562: Line 990:
  spesel.innerHTML="<option>ALL</option>"  spesel.innerHTML="<option>ALL</option>"
  var ordarr=[]  var ordarr=[]
- for (var i=0;i<arma.length-1;i++)+ for (var i=0;i<window.arma.length-1;i++)
  {  {
- if(clasel.value==arma[i].classis && arma[i].ordo!="") + if(clasel.value==window.arma[i].classis && window.arma[i].ordo!="") 
- ordarr.push(arma[i].ordo)+ ordarr.push(window.arma[i].ordo)
  }  }
  ordarr.sort()  ordarr.sort()
Line 586: Line 1014:
  spesel.innerHTML="<option>ALL</option>"  spesel.innerHTML="<option>ALL</option>"
  var famarr=[]  var famarr=[]
- for (var i=0;i<arma.length-1;i++)+ for (var i=0;i<window.arma.length-1;i++)
  {  {
- if(ordsel.value==arma[i].ordo && arma[i].familia!="") + if(ordsel.value==window.arma[i].ordo && window.arma[i].familia!="") 
- famarr.push(arma[i].familia)+ famarr.push(window.arma[i].familia)
  }  }
  famarr.sort()  famarr.sort()
Line 609: Line 1037:
  spesel.innerHTML="<option>ALL</option>"  spesel.innerHTML="<option>ALL</option>"
  var genarr=[]  var genarr=[]
- for (var i=0;i<arma.length-1;i++)+ for (var i=0;i<window.arma.length-1;i++)
  {  {
- if(famsel.value==arma[i].familia && arma[i].genus!="") + if(famsel.value==window.arma[i].familia && window.arma[i].genus!="") 
- genarr.push(arma[i].genus)+ genarr.push(window.arma[i].genus)
  }  }
  genarr.sort()  genarr.sort()
Line 633: Line 1061:
  spesel.innerHTML="<option>ALL</option>"  spesel.innerHTML="<option>ALL</option>"
  var spearr=[]  var spearr=[]
- for (var i=0;i<arma.length-1;i++)+ for (var i=0;i<window.arma.length-1;i++)
  {  {
- if(gensel.value==arma[i].genus && arma[i].specie!="") + if(gensel.value==window.arma[i].genus && window.arma[i].specie!="") 
- spearr.push(arma[i].specie)+ spearr.push(window.arma[i].specie)
  }  }
  spearr.sort()  spearr.sort()
Line 654: Line 1082:
 function armageddon() function armageddon()
 { {
 + console.log("a "+window.arma.length);
  var speval=document.getElementById("spe").value  var speval=document.getElementById("spe").value
  var genval=document.getElementById("gen").value  var genval=document.getElementById("gen").value
Line 665: Line 1094:
  if(speval!="ALL")  if(speval!="ALL")
  {  {
- for(var i=0;i<arma.length-1;i++) + for(var i=0;i<window.arma.length-1;i++) 
- if(arma[i].specie==speval && arma[i].genus==genval) // Check genus because of unknown "sp." + if(window.arma[i].specie==speval && window.arma[i].genus==genval) // Check genus because of unknown "sp." 
- a.push(arma[i])+ a.push(window.arma[i])
  }  }
  else if(genval!="ALL")  else if(genval!="ALL")
  {  {
- for(var i=0;i<arma.length-1;i++) + for(var i=0;i<window.arma.length-1;i++) 
- if(arma[i].genus==genval) + if(window.arma[i].genus==genval) 
- a.push(arma[i])+ a.push(window.arma[i])
  }  }
  else if(famval!="ALL")  else if(famval!="ALL")
  {  {
- for(var i=0;i<arma.length-1;i++) + for(var i=0;i<window.arma.length-1;i++) 
- if(arma[i].familia==famval) + if(window.arma[i].familia==famval) 
- a.push(arma[i])+ a.push(window.arma[i])
  }  }
  else if(ordval!="ALL")  else if(ordval!="ALL")
  {  {
- for(var i=0;i<arma.length-1;i++) + for(var i=0;i<window.arma.length-1;i++) 
- if(arma[i].ordo==ordval) + if(window.arma[i].ordo==ordval) 
- a.push(arma[i])+ a.push(window.arma[i])
  }  }
  else if(claval!="ALL")  else if(claval!="ALL")
  {  {
- for(var i=0;i<arma.length-1;i++) + for(var i=0;i<window.arma.length-1;i++) 
- if(arma[i].classis==claval) + if(window.arma[i].classis==claval) 
- a.push(arma[i])+ a.push(window.arma[i])
  }  }
  else if(phyval!="ALL")  else if(phyval!="ALL")
  {  {
- for(var i=0;i<arma.length-1;i++) + for(var i=0;i<window.arma.length-1;i++) 
- if(arma[i].phylum==phyval) + if(window.arma[i].phylum==phyval) 
- a.push(arma[i])+ a.push(window.arma[i])
  }  }
  else if(regval!="ALL")  else if(regval!="ALL")
  {  {
- for(var i=0;i<arma.length-1;i++) + for(var i=0;i<window.arma.length-1;i++) 
- if(arma[i].regnum==regval) + if(window.arma[i].regnum==regval) 
- a.push(arma[i])+ a.push(window.arma[i])
  }  }
  else // Regnum: ALL  else // Regnum: ALL
  {  {
- for(var i=0;i<arma.length-1;i++) + for(var i=0;i<window.arma.length-1;i++) 
- a.push(arma[i])+ a.push(window.arma[i])
  }  }
  
Line 717: Line 1146:
 { {
  var p=[]  var p=[]
- for(var i=0;i<arma.length-1;i++)+ for(var i=0;i<window.arma.length-1;i++)
  {  {
- if(arma[i].regnum==""|| + if(window.arma[i].regnum==""|| 
-      arma[i].phylum==""|| +      window.arma[i].phylum==""|| 
-      arma[i].classis==""|| +      window.arma[i].classis==""|| 
-      arma[i].ordo==""|| +      window.arma[i].ordo==""|| 
-      arma[i].familia==""|| +      window.arma[i].familia==""|| 
-      arma[i].genus=="") +      window.arma[i].genus=="") 
-   p.push(arma[i])+   p.push(window.arma[i])
  }  }
  icongeddon(p)  icongeddon(p)
Line 733: Line 1162:
 { {
  var p=[]  var p=[]
- for(var i=0;i<arma.length-1;i++)+ for(var i=0;i<window.arma.length-1;i++)
  {  {
- if(arma[i].phylum=="Platyhelminthes") + if(window.arma[i].phylum=="Platyhelminthes") 
- p.push(arma[i])+ p.push(window.arma[i])
  }  }
  icongeddon(p)  icongeddon(p)
Line 764: Line 1193:
  for(;i<a.length;i++) // -1 fix for last empty entry  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  // Pokracujem v hadovi
- if(a[i].locus == bylo)+ if(a[i].locality == bylo)
  {  {
  sam="";  sam="";
Line 774: Line 1206:
  else  else
  spoj+='<img src=./"'+ICON_biohazard+'" class="hadimg"></a></td>'  spoj+='<img src=./"'+ICON_biohazard+'" class="hadimg"></a></td>'
- spoj+="<td>"+a[i].qualis+"<br>"+a[i].quando+"</td>"+ spoj+="<td>"+a[i].title+"<br>"+a[i].takendate+"</td>"
  spoj+="</tr>"  spoj+="</tr>"
  ox=a[i].x  ox=a[i].x
Line 781: Line 1213:
  }  }
  
- if(a[i].specie=="sp.") + switch(a[i].specie) 
- wikisp="https://en.wikipedia.org/wiki/"+a[i].genus + { 
- else + case "sp.": 
- wikisp="https://en.wikipedia.org/wiki/"+a[i].genus+" "+a[i].specie+ { 
 + 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  // Bud prvni zaznam, nebo zmena pozice
Line 807: Line 1255:
  }  }
  
- bylo=a[i].locus+ bylo=a[i].locality
  spoj='<tr><td><a href="./det/'+a[i].detid+'.htm" target="_blank">'  spoj='<tr><td><a href="./det/'+a[i].detid+'.htm" target="_blank">'
  if(a[i].obr != "")  if(a[i].obr != "")
Line 813: Line 1261:
  else  else
  spoj+='<img src="./'+geticon(a,i)+'" class="hadimg"</a></td>'  spoj+='<img src="./'+geticon(a,i)+'" class="hadimg"</a></td>'
- spoj+='<td>'+a[i].qualis+'<br>'+a[i].quando+'</td>'+ spoj+='<td>'+a[i].title+'<br>'+a[i].takendate+'</td>'
  spoj+="</tr>"  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='<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+='<br><span class="butttext">'
- sam+='<b>Qualis:</b> <a href="'+wikisp+'" target="_blank">'+a[i].qualis+'</a><br>'+ sam+='<a href="'+wikisp+'" target="_blank">'+(a[i].title=="negative"?"Negative observation":a[i].title)+'</a><br>'
  if(a[i].imperium != "")  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>'+ 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 != "")  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>'+    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 != "")  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>'  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 != "")  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>'+ 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 != "")  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>'+ 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 != "")  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>' + 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 != "")+ 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>'  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 != "")  if(a[i].specie != "")
- sam+='<b>Specie:</b> <a href="'+wikisp+'" target="_blank">'+a[i].specie+'</a><br>' + sam+='<b>Species:</b> <a href="'+wikisp+'" target="_blank">'+a[i].specie+'</a><br>' 
- if(a[i].bio != "") + if(a[i].biotope != "") 
- sam+="<b>Biotope:</b> "+a[i].bio+"<br>" + sam+="<b>Biotope:</b> "+a[i].biotope+"<br>" 
- if(a[i].quando != "") + if(a[i].pov != "") 
- sam+="<b>Quando:</b> "+a[i].quando+"<br>" + sam+="<b>River:</b> "+a[i].pov+"<br>" 
- sam+="<b>Locus:</b> "+a[i].locus+" ("+a[i].locplain+")<br>" + if(a[i].temperature != "") 
- if(a[i].spec != "") + sam+="<b>Temperature:</b> "+a[i].temperature+" °C<br>" 
-  sam+="<b>Spectator:</b> "+a[i].spec+"<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 != "")  if(a[i].micro != "")
- sam+="<b>Microscopium:</b> "+a[i].micro+" ("+a[i].microtyp+")<br>" + sam+="<b>Microscope:</b> "+a[i].micro+" ("+a[i].microtyp+")<br>" 
- if(a[i].amp != "") + if(a[i].enlargement != "") 
- sam+="<b>Amplificatio:</b> "+a[i].amp+"<br>"+ sam+="<b>Amplification:</b> "+a[i].enlargement+"<br>"
  /* if [[ "$des" != "" ]]; then  /* if [[ "$des" != "" ]]; then
  #   sam="$sam<b>Depictio:</b> $des<br>"  #   sam="$sam<b>Depictio:</b> $des<br>"
  # fi */  # fi */
- if(a[i].vid != "") + //if(a[i].videolink != "") 
- sam+='<b>Video:</b> <a href="'+a[i].vid+'" target="_blank">'+a[i].vid+'</a><br>'+ // sam+='<b>Video:</b> <a href="'+a[i].videolink+'" target="_blank">'+a[i].videolink+'</a><br>'
  sam+="</span>"  sam+="</span>"
  
Line 868: Line 1326:
 } // Konec armageddonu } // Konec armageddonu
  
-var laycon = [vectorLayer,vectorLayerDynamic];+//var laycon = [vectorLayer,vectorLayerPonygon,vectorLayerDynamic,studlay]; 
 +var laycon = [vectorLayer,vectorLayerDynamic,studlay];
  
 var controls = {selector: new OpenLayers.Control.SelectFeature(laycon, { onSelect: createPopup, onUnselect: destroyPopup })}; var controls = {selector: new OpenLayers.Control.SelectFeature(laycon, { onSelect: createPopup, onUnselect: destroyPopup })};
Line 893: Line 1352:
 } }
  
-// Run armageddon on initial load + 
-armageddon()+// 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(); 
 +} 
 </code> </code>
  
-==== Taxonomie dle rodoveho jmena ====+==== Springs ====
  
-Script bere jako jediny parametr rodove jmeno a z wikipedie vyparsuje zbytek taxonomie. +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/]]. 
-<code bash tax.sh>+ 
 +<code bash studanky.sh>
 #!/bin/bash #!/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 "$json{}]}"
 +</code>
 +
 +=== LocalityID ===
 +<code bash ajdy.sh>
 +#!/bin/bash
 +
 +T=$(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")
  
-wat=$(wget -q -O - "https://en.wikipedia.org/wiki/Template:Taxonomy/$1" 2>/dev/null | tr -d '\n' | sed -e $'s/<\/tr>/<\/tr>\\n/g' | grep "<tr>" | sed -e 's/<[^>]*>//g' | grep -o -e "^[a-zA-Z]*:[a-zA-Z]*")+D=$(mktemp -d) 
 +cp -f "$T" "$D/tellico.xml" 
 +zip -j "./micro_new.tc" "$D/tellico.xml"
  
-echo $(echo "$wat" | grep "Domain:") +rm -rfv "$T" 
-echo $(echo "$wat" | grep "Kingdom:") +rm -rfv "$D"
-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:")+
 </code> </code>
project/bioosm/start.1535410549.txt.gz · Last modified: 2018/08/27 22:55 by sachy