Replace equalArrays with lodash.isEqual

scripts/get-data.sh

@@ -1,17 +1,83 @@
 #!/bin/bash
 
 data_files=(
-  "entropy-test-data_hepB.json" \
-  "entropy-test-data_ncov.json" \
+  "dengue_all.json" "dengue_denv1.json" "dengue_denv2.json" "dengue_denv3.json" "dengue_denv4.json"\
+  "ebola.json" "ebola_root-sequence.json" \
+  "ebola_2019-09-14-no-epi-id_meta.json" "ebola_2019-09-14-no-epi-id_tree.json" \
+  "lassa_s_tree.json" "lassa_s_meta.json" \
+  "lassa_l_tree.json" "lassa_l_meta.json" \
+  "measles.json" \
+  "mers_tree.json" "mers_meta.json" \
+  "mumps_global.json" "mumps_na.json" \
+  "WNV_NA_tree.json" "WNV_NA_meta.json" \
   "zika.json" \
-  "monkeypox_mpxv.json" \
+  "tb_global_meta.json" "tb_global_tree.json" \
+  "enterovirus_d68_genome_meta.json" "enterovirus_d68_genome_tree.json" \
+  "enterovirus_d68_vp1_meta.json" "enterovirus_d68_vp1_tree.json" \
+  ##############              AVIAN FLU           ##############
+  "flu_avian_h7n9_ha.json" \
+  "flu_avian_h7n9_mp.json" \
+  "flu_avian_h7n9_na.json" \
+  "flu_avian_h7n9_np.json" \
+  "flu_avian_h7n9_ns.json" \
+  "flu_avian_h7n9_pa.json" \
+  "flu_avian_h7n9_pb1.json" \
+  "flu_avian_h7n9_pb2.json" \
+  ##############              SEASONAL FLU           ##############
+  "flu_seasonal_h3n2_ha_2y.json" "flu_seasonal_h3n2_ha_2y_tip-frequencies.json" \
+  "flu_seasonal_h3n2_ha_3y.json" "flu_seasonal_h3n2_ha_3y_tip-frequencies.json" \
+  "flu_seasonal_h3n2_ha_6y.json" "flu_seasonal_h3n2_ha_6y_tip-frequencies.json" \
+  "flu_seasonal_h3n2_ha_12y.json" "flu_seasonal_h3n2_ha_12y_tip-frequencies.json" \
+  "flu_seasonal_h3n2_na_2y.json" "flu_seasonal_h3n2_na_2y_tip-frequencies.json" \
+  "flu_seasonal_h3n2_na_3y.json" "flu_seasonal_h3n2_na_3y_tip-frequencies.json" \
+  "flu_seasonal_h3n2_na_6y.json" "flu_seasonal_h3n2_na_6y_tip-frequencies.json" \
+  "flu_seasonal_h3n2_na_12y.json" "flu_seasonal_h3n2_na_12y_tip-frequencies.json" \
+  "flu_seasonal_h1n1pdm_ha_2y.json" "flu_seasonal_h1n1pdm_ha_2y_tip-frequencies.json" \
+  "flu_seasonal_h1n1pdm_ha_3y.json" "flu_seasonal_h1n1pdm_ha_3y_tip-frequencies.json" \
+  "flu_seasonal_h1n1pdm_ha_6y.json" "flu_seasonal_h1n1pdm_ha_6y_tip-frequencies.json" \
+  "flu_seasonal_h1n1pdm_ha_12y.json" "flu_seasonal_h1n1pdm_ha_12y_tip-frequencies.json" \
+  "flu_seasonal_h1n1pdm_ha_pandemic_meta.json" "flu_seasonal_h1n1pdm_ha_pandemic_tree.json" "flu_seasonal_h1n1pdm_ha_pandemic_tip-frequencies.json" \
+  "flu_seasonal_h1n1pdm_na_2y.json" "flu_seasonal_h1n1pdm_na_2y_tip-frequencies.json" \
+  "flu_seasonal_h1n1pdm_na_3y.json" "flu_seasonal_h1n1pdm_na_3y_tip-frequencies.json" \
+  "flu_seasonal_h1n1pdm_na_6y.json" "flu_seasonal_h1n1pdm_na_6y_tip-frequencies.json" \
+  "flu_seasonal_h1n1pdm_na_12y.json" "flu_seasonal_h1n1pdm_na_12y_tip-frequencies.json" \
+  "flu_seasonal_h1n1pdm_na_pandemic_tree.json" "flu_seasonal_h1n1pdm_na_pandemic_meta.json" "flu_seasonal_h1n1pdm_na_pandemic_tip-frequencies.json" \
+  "flu_seasonal_vic_ha_2y.json" "flu_seasonal_vic_ha_2y_tip-frequencies.json" "flu_seasonal_vic_ha_2y_root-sequence.json" \
+  "flu_seasonal_vic_ha_3y.json" "flu_seasonal_vic_ha_3y_tip-frequencies.json" "flu_seasonal_vic_ha_3y_root-sequence.json" \
+  "flu_seasonal_vic_ha_6y.json" "flu_seasonal_vic_ha_6y_tip-frequencies.json" "flu_seasonal_vic_ha_6y_root-sequence.json" \
+  "flu_seasonal_vic_ha_12y.json" "flu_seasonal_vic_ha_12y_tip-frequencies.json" "flu_seasonal_vic_ha_12y_root-sequence.json" \
+  "flu_seasonal_vic_na_2y.json" "flu_seasonal_vic_na_2y_tip-frequencies.json" "flu_seasonal_vic_na_2y_root-sequence.json" \
+  "flu_seasonal_vic_na_3y.json" "flu_seasonal_vic_na_3y_tip-frequencies.json" "flu_seasonal_vic_na_3y_root-sequence.json" \
+  "flu_seasonal_vic_na_6y.json" "flu_seasonal_vic_na_6y_tip-frequencies.json" "flu_seasonal_vic_na_6y_root-sequence.json" \
+  "flu_seasonal_vic_na_12y.json" "flu_seasonal_vic_na_12y_tip-frequencies.json" "flu_seasonal_vic_na_12y_root-sequence.json" \
+  "flu_seasonal_yam_ha_2y.json" "flu_seasonal_yam_ha_2y_tip-frequencies.json" "flu_seasonal_yam_ha_2y_root-sequence.json" \
+  "flu_seasonal_yam_ha_3y.json" "flu_seasonal_yam_ha_3y_tip-frequencies.json" "flu_seasonal_yam_ha_3y_root-sequence.json" \
+  "flu_seasonal_yam_ha_6y.json" "flu_seasonal_yam_ha_6y_tip-frequencies.json" "flu_seasonal_yam_ha_6y_root-sequence.json" \
+  "flu_seasonal_yam_ha_12y.json" "flu_seasonal_yam_ha_12y_tip-frequencies.json" "flu_seasonal_yam_ha_12y_root-sequence.json" \
+  "flu_seasonal_yam_na_2y.json" "flu_seasonal_yam_na_2y_tip-frequencies.json" "flu_seasonal_yam_na_2y_root-sequence.json" \
+  "flu_seasonal_yam_na_3y.json" "flu_seasonal_yam_na_3y_tip-frequencies.json" "flu_seasonal_yam_na_3y_root-sequence.json" \
+  "flu_seasonal_yam_na_6y.json" "flu_seasonal_yam_na_6y_tip-frequencies.json" "flu_seasonal_yam_na_6y_root-sequence.json" \
+  "flu_seasonal_yam_na_12y.json" "flu_seasonal_yam_na_12y_tip-frequencies.json" "flu_seasonal_yam_na_12y_root-sequence.json" \
+  ##############            LATEST CORE SARS-CoV-2 (COVID-19) BUILDS            ##############
+  "ncov_gisaid_global.json" "ncov_gisaid_global_tip-frequencies.json" \
+  "ncov_gisaid_africa.json" "ncov_gisaid_africa_tip-frequencies.json" \
+  "ncov_gisaid_asia.json" "ncov_gisaid_asia_tip-frequencies.json" \
+  "ncov_gisaid_europe.json" "ncov_gisaid_europe_tip-frequencies.json" \
+  "ncov_gisaid_north-america.json" "ncov_gisaid_north-america_tip-frequencies.json" \
+  "ncov_gisaid_oceania.json" "ncov_gisaid_oceania_tip-frequencies.json" \
+  "ncov_gisaid_south-america.json" "ncov_gisaid_south-america_tip-frequencies.json" \
+  ##############            TIMESTAMPED  SARS-CoV-2 BUILDS USED IN NARRATIVES           #############
+  "ncov_2020-01-23.json" "ncov_2020-01-25.json" "ncov_2020-01-26.json" "ncov_2020-01-30.json" \
+  "ncov_2020-03-04.json" "ncov_2020-03-05.json" "ncov_2020-03-11.json" "ncov_2020-03-13.json" \
+  "ncov_2020-03-20.json" "ncov_2020-03-27.json" "ncov_2020-04-03.json" \
+  "ncov_global_2020-04-09.json" "ncov_north-america_2020-04-17.json" \
 )
 
 rm -rf data/
 mkdir -p data/
 for i in "${data_files[@]}"
 do
-  curl http://staging.nextstrain.org/"${i}" --compressed -o data/"${i}"
+  curl http://data.nextstrain.org/"${i}" --compressed -o data/"${i}"
 done
 
 echo "Copying the test datasets from test/data to data"

src/actions/entropy.js

@@ -1,6 +1,6 @@
-import { debounce } from 'lodash';
+import { debounce, isEqual } from 'lodash';
 import { calcEntropyInView } from "../util/entropy";
-import { nucleotide_gene, equalArrays } from "../util/globals";
+import { nucleotide_gene } from "../util/globals";
 import * as types from "./types";
 import { isColorByGenotype, decodeColorByGenotype, getCdsFromGenotype} from "../util/getGenotype";
 
@@ -18,18 +18,18 @@ export const updateEntropyVisibility = debounce((dispatch, getState) => {
 }, 500, { leading: true, trailing: true });
 
 /**
- * Returns a thunk which makes zero or one dispatches to update the entropy reducer 
+ * Returns a thunk which makes zero or one dispatches to update the entropy reducer
  * if the selected CDS and/or positions need updating.
- * 
+ *
  * The argument may vary:
  *   - It may be a colorBy string, which may or may not be a genotype coloring
  *   - It may be a CDS (Object)
  *   - It may be the constant `nucleotide_gene`
- * 
+ *
  * The expected state updates to (selectedCds, selectedPositions) are as follows:
  * (nuc = nucleotide_gene, x,y,z are positions, [*] means any (or no) positions selected,
  * no-op means that no dispatches are made and thus the state is unchanged):
- * 
+ *
  * -----------------------------------------------------------------------------------
  * PREVIOUS STATE  | EXAMPLE ARGUMENT      |  NEW STATE ($ = entropy bar recalc needed)
  * -----------------------------------------------------------------------------------
@@ -49,13 +49,16 @@ export const updateEntropyVisibility = debounce((dispatch, getState) => {
  * CdsA, [*]       | CdsB                  | CdsB, [] $
  * CdsA, [*]       | nucleotide_gene       | nuc, [] $
  * -----------------------------------------------------------------------------------
- * 
+ *
  * @returns {ReduxThunk}
  */
 export const changeEntropyCdsSelection = (arg) => (dispatch, getState) => {
   const action = {type: types.CHANGE_ENTROPY_CDS_SELECTION}
   const entropy = getState().entropy;
 
+  // no-op if the entropy data isn't present
+  if (!entropy.loaded) return;
+
   if (arg === nucleotide_gene) {
     if (entropy.selectedCds === nucleotide_gene) {
       return
@@ -91,7 +94,7 @@ export const changeEntropyCdsSelection = (arg) => (dispatch, getState) => {
     const [data, maxYVal] = calcEntropyInView(state.tree.nodes, state.tree.visibility, action.selectedCds, entropy.showCounts);
     action.bars = data;
     action.maxYVal = maxYVal;
-  } else if (equalArrays(action.selectedPositions, entropy.selectedPositions)) {
+  } else if (isEqual(action.selectedPositions, entropy.selectedPositions)) {
     return;
   }
 

src/components/entropy/index.js

@@ -5,6 +5,7 @@ import { select } from "d3-selection";
 import { withTranslation } from "react-i18next";
 import 'd3-transition';
 import { FaInfoCircle } from "react-icons/fa";
+import { isEqual } from 'lodash';
 import Card from "../framework/card";
 import { changeColorBy } from "../../actions/colors";
 import { tabGroup, tabGroupMember, tabGroupMemberSelected } from "../../globalStyles";
@@ -13,7 +14,7 @@ import InfoPanel from "./infoPanel";
 import { changeEntropyCdsSelection, showCountsNotEntropy } from "../../actions/entropy";
 import { timerStart, timerEnd } from "../../util/perf";
 import { encodeColorByGenotype } from "../../util/getGenotype";
-import { nucleotide_gene, equalArrays } from "../../util/globals";
+import { nucleotide_gene } from "../../util/globals";
 import { getCdsByName } from "../../util/entropy";
 import { StyledTooltip } from "../controls/styles";
 import "../../css/entropy.css";
@@ -228,7 +229,7 @@ class Entropy extends React.Component {
       if (this.props.showCounts !== nextProps.showCounts) {
         updateParams.showCounts = nextProps.showCounts;
       }
-      if (!equalArrays(this.props.selectedPositions, nextProps.selectedPositions)) {
+      if (!isEqual(this.props.selectedPositions, nextProps.selectedPositions)) {
         updateParams.selectedPositions = nextProps.selectedPositions
       }
       if (Object.keys(updateParams).length) {

src/util/globals.js

@@ -247,5 +247,3 @@ const aminoAcids = {
 };
 
 export const getAminoAcidName = (x) => aminoAcids[x.toUpperCase()] || "Unknown";
-
-export const equalArrays = (a,b) => a.length===b.length && a.every((el, idx) => b[idx]===el);