updating deps; removing validate.io-nonnegative-integer-array

TeselaGen · Sep 23, 2021 · e5e0f6d · e5e0f6d
1 parent 7221639
commit e5e0f6d
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Showing 7 changed files with 19 additions and 76 deletions.
diff --git a/package.json b/package.json
@@ -39,8 +39,7 @@
     "bson-objectid": "^1.1.1",
     "escape-string-regexp": "^1.0.5",
     "jsondiffpatch": "^0.3.11",
-    "string-splice": "^1.3.0",
-    "validate.io-nonnegative-integer-array": "^1.0.1"
+    "string-splice": "^1.3.0"
   },
   "devDependencies": {
     "@types/jest": "^23.3.11",
@@ -59,7 +58,6 @@
     "npm-check": "^5.0.1",
     "nwb": "^0.23.0",
     "prettier": "^1.15.3",
-    "ve-range-utils": "2.5.5",
-    "ve-sequence-utils": "^3.3.16"
+    "ve-range-utils": "2.6.3"
   }
 }
diff --git a/src/getOrfsFromSequence.js b/src/getOrfsFromSequence.js
@@ -1,4 +1,3 @@
-// const areNonNegativeIntegers = require('validate.io-nonnegative-integer-array');
 const ObjectId = require("bson-objectid");
 const getReverseComplementSequenceString = require("./getReverseComplementSequenceString");
 // const ac = require('ve-api-check');

diff --git a/src/mapAnnotationsToRows.js b/src/mapAnnotationsToRows.js
@@ -1,13 +1,4 @@
-// const ac = require('ve-api-check');
-// ac.throw([ac.string,ac.bool],arguments);
-const {
-  each,
-  forEach,
-  startsWith,
-  filter
-  // some, sortBy, uniq
-} = require("lodash");
-// const areNonNegativeIntegers = require('validate.io-nonnegative-integer-array');
+const { each, forEach, startsWith, filter } = require("lodash");
 const {
   getYOffsetForPotentiallyCircularRange,
   splitRangeIntoTwoPartsIfItIsCircular
@@ -18,14 +9,6 @@ module.exports = function mapAnnotationsToRows(
   sequenceLength,
   bpsPerRow
 ) {
-  // ac.throw(ac.arrayOf(ac.shape({
-  //     start: ac.posInt,
-  //     end: ac.posInt,
-  //     // id: ac.oneOfType([ac.object, ac.string])
-  // })), annotations);
-  // ac.throw(ac.posInt, sequenceLength);
-  // ac.throw(ac.posInt, bpsPerRow);
-
   const annotationsToRowsMap = {};
   const yOffsetLevelMap = {};
   const wrappedAnnotations = {};

diff --git a/src/tidyUpAnnotation.js b/src/tidyUpAnnotation.js
@@ -1,7 +1,6 @@
 const { cloneDeep } = require("lodash");
 const FeatureTypes = require("./FeatureTypes.js");
 const featureColors = require("./featureColors");
-const areNonNegativeIntegers = require("validate.io-nonnegative-integer-array");
 const bsonObjectid = require("bson-objectid");
 
 module.exports = function tidyUpAnnotation(
@@ -124,7 +123,11 @@ function coerceLocation({
     location.start = location.start * 3;
     location.end = location.end * 3 + 2;
   }
-  if (!areNonNegativeIntegers([location.start]) || location.start > size - 1) {
+  if (
+    location.start < 0 ||
+    !(location.start <= size - 1) ||
+    location.start > size - 1
+  ) {
     messages.push(
       "Invalid annotation start: " +
         location.start +
@@ -135,7 +138,11 @@ function coerceLocation({
     ); //setting it to 0 internally, but users will see it as 1
     location.start = size - (isProtein ? 3 : 1);
   }
-  if (!areNonNegativeIntegers([location.end]) || location.end > size - 1) {
+  if (
+    location.end < 0 ||
+    !(location.end <= size - 1) ||
+    location.end > size - 1
+  ) {
     messages.push(
       "Invalid annotation end:  " +
         location.end +

diff --git a/src/tidyUpSequenceData.js b/src/tidyUpSequenceData.js
@@ -2,7 +2,6 @@
 const bsonObjectid = require("bson-objectid");
 const getAminoAcidDataForEachBaseOfDna = require("./getAminoAcidDataForEachBaseOfDna");
 const { cloneDeep } = require("lodash");
-const areNonNegativeIntegers = require("validate.io-nonnegative-integer-array");
 const annotationTypes = require("./annotationTypes");
 const filterSequenceString = require("./filterSequenceString");
 const tidyUpAnnotation = require("./tidyUpAnnotation");
@@ -140,7 +139,7 @@ module.exports = function tidyUpSequenceData(pSeqData, options = {}) {
     annotationTypes.forEach(function(name) {
       seqData[name] = seqData[name].reduce(function(acc, item) {
         let itemId;
-        if (areNonNegativeIntegers(item.id) || item.id) {
+        if (item.id || item.id === 0) {
           itemId = item.id;
         } else {
           itemId = bsonObjectid().str;

diff --git a/src/tidyUpSequenceData.test.js b/src/tidyUpSequenceData.test.js
@@ -14,7 +14,7 @@ describe("tidyUpSequenceData", function() {
             end: 20,
             locations: [
               {
-                start: 3,
+                start: "3", //this should be converted to an int :)
                 end: 5
               },
               {

diff --git a/yarn.lock b/yarn.lock
@@ -11004,60 +11004,17 @@ validate-npm-package-license@^3.0.1:
     spdx-correct "^3.0.0"
     spdx-expression-parse "^3.0.0"
 
-validate.io-array@^1.0.3:
-  version "1.0.6"
-  resolved "https://registry.yarnpkg.com/validate.io-array/-/validate.io-array-1.0.6.tgz#5b5a2cafd8f8b85abb2f886ba153f2d93a27774d"
-  integrity sha1-W1osr9j4uFq7L4hroVPy2Tond00=
-
-validate.io-integer@^1.0.5:
-  version "1.0.5"
-  resolved "https://registry.yarnpkg.com/validate.io-integer/-/validate.io-integer-1.0.5.tgz#168496480b95be2247ec443f2233de4f89878068"
-  integrity sha1-FoSWSAuVviJH7EQ/IjPeT4mHgGg=
-  dependencies:
-    validate.io-number "^1.0.3"
-
-validate.io-nonnegative-integer-array@^1.0.1:
-  version "1.0.1"
-  resolved "https://registry.yarnpkg.com/validate.io-nonnegative-integer-array/-/validate.io-nonnegative-integer-array-1.0.1.tgz#66330a665f5598b96f25f69081f81f632ea4db4f"
-  integrity sha1-ZjMKZl9VmLlvJfaQgfgfYy6k208=
-  dependencies:
-    validate.io-array "^1.0.3"
-    validate.io-nonnegative-integer "^1.0.0"
-
-validate.io-nonnegative-integer@^1.0.0:
-  version "1.0.0"
-  resolved "https://registry.yarnpkg.com/validate.io-nonnegative-integer/-/validate.io-nonnegative-integer-1.0.0.tgz#8069243a08c5f98e95413c929dfd7b18f3f6f29f"
-  integrity sha1-gGkkOgjF+Y6VQTySnf17GPP28p8=
-  dependencies:
-    validate.io-integer "^1.0.5"
-
-validate.io-number@^1.0.3:
-  version "1.0.3"
-  resolved "https://registry.yarnpkg.com/validate.io-number/-/validate.io-number-1.0.3.tgz#f63ffeda248bf28a67a8d48e0e3b461a1665baf8"
-  integrity sha1-9j/+2iSL8opnqNSODjtGGhZluvg=
-
 vary@~1.1.2:
   version "1.1.2"
   resolved "https://registry.yarnpkg.com/vary/-/vary-1.1.2.tgz#2299f02c6ded30d4a5961b0b9f74524a18f634fc"
   integrity sha1-IpnwLG3tMNSllhsLn3RSShj2NPw=
 
-ve-range-utils@2.5.5:
-  version "2.5.5"
-  resolved "https://registry.yarnpkg.com/ve-range-utils/-/ve-range-utils-2.5.5.tgz#54d8bb442666b10b4cfe9bfef457c3f6cbd7a1a0"
-  integrity sha512-rxdps7rO3WO0btj5zrR34aPTolYxSHxAPNkX+AyuufaaiggAoinRcsu9Xx1sTmVa7uwQuLeTKr8U7j9VhZAPZw==
+ve-range-utils@2.6.3:
+  version "2.6.3"
+  resolved "https://registry.yarnpkg.com/ve-range-utils/-/ve-range-utils-2.6.3.tgz#ef7e36efcfba563860f6ff89350ad8f6ae28f244"
+  integrity sha512-HiUuyaiqKRirrc1/5P4/XpnFOvb1Z+lpcwyHn+mc1LecXipNViBIVfCQU8LIxbScFXuvTzgClS1ywdJRvs6HWA==
   dependencies:
     lodash "^4.17.4"
-    validate.io-nonnegative-integer-array "^1.0.1"
-
-ve-sequence-utils@^3.3.16:
-  version "3.3.16"
-  resolved "https://registry.yarnpkg.com/ve-sequence-utils/-/ve-sequence-utils-3.3.16.tgz#ac1a7bdf4187953b0990b16b3154decd07066a1b"
-  integrity sha512-JTARqUoYZECY2OpMZFhG6P3+YtpovgNbju36hWeYFaxfMXB8LE7L33BJ4TvIyI+OKP5UCf/gRMZMmTzZUa+9AA==
-  dependencies:
-    bson-objectid "^1.1.1"
-    escape-string-regexp "^1.0.5"
-    string-splice "^1.3.0"
-    validate.io-nonnegative-integer-array "^1.0.1"
 
 [email protected]:
   version "1.10.0"