;

; STBioData is an application to integrate, retrieve, and visualize biodiversity data using

; spatiotemporal information. It uses semantics, data visualization and mapping

; techniques to achieve that.

;

; Copyright (c) 2018-2024 Dilvan A. Moreira

;

; This program is free software: you can redistribute it and/or modify

; it under the terms of the GNU General Public License as published by

; the Free Software Foundation, either version 3 of the License, or

; (at your option) any later version.

;

; This program is distributed in the hope that it will be useful,

; but WITHOUT ANY WARRANTY; without even the implied warranty of

; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the

; GNU General Public License for more details.

;

; You should have received a copy of the GNU General Public License

; along with this program. If not, see <https://www.gnu.org/licenses/>.

;

(ns stbiodata.core

(:require [cljsjs.material-ui]

[cljs-react-material-ui.core :refer [get-mui-theme color]]

[cljs-react-material-ui.reagent :as rui]

[cljs-react-material-ui.icons :as ic]

[reagent.core :as reagent :refer [atom]]

[cljs-time.core :as time]

[stbiodata.table :as table]

[testdouble.cljs.csv :as csv]

[ajax.core :as ajax :refer [GET ajax-request transit-request-format transit-response-format text-request-format text-response-format]]))

;; -------------------------

;; Variables

(def responseAtom (atom {}))

(def mymap (atom ()))

(def mymarkers (atom #js []))

(def markers-cluster (atom nil))

(def markers-spyder (atom nil))

(def user-position (atom ()))

(def csv-file (atom nil))

(def rdf-describe (atom nil))

(def species-list (atom ()))

(def start-datePicker (atom ""))

(def end-datePicker (atom ""))

(def stat (atom ()))

(def progress (atom "hidden"))

(def progress-data-sets (atom "inline-block"))

(def progress-country (atom "inline-block"))

(def progress-years (atom "inline-block"))

(def caseTitle (atom (str "Map")))

(def caseQuery (atom ()))

(def data-table (atom ()))

(def prov (atom {:scientificName "" :code "" :institutionCode "" :dateCollected "" :nameColleted "" :dateCataloguing "" :nameCataloguing ""}))

(def endpoint "http://java.icmc.usp.br:2190/repositories/bio")

(def drawer-status (reagent/atom false))

(def drawer-status2 (reagent/atom false))

(def statitics-bol (atom false))

(def list-item-selected (atom nil))

;; -------------------------

;; Maps Functions

;; Create marker in map

;; varmap - Map object

;; lat - latitude

;; long - longitude

;; title - Marker title

(defn create-marker [varmap lat long title]

(let [marker (clj->js (js/google.maps.Marker. (clj->js {:map varmap

:position (google.maps.LatLng. lat, long)

:title title

:icon "imgs/markers/marker.svg"})))]

(.push @mymarkers marker)

(reset! mymarkers @mymarkers)

(.addMarker @markers-spyder marker)

marker))

;; Remove all markers

(defn remove-markers []

(dotimes [i (count @mymarkers)] (.setMap (get @mymarkers i) (clj->js nil)))

(if-not (nil? @markers-cluster) (.clearMarkers @markers-cluster))

(reset! mymarkers #js []))

;; Map wrapper div

(defn map-render []

[:div#map {:class "col-xs-12" :style {:height "500px"}}])

;; Execute after mount map

(defn home-did-mount [this]

;; Put "this node" into map-canvas

(def map-canvas (reagent/dom-node this))

;; Gmaps config

(def map-options (clj->js {"center" (js/google.maps.LatLng. -15.794410 -47.877821)

"zoom" 4}))

;; Reset! myMap with a new MAP object

(reset! mymap (js/google.maps.Map. map-canvas map-options))

;; Center map based on actual user position

(.getCurrentPosition js/navigator.geolocation

(fn [position] (reset! user-position (js/google.maps.Circle. (clj->js {"strokeColor" (color :green700)

"strokeOpacity" 0.8

"strokeWeight" 2

"fillColor" (color :green200)

"fillOpacity" 0.35

"radius" 25000

"map" @mymap

"center" (js/google.maps.LatLng.

(-> position (aget "coords") (aget "latitude"))

(-> position (aget "coords") (aget "longitude")))})))

(.setCenter @mymap (js/google.maps.LatLng. (-> position (aget "coords") (aget "latitude")) (-> position (aget "coords") (aget "longitude"))))

(.setZoom @mymap 7))))

;; Function to create a map

(defn create-map "Render the map" [] (reagent/create-class {:reagent-render map-render :component-did-mount home-did-mount}))

;; -------------------------

;; Functions

(defn json->clj "Convert the ajax response in clj" [json-string]

(js->clj (.parse js/JSON json-string)))

(defn alert [str] (js/alert str))

;; Change provenance value

(defn provenance [scientificName code institutionCode dateCollected nameColleted dateCataloguing nameCataloguing]

(reset! prov {:scientificName scientificName

:code code

:institutionCode institutionCode

:dateCollected dateCollected

:nameColleted nameColleted

:dateCataloguing dateCataloguing

:nameCataloguing nameCataloguing}))

;; Convert response to CSV

(defn response-to-csv [response]

(reset! csv-file [["code" "scientificname" "kingdom" "phylum" "class" "order" "family" "genus" "institutionCode" "Status IUCN" "POINT (lat long)" "country" "dateCollected" "nameCollected" "dateCataloguing" "nameCataloguing" "Same as GBIF" "Same as IUCN"]])

(dotimes [i (count response)] ^{:key i}

(reset! csv-file (conj @csv-file [(-> response (get i) (get "code") (get "value"))

(-> response (get i) (get "scientificname") (get "value"))

(-> response (get i) (get "kingdom") (get "value"))

(-> response (get i) (get "phylum") (get "value"))

(-> response (get i) (get "class") (get "value"))

(-> response (get i) (get "order") (get "value"))

(-> response (get i) (get "family") (get "value"))

(-> response (get i) (get "genus") (get "value"))

(-> response (get i) (get "institutionCode") (get "value"))

(-> response (get i) (get "occurrenceStatusIUCN") (get "value"))

(-> response (get i) (get "wktA") (get "value"))

(-> response (get i) (get "country") (get "value"))

(-> response (get i) (get "dateCollected") (get "value"))

(str "\"" (-> response (get i) (get "nameCollected") (get "value")) "\"")

(-> response (get i) (get "dateCataloguing") (get "value"))

(str "\"" (-> response (get i) (get "nameCataloguing") (get "value")) "\"")

(-> response (get i) (get "sameAsGBIF") (get "value"))

(-> response (get i) (get "sameAsIUCN") (get "value"))]))))

;; Draw statistics charts

(defn draw-charts "1-Pie 2-Colum 3-Donnut 4-Geo 5-line 6-Scatter" [id title vec type]

(let [container (.getElementById js/document id)

chart (case type

1 (js/google.visualization.PieChart. container)

2 (js/google.visualization.ColumnChart. container)

4 (js/google.visualization.GeoChart. container)

5 (js/google.visualization.LineChart. container)

6 (js/google.visualization.ScatterChart. container)

(js/google.visualization.PieChart. container))

options (clj->js {:title title :region "005" :pieHole (if (= type 3) 0.4 0) :colorAxis {:colors [(color :amber300) (color :lime400) (color :light-green400) (color :green300)]} :chartArea {:left 10 :top 10 :width "100%" :height 160} :titleTextStyle {:fontSize 14}})

data-table (js/google.visualization.DataTable.)]

;;Processes data according to specified type

(case type

4 (doto data-table

(.addColumn "string" "Country")

(.addColumn "number" "Ocurrences")

(.addRows (clj->js vec)))

(doto data-table

(.addColumn "string" "Topping")

(.addColumn "number" "Slices")

(.addRows (clj->js vec))))

(.draw chart data-table options)))

(defn print-sparql

"Print sparql query" [query]

[:div (for [i (range (count query))] (if (= (get query i) "\n") (reagent/as-element [:br]) (get query i)))])

;; Function to download csv file

(defn save-file [filename t s]

(if js/Blob

(let [b (js/Blob. s #js {:type t})]

(if js/window.navigator.msSaveBlob

(js/window.navigator.msSaveBlob b filename)

(let [link (js/document.createElement "a")]

(aset link "download" filename)

(if js/window.webkitURL

(aset link "href" (js/window.webkitURL.createObjectURL b))

(do

(aset link "href" (js/window.URL.createObjectURL b))

(aset link "onclick" (fn destroy-clicked [e]

(.removeChild (.-body js/document) (.-target e))))

(aset link "style" "display" "none")

(.appendChild (.-body js/document) link)))

(.click link))))

(js/console.log "Browser does not support Blob")))

;; -------------------------

;; Handlers

;; Handler of consult function

(defn handler [response]

;; Convert response JSON into CLJ

(def response-json (json->clj response))

;; Extract results and put in responseAtom

(reset! responseAtom (-> response-json (get "results") (get "bindings")))

;; Get size of response

(def msize (atom (count @responseAtom)))

;; If has a response

(if (> @msize 0) (response-to-csv @responseAtom) (do (reset! csv-file nil) (reset! rdf-describe nil)))

;; Create a new table and put! in data-table

(reset! data-table (table/create-table-geobio @responseAtom))

;; Add spiderfy plugin in map

(reset! markers-spyder (js/OverlappingMarkerSpiderfier. @mymap (clj->js {"keepSpiderfied" true "event" "mouseover"})))

(def iw (js/google.maps.InfoWindow.))

(.addListener @markers-spyder "format" (fn [marker status] (if (= 0 (compare status "SPIDERFIED"))

(.setIcon marker (clj->js {:url "imgs/markers/marker-highlight.svg" :scaledSize (js/google.maps.Size. 23 32)}))

(if (= 0 (compare status "SPIDERFIABLE"))

(.setIcon marker (clj->js {:url "imgs/markers/marker-plus.svg" :scaledSize (js/google.maps.Size. 23 32)}))

(if (= 0 (compare status "UNSPIDERFIABLE"))

(.setIcon marker (clj->js {:url "imgs/markers/marker.svg" :scaledSize (js/google.maps.Size. 23 32)})))))))

(.addListener @markers-spyder "click" (fn [marker e] (.setContent iw (aget marker "title")) (.open iw @mymap marker)))

(.addListener @markers-spyder "spiderfy" (fn [markers] (.close iw)))

;; Clear all old markers

(remove-markers)

;; Add in markers function to show profenance

(dotimes [i @msize]

(let [latlng (-> @responseAtom (get i) (get "wktA") (get "value") (clojure.string/replace "POINT(" "") (clojure.string/replace ")" "") (clojure.string/split " "))

scientificName (-> @responseAtom (get i) (get "scientificname") (get "value"))

code (-> @responseAtom (get i) (get "code") (get "value"))

institutionCode (-> @responseAtom (get i) (get "institutionCode") (get "value"))

dateCollected (-> @responseAtom (get i) (get "dateCollected") (get "value"))

nameColleted (-> @responseAtom (get i) (get "nameColleted") (get "value"))

dateCataloguing (-> @responseAtom (get i) (get "dateCataloguing") (get "value"))

nameCataloguing (-> @responseAtom (get i) (get "nameCataloguing") (get "value"))

mark (create-marker @mymap (get latlng 0) (get latlng 1) (str (+ i 1) ": " scientificName))]

(.addListener mark "click" (fn [] (provenance scientificName code institutionCode dateCollected nameColleted dateCataloguing nameCataloguing)))))

;; Update markers-cluster with new cluster

(reset! markers-cluster (js/MarkerClusterer. @mymap @mymarkers (clj->js {"imagePath" "https://developers.google.com/maps/documentation/javascript/examples/markerclusterer/m"})))

(.setMaxZoom @markers-cluster 12)

(reset! progress "hidden"))

;; General erro handler

(defn error-handler [{:keys [status status-text]}]

(.log js/console (str "something bad happened: " status " " status-text)))

;; Handler of consult-especies-list

(defn handler-species [response]

(let [result (-> (json->clj response) (get "results") (get "bindings"))]

(dotimes [i (count result)] (reset! species-list (conj @species-list (-> (get result i) (get "scientificname") (get "value")))))))

;; Handler of consult-statistics

(defn handler-statistics [response]

(let [result (-> (json->clj response) (get "results") (get "bindings") (get 0))]

(reset! stat {:ocurrences (-> result (get "Ocurrences") (get "value"))

:species (-> result (get "Species") (get "value"))

:animalia (-> result (get "Animalia") (get "value"))

:plantae (-> result (get "Plantae") (get "value"))

:geo-referenced (-> result (get "Georeference") (get "value"))})))

;; Handler of consult-statistics-data-sets

(defn handler-statistics-data-sets [response]

(let [result (-> (json->clj response) (get "results") (get "bindings") (get 0))]

(reset! progress-data-sets "none")

(draw-charts "chart-data-sets" "" [["Embrapa" (-> result (get "Embrapa") (get "value") (int))]

["IUCN" (-> result (get "IUCN") (get "value") (int))]

["INPA" (-> result (get "INPA") (get "value") (int))]

["SpeciesLink" (-> result (get "SpeciesLink") (get "value") (int))]] 3)))

;; Handler of consult-statistics-years

(defn handler-statistics-years [response]

(let [result (-> (json->clj response) (get "results") (get "bindings"))

list (atom [])]

(reset! progress-years "none")

(dotimes [i (count result)]

(reset! list (conj @list [(-> result (get i) (get "year") (get "value"))

(-> result (get i) (get "yearCT") (get "value") (int))])))

(draw-charts "chart-years" "" @list 3)))

;; Handler of statistics-country

(defn handler-statistics-country [response]

(let [result (-> (json->clj response) (get "results") (get "bindings"))

list (atom [])]

(reset! progress-country "none")

(dotimes [i (count result)]

(reset! list (conj @list [(-> result (get i) (get "Country") (get "value") (clojure.string/replace "http://dbpedia.org/resource/" ""))

(-> result (get i) (get "CountryST") (get "value") (int))])))

(draw-charts "chart-country" "" @list 4)))

;; Handler of download RDF

(defn handler-rdf [response]

(save-file (str "rdf(" (get @rdf-describe :name) ").n3") "text/n3" #js [response]))

;; -------------------------

;; Main Functions

;; Execute search according studyCase

(defn consult [serv estudyCase]

(reset! caseTitle (if-not (clojure.string/blank? (get estudyCase :title)) (get estudyCase :title) "Map"))

(reset! caseQuery (get estudyCase :query))

(ajax/GET (str "http://java.icmc.usp.br:2190/repositories/" serv) {:params {:query (clojure.string/replace (get estudyCase :query) #"#" "%23")}

:handler handler

:error-handler handler}))

;; Consult species list to populate combobox

(defn consult-especies-list []

(ajax/GET (str "http://java.icmc.usp.br:2190/repositories/" "Animalia")

{:params {:query "PREFIX dwc: <http://rs.tdwg.org/dwc/terms/>

SELECT DISTINCT ?scientificname

where {

?code dwc:scientificName ?scientificname

} ORDER BY ?scientificname"}

:handler handler-species

:error-handler (fn [response] (js/console.log response))}))

(defn consult-statistics []

(ajax/GET

(str "http://java.icmc.usp.br:2190/repositories/" "Animalia")

{:params

{:query (clojure.string/replace "PREFIX iucn: <http://java.icmc.usp.br/iucn/>

PREFIX bioprov: <http://java.icmc.usp.br/bioprov/>

PREFIX foaf: <http://xmlns.com/foaf/0.1/>

PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>

PREFIX geo: <http://www.opengis.net/ont/geosparql#>

PREFIX geof: <http://www.opengis.net/def/function/geosparql/>

PREFIX dwc: <http://rs.tdwg.org/dwc/terms/>

PREFIX time: <http://www.w3.org/2006/time#>

PREFIX prov: <http://www.w3.org/ns/prov#>

PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>

PREFIX geobio: <http://specieslink.br/extinsion>

PREFIX terms1: <http://rs.tdwg.org/dwc/terms/>

SELECT (COUNT(?code) as ?Ocurrences) (COUNT(DISTINCT ?species) as ?Species)

(sum(if(lcase(str(?kingdom)) = 'animalia', 1, 0)) as ?Animalia)

(sum(if(lcase(str(?kingdom)) = 'plantae', 1, 0)) as ?Plantae)

(COUNT(?wktA) as ?Georeference){

?code dwc:scientificName ?species.

?code geo:hasGeometry/geo:asWKT ?wktA.

?code dwc:kingdom ?kingdom.

}" #"#" "%23")}

:handler handler-statistics

:error-handler (fn [response] (js/console.log response))}))

(defn consult-statistics-data-sets []

(ajax/GET (str "http://java.icmc.usp.br:2190/repositories/" "Animalia") {:params {:query (clojure.string/replace "PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>

PREFIX dwc: <http://rs.tdwg.org/dwc/terms/>

SELECT (sum(if(lcase(str(?biospecie)) = 'http://java.icmc.usp.br/specieslink/biospecie', 1, 0)) as ?SpeciesLink)

(sum(if(lcase(str(?biospecie)) = 'http://java.icmc.usp.br/iucn/biospecie', 1, 0)) as ?IUCN)

(sum(if(lcase(str(?biospecie)) = 'http://java.icmc.usp.br/inpa/biospecie', 1, 0)) as ?INPA)

(sum(if(lcase(str(?biospecie)) = 'http://java.icmc.usp.br/embrapa/biospecie', 1, 0)) as ?Embrapa)

{ ?code rdf:type ?biospecie

} " #"#" "%23")}

:handler handler-statistics-data-sets

:error-handler (fn [response] (js/console.log response))}))

(defn consult-statistics-years []

(ajax/GET (str "http://java.icmc.usp.br:2190/repositories/" "Animalia") {:params {:query (clojure.string/replace "PREFIX iucn: <http://java.icmc.usp.br/iucn/>

PREFIX bioprov: <http://java.icmc.usp.br/bioprov/>

PREFIX foaf: <http://xmlns.com/foaf/0.1/>

PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>

PREFIX geo: <http://www.opengis.net/ont/geosparql#>

PREFIX geof: <http://www.opengis.net/def/function/geosparql/>

PREFIX dwc: <http://rs.tdwg.org/dwc/terms/>

PREFIX time: <http://www.w3.org/2006/time#>

PREFIX prov: <http://www.w3.org/ns/prov#>

PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>

PREFIX geobio: <http://specieslink.br/extinsion>

Select ?year (COUNT(?year) as ?yearCT)

where {

?code prov:hadMember/bioprov:wasCollectedBy/bioprov:yearcollected ?yearcollected.

bind( substr( str(?yearcollected), 1, 4) as ?year )

FILTER(!isBlank(?year))

} GROUP BY ?year

ORDER BY ?year

" #"#" "%23")}

:handler handler-statistics-years

:error-handler (fn [response] (js/console.log response))}))

(defn consult-statistics-country []

(ajax/GET (str "http://java.icmc.usp.br:2190/repositories/" "Animalia") {:params {:query "PREFIX dwc: <http://rs.tdwg.org/dwc/terms/>

SELECT ?Country (COUNT(?Country) as ?CountryST) {

?code dwc:country ?Country.

} GROUP BY ?Country

Order by ?Country"}

:handler handler-statistics-country

:error-handler (fn [response] (js/console.log response))}))

(defn download-csv []

(if-not (nil? @csv-file)

(save-file (str "csv(" (get @rdf-describe :name) ").csv") "text/csv" #js [(csv/write-csv @csv-file)])

(alert "No results")))

(defn download-rdf []

(if-not (nil? @rdf-describe)

(ajax/GET (str "http://java.icmc.usp.br:2190/repositories/" "Animalia") {:params {:query (str "PREFIX iucn: <http://java.icmc.usp.br/iucn/>

PREFIX bioprov: <http://java.icmc.usp.br/bioprov/>

PREFIX foaf: <http://xmlns.com/foaf/0.1/>

PREFIX xsd: <http://www.w3.org/2001/XMLSchema%23>

PREFIX geo: <http://www.opengis.net/ont/geosparql%23>

PREFIX geof: <http://www.opengis.net/def/function/geosparql/>

PREFIX dwc: <http://rs.tdwg.org/dwc/terms/>

PREFIX time: <http://www.w3.org/2006/time%23>

PREFIX prov: <http://www.w3.org/ns/prov%23>

PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns%23>

PREFIX geobio: <http://specieslink.br/extinsion>

Describe ?code

WHERE { "

(str " ?code dwc:scientificName '" (get @rdf-describe :name) "' . ")

" ?code dwc:scientificName ?scientificname.

?code dwc:institutionCode ?institutionCode.

?code geo:hasGeometry/geo:asWKT ?wktA.

?code prov:hadMember/bioprov:wasCollectedBy/prov:startedAtTime ?dateCollected.

?code prov:hadMember/bioprov:wasCatalguingBy/prov:startedAtTime ?dateCataloguing.

?code prov:hadMember/bioprov:wasCollectedBy/prov:wasAssociatedWith/foaf:givenName ?nameCollected.

?code prov:hadMember/bioprov:wasCatalguingBy/prov:wasAssociatedWith/foaf:givenName ?nameCataloguing.

?code prov:hadMember/bioprov:wasCollectedBy/bioprov:yearcollected ?yearcollected.

?code dwc:kingdom ?kingdom.

?code dwc:phylum ?phylum.

?code dwc:class ?class.

?code dwc:order ?order.

?code dwc:family ?family.

?code dwc:genus ?genus.

OPTIONAL { ?code dwc:country ?country. }

OPTIONAL { ?code bioprov:sameSynonymIUCN ?sameAsIUCN. }

OPTIONAL { ?code bioprov:sameSynonymGBIF ?sameAsGBIF. }

OPTIONAL { ?code bioprov:hasConservationStatus/dwc:occurrenceStatus ?occurrenceStatusIUCN1.}

OPTIONAL { ?code dwc:occurrenceStatus ?occurrenceStatusIUCN2. }

BIND(COALESCE(?occurrenceStatusIUCN1, ?occurrenceStatusIUCN2) as ?occurrenceStatusIUCN)

" (if-not (clojure.string/blank? (get @rdf-describe :start-date)) (str " FILTER (?yearcollected >= '" (get @rdf-describe :start-date) "')") " ")

(if-not (clojure.string/blank? (get @rdf-describe :end-date)) (str " FILTER (?yearcollected <= '" (get @rdf-describe :end-date) "')") " ") " }")}

:handler handler-rdf

:error-handler (fn [response] (js/console.log response))})

(alert "No results")))

(defn filter-query []

(let [name (-> (js/document.getElementById "specie-filter") (.-value))

start-date (-> (js/document.getElementById "start-date") (.-value))

end-date (-> (js/document.getElementById "end-date") (.-value))

query2 (str "PREFIX iucn: <http://java.icmc.usp.br/iucn/>

PREFIX bioprov: <http://java.icmc.usp.br/bioprov/>

PREFIX foaf: <http://xmlns.com/foaf/0.1/>

PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>

PREFIX geo: <http://www.opengis.net/ont/geosparql#>

PREFIX geof: <http://www.opengis.net/def/function/geosparql/>

PREFIX dwc: <http://rs.tdwg.org/dwc/terms/>

PREFIX time: <http://www.w3.org/2006/time#>

PREFIX prov: <http://www.w3.org/ns/prov#>

PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>

PREFIX geobio: <http://specieslink.br/extinsion>

Select ?code ?scientificname ?institutionCode ?occurrenceStatusIUCN ?sameAsGBIF ?sameAsIUCN ?country ?wktA ?dateCollected ?nameCollected ?dateCataloguing ?nameCataloguing ?kingdom ?phylum ?class ?order ?family ?genus

where { "

(if-not (clojure.string/blank? name) (str " ?code dwc:scientificName '" name "' . "))

" ?code dwc:scientificName ?scientificname.

?code dwc:institutionCode ?institutionCode.

?code geo:hasGeometry/geo:asWKT ?wktA.

?code prov:hadMember/bioprov:wasCollectedBy/prov:startedAtTime ?dateCollected.

?code prov:hadMember/bioprov:wasCatalguingBy/prov:startedAtTime ?dateCataloguing.

?code prov:hadMember/bioprov:wasCollectedBy/prov:wasAssociatedWith/foaf:givenName ?nameCollected.

?code prov:hadMember/bioprov:wasCatalguingBy/prov:wasAssociatedWith/foaf:givenName ?nameCataloguing.

?code prov:hadMember/bioprov:wasCollectedBy/bioprov:yearcollected ?yearcollected.

?code dwc:kingdom ?kingdom.

?code dwc:phylum ?phylum.

?code dwc:class ?class.

?code dwc:order ?order.

?code dwc:family ?family.

?code dwc:genus ?genus.

OPTIONAL { ?code dwc:country ?country. }

OPTIONAL { ?code bioprov:sameSynonymIUCN ?sameAsIUCN. }

OPTIONAL { ?code bioprov:sameSynonymGBIF ?sameAsGBIF. }

OPTIONAL { ?code bioprov:hasConservationStatus/dwc:occurrenceStatus ?occurrenceStatusIUCN1.}

OPTIONAL { ?code dwc:occurrenceStatus ?occurrenceStatusIUCN2. }

BIND(COALESCE(?occurrenceStatusIUCN1, ?occurrenceStatusIUCN2) as ?occurrenceStatusIUCN)

" (if-not (clojure.string/blank? start-date) (str " FILTER (?dateCollected >= '" start-date "'^^xsd:dateTime )") " ")

(if-not (clojure.string/blank? end-date) (str " FILTER (?dateCollected <= '" end-date "'^^xsd:dateTime )") " ") "}")]

(if-not (and (clojure.string/blank? name) (clojure.string/blank? start-date) (clojure.string/blank? end-date))

(do (reset! rdf-describe {:name name :start-date start-date :end-date end-date})

(reset! progress "visible")

(consult "Animalia" {:title name :query query2})))))

;; -------------------------

;; Views Functions

(defn drawer-click [] "Open drawer" (swap! drawer-status [true false]))

(defn drawer-click2 [] "Open drawer" (swap! drawer-status2 [true false]) (if (= @statitics-bol false) (do (consult-statistics)

(consult-statistics-data-sets)

(consult-statistics-years)

(consult-statistics-country)

(reset! statitics-bol true))))

(defn create-list "Create a list" [header]

(fn [] [rui/selectable-list

[rui/list-item {:value 0

:key 0

:style {:background-color (color :deep-orange300) :font-weight 500 :color (color :blue-grey900)}

:right-icon (ic/action-open-in-new {:style {:fill (color :blue-grey900)}})

:primary-text "Open Sparql Endpoint"

:on-click (fn [] (.open js/window "http://java.icmc.usp.br:2190/sparql" "_blank") (drawer-click))}]]))

(defn menu [app-content]

[:div

[rui/mui-theme-provider {:mui-theme (get-mui-theme {:palette {:primary1-color (color :blue500)}})}

[rui/drawer {:open @drawer-status

:id "drawer"

:style {:background-color (color :grey50)}}

[rui/app-bar {:title "Menu"

:icon-element-left (reagent/as-element [rui/icon-button

(ic/navigation-close)])

:onLeftIconButtonTouchTap (fn [e] (drawer-click))}]

[create-list "Use Cases"]]]

[:div#app-bar

[rui/mui-theme-provider {:mui-theme (get-mui-theme {:palette {:primary1-color (color :blue500)}})}

[rui/app-bar {:title "STBioData"

:titleStyle {:text-align "center"}

:icon-element-left (reagent/as-element [rui/flat-button {:label "Menu" :label-position "after" :icon (ic/navigation-menu) :style {:background-color "white" :margin-top "5px"}}])

:on-Left-Icon-Button-Touch-Tap (fn [e] (drawer-click))

:icon-element-right (reagent/as-element [rui/flat-button {:label "Statistics" :label-position "before" :icon (ic/navigation-menu) :style {:color "black" :background-color "white" :margin-top "5px"}}])

:on-right-Icon-Button-Touch-Tap (fn [e] (drawer-click2))}]]

[:div#app-content

app-content]]

[rui/mui-theme-provider {:mui-theme (get-mui-theme {:palette {:primary1-color (color :blue500)}})}

[rui/drawer {:open @drawer-status2

:id "drawer-statistics"

:width "100%"

:openSecondary true

:containerStyle {:background-color (color :blue-grey100)}}

[rui/app-bar {:title "Statistics"

:icon-element-left (reagent/as-element [rui/icon-button

(ic/navigation-close)])

:onLeftIconButtonTouchTap (fn [e] (drawer-click2))}]

[:div {:class "row" :style {:margin-right "0px" :margin-left "0px" :padding-top "10px"}}

[:div {:class "col-lg-3"}

[rui/mui-theme-provider {:mui-theme (get-mui-theme)}

[rui/card {:style {:height "400px"}} [rui/card-title {:title "Data metrics" :act-as-expander false :titleColor "white" :style {:background-color (color :orange700)}}]

[rui/card-text

[rui/list [rui/list-item {:value 0

:key 0

:left-icon (ic/social-public {:style {:fill (color :indigo700)}})

:primary-text (str "Ocurrences: " (get @stat :ocurrences))}]

[rui/divider]

[rui/list-item {:value 1

:key 1

:left-icon (ic/notification-adb {:style {:fill (color :brown700)}})

:primary-text (str "Species: " (get @stat :species))}]

[rui/divider]

[rui/list-item {:value 2

:key 2

:left-icon (ic/action-bug-report {:style {:fill (color :orange700)}})

:primary-text (str "Animalia: " (get @stat :animalia))}]

[rui/divider]

[rui/list-item {:value 3

:key 3

:left-icon (ic/maps-local-florist {:style {:fill (color :green700)}})

:primary-text (str "Plantae: " (get @stat :plantae))}]

[rui/divider]

[rui/list-item {:value 4

:key 4

:left-icon (ic/maps-place {:style {:fill (color :red700)}})

:primary-text (str "Georeferenced: " (get @stat :geo-referenced))}]]]]]]

[:div {:class "col-lg-3"}

[rui/mui-theme-provider {:mui-theme (get-mui-theme)}

[rui/card {:style {:height "400px"}} [rui/card-title {:title "Datasets" :act-as-expander false :titleColor "white" :style {:background-color (color :green700)}}]

[rui/card-text [rui/circular-progress {:size 60 :style {:top "50px" :left "calc(50% - 50px)" :display @progress-data-sets}}] [:div {:id "chart-data-sets" :style {:height "300px"}}]]]]]

[:div {:class "col-lg-3"}

[rui/mui-theme-provider {:mui-theme (get-mui-theme)}

[rui/card {:style {:height "400px"}} [rui/card-title {:title "Ocurrences in South America" :act-as-expander false :titleColor "white" :style {:background-color (color :deep-purple500)}}]

[rui/card-text [rui/circular-progress {:size 60 :style {:top "50px" :left "calc(50% - 50px)" :display @progress-country}}] [:div {:id "chart-country" :style {:max-height "250px"}}]]]]]

[:div {:class "col-lg-3"}

[rui/mui-theme-provider {:mui-theme (get-mui-theme)}

[rui/card {:style {:height "400px"}} [rui/card-title {:title "Occurrences by year collected" :act-as-expander false :titleColor "white" :style {:background-color (color :cyan700)}}]

[rui/card-text [rui/circular-progress {:size 60 :style {:top "50px" :left "calc(50% - 50px)" :display @progress-years}}] [:div {:id "chart-years" :style {:max-height "250px"}}]]]]]]]]])

;; -------------------------

;; Views

(defn home-page []

(menu [:div

[:div {:class "row" :style {:margin-right "0px" :margin-left "0px"}}

[:div {:class "col-xs-12 col-sm-12 col-md-4 col-lg-4"}

[rui/mui-theme-provider {:mui-theme (get-mui-theme)}

[rui/card [rui/card-title {:title "Search" :act-as-expander false :titleColor "white" :style {:background-color (color :orange700)}}]

[rui/card-text [:div [rui/auto-complete {:id "specie-filter"

:placeholder "Enter species name"

:listStyle {:max-height "200px" :overflow "auto"}

:filter (aget js/MaterialUI "AutoComplete" "caseInsensitiveFilter")

:maxSearchResults 60

:fullWidth true

:dataSource @species-list}]

[:div {:class "row"}

[:div {:class "col-xs-6" :style {:overflow "hidden"}}

[rui/date-picker {:id "start-date" :placeholder "Start date" :textFieldStyle {:max-width "100%"} :container "inline" :autoOk true :maxDate (time/now) :minDate (time/date-time 1750 1 1)

:value @start-datePicker

:onChange (fn [null date] (reset! start-datePicker date))

:cancelLabel "Clear" :onDismiss (fn [] (reset! start-datePicker ""))}]]

[:div {:class "col-xs-6" :style {:overflow "hidden"}}

[rui/date-picker {:id "end-date" :placeholder "End date" :textFieldStyle {:max-width "100%"} :container "inline" :autoOk true :maxDate (time/now) :minDate (time/date-time 1750 1 1)

:value @end-datePicker

:onChange (fn [null date] (reset! end-datePicker date))

:cancelLabel "Clear" :onDismiss (fn [] (reset! end-datePicker ""))}]]]

[:div {:style {:top "10px"}}

[rui/raised-button {:label "Submit" :label-position "before" :icon (ic/action-search) :label-color (color :white) :background-color (color :brown400) :on-click (fn [e] (filter-query))}]

[rui/circular-progress {:size 30 :style {:top "10px" :left "10px" :visibility @progress}}]]]]]]

[:div {:style {:margin-top "10px" :margin-bottom "10px"}}

[rui/mui-theme-provider {:mui-theme (get-mui-theme)}

[rui/card [rui/card-title {:title (reagent/as-element [:span {:style {:font-size "20px"}} "BioProv"])

:subtitle "A Provenance Model for Biodiversity Data"

:subtitleStyle (clj->js {:color "white"})

:act-as-expander false

:titleColor "white"

:style {:background-color (color :deep-purple500)}}]

[rui/card-text

[:div

[:span [:b "Scientific Name: "] (get @prov :scientificName)] [:br]

[:span [:b "Institution Code: "] (get @prov :institutionCode)] [:br]

[:span [:b "Date Collected: "] (get @prov :dateCollected)] [:br]

[:span [:b "Name Collected: "] (get @prov :nameColleted)] [:br]

[:span [:b "Date Cataloguing: "] (get @prov :dateCataloguing)] [:br]

[:span [:b "Species Authority: "] (get @prov :nameCataloguing)] [:br]]]]]]]

[:div {:class "col-xs-12 col-sm-12 col-md-8 col-lg-8"}

[rui/mui-theme-provider {:mui-theme (get-mui-theme)}

[rui/card [rui/card-title {:title @caseTitle :act-as-expander false :titleColor "white" :style {:background-color (color :green700)}}]

[rui/card-media [create-map]]]]]]

[:div {:class "row" :style {:margin-top "10px" :margin-right "0px" :margin-left "0px"}}

[:div {:class "col-xs-12 col-sm-12 col-md-12 col-lg-12"}

[rui/mui-theme-provider {:mui-theme (get-mui-theme)}

[rui/card {:style {:position "relative"}}

[rui/card-title {:title "Search result"

:act-as-expander false

:titleColor "white"

:style {:background-color (color :blue500)}

:children [(reagent/as-element

[rui/icon-menu {:style {:position "absolute" :top "16px" :right "16px" :z-index 2}

:icon-button-element (reagent/as-element [rui/raised-button {:label "Download"

:label-position "after"

:icon (ic/file-cloud-download)}])

:children [(reagent/as-element

[rui/menu-item {:value "1" :primary-text "CSV Format" :on-click (fn [] (download-csv))}])

(reagent/as-element

[rui/menu-item {:value "2" :primary-text "RDF Format" :on-click (fn [] (download-rdf))}])]}])]}]

[rui/card-text @data-table]]]]]]))

;; -------------------------

;; Initialize app

(defn mount-root []

(reagent/render [home-page] (.getElementById js/document "app")))

(defn init! []

(mount-root)

(consult-especies-list)

(.load js/google.charts "current" (clj->js {:packages ["corechart"]})))