Changed how blast queries are issued and the reporting UI, among othe…

…r things.

.gitignore

@@ -1,6 +1,7 @@
 /__pycache__
 *.pyc
 /.venv
+/logs
 /uploads
 /blast_db
 /static/node_modules

frontend/src/App.vue

@@ -19,9 +19,11 @@
             <router-link to="/debug" class="nav-link" tag="a">Debug</router-link>
           </li>
 
+          <!--
           <li class="nav-item">
             <router-link to="/designer" class="nav-link" tag="a">Designer</router-link>
           </li>
+          -->
         </ul>
       </div>
     </nav>

frontend/src/assets/main.css

@@ -101,4 +101,17 @@
 .slideup-enter, .slideup-leave-to /* .list-leave-active below version 2.1.8 */ {
   opacity: 0;
   transform: translateY(30px);
+}
+
+/* faster version of the slideup animation */
+.slideup_fast-item {
+  display: inline-block;
+  margin-bottom: 10px;
+}
+.slideup_fast-enter-active, .slideup_fast-leave-active {
+  transition: all 200s;
+}
+.slideup_fast-enter, .slideup_fast-leave-to /* .list-leave-active below version 2.1.8 */ {
+  opacity: 0;
+  transform: translateY(30px);
 }

frontend/src/components/Blaster.vue

@@ -14,22 +14,25 @@
       </button>
     </div>
 
-    <div v-if="blast_status || blast_hits">
-      <div class="status_pane">
-        <h4>Status:</h4>
-
-        <transition-group name="slideright" tag="ol">
-          <li v-for="(rec, idx) in blast_status" :key="idx">
-            {{ rec.status }}
-            <fa-icon v-if="blast_pending && idx === blast_status.length - 1" icon="spinner" pulse />
-          </li>
-        </transition-group>
-      </div>
+    <div v-if="blast_status || blast_hits" class="status_and_results">
+      <transition-group name="slideup" mode="out-in">
+
+        <div class="status_pane" key="status_pane" v-if="!blast_result || !blast_first_five || blast_first_five.length <= 0">
+          <h4>Status:</h4>
+
+          <div class="status_scroller" ref="status_scroller">
+            <transition-group name="slideright" tag="ol">
+              <li v-for="(rec, idx) in blast_status" :key="idx">
+                {{ rec.status }}
+                <fa-icon v-if="blast_pending && idx === blast_status.length - 1" icon="circle-notch" spin />
+              </li>
+            </transition-group>
+            </div>
+        </div>
 
-      <div class="results_pane">
-        <transition name="slideup">
-          <div v-if="blast_result">
-            <h3 style="text-align: left;">Hits:</h3>
+        <div class="results_pane" key="results_pane" v-if="blast_result">
+          <div>
+            <h3 style="text-align: left;">Hits ({{ blast_first_five.length }}):</h3>
             <hr />
 
             <div v-if="blast_first_five.length > 0" class="species-tiles">
@@ -38,13 +41,14 @@
               </div>
             </div>
             <div v-else class="no-results">
-                No matching species found! <fa-icon icon="sad-cry" />
-                <br />
-                Try again with another sequence!
+              No matching species found.
+              <br />
+              Try again with another sequence!
             </div>
           </div>
-        </transition>
-      </div>
+        </div>
+
+      </transition-group>
     </div>
 
     <Sidebar ref="sidedar">
@@ -72,8 +76,8 @@
 
               <div class="mini-sec"><b>Bases:</b>
                 <div class="alignment">{{ hit.qseq }}
-{{ hit.midline }}
-{{ hit.hseq }}
+                  {{ hit.midline }}
+                  {{ hit.hseq }}
                 </div>
               </div>
             </div>
@@ -87,6 +91,7 @@
 <script>
 import * as oboe from 'oboe';
 import uniqBy from "lodash/uniqBy";
+import countBy from "lodash/countBy";
 import {col_to_base} from "../constants";
 import SpeciesResult from "./SpeciesResult";
 import Sidebar from "./Sidebar";
@@ -127,6 +132,8 @@ export default {
             return uniqBy(this.blast_hits, x => x.sciname);
         },
         blast_first_five() {
+            if (!this.blast_unique_hits)
+                return null;
             return this.blast_unique_hits.slice(0, 6);
         }
     },
@@ -144,7 +151,13 @@ export default {
                 })
                 .node('!.{status}', rec => {
                     console.log(rec);
-                    this.blast_status.push(rec)
+                    this.blast_status.push(rec);
+                    const status_scroller = this.$refs.status_scroller;
+                    if (status_scroller) {
+                        setTimeout(() => {
+                          status_scroller.scrollTop = status_scroller.scrollHeight;
+                        }, 10);
+                    }
                 })
                 .node('!.{results}', rec => {
                     console.log("Done: ", rec);
@@ -163,7 +176,7 @@ export default {
                 })
         },
         show_details(options) {
-          this.$refs.sidedar.showModal(options);
+            this.$refs.sidedar.showModal(options);
         }
     }
 }
@@ -187,6 +200,10 @@ export default {
   font-size: 20px;
   /*border: solid 1px #ccc; border-radius: 5px;*/
 }
+.status_pane .status_scroller {
+  max-height: 6.5em;
+  overflow-y: auto;
+}
 
 .species-tiles {
   display: flex; flex-wrap: wrap; justify-content: space-around;

frontend/src/components/SpeciesResult.vue

@@ -9,7 +9,8 @@
     <div class="card-body">
       <h5 class="card-title">{{ species }}</h5>
       <p class="card-text">Score: {{ score }}</p>
-      <a href="#" @click.stop="show_details" class="btn btn-primary">Details</a>
+      <a href="#" @click.stop="show_details" class="btn btn-primary">Details</a>&nbsp;
+      <a :href="gsearch_url" target="_blank" class="btn btn-success">Search <fa-icon icon="external-link-alt" /></a>
     </div>
   </div>
 </template>
@@ -29,6 +30,11 @@ export default {
             error: null
         }
     },
+    computed: {
+        gsearch_url() {
+            return `https://www.google.com/search?safe=active&q=%22${this.species}%22`;
+        }
+    },
     mounted() {
         // fire off a request to our API for the image
         this.loading = true;

frontend/src/main.js

@@ -17,11 +17,11 @@ import './assets/modal-sidebar.css';
 // font-awesome stuff
 import { library } from '@fortawesome/fontawesome-svg-core'
 import {
-  faUserSecret, faSpinner, faTrash, faCircleNotch, faAngleDoubleDown, faQuestion, faSadCry
+  faUserSecret, faSpinner, faTrash, faCircleNotch, faAngleDoubleDown, faQuestion, faSadCry, faExternalLinkAlt
 } from '@fortawesome/free-solid-svg-icons'
 import { FontAwesomeIcon } from '@fortawesome/vue-fontawesome'
 
-library.add(faUserSecret, faSpinner, faTrash, faCircleNotch, faAngleDoubleDown, faQuestion, faSadCry);
+library.add(faUserSecret, faSpinner, faTrash, faCircleNotch, faAngleDoubleDown, faQuestion, faSadCry, faExternalLinkAlt);
 
 Vue.component('fa-icon', FontAwesomeIcon);
 

sequencer/__init__.py

@@ -14,6 +14,7 @@ def create_app(test_config=None):
     app.config.from_mapping(
         SECRET_KEY='dev',
         DATABASE=os.path.join(app.instance_path, 'sequencer.sqlite'),
+        BLAST_DB_DIR=os.path.join(app.root_path, 'blast_db'),
         # CACHE_DIR=os.path.join(app.instance_path, 'cache'),
         # CACHE_TYPE="filesystem"
     )
@@ -49,7 +50,8 @@ def create_app(test_config=None):
     app.register_blueprint(
         api.bp,
         GCE_KEY=app.config['GCE_KEY'],
-        GCE_PROJECT_CX=app.config['GCE_PROJECT_CX']
+        GCE_PROJECT_CX=app.config['GCE_PROJECT_CX'],
+        BLAST_DB_DIR=app.config['BLAST_DB_DIR']
     )
 
     # inject frontend-serving bits

sequencer/api.py

@@ -14,14 +14,15 @@
 )
 
 from sequencer import cache
-from sequencer.default_settings import MOCK_BLAST_HAS_RESULTS
+from sequencer.default_settings import MOCK_BLAST_HAS_RESULTS, USE_GIS_CACHING, BLAST_TIMEOUT
 from sequencer.support import ev3_reader
 from sequencer.db import get_db
-from sequencer.support.blaster import blast_sequence
+from sequencer.support.blaster import blast_sequence, blast_sequence_local
 from sequencer.support.ev3_reader import query_full_sequence
 
 GCE_KEY = None
 GCE_PROJECT_CX = None
+BLAST_DB_DIR = None
 
 
 class APIBlueprint(Blueprint):
@@ -31,6 +32,7 @@ def register(self, app, options, first_registration=False):
         config = app.config
         GCE_KEY = config.get('GCE_KEY')
         GCE_PROJECT_CX = config.get('GCE_PROJECT_CX')
+        BLAST_DB_DIR = config.get('BLAST_DB_DIR')
 
         super(APIBlueprint, self).register(app, options, first_registration)
 
@@ -50,6 +52,10 @@ def ping():
     return jsonify({'msg': 'pong!'})
 
 
+# ------------------------------------------------------
+# --- LEGO Brick Comm.
+# ------------------------------------------------------
+
 @bp.route('/nudge/<direction>', defaults={'amount': 1})
 @bp.route('/nudge/<direction>/<amount>')
 def nudge(direction, amount):
@@ -99,6 +105,10 @@ def g():
         }), 500)
 
 
+# ------------------------------------------------------
+# --- BLAST proxy
+# ------------------------------------------------------
+
 @bp.route('/blast')
 def blast():
     try:
@@ -107,7 +117,29 @@ def blast():
         return jsonify({'error': 'must specify a sequence'})
 
     def g():
-        gen = blast_sequence(sequence, "nr")
+        gen = blast_sequence(sequence, timeout=BLAST_TIMEOUT)
+        not_first = False
+        yield "["
+        for rec in gen:
+            if not_first:
+                yield ","
+            not_first = True
+            yield json.dumps(rec)
+        yield "]"
+
+    # incrementally yields json objects
+    return Response(stream_with_context(g()))
+
+
+@bp.route('/local_blast')
+def local_blast():
+    try:
+        sequence = request.args['sequence']
+    except KeyError:
+        return jsonify({'error': 'must specify a sequence'})
+
+    def g():
+        gen = blast_sequence_local(sequence, blast_db_dir=BLAST_DB_DIR)
         not_first = False
         yield "["
         for rec in gen:
@@ -121,6 +153,43 @@ def g():
     return Response(stream_with_context(g()))
 
 
+# ------------------------------------------------------
+# --- GIS species images
+# ------------------------------------------------------
+
+@bp.route('/species_img')
+def species_img():
+    species_name = request.args.get('species')
+    # species_name = "Homo sapiens"
+
+    cache_key = 'SPECIES_IMG:%s' % species_name
+    cached_val = cache.get(cache_key) if USE_GIS_CACHING else None
+
+    if not cached_val:
+        resp = requests.get('https://www.googleapis.com/customsearch/v1/siterestrict', params={
+            "key": GCE_KEY,
+            "cx": GCE_PROJECT_CX,
+            "safe": "high",
+            "fileType": "png|jpg|gif",
+            "imgType": "photo",
+            "searchType": "image",
+            "limit": 1,
+            "q": species_name
+        })
+        result = resp.json()
+
+        cached_val = [x['link'] for x in result['items']]
+        cache.set(cache_key, cached_val)
+
+    return jsonify({
+        'results': cached_val
+    })
+
+
+# ------------------------------------------------------
+# --- mocked endpoints
+# ------------------------------------------------------
+
 @bp.route('/mock_blast', methods=['GET','POST'])
 def mock_blast():
     """
@@ -156,30 +225,3 @@ def mock_blast():
         elif arg_set.get('FORMAT_TYPE') == 'JSON2_S':
             return send_file("mockdata/canned_blast.json") if MOCK_BLAST_HAS_RESULTS else send_file("mockdata/canned_blast_noresults.json")
 
-
-@bp.route('/species_img')
-def species_img():
-    species_name = request.args.get('species')
-
-    cache_key = 'SPECIES_IMG:%s' % species_name
-    cached_val = cache.get(cache_key)
-
-    if not cached_val:
-        resp = requests.get('https://www.googleapis.com/customsearch/v1/siterestrict', params={
-            "key": GCE_KEY,
-            "cx": GCE_PROJECT_CX,
-            "safe": "high",
-            "fileType": "png|jpg|gif",
-            "imgType": "photo",
-            "searchType": "image",
-            "limit": 1,
-            "q": species_name
-        })
-        result = resp.json()
-
-        cached_val = [x['link'] for x in result['items']]
-        cache.set(cache_key, cached_val)
-
-    return jsonify({
-        'results': cached_val
-    })