gramene-bins-client - npm Package Compare versions

Comparing version 2.2.8 to 2.2.9

npm-shrinkwrap.json

 {
   "name": "gramene-bins-client",
-  "version": "2.2.8",
+  "version": "2.2.9",
   "dependencies": {
@@ -113,2 +113,456 @@ "argparse": {
     },
+    "gramene-taxonomy-with-genomes": {
+      "version": "3.0.6",
+      "from": "gramene-taxonomy-with-genomes@3.0.6",
+      "dependencies": {
+        "gramene-bins-client": {
+          "version": "2.2.8",
+          "from": "gramene-bins-client@2.2.8",
+          "dependencies": {
+            "argparse": {
+              "version": "1.0.3",
+              "from": "argparse@>=1.0.2 <2.0.0",
+              "resolved": "https://registry.npmjs.org/argparse/-/argparse-1.0.3.tgz"
+            },
+            "async": {
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+              "from": "async@>=0.9.0 <0.10.0",
+              "resolved": "https://registry.npmjs.org/async/-/async-0.9.2.tgz"
+            },
+            "btoa": {
+              "version": "1.1.2",
+              "from": "btoa@>=1.1.2 <2.0.0",
+              "resolved": "https://registry.npmjs.org/btoa/-/btoa-1.1.2.tgz"
+            },
+            "combined-stream": {
+              "version": "0.0.7",
+              "from": "combined-stream@>=0.0.4 <0.1.0",
+              "resolved": "https://registry.npmjs.org/combined-stream/-/combined-stream-0.0.7.tgz"
+            },
+            "component-emitter": {
+              "version": "1.1.2",
+              "from": "component-emitter@1.1.2",
+              "resolved": "https://registry.npmjs.org/component-emitter/-/component-emitter-1.1.2.tgz"
+            },
+            "cookiejar": {
+              "version": "2.0.6",
+              "from": "cookiejar@>=2.0.1 <3.0.0",
+              "resolved": "https://registry.npmjs.org/cookiejar/-/cookiejar-2.0.6.tgz"
+            },
+            "core-util-is": {
+              "version": "1.0.2",
+              "from": "core-util-is@>=1.0.0 <1.1.0",
+              "resolved": "https://registry.npmjs.org/core-util-is/-/core-util-is-1.0.2.tgz"
+            },
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+              "from": "debug@>=2.0.0 <3.0.0",
+              "resolved": "https://registry.npmjs.org/debug/-/debug-2.2.0.tgz"
+            },
+            "delayed-stream": {
+              "version": "0.0.5",
+              "from": "delayed-stream@0.0.5",
+              "resolved": "https://registry.npmjs.org/delayed-stream/-/delayed-stream-0.0.5.tgz"
+            },
+            "esprima": {
+              "version": "2.7.1",
+              "from": "esprima@>=2.6.0 <3.0.0",
+              "resolved": "https://registry.npmjs.org/esprima/-/esprima-2.7.1.tgz"
+            },
+            "extend": {
+              "version": "1.2.1",
+              "from": "extend@1.2.1",
+              "resolved": "https://registry.npmjs.org/extend/-/extend-1.2.1.tgz"
+            },
+            "form-data": {
+              "version": "0.2.0",
+              "from": "form-data@0.2.0",
+              "resolved": "https://registry.npmjs.org/form-data/-/form-data-0.2.0.tgz"
+            },
+            "formidable": {
+              "version": "1.0.14",
+              "from": "formidable@1.0.14",
+              "resolved": "https://registry.npmjs.org/formidable/-/formidable-1.0.14.tgz"
+            },
+            "gramene-search-client": {
+              "version": "2.6.2",
+              "from": "gramene-search-client@2.6.2",
+              "dependencies": {
+                "lodash": {
+                  "version": "3.10.1",
+                  "from": "lodash@>=3.6.0 <4.0.0",
+                  "resolved": "https://registry.npmjs.org/lodash/-/lodash-3.10.1.tgz"
+                },
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+                  "from": "q@>=1.2.0 <2.0.0",
+                  "resolved": "https://registry.npmjs.org/q/-/q-1.4.1.tgz"
+                }
+              }
+            },
+            "inherit": {
+              "version": "2.2.2",
+              "from": "inherit@>=2.2.2 <3.0.0",
+              "resolved": "https://registry.npmjs.org/inherit/-/inherit-2.2.2.tgz"
+            },
+            "is-number": {
+              "version": "1.1.2",
+              "from": "is-number@>=1.1.2 <2.0.0",
+              "resolved": "https://registry.npmjs.org/is-number/-/is-number-1.1.2.tgz"
+            },
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+              "version": "0.0.1",
+              "from": "isarray@0.0.1",
+              "resolved": "https://registry.npmjs.org/isarray/-/isarray-0.0.1.tgz"
+            },
+            "js-yaml": {
+              "version": "3.4.6",
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+              "resolved": "https://registry.npmjs.org/js-yaml/-/js-yaml-3.4.6.tgz"
+            },
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+              "from": "lodash@>=3.6.0 <4.0.0",
+              "resolved": "https://registry.npmjs.org/lodash/-/lodash-3.10.1.tgz"
+            },
+            "lodash-compat": {
+              "version": "3.10.1",
+              "from": "lodash-compat@>=3.5.0 <4.0.0",
+              "resolved": "https://registry.npmjs.org/lodash-compat/-/lodash-compat-3.10.1.tgz"
+            },
+            "methods": {
+              "version": "1.0.1",
+              "from": "methods@1.0.1",
+              "resolved": "https://registry.npmjs.org/methods/-/methods-1.0.1.tgz"
+            },
+            "mime": {
+              "version": "1.3.4",
+              "from": "mime@1.3.4",
+              "resolved": "https://registry.npmjs.org/mime/-/mime-1.3.4.tgz"
+            },
+            "mime-db": {
+              "version": "1.12.0",
+              "from": "mime-db@>=1.12.0 <1.13.0",
+              "resolved": "https://registry.npmjs.org/mime-db/-/mime-db-1.12.0.tgz"
+            },
+            "mime-types": {
+              "version": "2.0.14",
+              "from": "mime-types@>=2.0.3 <2.1.0",
+              "resolved": "https://registry.npmjs.org/mime-types/-/mime-types-2.0.14.tgz"
+            },
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+            },
+            "query-string": {
+              "version": "3.0.0",
+              "from": "query-string@*",
+              "resolved": "https://registry.npmjs.org/query-string/-/query-string-3.0.0.tgz"
+            },
+            "readable-stream": {
+              "version": "1.0.27-1",
+              "from": "readable-stream@1.0.27-1",
+              "resolved": "https://registry.npmjs.org/readable-stream/-/readable-stream-1.0.27-1.tgz",
+              "dependencies": {
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+                  "from": "inherits@>=2.0.1 <2.1.0",
+                  "resolved": "https://registry.npmjs.org/inherits/-/inherits-2.0.1.tgz"
+                }
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+            },
+            "reduce-component": {
+              "version": "1.0.1",
+              "from": "reduce-component@1.0.1",
+              "resolved": "https://registry.npmjs.org/reduce-component/-/reduce-component-1.0.1.tgz"
+            },
+            "sprintf-js": {
+              "version": "1.0.3",
+              "from": "sprintf-js@>=1.0.2 <1.1.0",
+              "resolved": "https://registry.npmjs.org/sprintf-js/-/sprintf-js-1.0.3.tgz"
+            },
+            "strict-uri-encode": {
+              "version": "1.1.0",
+              "from": "strict-uri-encode@>=1.0.0 <2.0.0",
+              "resolved": "https://registry.npmjs.org/strict-uri-encode/-/strict-uri-encode-1.1.0.tgz"
+            },
+            "string_decoder": {
+              "version": "0.10.31",
+              "from": "string_decoder@>=0.10.0 <0.11.0",
+              "resolved": "https://registry.npmjs.org/string_decoder/-/string_decoder-0.10.31.tgz"
+            },
+            "superagent": {
+              "version": "1.6.1",
+              "from": "superagent@>=1.2.0 <2.0.0",
+              "resolved": "https://registry.npmjs.org/superagent/-/superagent-1.6.1.tgz"
+            },
+            "swagger-client": {
+              "version": "2.1.10",
+              "from": "swagger-client@>=2.1.6 <3.0.0",
+              "resolved": "https://registry.npmjs.org/swagger-client/-/swagger-client-2.1.10.tgz"
+            },
+            "swagger-model-validator": {
+              "version": "2.0.4",
+              "from": "swagger-model-validator@>=2.0.3 <3.0.0",
+              "resolved": "https://registry.npmjs.org/swagger-model-validator/-/swagger-model-validator-2.0.4.tgz"
+            }
+          }
+        },
+        "gramene-trees-client": {
+          "version": "2.4.4",
+          "from": "gramene-trees-client@2.4.4",
+          "dependencies": {
+            "flat-to-nested": {
+              "version": "1.0.2",
+              "from": "flat-to-nested@>=1.0.1 <2.0.0",
+              "resolved": "https://registry.npmjs.org/flat-to-nested/-/flat-to-nested-1.0.2.tgz"
+            },
+            "gramene-search-client": {
+              "version": "2.6.2",
+              "from": "gramene-search-client@2.6.2",
+              "dependencies": {
+                "query-string": {
+                  "version": "3.0.0",
+                  "from": "https://registry.npmjs.org/query-string/-/query-string-3.0.0.tgz",
+                  "resolved": "https://registry.npmjs.org/query-string/-/query-string-3.0.0.tgz",
+                  "dependencies": {
+                    "strict-uri-encode": {
+                      "version": "1.1.0",
+                      "from": "https://registry.npmjs.org/strict-uri-encode/-/strict-uri-encode-1.1.0.tgz",
+                      "resolved": "https://registry.npmjs.org/strict-uri-encode/-/strict-uri-encode-1.1.0.tgz"
+                    }
+                  }
+                },
+                "swagger-client": {
+                  "version": "2.1.10",
+                  "from": "https://registry.npmjs.org/swagger-client/-/swagger-client-2.1.10.tgz",
+                  "resolved": "https://registry.npmjs.org/swagger-client/-/swagger-client-2.1.10.tgz",
+                  "dependencies": {
+                    "btoa": {
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+                      "resolved": "https://registry.npmjs.org/btoa/-/btoa-1.1.2.tgz"
+                    },
+                    "cookiejar": {
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+                      "resolved": "https://registry.npmjs.org/cookiejar/-/cookiejar-2.0.6.tgz"
+                    },
+                    "js-yaml": {
+                      "version": "3.4.6",
+                      "from": "https://registry.npmjs.org/js-yaml/-/js-yaml-3.4.6.tgz",
+                      "resolved": "https://registry.npmjs.org/js-yaml/-/js-yaml-3.4.6.tgz",
+                      "dependencies": {
+                        "argparse": {
+                          "version": "1.0.3",
+                          "from": "https://registry.npmjs.org/argparse/-/argparse-1.0.3.tgz",
+                          "resolved": "https://registry.npmjs.org/argparse/-/argparse-1.0.3.tgz",
+                          "dependencies": {
+                            "sprintf-js": {
+                              "version": "1.0.3",
+                              "from": "https://registry.npmjs.org/sprintf-js/-/sprintf-js-1.0.3.tgz",
+                              "resolved": "https://registry.npmjs.org/sprintf-js/-/sprintf-js-1.0.3.tgz"
+                            }
+                          }
+                        },
+                        "esprima": {
+                          "version": "2.7.1",
+                          "from": "https://registry.npmjs.org/esprima/-/esprima-2.7.1.tgz",
+                          "resolved": "https://registry.npmjs.org/esprima/-/esprima-2.7.1.tgz"
+                        },
+                        "inherit": {
+                          "version": "2.2.2",
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+                          "resolved": "https://registry.npmjs.org/inherit/-/inherit-2.2.2.tgz"
+                        }
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+                    },
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+                      "resolved": "https://registry.npmjs.org/superagent/-/superagent-1.6.1.tgz",
+                      "dependencies": {
+                        "component-emitter": {
+                          "version": "1.1.2",
+                          "from": "https://registry.npmjs.org/component-emitter/-/component-emitter-1.1.2.tgz",
+                          "resolved": "https://registry.npmjs.org/component-emitter/-/component-emitter-1.1.2.tgz"
+                        },
+                        "debug": {
+                          "version": "2.2.0",
+                          "from": "https://registry.npmjs.org/debug/-/debug-2.2.0.tgz",
+                          "resolved": "https://registry.npmjs.org/debug/-/debug-2.2.0.tgz",
+                          "dependencies": {
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+                        },
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+                          "resolved": "https://registry.npmjs.org/form-data/-/form-data-0.2.0.tgz",
+                          "dependencies": {
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+                              "resolved": "https://registry.npmjs.org/async/-/async-0.9.2.tgz"
+                            },
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+                              "resolved": "https://registry.npmjs.org/combined-stream/-/combined-stream-0.0.7.tgz",
+                              "dependencies": {
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+                              "resolved": "https://registry.npmjs.org/mime-types/-/mime-types-2.0.14.tgz",
+                              "dependencies": {
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+                                  "resolved": "https://registry.npmjs.org/mime-db/-/mime-db-1.12.0.tgz"
+                                }
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+                            }
+                          }
+                        },
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+                          "resolved": "https://registry.npmjs.org/formidable/-/formidable-1.0.14.tgz"
+                        },
+                        "methods": {
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+                          "resolved": "https://registry.npmjs.org/methods/-/methods-1.0.1.tgz"
+                        },
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+                          "resolved": "https://registry.npmjs.org/mime/-/mime-1.3.4.tgz"
+                        },
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+                        },
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+                          "resolved": "https://registry.npmjs.org/readable-stream/-/readable-stream-1.0.27-1.tgz",
+                          "dependencies": {
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+                              "resolved": "https://registry.npmjs.org/core-util-is/-/core-util-is-1.0.2.tgz"
+                            },
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+                            },
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+                        }
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+                  "resolved": "https://registry.npmjs.org/swagger-model-validator/-/swagger-model-validator-2.0.4.tgz"
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+              "from": "q@>=1.2.0 <2.0.0",
+              "resolved": "https://registry.npmjs.org/q/-/q-1.4.1.tgz"
+            },
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+              "version": "1.0.4",
+              "from": "tree-model@>=1.0.0 <2.0.0",
+              "resolved": "https://registry.npmjs.org/tree-model/-/tree-model-1.0.4.tgz",
+              "dependencies": {
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+                  "version": "0.0.1",
+                  "from": "find-insert-index@0.0.1",
+                  "resolved": "https://registry.npmjs.org/find-insert-index/-/find-insert-index-0.0.1.tgz"
+                },
+                "mergesort": {
+                  "version": "0.0.1",
+                  "from": "mergesort@0.0.1",
+                  "resolved": "https://registry.npmjs.org/mergesort/-/mergesort-0.0.1.tgz"
+                }
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+            }
+          }
+        },
+        "is-number": {
+          "version": "1.1.2",
+          "from": "is-number@>=1.1.2 <2.0.0",
+          "resolved": "https://registry.npmjs.org/is-number/-/is-number-1.1.2.tgz"
+        },
+        "lodash": {
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+          "from": "lodash@>=3.7.0 <4.0.0",
+          "resolved": "https://registry.npmjs.org/lodash/-/lodash-3.10.1.tgz"
+        },
+        "q": {
+          "version": "1.4.1",
+          "from": "q@>=1.2.0 <2.0.0",
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+        }
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     "growl": {
@@ -115,0 +569,0 @@ "version": "1.7.0",

package.json

 {
   "name": "gramene-bins-client",
-  "version": "2.2.8",
+  "version": "2.2.9",
   "description": "Provide API for working with gene distribution bins provided by data.gramene.org/genes",
@@ -5,0 +5,0 @@ "main": "index.js",

spec/bins/BinSpec.js

@@ -697,3 +697,11 @@ describe('Bins', function () {
 
+  it('should not fail if the bin with assignment fails to converge', function() {
+    var dodgyGenome = [{"_id":"GCA_000341285.1","db":"plants_rhodophyta1_collection_core_51_85_1","taxon_id":130081,"system_name":"galdieria_sulphuraria","type":"genome","length":180086,"regions":{"names":["Pt","UNANCHORED"],"lengths":[180086,104800334]},"num_genes":16564}];
+    var dodgyBins = binsGenerator(dodgyGenome);
 
+    // this used to be an infinite loop.
+    var dodgyMapper = dodgyBins.fixedBinMapper(1000);
+
+    expect(true).toBe(true);
+  });
 });

src/bins.js

@@ -211,3 +211,3 @@ 'use strict';
           var b = binSize;
-          while (countBins(a) != binsPerGenome) {
+          while (a != b && countBins(a) != binsPerGenome) {
             var m = Math.floor((a+b)/2);
@@ -214,0 +214,0 @@ var mbins = countBins(m);

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Improved metrics

Total package byte prevSize

1109550

increased by2.07%

Lines of code

37627

increased by1.24%

No dependency changes