auspice/src/actions/loadData.js

Web app for visualizing pathogen evolution

import queryString from "query-string";
import * as types from "./types";
import { charonAPIAddress } from "../util/globals";
import { goTo404 } from "./navigation";
import { createStateFromQueryOrJSONs, createTreeTooState } from "./recomputeReduxState";
import { loadFrequencies } from "./frequencies";
import { fetchJSON } from "../util/serverInteraction";
import { warningNotification } from "./notifications";
import { hasExtension, getExtension } from "../util/extensions";


/* TODO: make a default auspice server (not charon) and make charon the nextstrain server. Or vice versa. */
const serverAddress = hasExtension("serverAddress") ? getExtension("serverAddress") : charonAPIAddress;

const getDatasetFromCharon = (prefix, {type, narrative=false}={}) => {
  let path = `${serverAddress}/${narrative?"getNarrative":"getDataset"}`;
  path += `?prefix=${prefix}`;
  if (type) path += `&type=${type}`;

  const p = fetch(path)
    .then((res) => {
      if (res.status !== 200) {
        throw new Error(res.statusText);
      }
      return res;
    })
    .then((res) => res.json());
  return p;
};

const getHardcodedData = (prefix, {type="mainJSON", narrative=false}={}) => {
  /* we currently expect a single dataset to be present in "hardcodedDataPaths".
  This may be extended to multiple in the future... */
  const datapaths = getExtension("hardcodedDataPaths");
  console.log("FETCHING", datapaths[type]);
  const p = fetch(datapaths[type])
    .then((res) => {
      if (res.status !== 200) {
        throw new Error(res.statusText);
      }
      return res;
    })
    .then((res) => res.json());
  return p;
};

// const fetchData = hasExtension("hardcodedDataPaths") ? getHardcodedData : getDatasetFromCharon;
const getDataset = hasExtension("hardcodedDataPaths") ? getHardcodedData : getDatasetFromCharon;


const fetchDataAndDispatch = (dispatch, url, query, narrativeBlocks) => {
  let warning = false;
  let fetchExtras = "";
  /* currently we support backwards compatability with the old (deprecated) tt=... URL query
  syntax for defining the second tree. This is not guaranteed to stay around */
  if (query.tt) { /* deprecated form of adding a second tree */
    warning = {
      message: `Specifing a second tree via "tt=${query.tt}" is deprecated.`,
      details: "The URL has been updated to reflect the new syntax 🙂"
    };
    fetchExtras += `&deprecatedSecondTree=${query.tt}`;
  }


  // fetchJSON(`${charonAPIAddress}request=mainJSON&url=${url}${fetchExtras}`)
  getDataset(`${url}${fetchExtras}`)
    .then((json) => {
      dispatch({
        type: types.CLEAN_START,
        ...createStateFromQueryOrJSONs({json, query, narrativeBlocks})
      });
      return {
        frequencies: (json.meta.panels && json.meta.panels.indexOf("frequencies") !== -1)
      };
    })
    .then((result) => {
      if (result.frequencies === true) {
        getDataset(url, {type: "tip-frequencies"})
          .then((res) => dispatch(loadFrequencies(res)))
          .catch((err) => console.error("Frequencies failed to fetch", err.message));
      }
      return false;
    })
    .then(() => {
      /* Get available datasets -- this is needed for the sidebar dataset-change dropdowns etc */
      fetchJSON(`${charonAPIAddress}/getAvailable?prefix=${window.location.pathname}`)
        .then((res) => dispatch({type: types.SET_AVAILABLE, data: res}));
    })
    .catch((err) => {
      if (err.message === "No Content") { // status code 204
        /* TODO: add more helper functions for moving between pages in auspice */
        return dispatch({
          type: types.PAGE_CHANGE,
          displayComponent: "splash",
          pushState: true
        });
      }
      console.warn(err, err.message);
      dispatch(goTo404(`Couldn't load JSONs for ${url}`));
    });
  if (warning) {
    dispatch(warningNotification(warning));
  }
};

export const loadJSONs = ({url = window.location.pathname, search = window.location.search} = {}) => {
  return (dispatch, getState) => {
    const { tree } = getState();
    if (tree.loaded) {
      dispatch({type: types.DATA_INVALID});
    }
    const query = queryString.parse(search);

    if (url.indexOf("narratives") !== -1) {
      /* we want to have an additional fetch to get the narrative JSON, which in turn
      tells us which data JSON to fetch... */
      getDatasetFromCharon(url, {narrative: true})
        .then((blocks) => {
          const firstURL = blocks[0].dataset;
          const firstQuery = queryString.parse(blocks[0].query);
          if (query.n) firstQuery.n = query.n;
          fetchDataAndDispatch(dispatch, firstURL, firstQuery, blocks);
        })
        .catch((err) => {
          console.error("Error obtaining narratives", err.message);
          dispatch(goTo404(`Couldn't load narrative for ${url}`));
        });
    } else {
      fetchDataAndDispatch(dispatch, url, query);
    }
  };
};

export const loadTreeToo = (name, fields) => (dispatch, getState) => {
  const oldState = getState();
  getDataset(fields.join("/"), {type: "tree"})
    .then((json) => {
      const newState = createTreeTooState({treeTooJSON: json.tree, oldState, segment: name});
      dispatch({type: types.TREE_TOO_DATA, segment: name, ...newState});
    })
    .catch((err) => console.error("Failed to fetch additional tree", err.message));
};