Skip to content

Commit

Permalink
Merge pull request maximilianh#203 from mxposed/nick-dec-2020
Browse files Browse the repository at this point in the history 
A bunch of small fixes and improvements
  • Loading branch information
@maximilianh
maximilianh committed Dec 21, 2020
2 parents 6a2a0bb + 898cdef commit 182a259
Show file tree
Hide file tree
Showing 4 changed files with 321 additions and 273 deletions.
Binary file removed src/cbPyLib/RangeHTTPServer/__pycache__/__init__.cpython-37.pyc
View file
Binary file not shown.
90 changes: 45 additions & 45 deletions src/cbPyLib/cellbrowser/cbWeb/js/cbData.js
View file
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
// scDb: a class accessing single cell data from a URL
'use strict';
/*jshint globalstrict: true*/
/* jshint -W104 */ // allow some es6 parts (const)
/* jshint -W104 */ // allow some es6 parts (const)
/* jshint -W117 */ // ignore undefined classes

/* a module with some helper functions */
Expand Down Expand Up @@ -36,7 +36,7 @@ var cbUtil = (function () {
my.loadJson = function(url, onSuccess, silent) {
/* load json file from url and run onSuccess when done. Alert if it doesn't work. */
var req = jQuery.ajax({
"url" : url,
"url" : url,
type : "GET",
dataType : "json",
//mimeType : 'text/plain; charset=x-user-defined', // for local files, avoids errors
Expand All @@ -50,15 +50,15 @@ var cbUtil = (function () {
"contact the administrator of this server, "+
"or cells@ucsc.edu if this is running at UCSC. ");
else
alert("Could not load "+url);
alert("Could not load "+url);
onSuccess(null);
}
});
};

my.loadFile = function(url, arrType, onDone, onProgress, otherInfo, start, end) {
/* load text or binary file with HTTP GET into fileData variable and call function
* onDone(fileData, otherInfo) when done.
* onDone(fileData, otherInfo) when done.
* convert the data to arrType. arrType can be either a class like
* Uint8Array or the value 'string', for normal text or 'comprText'
* for gzip'ed string. To switch off type casting, set arrType=null
Expand Down Expand Up @@ -113,7 +113,7 @@ var cbUtil = (function () {
alert("Could not load "+url+", error " + oEvent.statusText);
return;
}

var binData = this.response;

if (!binData) {
Expand All @@ -123,7 +123,7 @@ var cbUtil = (function () {

// if the user wants only a byte range...
if (this._start!==undefined) {
// check if the expected length is OK. Some webservers don't support byte range
// check if the expected length is OK. Some webservers don't support byte range
// requests.
var expLength = this._end-this._start+1; // byte range is inclusive

Expand Down Expand Up @@ -164,7 +164,7 @@ var cbUtil = (function () {
var arr = pako.ungzip(binData);
// https://stackoverflow.com/questions/6965107/converting-between-strings-and-arraybuffers
// convert byte array to strin
// I used the apply() function originally, that's more compatible, but leads to a
// I used the apply() function originally, that's more compatible, but leads to a
// stack overflow in bigger datasets
//binData = String.fromCharCode.apply(null, arr);
var dec = new TextDecoder("utf-8");
Expand Down Expand Up @@ -241,17 +241,17 @@ var cbUtil = (function () {


function CbDbFile(url) {
// a class that loads all data from binary files loading for the cell browser:
// a class that loads all data from binary files loading for the cell browser:
// loading coordinates, loading meta data, resolve sample names to sample
// indices, resolve sample indices to sample names load meta for a given
// cell index
var self = this; // this has two conflicting meanings in javascript.
var self = this; // this has two conflicting meanings in javascript.
// we use 'self' to refer to object variables and 'this' to refer to the calling object

self.name = url;
self.url = url;
self.geneOffsets = null;
self.exprBinCount = 10;
self.exprBinCount = 10;

self.exprCache = {}; // cached compressed expression arrays
self.metaCache = {}; // cached compressed meta arrays
Expand Down Expand Up @@ -351,7 +351,7 @@ function CbDbFile(url) {
}
return null;
}

this.fieldNameToIndex = function(fieldName) {
/* given a meta field name, return its meta table index or null */
var idx = cbUtil.findIdxWhereEq(self.conf.metaFields, "name", fieldName);
Expand All @@ -366,21 +366,21 @@ function CbDbFile(url) {
var binUrl = cbUtil.joinPaths([self.url, "metaFields", fieldName+".bin.gz"]);
if (metaInfo.md5)
binUrl += "?"+metaInfo.md5;
cbUtil.loadFile(binUrl, arrType,
cbUtil.loadFile(binUrl, arrType,
onMetaDone,
onProgress, metaInfo);
}

this.loadMetaVec = function(metaInfo, onDone, onProgress, otherInfo) {
/* get an array of numbers, one per cell, that reflect the meta field contents
* and an object with some info about the field. call onDone(arr, metaInfo) when done.
* and an object with some info about the field. call onDone(arr, metaInfo) when done.
* Keep all compressed arrays in metaCache;
* Numerical meta data (int/float) is discretized, binning info is written to metaInfo.binInfo
* and the original data is added to metaInfo.origVals
* */

function onMetaDone(comprBytes, metaInfo) {
self.metaCache[metaInfo.name] = comprBytes;
self.metaCache[metaInfo.name] = comprBytes;
var ArrType = cbUtil.makeType(metaInfo.arrType);

var bytes = comprBytes; // some Apache/InternetBrowser combinations silently uncompress
Expand Down Expand Up @@ -448,18 +448,18 @@ function CbDbFile(url) {
var lineLen = cbUtil.baReadUint16(arr, 4);
// now get the line from the .tsv file
var url = cbUtil.joinPaths([self.url, "meta.tsv"]);
cbUtil.loadFile(url+"?"+cellIdx, "string", lineDone, onProgress, null,
cbUtil.loadFile(url+"?"+cellIdx, "string", lineDone, onProgress, null,
offset, offset+lineLen);
}

// chrome caching sometimes fails with byte range requests, so add cellidx to the URL
cbUtil.loadFile(url+"?"+cellIdx, Uint8Array, function(byteArr) { offsetDone(byteArr); },
cbUtil.loadFile(url+"?"+cellIdx, Uint8Array, function(byteArr) { offsetDone(byteArr); },
undefined, null, start, end);
};

function sortArrOfArr(arr, j) {
/* sort an array of arrays by the j-th element */
arr.sort(function(a, b) {
arr.sort(function(a, b) {
return a[j] > b[j] ? 1 : -1;
});
}
Expand All @@ -468,7 +468,7 @@ function CbDbFile(url) {
/* given an array of numbers, count how often each number appears.
* return an obj with two keys:
* - dArr is the new array with the index of each value
* - binInfo is an array with for each index a tuple of (value, value, count)
* - binInfo is an array with for each index a tuple of (value, value, count)
*/
// replace values in array with their enum-index
// -> make a mapping value -> bin
Expand Down Expand Up @@ -503,8 +503,8 @@ function CbDbFile(url) {
Find the bin index for the break defined by breakVals for every value in numVals.
The comparison uses "<=" ("left"). Also returns an array with the count for every bin.
*/
var dArr = new Uint8Array(numVals.length);

var dArr = new Uint8Array(numVals.length);
var binCounts = new Uint32Array(breakVals.length+1); // bin0 is a special bin, so +1

for (var i=0; i<numVals.length; i++) {
Expand All @@ -526,12 +526,12 @@ function CbDbFile(url) {
NaN is encoded in numVals as nanValues, which has to smaller than any other value.
Find the bin index for the break defined by breakVals for every value in numVals.
The comparison uses "<=" ("left").
The comparison uses "<=" ("left").
Also returns an array with the count for every bin.
*/
var dArr = new Uint8Array(numVals.length);

var dArr = new Uint8Array(numVals.length);
var binCounts = new Uint32Array(breakVals.length-1);
var breaks = breakVals.slice(2);

Expand Down Expand Up @@ -561,7 +561,7 @@ function CbDbFile(url) {
// From now on, we treat NAs/0s separately, so remove their counts
if (counts[0][0]===bin0Val) // NA is always first, as we defined it as -inf
counts.shift(); // remove first element

// make array of count-indices of the breaks
// e.g. if maxBinCount=10, breakPercs is [0.0, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9]
var breakPercs = [];
Expand All @@ -588,7 +588,7 @@ function CbDbFile(url) {
var breakVal = counts[breakIdx][0];
breakValues.push( breakVal );
}

var fb = findBins(arr, bin0Val, breakValues);
var dArr = fb.dArr;
var binCounts = fb.binCounts;
Expand Down Expand Up @@ -657,7 +657,7 @@ function CbDbFile(url) {
//# - len(descStr) bytes: the descriptive string descStr
//# - 132 bytes: 11 deciles, encoded as 11 * 3 floats (=min, max, count)
//# - array of n bytes, n = number of cells

// read the gene description
var descLen = cbUtil.baReadUint16(buf, 0);
var arr = buf.slice(2, 2+descLen);
Expand Down Expand Up @@ -691,7 +691,7 @@ function CbDbFile(url) {
if (geneSym in this.exprCache)
onGeneDone(this.exprCache[geneSym], geneSym);
else
cbUtil.loadFile(url+"?"+geneSym, Uint8Array, onGeneDone, onProgress, geneSym,
cbUtil.loadFile(url+"?"+geneSym, Uint8Array, onGeneDone, onProgress, geneSym,
start, end);
};

Expand All @@ -715,7 +715,7 @@ function CbDbFile(url) {
this.addCustomMetaField = function(metaInfo) {
//if (!self.customMeta)
//self.customMeta = [];
//self.customMeta.push(metaInfo);
//self.customMeta.push(metaInfo);
metaInfo.isCustom = true;
self.conf.metaFields.unshift(metaInfo);
}
Expand Down Expand Up @@ -746,7 +746,7 @@ function CbDbFile(url) {

var idList = [];
for (var i=0; i<idxArray.length; i++) {
var cellIdx = idxArray[i];
var cellIdx = idxArray[i];
idList.push(self.cellIds[cellIdx]);
}
return idList;
Expand Down Expand Up @@ -779,7 +779,7 @@ function CbDbFile(url) {
if (hasWildcards) {
var foundIds = {}; // = set = removes any duplicates
for (var i=0; i<findIds.length; i++) {
var searchId = findIds[i];
var searchId = findIds[i];
var searchRe = new RegExp(searchId);
var foundOne = false;
for (var cellIdx = 0; cellIdx<cellIds.length; cellIdx++) {
Expand All @@ -797,7 +797,7 @@ function CbDbFile(url) {
}
else {
for (let i=0; i<findIds.length; i++) {
let searchId = findIds[i];
let searchId = findIds[i];
var foundIdx = cellIds.indexOf(searchId);
if (foundIdx===-1)
notFoundIds.push(searchId);
Expand All @@ -815,7 +815,7 @@ function CbDbFile(url) {
onSearchDone(mapIdsToIdx(findIds));
}

if (self.cellIds===undefined)
if (self.cellIds===undefined)
// trigger the cellId load
self._startMetaLoad(self.getMetaFields()[0], "comprText", onIdsDone, onProgress)
else
Expand All @@ -842,12 +842,12 @@ function CbDbFile(url) {
var lineLen = cbUtil.baReadUint16(arr, 4);
// now get the line from the .tsv file
var url = cbUtil.joinPaths([self.url, "meta.tsv"]);
cbUtil.loadFile(url+"?"+cellIdx, "string", lineDone, onProgress, null,
cbUtil.loadFile(url+"?"+cellIdx, "string", lineDone, onProgress, null,
offset, offset+lineLen);
}

// chrome caching sometimes fails with byte range requests, so add cellidx to the URL
cbUtil.loadFile(url+"?"+cellIdx, Uint8Array, function(byteArr) { offsetDone(byteArr); },
cbUtil.loadFile(url+"?"+cellIdx, Uint8Array, function(byteArr) { offsetDone(byteArr); },
undefined, null, start, end);
};

Expand Down Expand Up @@ -875,12 +875,12 @@ function CbDbFile(url) {
var i;
while(lo <= hi) {
i = ((lo + hi) >> 1);
if(arr[i] >= find)
if(arr[i] >= find)
hi = i - 1;
else
//if (arr[i] < find)
//if (arr[i] < find)
lo = i + 1;
//else
//else
//{ return lo; }
}
return lo;
Expand All @@ -902,7 +902,7 @@ function CbDbFile(url) {
//# - len(descStr) bytes: the descriptive string descStr
//# - 132 bytes: 11 deciles, encoded as 11 * 3 floats (=min, max, count)
//# - array of n bytes, n = number of cells

// read the gene description
var descLen = cbUtil.baReadUint16(buf, 0);
var arr = buf.slice(2, 2+descLen);
Expand Down Expand Up @@ -936,7 +936,7 @@ function CbDbFile(url) {
if (geneSym in this.exprCache)
onGeneDone(this.exprCache[geneSym], geneSym);
else
cbUtil.loadFile(url+"?"+geneSym, Uint8Array, onGeneDone, onProgress, geneSym,
cbUtil.loadFile(url+"?"+geneSym, Uint8Array, onGeneDone, onProgress, geneSym,
start, end);
};

Expand Down Expand Up @@ -988,7 +988,7 @@ function CbDbFile(url) {
self.allMeta = {};

function doneMetaVec(arr, metaInfo, otherInfo) {
self.allMeta[metaInfo.name] = arr;
self.allMeta[metaInfo.name] = arr;
delete self.metaCache[fieldIdx];
}

Expand Down Expand Up @@ -1024,11 +1024,11 @@ function CbDbFile(url) {
}

self.loadExprAndDiscretize(
sym,
function(exprVec, discExprVec, geneSym, geneDesc, binInfo) {
sym,
function(exprVec, discExprVec, geneSym, geneDesc, binInfo) {
self.quickExpr[geneSym] = [discExprVec, geneDesc, binInfo];
loadCounter++;
if (loadCounter===geneSyms.length) onDone();
loadCounter++;
if (loadCounter===geneSyms.length) onDone();
},
onProgress);
}
Expand Down

0 comments on commit 182a259

Please sign in to comment.