@sjcrh/proteinpaint-client 2.196.0 → 2.198.0

package/dist/chunk-M2G5R4WB.js

@@ -0,0 +1,142 @@
+import {
+  runproteinpaint
+} from "./chunk-VJ6UFVGC.js";
+
+// test/front.helpers.js
+var serverData = /* @__PURE__ */ Object.create(null);
+function getRunPp(appname = "", defaultArgs = {}, _host = "http://localhost:3000") {
+  const host = window.testHost || _host;
+  const arg = {
+    host: window.testHost || _host,
+    noheader: 1,
+    nobox: true,
+    debug: 1,
+    norecover: true
+  };
+  if (appname == "mass" || appname == "termdb") {
+    defaultArgs.debounceInterval = 0;
+  }
+  if (appname) arg[appname] = defaultArgs;
+  else copyMerge(arg, defaultArgs);
+  const argStr = JSON.stringify(arg);
+  return function runpp(overrides = {}) {
+    const argCopy = JSON.parse(argStr);
+    if (appname) copyMerge(argCopy[appname], overrides);
+    else copyMerge(argCopy, overrides);
+    if (appname && defaultArgs.fetchOpts) {
+      argCopy[appname].fetchOpts = defaultArgs.fetchOpts;
+    }
+    return runproteinpaint(Object.assign(argCopy, { serverData }));
+  };
+}
+function copyMerge(base, ...args) {
+  const target = typeof base == "string" ? JSON.parse(base) : base;
+  for (const arg of args) {
+    if (arg) {
+      const source = typeof base == "string" ? JSON.parse(JSON.stringify(arg)) : arg;
+      for (const key in source) {
+        if (!target[key] || Array.isArray(target[key]) || typeof target[key] !== "object") target[key] = source[key];
+        else copyMerge(target[key], source[key]);
+      }
+    }
+  }
+  return target;
+}
+function rideInit(opts = {}) {
+  const self = new Ride(opts);
+  const rideApi = {
+    // ride on the default event bus
+    to(callback, sub = {}) {
+      self.addToThen(callback, Object.assign({}, opts, sub));
+      return rideApi;
+    },
+    use(triggerFxn, sub = {}) {
+      self.addUseThen(triggerFxn, Object.assign({}, opts, sub));
+      return rideApi;
+    },
+    change(sub = {}) {
+      Object.assign(opts, sub);
+      return rideApi;
+    },
+    // run callback without using bus, with or without timeout
+    run(callback, after = 0) {
+      self.addRunThen(callback, after, opts);
+      return rideApi;
+    },
+    // close the event bus
+    done(test) {
+      if (opts.bus) self.resolved.then(() => opts.bus.on(opts.eventType, null));
+      self.resolved.then(() => {
+        test.end();
+        if (!opts.preserve && test._ok && opts.arg.Inner.app && typeof opts.arg.Inner.app.destroy == "function") {
+          opts.arg.Inner.app.destroy();
+        }
+      }).catch(console.log);
+      return rideApi;
+    }
+  };
+  return Object.freeze(rideApi);
+}
+var Ride = class {
+  // mutable but private access props and methods
+  // when used inside rideInit()
+  constructor(opts) {
+    this.validateOpts(opts);
+    this.resolved = Promise.resolve();
+  }
+  validateOpts(opts) {
+    try {
+      if (opts.eventType && !opts.bus) {
+        if (!opts.arg) throw "must specify opts.bus or opts.arg for rideInit() argument";
+        opts.bus = opts.arg;
+      }
+      if (opts.bus) {
+        if (typeof opts.eventType !== "string") throw "invalid default.eventType";
+        opts.bus.on(opts.eventType, null);
+        return opts;
+      }
+    } catch (e) {
+      console.log(e);
+    }
+  }
+  addToThen(callback, opts) {
+    this.resolved = this.resolved.then(async (triggerFxn) => {
+      opts.bus.on(opts.eventType, null);
+      return new Promise(async (resolve, reject) => {
+        opts.bus.on(opts.eventType, async () => {
+          await sleep(opts.wait);
+          callback(opts.arg);
+          resolve();
+        });
+        if (triggerFxn) await triggerFxn();
+      });
+    });
+  }
+  // prepare a trigger function for use in the pattern
+  // rideInit().use(triggerFxn).to(...)
+  //
+  // .use() enables setting a different opts.arg to be used for triggerFxn
+  //
+  addUseThen(triggerFxn, opts) {
+    this.resolved = this.resolved.then(async (prevTriggerFxn) => {
+      if (typeof prevTriggerFxn == "function") await prevTriggerFxn();
+      await sleep(isNaN(opts.wait) ? 0 : opts.wait);
+      return () => triggerFxn(opts.arg);
+    });
+  }
+  addRunThen(callback, after, opts) {
+    this.resolved = this.resolved.then(async () => {
+      await sleep(typeof after == "number" ? after : 0);
+      callback(opts.arg);
+    });
+  }
+};
+function sleep(ms) {
+  return new Promise((resolve) => setTimeout(resolve, ms));
+}
+
+export {
+  getRunPp,
+  rideInit
+};
+//# sourceMappingURL=chunk-M2G5R4WB.js.map

package/dist/chunk-M4TTGGT4.js

@@ -0,0 +1,102 @@
+import {
+  addGeneSearchbox,
+  first_genetrack_tolist,
+  getDNAMethUnit,
+  sayerror
+} from "./chunk-5VOPABBA.js";
+import {
+  Menu
+} from "./chunk-HYOEWQ5P.js";
+import {
+  DNA_METHYLATION
+} from "./chunk-I6WR4CG7.js";
+
+// termdb/handlers/dnaMethylation.ts
+var SearchHandler = class {
+  init(opts) {
+    this.opts = opts;
+    this.callback = opts.callback;
+    this.app = opts.app;
+    const holder = opts.holder.append("div").style("margin", "10px 0px");
+    this.dom = {};
+    this.dom.errDiv = holder.append("div").style("margin", "5px 0px").style("display", "none");
+    this.dom.geneSearchDiv = holder.append("div");
+    this.dom.blockDiv = holder.append("div").style("display", "none").style("margin", "15px 4px");
+    const geneSearch = addGeneSearchbox({
+      tip: new Menu({ padding: "0px" }),
+      genome: opts.genomeObj,
+      row: this.dom.geneSearchDiv,
+      callback: async () => {
+        try {
+          this.dom.errDiv.style("display", "none");
+          await this.handleGeneSearch(geneSearch);
+        } catch (e) {
+          this.dom.errDiv.style("display", "block");
+          sayerror(this.dom.errDiv, "Error: " + (e.message || e));
+          if (e.stack) console.log(e.stack);
+        }
+      }
+    });
+  }
+  async handleGeneSearch(geneSearch) {
+    if (geneSearch.geneSymbol) {
+      const { chr, start, stop } = geneSearch;
+      if (!chr || !Number.isInteger(start) || !Number.isInteger(stop))
+        throw new Error("unable to retrieve gene coordinate");
+      this.dom.blockDiv.selectAll("*").remove();
+      this.dom.blockDiv.style("display", "block");
+      this.dom.blockDiv.append("div").style("opacity", 0.6).text("Navigate genome browser to desired region");
+      const arg = {
+        holder: this.dom.blockDiv,
+        genome: this.opts.genomeObj,
+        // genome obj
+        chr,
+        start,
+        stop,
+        tklst: [],
+        nobox: true,
+        width: 500,
+        hidegenelegend: true,
+        debugmode: this.opts.debug
+      };
+      first_genetrack_tolist(this.opts.genomeObj, arg.tklst);
+      const _ = await import("./block-NBTCOT3H.js");
+      this.blockInstance = new _.Block(arg);
+      this.dom.submitBtn = this.dom.blockDiv.append("div").attr("data-testid", "sjpp-dnaMethylation-submitDiv").style("margin", "10px 0px").append("button").style("border", "none").style("border-radius", "20px").style("padding", "10px 15px").text("Submit Region").on("click", async () => {
+        const { chr: chr2, start: start2, stop: stop2 } = this.blockInstance.rglst[0];
+        const term = this.makeTerm({ chr: chr2, start: start2, stop: stop2 });
+        await this.callback(term);
+      });
+    } else if (geneSearch.chr && Number.isInteger(geneSearch.start) && Number.isInteger(geneSearch.stop)) {
+      const { chr } = geneSearch;
+      let { start, stop } = geneSearch;
+      if (geneSearch.actualposition?.len <= 1) {
+        start = geneSearch.actualposition.position;
+        stop = start + 1;
+      }
+      const term = this.makeTerm({ chr, start, stop });
+      await this.callback(term);
+    } else {
+      throw new Error("invalid gene search input");
+    }
+  }
+  makeTerm(opts) {
+    const { chr, start, stop } = opts;
+    if (!chr || !Number.isInteger(start) || !Number.isInteger(stop)) throw new Error("invalid coordinate");
+    const unit = getDNAMethUnit("region", this.app.vocabApi);
+    const term = {
+      chr,
+      start,
+      stop,
+      type: DNA_METHYLATION,
+      unit,
+      genomicFeatureType: "region"
+    };
+    return term;
+  }
+};
+
+export {
+  SearchHandler
+};
+//# sourceMappingURL=chunk-M4TTGGT4.js.map