Merge branch 'master' of github.com:intermine/imcljs

.gitignore

@@ -26,3 +26,4 @@ out
 .lein-*
 /resources/public/js
 /resources/public/js/test
+node_modules/

.travis.yml

@@ -0,0 +1,3 @@
+language: clojure
+lein: lein2
+script: lein2 doo phantom test once

README.md

@@ -1,5 +1,7 @@
 # imcljs
 
+[![Build Status](https://travis-ci.org/intermine/imcljs.svg?branch=master)](https://travis-ci.org/intermine/imcljs)
+
 A library for interacting with Intermine's web services.
 
 ## Getting Start

src/imcljs/core.cljs

@@ -8,147 +8,18 @@
             [imcljs.save :as save]
             [imcljs.entity :as entity]))
 
-
-
-
-
 (enable-console-print!)
 
-(defn on-js-reload []
-  (def flymine {:root  "beta.flymine.org/beta"
-                :model {:name "genomic"}})
-
-  (def flymine-beta {:root  "beta.flymine.org/beta"
-                     :model {:name "genomic"}})
-
-  (def mousemine {:root  "www.mousemine.org/mousemine"
-                  :model {:name "genomic"}})
-
-  (def a-query {:select  ["Gene.symbol" "Gene.secondaryIdentifier" "Gene.homologues.homologue.name"]
-                :orderBy [{:symbol "asc"}]
-                :where   [{:path  "symbol"
-                           :op    "="
-                           :value "ab*"}]})
-
-
-  (def region {:from    "SequenceFeature"
-               :select  ["SequenceFeature.id"]
-               :orderBy [["SequenceFeature.id" "asc"]]
-               :where   [{:path   "SequenceFeature"
-                          :op     "ISA"
-                          :values ["Exon" "Intron" "Gene"]}]})
-
-
-
-  (def bigr {:from   "SequenceFeature"
-             :select ["SequenceFeature.id"
-                      "SequenceFeature.name"
-                      "SequenceFeature.primaryIdentifier"
-                      "SequenceFeature.symbol"
-                      "SequenceFeature.chromosomeLocation.start"
-                      "SequenceFeature.chromosomeLocation.end"
-                      "SequenceFeature.chromosomeLocation.locatedOn.primaryIdentifier"]
-             :where  [{:path   "SequenceFeature.chromosomeLocation"
-                       :op     "OVERLAPS"
-                       :values ["2L:14615455..14619002"
-                                "2R:5866646..5868384"
-                                "3R:2578486..2580016"]}
-                      {:path  "SequenceFeature.organism.shortName"
-                       :op    "="
-                       :value "D. melanogaster"}]})
-
+(def service {:root  "beta.flymine.org/beta"
+              :model {:name "genomic"}})
 
-  (def ids-constraint-shortcut
-    {:from   "Gene"
-     :select ["Gene.symbol"]
-     :where  [{:path "Gene"
-               :ids  [1000100 1000781 1001050 1001183 1001292]}]})
-
-  (def subclass-query
-    {:from    "OntologyAnnotation",
-     :select  ["subject.primaryIdentifier"
-               "subject.symbol"
-               "evidence.baseAnnotations.subject.symbol"
-               "evidence.baseAnnotations.subject.background.name"
-               "evidence.baseAnnotations.subject.zygosity"
-               "ontologyTerm.identifier"
-               "ontologyTerm.name"],
-     :orderBy [{:path "subject.symbol", :direction "ASC"}],
-     :where   [{:path "ontologyTerm.parents", :type "MPTerm"}
-               {:path "ontologyTerm", :type "MPTerm"}
-               {:path "subject", :type "SequenceFeature"}
-               {:path "evidence.baseAnnotations.subject", :type "Genotype"}
-               {:path "ontologyTerm.parents", :op "LOOKUP", :value "*circulating glucose*", :code "A"}]})
-
-  (def subclass-query-2
-    {:name            "Lookup_MPhenotype",
-     :title           "Lookup --> Mammalian phenotypes (MP terms)",
-     :description     "Returns MP terms whose names match the specified search terms.",
-     :constraintLogic "A and B",
-     :from            "MPTerm",
-     :select          ["name" "identifier" "description"],
-     :orderBy         [{:path "name", :direction "ASC"}],
-     :where           [{:path       "obsolete",
-                        :op         "=",
-                        :value      "false", :code "B",
-                        :editable   false,
-                        :switched   "LOCKED",
-                        :switchable false}
-                       {:path       "name",
-                        :op         "CONTAINS",
-                        :value      "hemoglobin",
-                        :code       "A",
-                        :editable   true,
-                        :switched   "LOCKED",
-                        :switchable false}]})
-
-  (def constraint-query
-    {:from    "Gene"
-     :select  ["Gene.symbol" "Gene.secondaryIdentifier"]
-     :orderBy [{:symbol "asc"}]
-     :where   [{:path  "Gene"
-                :op    "IN"
-                :value "PL FlyAtlas_maleglands_top"}
-               {:path  "Gene.symbol"
-                :op    "<="
-                :value "100"
-                :code  "A"}]})
-
-  (def big-query
-    {:from    "Gene"
-     :select  ["Gene.symbol" "Gene.secondaryIdentifier"]
-     :orderBy [{:symbol "asc"}]})
-
-  (go
-    (let [fm (assoc flymine-beta :token (<! (fetch/session flymine-beta)))]
-      (save/im-list-union fm "UNION" ["pie" "five_genes"])))
+(def query {:from "Gene" :select ["Gene.organism.name"]})
 
+(defn on-js-reload []
   (go
-    (let [fm (assoc flymine-beta :token (<! (fetch/session flymine-beta)))]
-      (.log js/console "D" (<! (save/im-list-copy fm "cookies" "cookies2")))))
-
-
-  #_(go
-    (.log js/console "d" (<! (fetch/table-rows flymine big-query {:start 50 :size 1}))))
-
-
-
-
-
+    (let [model (<! (fetch/model service))]
+      (println "adjusted" (path/adjust-path-to-last-class model "Gene.organism.name")))))
 
-  #_(go
-      (let [model (<! (fetch/model flymine))]
-        (.log js/console (fetch/table-rows flymine constraint-query))))
 
 
-  ;(go
-  ;  (let [fm (assoc flymine :token (<! (fetch/session flymine)))]
-  ;    (save/im-list fm a-query)))
-  #_(go
-      (let [model (<! (fetch/model flymine))]
-        (.log js/console (query/deconstruct-by-class model a-query))))
 
-  ;(go (.log js/console "templates" (<! (fetch/templates flymine))))
-  ;(go (.log js/console "enrichment" (<! (fetch/enrichment flymine {:list "PL FlyTF_putativeTFs"}))))
-  ;(go (.log js/console "rows" (<! (fetch/rows flymine a-query))))
-  )

src/imcljs/fetch.cljs

@@ -1,5 +1,7 @@
 (ns imcljs.fetch
-  (:require [imcljs.internal.io :refer [restful]]))
+  (:require-macros [cljs.core.async.macros :refer [go]])
+  (:require [imcljs.internal.io :refer [restful]]
+            [cljs.core.async :refer [<! >! chan]]))
 
 ; Quicksearch
 
@@ -30,6 +32,22 @@
   [service query & [options]]
   (restful :post "/query/results" service (merge {:query query :format "count"} options)))
 
+(defn possible-values
+  [service path & [options]]
+  (restful :get "/path/values" service (merge {:path path :format "json"} options)))
+
+(defn unique-values
+  "Fetches unique values for a path within a query. Providing a limit shortcircuits the request
+  and returns false if the unique values exceed the limit"
+  [service query path & [limit]]
+  (let [return-chan (chan)]
+    (go
+      (let [{unique-count :uniqueValues} (<! (rows service query {:summaryPath path :size 1 :format "jsonrows"}))]
+        (if (or (not limit) (<= unique-count limit))
+          (>! return-chan (<! (rows service query {:summaryPath path :size limit :format "jsonrows"})))
+          (>! return-chan false))))
+    return-chan))
+
 ; Assets
 
 (defn lists

src/imcljs/internal/io.cljs

@@ -54,13 +54,13 @@
 
 (defmethod restful :post [method path service options & [xform]]
   ;(body- (post-wrapper- path service options) xform)
-  (post-wrapper- path service options xform)
-  )
+  (post-wrapper- path service options xform))
+
 
 (defmethod restful :get [method path service options & [xform]]
   ;(body- (request-wrapper- path service options) xform)
-  (request-wrapper- path service options xform)
-  )
+  (request-wrapper- path service options xform))
+
 
 (defmethod restful :delete [method path service options & [xform]]
   (delete-wrapper- path service options xform))

src/imcljs/internal/utils.cljs

@@ -1,4 +1,5 @@
-(ns imcljs.internal.utils)
+(ns imcljs.internal.utils
+  (:require [clojure.string :refer [split]]))
 
 (def does-not-contain? (complement contains?))
 
@@ -10,7 +11,7 @@
 
 (defn append- [text val] (str val text))
 
-(def alphabet (apply sorted-set (clojure.string/split "ABCDEFGHIJKLMNOPQRSTUVWXYZ" "")))
+(def alphabet (apply sorted-set (split "ABCDEFGHIJKLMNOPQRSTUVWXYZ" "")))
 
 (defn scrub-url
   "Ensures that a url starts with an http protocol and ends with /service"