Release/1.22.0 -> Master (#2635)

* PRTL-2543 add box plot table

* fix ClinicalVariableCard no data errors

* [PRTL-2459] Update References to Moved Properties for Pinwheel (#2516)

* Changed property as described.

* Updated version of tableColumns.

* Changed the return value of rehydrate

* Prtl 2528 biospecimen & clinical columns (#2540)

* eslint change

* alphabetize

* add table styling

* add constant for projects categories

* add conditions to table headers & columns

* add project link

* remove comment

* refactor/rename

* fix typo

* change file count to case count

* update table version

* 🐛 feature/PRTL-2550 fix small ranges (#2544)

* [PRTL-2568] Remove From Set - Default to Current Cohort (#2547)

* Added default set in removeSetModal; sort the list of sets.

* Added highlight for selected set.

* fix bug with p-value cut off in windows chrome (#2549)

* [PRTL-2580] histogram download (PR #2551)

* make css selector more specific for histogram svg/png function
* remove console log

* [PRT-2580] histogram improvements (PR #2553)

* add labels to histogram json

* possible fix for loading old set id

* [PRTL-2581] fix case removal of “_missing” and other values

Currently, when combining “_missing” and any other values creates a logical error in the query.

* [PRTL-2559] Create Modal Layout for Custom Categorical Binning (#2546)

* Added the GroupValuesModal and bins objects.

* Created function to update the group bins.

* Changed the way to get groupName

* Changed the modal based on feedback.

* Removed bins with empty key from customBins.

* Improved onclick function of '<<' button

* Create pull_request_template (#2560)

* Create pull_request_template

* change x-axis length from 8 to 10 (#2562)

* [PRTL-2545] add box plot package

* [PRTL-2582] add Synchronous Malignancy @ case entities

* [PRTL-2584] add Pack Years Smoked @ case entities

* [PRTL-2594] add tooltip to truncated tab label

* [PRTL-2547] add publications app shortcut

* [PRTL-2593] add box plot tooltips

* Prtl 2570 qq box viz download (#2569)

* wip using case_ssms

* collect qq data points for all clinical types

* reduce dropdown char limit to accommodate all caps

* watch filters prop to update plot

* PRTL-2537 qq slope, data download (#2548)

* wip calculate slope from q1 and q3

* truncate data, log values to test in R

* wip clip path for qqline

* download tsv button

* add json download

* fix runaway qqline

* fix bug with p-value cut off in windows chrome (#2550)

* PRTL-2580 [bug] histogram download (#2551)

* make css selector more specific for histogram svg/png function

* Prtl 2580 histogram improvements (#2553)

* add labels to histogram json

* [PRTL-2581] fix case removal of “_missing” and other values

Currently, when combining “_missing” and any other values creates a logical error in the query.

* add boxplot wrapper

* styling changes. fix qq resize and clip path.

* increase chart heights. add scroll action on cards with no data

* update boxplot package. set qq data for export.

* add styles for img export. some fixes for box resizing

* release/1.21.0 into develop. (#2538)

* version bump.

* [PRTL-2459] Update References to Moved Properties for Pinwheel (#2542)

* Changed property as described.

* fix api url (#2545)

* fix api url

* remove console.logs (#2563)

* revert UNSAFE method changes (#2570)

* [PRTL-2534] update schema with CIViC attributes.

* [PRTL-2534] add queries and view for civic data at gene and ssms entities

* 💄 enable cdave launch demo button (#2573)

* 💄Feature/PRTL-2585 style set action menu (#2572)

* 💄 styling for set action dropdown

* default border radius for dropdowns. positioning for bin dropdown

* [PRTL-2596] Binning UX/Styling Improvements (#2568)

* Added the GroupValuesModal and bins objects.

* Created function to update the group bins.

* Changed the way to get groupName

* Changed the modal based on feedback.

* Removed empty line.

* Removed bins with empty key from customBins.

* Removed console.

* Improved onclick function of '<<' button

* Added style to model.

* Updated the groupValuesModal.

* changed the warning message; added the numbers of data in hidden value list.

* Added outsideClickHandlerDisabled to false in GroupValuesModal.

* Sorted the binData before displaying it.

* Updated bins when setId and totalDocs number changes.

* Added warning after each group name. Changed toggleEditingAndSave function in EditableLabel.

* Created a new file to handle editable row in GroupValuesModal.

* Removed values that equal to 0 when switch cohort.

* Restored old editablelabel since I create a new one for groupvaluesmodal.

* Improved types. Added cardFilters variable.

* Fixed comments.

* removessss extra s'ssssss (#2576)

* removessss extra s'ssssss

* change condition syntax

* Changed reset function in groupValuesModal. (#2574)

* [PRTL-2610] Fix On Switch Cohort (#2577)

* Change the withPropsOnChange listener.

* 🚸PRTL-2603 default analysis name (#2579)

* 🚸 default analysis name to num set + 1

* update qq plot when data buckets change

* [PRTL-2566] Added Range to Continuous Binning Query (#2575)

* Added range in continuousAggregation.

* Added analysis colors for each category of buckets.

* Changed one of the color.

* Assign a default value to legend in survivalplotwrapper to prevent undefined error. (#2608)

* bump version

* Revert "Merge pull request #2571 from NCI-GDC/feature/PRTL-2534"

This reverts commit 79dfb87, reversing
changes made to 83a1759.

* 🐛 PRTL-2706 Fix incorrect string coercion (#2642)

.eslintrc.js

@@ -29,6 +29,7 @@ module.exports = {
     '@typescript-eslint',
     'react',
     'react-hooks',
+    'sort-destructure-keys'
     // 'jest'
   ],
   rules: {
@@ -42,7 +43,9 @@ module.exports = {
     }],
     'arrow-body-style': 'off',
     'arrow-parens': 'off',
-    'camelcase': 'warn',
+    'camelcase': ['warn', {
+      allow: ["^UNSAFE_", "doc_count", "^active_"],
+    }],
     'comma-dangle': ['warn', 'always-multiline'],
     'func-names': ['warn', 'as-needed'],
     'function-paren-newline': ['warn', 'consistent'],
@@ -88,6 +91,9 @@ module.exports = {
       commentPattern: 'break[\\s\\w]*omitted',
     }],
     'no-nested-ternary': 'off',
+    'no-unused-expressions': ['warn', {
+      allowShortCircuit: true,
+    }],
     'no-var': 'error', // Must use const or let.
     'object-property-newline': ['warn', {
       // allowAllPropertiesOnSameLine: false,
@@ -173,6 +179,9 @@ module.exports = {
     'react/sort-comp': 'warn',
     'react/sort-prop-types': 'error',
     'react/prop-types': 'off', // Disable prop-types as TS is used for type checking.
+    'sort-destructure-keys/sort-destructure-keys': ['warn', {
+      caseSensitive: false,
+    }],
     '@typescript-eslint/explicit-function-return-type': 'off', // Allows functional components, should be fixed soon: https://github.com/typescript-eslint/typescript-eslint/issues/149
     '@typescript-eslint/explicit-member-accessibility': 'off', // Allows not having to set public/private on class properties.
   },

.gitignore

@@ -3,20 +3,25 @@ logs
 *.log
 npm-debug.log*
 lerna-debug.log*
+yarn-debug.log*
 yarn-error.log*
 *.swp
 
 # Runtime data
 pids
+.env.local
+.env.development.local
+.env.test.local
+.env.production.local
 *.pid
 *.seed
 
-# Coverage directory used by tools like istanbul
+# Testing
 coverage
 
-# Dependency directories
-/node_modules
-/jspm_packages
+# Dependencies
+node_modules
+jspm_packages
 
 # Optional npm cache directory
 .npm
@@ -32,10 +37,13 @@ coverage
 *.iml
 .vscode/chrome
 
-# build folders
+# production folders
 dist
 build
 
 # OS
 .DS_Store
-__generated__
+__generated__
+
+#OncoJS development
+/src/packages/@oncojs

config-overrides.js

@@ -1,21 +1,29 @@
-const { injectBabelPlugin } = require("react-app-rewired");
+const { injectBabelPlugin } = require('react-app-rewired');
 
 module.exports = function override(config, env) {
   config = injectBabelPlugin(
     [
-      "import-inspector",
+      'import-inspector',
       {
         serverSideRequirePath: false,
-        webpackRequireWeakId: true
-      }
+        webpackRequireWeakId: true,
+      },
     ],
     config
   );
 
   config = injectBabelPlugin(
-    ["relay", { compat: true, schema: "data/schema.graphql" }],
+    [
+      'relay',
+      {
+        compat: true,
+        schema: 'data/schema.graphql',
+      },
+    ],
     config
   );
 
+  env === 'development' && (config.devtool = 'eval-source-map');
+
   return config;
 };