@abi-software/flatmapvuer 0.4.6-fixes-2 → 0.5.0

package/package-lock.json

@@ -1,6 +1,6 @@
 {
   "name": "@abi-software/flatmapvuer",
-  "version": "0.4.6-fixes-2",
+  "version": "0.5.0",
   "lockfileVersion": 1,
   "requires": true,
   "dependencies": {
@@ -384,7 +384,8 @@
     "@babel/parser": {
       "version": "7.20.5",
       "resolved": "https://registry.npmjs.org/@babel/parser/-/parser-7.20.5.tgz",
-      "integrity": "sha512-r27t/cy/m9uKLXQNWWebeCUHgnAZq0CpG1OwKRxzJMP1vpSU4bSIK2hq+/cp0bQxetkXx38n09rNu8jVkcK/zA=="
+      "integrity": "sha512-r27t/cy/m9uKLXQNWWebeCUHgnAZq0CpG1OwKRxzJMP1vpSU4bSIK2hq+/cp0bQxetkXx38n09rNu8jVkcK/zA==",
+      "dev": true
     },
     "@babel/plugin-bugfix-safari-id-destructuring-collision-in-function-expression": {
       "version": "7.18.6",
@@ -2170,16 +2171,6 @@
         "strip-ansi": "^6.0.0"
       }
     },
-    "@vue/compiler-sfc": {
-      "version": "2.7.14",
-      "resolved": "https://registry.npmjs.org/@vue/compiler-sfc/-/compiler-sfc-2.7.14.tgz",
-      "integrity": "sha512-aNmNHyLPsw+sVvlQFQ2/8sjNuLtK54TC6cuKnVzAY93ks4ZBrvwQSnkkIh7bsbNhum5hJBS00wSDipQ937f5DA==",
-      "requires": {
-        "@babel/parser": "^7.18.4",
-        "postcss": "^8.4.14",
-        "source-map": "^0.6.1"
-      }
-    },
     "@vue/component-compiler-utils": {
       "version": "3.3.0",
       "resolved": "https://registry.npmjs.org/@vue/component-compiler-utils/-/component-compiler-utils-3.3.0.tgz",
@@ -2784,6 +2775,51 @@
       "integrity": "sha512-Wm6ukoaOGJi/73p/cl2GvLjTI5JM1k/O14isD73YML8StrH/7/lRFgmg8nICZgD3bZZvjwCGxtMOD3wWNAu8cg==",
       "dev": true
     },
+    "auto-changelog": {
+      "version": "2.4.0",
+      "resolved": "https://registry.npmjs.org/auto-changelog/-/auto-changelog-2.4.0.tgz",
+      "integrity": "sha512-vh17hko1c0ItsEcw6m7qPRf3m45u+XK5QyCrrBFViElZ8jnKrPC1roSznrd1fIB/0vR/zawdECCRJtTuqIXaJw==",
+      "dev": true,
+      "requires": {
+        "commander": "^7.2.0",
+        "handlebars": "^4.7.7",
+        "node-fetch": "^2.6.1",
+        "parse-github-url": "^1.0.2",
+        "semver": "^7.3.5"
+      },
+      "dependencies": {
+        "commander": {
+          "version": "7.2.0",
+          "resolved": "https://registry.npmjs.org/commander/-/commander-7.2.0.tgz",
+          "integrity": "sha512-QrWXB+ZQSVPmIWIhtEO9H+gwHaMGYiF5ChvoJ+K9ZGHG/sVsa6yiesAD1GC/x46sET00Xlwo1u49RVVVzvcSkw==",
+          "dev": true
+        },
+        "lru-cache": {
+          "version": "6.0.0",
+          "resolved": "https://registry.npmjs.org/lru-cache/-/lru-cache-6.0.0.tgz",
+          "integrity": "sha512-Jo6dJ04CmSjuznwJSS3pUeWmd/H0ffTlkXXgwZi+eq1UCmqQwCh+eLsYOYCwY991i2Fah4h1BEMCx4qThGbsiA==",
+          "dev": true,
+          "requires": {
+            "yallist": "^4.0.0"
+          }
+        },
+        "semver": {
+          "version": "7.5.1",
+          "resolved": "https://registry.npmjs.org/semver/-/semver-7.5.1.tgz",
+          "integrity": "sha512-Wvss5ivl8TMRZXXESstBA4uR5iXgEN/VC5/sOcuXdVLzcdkz4HWetIoRfG5gb5X+ij/G9rw9YoGn3QoQ8OCSpw==",
+          "dev": true,
+          "requires": {
+            "lru-cache": "^6.0.0"
+          }
+        },
+        "yallist": {
+          "version": "4.0.0",
+          "resolved": "https://registry.npmjs.org/yallist/-/yallist-4.0.0.tgz",
+          "integrity": "sha512-3wdGidZyq5PB084XLES5TpOSRA3wjXAlIWMhum2kRcv/41Sn2emQ0dycQW4uZXLejwKvg6EsvbdlVL+FYEct7A==",
+          "dev": true
+        }
+      }
+    },
     "autoprefixer": {
       "version": "9.8.8",
       "resolved": "https://registry.npmjs.org/autoprefixer/-/autoprefixer-9.8.8.tgz",
@@ -4288,9 +4324,9 @@
       }
     },
     "core-js": {
-      "version": "3.26.1",
-      "resolved": "https://registry.npmjs.org/core-js/-/core-js-3.26.1.tgz",
-      "integrity": "sha512-21491RRQVzUn0GGM9Z1Jrpr6PNPxPi+Za8OM9q4tksTSnlbXXGKK1nXNg/QvwFYettXvSX6zWKCtHHfjN4puyA=="
+      "version": "3.30.2",
+      "resolved": "https://registry.npmjs.org/core-js/-/core-js-3.30.2.tgz",
+      "integrity": "sha512-uBJiDmwqsbJCWHAwjrx3cvjbMXP7xD72Dmsn5LOJpiRmE3WbBbN5rCqQ2Qh6Ek6/eOrjlWngEynBWo4VxerQhg=="
     },
     "core-js-compat": {
       "version": "3.26.1",
@@ -4698,11 +4734,6 @@
         }
       }
     },
-    "csstype": {
-      "version": "3.1.1",
-      "resolved": "https://registry.npmjs.org/csstype/-/csstype-3.1.1.tgz",
-      "integrity": "sha512-DJR/VvkAvSZW9bTouZue2sSxDwdTN92uHjqeKVm+0dAqdfNykRzQ95tay8aXMBAAPpUiq4Qcug2L7neoRh2Egw=="
-    },
     "current-script-polyfill": {
       "version": "1.0.0",
       "resolved": "https://registry.npmjs.org/current-script-polyfill/-/current-script-polyfill-1.0.0.tgz",
@@ -4735,7 +4766,7 @@
     "de-indent": {
       "version": "1.0.2",
       "resolved": "https://registry.npmjs.org/de-indent/-/de-indent-1.0.2.tgz",
-      "integrity": "sha1-sgOOhG3DO6pXlhKNCAS0VbjB4h0=",
+      "integrity": "sha512-e/1zu3xH5MQryN2zdVaF0OrdNLUbvWxzMbi+iNA6Bky7l1RoP8a2fIbRocyHclXt/arDrrR6lL3TqFD9pMQTsg==",
       "dev": true
     },
     "debug": {
@@ -6603,6 +6634,19 @@
       "integrity": "sha512-9Qn4yBxelxoh2Ow62nP+Ka/kMnOXRi8BXnRaUwezLNhqelnN49xKz4F/dPP8OYLxLxq6JDtZb2i9XznUQbNPTg==",
       "dev": true
     },
+    "handlebars": {
+      "version": "4.7.7",
+      "resolved": "https://registry.npmjs.org/handlebars/-/handlebars-4.7.7.tgz",
+      "integrity": "sha512-aAcXm5OAfE/8IXkcZvCepKU3VzW1/39Fb5ZuqMtgI/hT8X2YgoMvBY5dLhq/cpOvw7Lk1nK/UF71aLG/ZnVYRA==",
+      "dev": true,
+      "requires": {
+        "minimist": "^1.2.5",
+        "neo-async": "^2.6.0",
+        "source-map": "^0.6.1",
+        "uglify-js": "^3.1.4",
+        "wordwrap": "^1.0.0"
+      }
+    },
     "har-schema": {
       "version": "2.0.0",
       "resolved": "https://registry.npmjs.org/har-schema/-/har-schema-2.0.0.tgz",
@@ -8589,11 +8633,6 @@
       "integrity": "sha512-2ZTgtl0nJsO0KQCjEpxcIr5D+Yv90plTitZt9JBfQvVJDS5seMl3FOvsh3+9CoYWXf/1l5OaZzzF6nDm4cagaQ==",
       "dev": true
     },
-    "nanoid": {
-      "version": "3.3.4",
-      "resolved": "https://registry.npmjs.org/nanoid/-/nanoid-3.3.4.tgz",
-      "integrity": "sha512-MqBkQh/OHTS2egovRtLk45wEyNXwF+cokD+1YPf9u5VfJiRdAiRwB2froX5Co9Rh20xs4siNPm8naNotSD6RBw=="
-    },
     "nanomatch": {
       "version": "1.2.13",
       "resolved": "https://registry.npmjs.org/nanomatch/-/nanomatch-1.2.13.tgz",
@@ -8646,6 +8685,15 @@
         "lower-case": "^1.1.1"
       }
     },
+    "node-fetch": {
+      "version": "2.6.11",
+      "resolved": "https://registry.npmjs.org/node-fetch/-/node-fetch-2.6.11.tgz",
+      "integrity": "sha512-4I6pdBY1EthSqDmJkiNk3JIT8cswwR9nfeW/cPdUagJYEQG7R95WRH74wpz7ma8Gh/9dI9FP+OU+0E4FvtA55w==",
+      "dev": true,
+      "requires": {
+        "whatwg-url": "^5.0.0"
+      }
+    },
     "node-forge": {
       "version": "0.10.0",
       "resolved": "https://registry.npmjs.org/node-forge/-/node-forge-0.10.0.tgz",
@@ -9266,6 +9314,12 @@
         "safe-buffer": "^5.1.1"
       }
     },
+    "parse-github-url": {
+      "version": "1.0.2",
+      "resolved": "https://registry.npmjs.org/parse-github-url/-/parse-github-url-1.0.2.tgz",
+      "integrity": "sha512-kgBf6avCbO3Cn6+RnzRGLkUsv4ZVqv/VfAYkRsyBcgkshNvVBkRn1FEZcW0Jb+npXQWm2vHPnnOqFteZxRRGNw==",
+      "dev": true
+    },
     "parse-json": {
       "version": "5.2.0",
       "resolved": "https://registry.npmjs.org/parse-json/-/parse-json-5.2.0.tgz",
@@ -9409,7 +9463,8 @@
     "picocolors": {
       "version": "1.0.0",
       "resolved": "https://registry.npmjs.org/picocolors/-/picocolors-1.0.0.tgz",
-      "integrity": "sha512-1fygroTLlHu66zi26VoTDv8yRgm0Fccecssto+MhsZ0D/DGW2sm8E8AjW7NU5VVTRt5GxbeZ5qBuJr+HyLYkjQ=="
+      "integrity": "sha512-1fygroTLlHu66zi26VoTDv8yRgm0Fccecssto+MhsZ0D/DGW2sm8E8AjW7NU5VVTRt5GxbeZ5qBuJr+HyLYkjQ==",
+      "dev": true
     },
     "picomatch": {
       "version": "2.3.1",
@@ -9492,16 +9547,6 @@
       "integrity": "sha1-AerA/jta9xoqbAL+q7jB/vfgDqs=",
       "dev": true
     },
-    "postcss": {
-      "version": "8.4.19",
-      "resolved": "https://registry.npmjs.org/postcss/-/postcss-8.4.19.tgz",
-      "integrity": "sha512-h+pbPsyhlYj6N2ozBmHhHrs9DzGmbaarbLvWipMRO7RLS+v4onj26MPFXA5OBYFxyqYhUJK456SwDcY9H2/zsA==",
-      "requires": {
-        "nanoid": "^3.3.4",
-        "picocolors": "^1.0.0",
-        "source-map-js": "^1.0.2"
-      }
-    },
     "postcss-calc": {
       "version": "7.0.5",
       "resolved": "https://registry.npmjs.org/postcss-calc/-/postcss-calc-7.0.5.tgz",
@@ -12078,12 +12123,8 @@
     "source-map": {
       "version": "0.6.1",
       "resolved": "https://registry.npmjs.org/source-map/-/source-map-0.6.1.tgz",
-      "integrity": "sha512-UjgapumWlbMhkBgzT7Ykc5YXUT46F0iKu8SGXq0bcwP5dz/h0Plj6enJqjz1Zbq2l5WaqYnrVbwWOWMyF3F47g=="
-    },
-    "source-map-js": {
-      "version": "1.0.2",
-      "resolved": "https://registry.npmjs.org/source-map-js/-/source-map-js-1.0.2.tgz",
-      "integrity": "sha512-R0XvVJ9WusLiqTCEiGCmICCMplcCkIwwR11mOSD9CR5u+IXYdiseeEuXCVAjS54zqwkLcPNnmU4OeJ6tUrWhDw=="
+      "integrity": "sha512-UjgapumWlbMhkBgzT7Ykc5YXUT46F0iKu8SGXq0bcwP5dz/h0Plj6enJqjz1Zbq2l5WaqYnrVbwWOWMyF3F47g==",
+      "dev": true
     },
     "source-map-resolve": {
       "version": "0.5.3",
@@ -12860,6 +12901,12 @@
         "punycode": "^2.1.1"
       }
     },
+    "tr46": {
+      "version": "0.0.3",
+      "resolved": "https://registry.npmjs.org/tr46/-/tr46-0.0.3.tgz",
+      "integrity": "sha512-N3WMsuqV66lT30CrXNbEjx4GEwlow3v6rr4mCcv6prnfwhS01rkgyFdjPNBYd9br7LpXV1+Emh01fHnq2Gdgrw==",
+      "dev": true
+    },
     "trim-newlines": {
       "version": "1.0.0",
       "resolved": "https://registry.npmjs.org/trim-newlines/-/trim-newlines-1.0.0.tgz",
@@ -13299,13 +13346,9 @@
       }
     },
     "vue": {
-      "version": "2.7.14",
-      "resolved": "https://registry.npmjs.org/vue/-/vue-2.7.14.tgz",
-      "integrity": "sha512-b2qkFyOM0kwqWFuQmgd4o+uHGU7T+2z3T+WQp8UBjADfEv2n4FEMffzBmCKNP0IGzOEEfYjvtcC62xaSKeQDrQ==",
-      "requires": {
-        "@vue/compiler-sfc": "2.7.14",
-        "csstype": "^3.1.0"
-      }
+      "version": "2.6.14",
+      "resolved": "https://registry.npmjs.org/vue/-/vue-2.6.14.tgz",
+      "integrity": "sha512-x2284lgYvjOMj3Za7kqzRcUSxBboHqtgRE2zlos1qWaOye5yUmHn42LB1250NJBLRwEcdrB0JRwyPTEPhfQjiQ=="
     },
     "vue-eslint-parser": {
       "version": "5.0.0",
@@ -13380,13 +13423,13 @@
       }
     },
     "vue-template-compiler": {
-      "version": "2.7.14",
-      "resolved": "https://registry.npmjs.org/vue-template-compiler/-/vue-template-compiler-2.7.14.tgz",
-      "integrity": "sha512-zyA5Y3ArvVG0NacJDkkzJuPQDF8RFeRlzV2vLeSnhSpieO6LK2OVbdLPi5MPPs09Ii+gMO8nY4S3iKQxBxDmWQ==",
+      "version": "2.6.14",
+      "resolved": "https://registry.npmjs.org/vue-template-compiler/-/vue-template-compiler-2.6.14.tgz",
+      "integrity": "sha512-ODQS1SyMbjKoO1JBJZojSw6FE4qnh9rIpUZn2EUT86FKizx9uH5z6uXiIrm4/Nb/gwxTi/o17ZDEGWAXHvtC7g==",
       "dev": true,
       "requires": {
         "de-indent": "^1.0.2",
-        "he": "^1.2.0"
+        "he": "^1.1.0"
       }
     },
     "vue-template-es2015-compiler": {
@@ -13543,6 +13586,12 @@
         "defaults": "^1.0.3"
       }
     },
+    "webidl-conversions": {
+      "version": "3.0.1",
+      "resolved": "https://registry.npmjs.org/webidl-conversions/-/webidl-conversions-3.0.1.tgz",
+      "integrity": "sha512-2JAn3z8AR6rjK8Sm8orRC0h/bcl/DqL7tRPdGZ4I1CjdF+EaMLmYxBHyXuKL849eucPFhvBoxMsflfOb8kxaeQ==",
+      "dev": true
+    },
     "webpack": {
       "version": "4.46.0",
       "resolved": "https://registry.npmjs.org/webpack/-/webpack-4.46.0.tgz",
@@ -14049,6 +14098,16 @@
       "integrity": "sha512-OqedPIGOfsDlo31UNwYbCFMSaO9m9G/0faIHj5/dZFDMFqPTcx6UwqyOy3COEaEOg/9VsGIpdqn62W5KhoKSpg==",
       "dev": true
     },
+    "whatwg-url": {
+      "version": "5.0.0",
+      "resolved": "https://registry.npmjs.org/whatwg-url/-/whatwg-url-5.0.0.tgz",
+      "integrity": "sha512-saE57nupxk6v3HY35+jzBwYa0rKSy0XR8JSxZPwgLr7ys0IBzhGviA1/TUGJLmSVqs8pb9AnvICXEuOHLprYTw==",
+      "dev": true,
+      "requires": {
+        "tr46": "~0.0.3",
+        "webidl-conversions": "^3.0.0"
+      }
+    },
     "which": {
       "version": "1.3.1",
       "resolved": "https://registry.npmjs.org/which/-/which-1.3.1.tgz",
@@ -14091,6 +14150,12 @@
       "integrity": "sha512-Hz/mrNwitNRh/HUAtM/VT/5VH+ygD6DV7mYKZAtHOrbs8U7lvPS6xf7EJKMF0uW1KJCl0H701g3ZGus+muE5vQ==",
       "dev": true
     },
+    "wordwrap": {
+      "version": "1.0.0",
+      "resolved": "https://registry.npmjs.org/wordwrap/-/wordwrap-1.0.0.tgz",
+      "integrity": "sha512-gvVzJFlPycKc5dZN4yPkP8w7Dc37BtP1yczEneOb4uq34pXZcvrtRTmWV8W+Ume+XCxKgbjM+nevkyFPMybd4Q==",
+      "dev": true
+    },
     "worker-farm": {
       "version": "1.7.0",
       "resolved": "https://registry.npmjs.org/worker-farm/-/worker-farm-1.7.0.tgz",

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@abi-software/flatmapvuer",
-  "version": "0.4.6-fixes-2",
+  "version": "0.5.0",
   "license": "Apache-2.0",
   "main": "./dist/flatmapvuer.common.js",
   "files": [
@@ -19,23 +19,29 @@
     "serve": "vue-cli-service serve --port 8082",
     "build": "vue-cli-service build --dest test_html --mode staging",
     "build-bundle": "vue-cli-service build --target lib --name flatmapvuer ./src/components/index.js",
-    "lint": "vue-cli-service lint"
+    "lint": "vue-cli-service lint",
+    "release:beta": "npm version prerelease --preid=beta; npm publish --tag beta",
+    "release:minor": "npm version minor; npm publish",
+    "release:patch": "npm version patch;  npm publish",
+    "changelog": "auto-changelog -p --output CHANGELOG.md --template keepachangelog",
+    "version": "npm run build-bundle;npm run changelog; git add CHANGELOG.md"
   },
   "dependencies": {
     "@abi-software/flatmap-viewer": "^2.3.3-b.4",
     "@abi-software/svg-sprite": "^0.1.14",
-    "core-js": "^3.3.2",
+    "core-js": "^3.30.1",
     "css-element-queries": "^1.2.2",
     "current-script-polyfill": "^1.0.0",
     "element-ui": "^2.13.0",
     "file-loader": "^5.0.2",
     "lodash": "^4.17.21",
-    "vue": "^2.6.10"
+    "vue": "2.6.14"
   },
   "devDependencies": {
-    "@vue/cli-plugin-babel": "^4.0.0",
-    "@vue/cli-plugin-eslint": "^4.0.0",
-    "@vue/cli-service": "^4.5.13",
+    "@vue/cli-plugin-babel": "^4.5.19",
+    "@vue/cli-plugin-eslint": "^4.5.19",
+    "@vue/cli-service": "^4.5.19",
+    "auto-changelog": "^2.4.0",
     "babel-eslint": "^10.0.3",
     "babel-plugin-component": "^1.1.1",
     "base64-inline-loader": "^2.0.1",
@@ -43,7 +49,7 @@
     "eslint-plugin-vue": "^5.0.0",
     "node-sass": "^4.14.1",
     "sass-loader": "^8.0.2",
-    "vue-template-compiler": "^2.6.10",
+    "vue-template-compiler": "2.6.14",
     "webpack-node-externals": "^2.5.2"
   },
   "eslintConfig": {

package/src/components/FlatmapVuer.vue

@@ -525,15 +525,12 @@ export default {
     checkAndCreatePopups:  async function(data) {
       // Call flatmap database to get the connection data
       let results = await this.flatmapQueries.retrieveFlatmapKnowledgeForEvent(data)
-      if(!results){
-        if(data.feature.hyperlinks && data.feature.hyperlinks.length > 0){
-          this.resourceForTooltip =  data.resource[0];
-          this.createTooltipFromNeuronCuration(data);
-        }
-      } else {
+      // The line below only creates the tooltip if some data was found on the path 
+      // result 0 is the connection, result 1 is the pubmed results from flatmap
+      if(results[0] || results[1] ||( data.feature.hyperlinks && data.feature.hyperlinks.length > 0)){
         this.resourceForTooltip =  data.resource[0];
         this.createTooltipFromNeuronCuration(data);
-      }
+      } 
     },
     popUpCssHacks: function() {
       // Below is a hack to remove flatmap tooltips while popup is open

package/src/services/flatmapQueries.js

@@ -210,9 +210,9 @@ let FlatmapQueries = function(){
           resolve(false)
         })
       })
-      let prom2 = this.pubmedQueryOnIds(eventData)
+      let prom2 = await this.pubmedQueryOnIds(eventData)
       let results = await Promise.all([prom1, prom2])
-      return results.every(Boolean)
+      return results
   }
 
   this.connectivityExists = function(data){
@@ -344,21 +344,24 @@ let FlatmapQueries = function(){
       console.error('Error:', error)
     })
   }
-
+  // Note that this functin WILL run to the end, as it doesn not catch the second level of promises
   this.pubmedQueryOnIds = function(eventData){
-    const keastIds = eventData.resource
-    const source = eventData.feature.source
-    if(!keastIds || keastIds.length === 0) return
-    const sql = this.buildPubmedSqlStatement(keastIds)
-    return this.flatmapQuery(sql).then(data=>{
-      // Create pubmed url on paths if we have them
-      if (data.values.length > 0){
-        this.urls = [this.pubmedSearchUrl(data.values.map(id=>this.stripPMIDPrefix(id[0])))]
-        return true
-      } else { // Create pubmed url on models
-        this.pubmedQueryOnModels(source).then(()=>{return true})
-      }
-      return false
+    return new Promise(resolve=>{
+      const keastIds = eventData.resource
+      const source = eventData.feature.source
+      if(!keastIds || keastIds.length === 0) return
+      const sql = this.buildPubmedSqlStatement(keastIds)
+      this.flatmapQuery(sql).then(data=>{
+        // Create pubmed url on paths if we have them
+        if (data.values.length > 0){
+          this.urls = [this.pubmedSearchUrl(data.values.map(id=>this.stripPMIDPrefix(id[0])))]
+          resolve(true)
+        } else { // Create pubmed url on models
+          this.pubmedQueryOnModels(source).then(result=>{
+            resolve(result)
+          })
+        }
+      })
     })
   }
 
@@ -366,10 +369,11 @@ let FlatmapQueries = function(){
     return this.flatmapQuery(this.buildPubmedSqlStatementForModels(source)).then(data=>{
       if (Array.isArray(data.values) && data.values.length > 0){
         this.urls = [this.pubmedSearchUrl(data.values.map(id=>this.stripPMIDPrefix(id[0])))]
+        return true
       } else {
         this.urls = [] // Clears the pubmed search button 
       } 
-      return
+      return false
     })
   }