more WIP
parent
ea2aea1fc8
commit
5e53eeb565
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@ -20,6 +20,7 @@ function testSearchPubmed(query) {
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});
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}
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function testSearchGene(query) {
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fetch(`${url}/esearch.fcgi?db=gene&term=${query}`)
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.then((res) => {
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@ -31,6 +32,7 @@ function testSearchGene(query) {
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});
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}
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function testLookupGeneById(ids) {
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fetch(`${url}/esummary.fcgi?db=gene&id=${String(ids)}`)
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.then(res => {
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@ -1,5 +1,7 @@
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@import url('https://fonts.googleapis.com/css2?family=Inter:wght@400;500;600;700&display=swap');
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body {
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font-family: 'Helvetica Neue', Verdana, Helvetica, Arial, sans-serif;
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font-family: 'Inter', sans-serif;
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max-width: 600px;
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margin: 0 auto;
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padding-top: 72px;
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@ -42,6 +44,40 @@ a:hover {
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position: absolute;
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}
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.menu-item {
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.menu-dropdown-item {
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width: 5rem;
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}
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.menu-button {
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font-size: 12pt;
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background-color: #efefef;
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border-color: black;
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border-width: 1px;
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}
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.menu-button:hover {
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background-color: #dedede;
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}
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.searchbar {
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font-size: 14pt;
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padding: 2px 8px;
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}
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.searchbar:focus {
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outline: #000;
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outline-width: 4px;
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}
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.button-primary {
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border-radius: 6px;
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border: none;
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padding: 6px 10px;
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background-color: black;
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color: white;
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font-weight: 600;
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}
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.button-primary:hover {
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background-color: #353535;
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cursor: pointer;
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}
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@ -4,37 +4,64 @@
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[reagent.dom :as d]))
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;; -------------------------
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;; Component data (custom)
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;; Global state
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;; use this later
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(def state {:search-query ""
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:searching false})
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(def search-query "")
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;; -------------------------
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;; Component data
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(def action-btns [{:text "tools" :action #(js/console.log "hi")}
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{:text "search" :action #((go (let [res (<! (ncbi-search "pubmed" "science[journal]+AND+breast+cancer+AND+2008[pdat]"))]
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(js/console.log res))))}
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{:text "help" :action #(js/console.log "test4")}])
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;; -------------------------
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;; Menus
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;; Components
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(defn dropdown-or-action
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"Render dropdown menu for an action button/menu"
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[btn-item is-dropdown]
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[:button {:class (if is-dropdown "menu-button" "")}
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[:button {:class (if is-dropdown
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"menu-button menu-dropdown-item"
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"menu-button")}
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:text (:text btn-item)
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:on-click (let [action (:action btn-item)]
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(if (nil? action)
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#(dropdown-or-action btn-item true)
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action))])
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(defn search-form
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"For searching for NCBI data"
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[placeholder]
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[:div {:style {:display "flex" :flex-direction "row" :align-items "center"}}
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[:input {:on-change (fn [val] (set! search-query val))
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:class "searchbar"
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:style {:margin-right 8 :width 300}
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:placeholder placeholder}]
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[:select {:id "search_type" :class "searchbar" :style {:margin-right 8}}
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[:option {:value "gene"} "Gene"]
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[:option {:value "protein"} "Protein"]]
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[:button {:class "searchbar button-primary" :on-click #(js/console.log "hi")} "Search!"]])
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;; -------------------------
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;; Views
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(defn home-page []
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[:div
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[:h2 "Reagent Playground"]
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[:h2 "NCBI Database Search"]
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[:p "A groundbreaking, revolutionary app that does stuff."]
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[:div {:class "button-container"}
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(map (fn [btn] [:button
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{:on-click #(dropdown-or-action btn false)}
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(:text btn)]) action-btns)]])
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{:on-click #(dropdown-or-action btn false)
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:class "menu-button"
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:style {:margin-right -1}}
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(:text btn)]) action-btns)]
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[:br]
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(search-form "Enter query...")])
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;; -------------------------
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;; Initialize app
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@ -7,27 +7,33 @@
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(def base-url "https://eutils.ncbi.nlm.nih.gov/entrez/eutils")
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(defn ncbi-db-search
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(defn ncbi-search
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"Send search query to NCBI database, and get back a list of ID strings.
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[More info](https://www.ncbi.nlm.nih.gov/books/NBK25500/#_chapter1_Searching_a_Database_)
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Example Query: `science[journal]+AND+breast+cancer+AND+2008[pdat]`"
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[db-id query]
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(go (let [res (<! (http/get (gstring/format
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"%s/esearch.fcgi?db=%s&term=%s"
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base-url db-id query)))
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(go (let [res (<! (http/get (gstring/format "%s/esearch.fcgi?db=%s&id=%s")))
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xml-doc (loadXml res)]
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(. xml-doc getElementByTagName "Id"))))
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(defn ncbi-db-get-summary
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(defn ncbi-get-summary
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"Get summary by ID.
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[More info](https://www.ncbi.nlm.nih.gov/books/NBK25500/#_chapter1_Downloading_Document_Summaries_)"
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[db-id id]
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(go (let [res (<! (http/get (gstring/format
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"%s/esummary.fcgi?db=%s&id=%s"
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"%s/esummary.fcgi?db=%s&id=%s"
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base-url db-id id)))
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xml-doc (loadXml res)]
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(js/console.log "hi"))))
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(defn ncbi-search-gene [query] (ncbi-db-search "gene" query))
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(defn ncbi-id-gene [query] (ncbi-db-search "gene" query))
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(defn ncbi-search-gene [query] (ncbi-search "gene" query))
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;; currently not needed
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;; (defn ncbi-query
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;; "Query ncbi endpoint specifying databse & params (`http/get`)"
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;; [endpoint dbid opts]
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;; (let [opts-str (doseq [k (keys opts)
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;; v (vals opts)]
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;; (gstring/format "&%s=%s" (str k) (str v)))]
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;; (http/get (gstring/format "%s/%s.fcgi?db=%s%s" endpoint dbid opts-str))))
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Reference in New Issue