2118

pending completion

Build # 2118

Build Type

push

travis-ci-com

Committed by

eweitz

Commit Message

Consolidate Gene Hints into Gene Leads

Run Details

1766 of 2271 branches covered (77.76%)

Branch coverage included in aggregate %.

6 of 6 new or added lines in 2 files covered. (100.0%)

4626 of 5173 relevant lines covered (89.43%)

34820.84 hits per line

Source File
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95.38

/src/js/init/init.js

/**
 * @fileoveriew Methods for initialization
 */

import {d3, slug} from '../lib';
import {configure} from './configure';
import {finishInit} from './finish-init';
import {writeContainer} from './write-container';
import {shouldFetchBands, fetchBands} from '../bands/fetch';
import {organismMetadata} from './organism-metadata';

function isHeterogameticChromosome(chrModel, chrIndex, ideo) {
  var ploidy = ideo.config.ploidy;
  return (
    'sex' in ideo.config &&
      (
        ploidy === 2 && ideo.sexChromosomes.index + 1 === chrIndex ||
        ideo.config.sex === 'female' && chrModel.name === 'Y'
      )
  );
}

function prepareChromosomes(bandsArray, chrs, taxid, ideo) {
  var j, bands, chromosome, chrModel, chrIndex;

  for (j = 0; j < chrs.length; j++) {
    chromosome = chrs[j];
    if (typeof bandsArray !== 'undefined') bands = bandsArray[j];

    chrIndex = j + ideo.config.taxids.indexOf(taxid);
    chrModel = ideo.getChromosomeModel(bands, chromosome, taxid, chrIndex);

    if (typeof chromosome !== 'string') {
      chromosome = chromosome.name.split(' ').slice(-1)[0].replace('chr', '');
    }

    ideo.chromosomes[taxid][chromosome] = chrModel;
    ideo.chromosomesArray.push(chrModel);

    if (isHeterogameticChromosome(chrModel, j, ideo)) continue;

    ideo.drawChromosome(chrModel);
  }
}

function setCoordinateSystem(chrs, ideo) {
  if (
    typeof chrBands !== 'undefined' &&
    chrs.length >= chrBands.length / 2
  ) {
    ideo.coordinateSystem = 'bp';
  }
}

/**
 * Configures chromosome data and calls downstream chromosome drawing functions
 */
function initDrawChromosomes() {
  var taxid, i, chrs, bandsArray,
    ideo = this,
    taxids = ideo.config.taxids;

  for (i = 0; i < taxids.length; i++) {
    taxid = taxids[i];
    chrs = ideo.config.chromosomes[taxid];

    bandsArray = ideo.bandsArray[taxid];

    if (!ideo.config.showNonNuclearChromosomes) {
      // Remove MT
      // TODO: Handle other non-nuclear chromosomes, e.g. CP, AP
      chrs = chrs.filter(chr => chr !== 'MT');
      if (typeof bandsArray !== 'undefined') {
        bandsArray = bandsArray.filter(bands => {
          return bands[0].chr !== 'MT';
        });
      }
    }

    setCoordinateSystem(chrs, ideo);

    ideo.chromosomes[taxid] = {};
    ideo.setSexChromosomes(chrs);

    prepareChromosomes(bandsArray, chrs, taxid, ideo);

    if (ideo.config.showBandLabels) ideo.drawBandLabels(ideo.chromosomes);
    ideo.handleRotateOnClick();
    ideo._gotChrModels = true; // Prevent issue with errant rat centromeres
  }
}

/**
 * Attach any click handlers to rotate and toggle chromosomes
 */
function handleRotateOnClick() {
  var ideo = this;

  if (!('rotatable' in ideo.config && ideo.config.rotatable === false)) {
    d3.selectAll(ideo.selector + ' .chromosome-set').on('click', function() {
      // Handles click on chromosome graphic or label.
      // Label click needed to toggle e.g. human MT
      const element = this.children[1];

      ideo.rotateAndToggleDisplay(element);
    });
  } else {
    d3.selectAll(ideo.selector).style('cursor', 'default');
  }
}

/**
 * Called when Ideogram has finished initializing.
 * Accounts for certain ideogram properties not being set until
 * asynchronous requests succeed, etc.
 */
function onLoad() {
  call(this.onLoadCallback);
}

function getBandFileName(taxid, accession, ideo) {
  var organism = ideo.organisms[taxid];
  var bandFileName = [slug(organism.scientificName)];
  var assemblies = organism.assemblies;
  var resolution = ideo.config.resolution;

  if (accession !== assemblies.default) {
    bandFileName.push(accession);
  }
  if (
    taxid === '9606' &&
    (accession in assemblies === 'false' &&
      Object.values(assemblies).includes(config.assembly) ||
      (resolution !== '' && resolution !== 850))
  ) {
    bandFileName.push(resolution);
  }

  bandFileName = bandFileName.join('-');

  var fullyBandedTaxids = ['9606', '10090', '10116'];
  if (fullyBandedTaxids.includes(taxid) && !ideo.config.showFullyBanded) {
    bandFileName += '-no-bands';
  }

  bandFileName += '.json';

  return bandFileName;
}

function getBandFileNames(taxid, bandFileNames, ideo) {
  var organism, assemblies, accession, bandFileName,
    config = ideo.config;

  organism = ideo.organisms[taxid];

  if (!config.assembly) ideo.config.assembly = 'default';

  assemblies = organism.assemblies;

  if (ideo.assemblyIsAccession()) {
    accession = config.assembly;
  } else {
    accession = assemblies[config.assembly];
  }

  bandFileName = getBandFileName(taxid, accession, ideo);
  var isCustomOrganism = taxid === '-1';

  if (taxid in ideo.organismsWithBands || isCustomOrganism) {
    bandFileNames[taxid] = bandFileName;
  }
  return bandFileNames;
}

function prepareContainer(taxid, bandFileNames, t0, ideo) {

  if (shouldFetchBands(bandFileNames, taxid, ideo)) {
    return fetchBands(bandFileNames, taxid, t0, ideo).then(function() {
      return ideo.processBandData(taxid);
    });
  } else {
    return new Promise(function(resolve) {
      ideo.processBandData(taxid);
      resolve([taxid, undefined]);
    });
  }
}

function initializeTaxids(ideo) {
  return new Promise(function(resolve) {
    var organism = ideo.config.organism;
    if (typeof organism === 'number') {
      // 'organism' is a taxid, e.g. 9606
      ideo.getOrganismFromEutils(organism, function() {
        ideo.getTaxids(resolve);
      });
    } else {
      ideo.getTaxids(resolve);
    }

  });
}

function getBandsAndPrepareContainer(taxids, t0, ideo) {
  var bandFileNames, i, taxid,
    promises = [];

  bandFileNames = {};
  for (taxid in organismMetadata) {
    bandFileNames[taxid] = '';
  }

  for (i = 0; i < taxids.length; i++) {
    taxid = String(taxids[i]);
    bandFileNames = getBandFileNames(taxid, bandFileNames, ideo);
    promises.push(prepareContainer(taxid, bandFileNames, t0, ideo));
  }

  Promise.all(promises).then(function(taxidsAndBandsArrays) {
    var taxidAndBandsArray, taxid, bandsArray;

    for (i = 0; i < taxidsAndBandsArrays.length; i++) {
      taxidAndBandsArray = taxidsAndBandsArrays[i];
      taxid = taxidAndBandsArray[0];
      bandsArray = taxidAndBandsArray[1];

      if ('bandsArray' in ideo === false) {
        ideo.bandsArray = {};
      }

      ideo.bandsArray[taxid] = bandsArray;
    }
    ideo.writeContainer(t0);
  });
}

/**
 * Initializes an ideogram.
 * Sets some high-level properties based on instance configuration,
 * fetches band and annotation data if needed, and
 * writes an SVG element to the document to contain the ideogram
 */
// Prevents race condition when init is called multiple times in
// quick succession.
// See https://github.com/eweitz/ideogram/pull/154.
var ideoNext = {};
var ideoQueued = {};
var ideoWait = {};

function init(ideo) {
  ideo = ideo || this;
  var containerId = ideo.config.container;

  if (ideoWait[containerId]) {
    ideoQueued[containerId] = true;
    ideoNext[containerId] = ideo;
  } else {
    ideoWait[containerId] = true;
    initializeTaxids(ideo)
      .then(function(taxids) {

        var taxid = taxids[0];
        ideo.config.taxid = taxid;
        ideo.config.taxids = taxids;

        ideo.organismScientificName =
          ideo.getScientificName(ideo.config.taxid);

        var t0 = new Date().getTime();
        getBandsAndPrepareContainer(taxids, t0, ideo);

        ideoWait[containerId] = false;
        if (ideoQueued[containerId]) {
          ideoQueued[containerId] = false;
          init(ideoNext[containerId]);
        }
      });
  }
}

export {
  configure, initDrawChromosomes, handleRotateOnClick,
  onLoad, init, finishInit, writeContainer
};

1	/**
2	* @fileoveriew Methods for initialization
3	*/
4
5	import {d3, slug} from '../lib';
6	import {configure} from './configure';
7	import {finishInit} from './finish-init';
8	import {writeContainer} from './write-container';
9	import {shouldFetchBands, fetchBands} from '../bands/fetch';
10	import {organismMetadata} from './organism-metadata';
11
12	function isHeterogameticChromosome(chrModel, chrIndex, ideo) {
13	var ploidy = ideo.config.ploidy;	1,751✔
14	return (	1,751✔
15	'sex' in ideo.config &&	2,032✔
16	(
17	ploidy === 2 && ideo.sexChromosomes.index + 1 === chrIndex \|\|
18	ideo.config.sex === 'female' && chrModel.name === 'Y'
19	)
20	);
21	}
22
23	function prepareChromosomes(bandsArray, chrs, taxid, ideo) {
24	var j, bands, chromosome, chrModel, chrIndex;
25
26	for (j = 0; j < chrs.length; j++) {	89✔
27	chromosome = chrs[j];	1,751✔
28	if (typeof bandsArray !== 'undefined') bands = bandsArray[j];	1,751✔
29
30	chrIndex = j + ideo.config.taxids.indexOf(taxid);	1,751✔
31	chrModel = ideo.getChromosomeModel(bands, chromosome, taxid, chrIndex);	1,751✔
32
33	if (typeof chromosome !== 'string') {	1,751✔
34	chromosome = chromosome.name.split(' ').slice(-1)[0].replace('chr', '');	32✔
35	}
36
37	ideo.chromosomes[taxid][chromosome] = chrModel;	1,751✔
38	ideo.chromosomesArray.push(chrModel);	1,751✔
39
40	if (isHeterogameticChromosome(chrModel, j, ideo)) continue;	1,751✔
41
42	ideo.drawChromosome(chrModel);	1,748✔
43	}
44	}
45
46	function setCoordinateSystem(chrs, ideo) {
47	if (	89✔
48	typeof chrBands !== 'undefined' &&	177✔
49	chrs.length >= chrBands.length / 2
50	) {
51	ideo.coordinateSystem = 'bp';	25✔
52	}
53	}
54
55	/**
56	* Configures chromosome data and calls downstream chromosome drawing functions
57	*/
58	function initDrawChromosomes() {
59	var taxid, i, chrs, bandsArray,
60	ideo = this,	83✔
61	taxids = ideo.config.taxids;	83✔
62
63	for (i = 0; i < taxids.length; i++) {	83✔
64	taxid = taxids[i];	89✔
65	chrs = ideo.config.chromosomes[taxid];	89✔
66
67	bandsArray = ideo.bandsArray[taxid];	89✔
68
69	if (!ideo.config.showNonNuclearChromosomes) {	89✔
70	// Remove MT
71	// TODO: Handle other non-nuclear chromosomes, e.g. CP, AP
72	chrs = chrs.filter(chr => chr !== 'MT');	1,730✔
73	if (typeof bandsArray !== 'undefined') {	86✔
74	bandsArray = bandsArray.filter(bands => {	85✔
75	return bands[0].chr !== 'MT';	1,698✔
76	});
77	}
78	}
79
80	setCoordinateSystem(chrs, ideo);	89✔
81
82	ideo.chromosomes[taxid] = {};	89✔
83	ideo.setSexChromosomes(chrs);	89✔
84
85	prepareChromosomes(bandsArray, chrs, taxid, ideo);	89✔
86
87	if (ideo.config.showBandLabels) ideo.drawBandLabels(ideo.chromosomes);	89✔
88	ideo.handleRotateOnClick();	89✔
89	ideo._gotChrModels = true; // Prevent issue with errant rat centromeres	89✔
90	}
91	}
92
93	/**
94	* Attach any click handlers to rotate and toggle chromosomes
95	*/
96	function handleRotateOnClick() {
97	var ideo = this;	95✔
98
99	if (!('rotatable' in ideo.config && ideo.config.rotatable === false)) {	95✔
100	d3.selectAll(ideo.selector + ' .chromosome-set').on('click', function() {	80✔
101	// Handles click on chromosome graphic or label.
102	// Label click needed to toggle e.g. human MT
103	const element = this.children[1];	9✔
104
105	ideo.rotateAndToggleDisplay(element);	9✔
106	});
107	} else {
108	d3.selectAll(ideo.selector).style('cursor', 'default');	15✔
109	}
110	}
111
112	/**
113	* Called when Ideogram has finished initializing.
114	* Accounts for certain ideogram properties not being set until
115	* asynchronous requests succeed, etc.
116	*/
117	function onLoad() {
118	call(this.onLoadCallback);	×
119	}
120
121	function getBandFileName(taxid, accession, ideo) {
122	var organism = ideo.organisms[taxid];	90✔
123	var bandFileName = [slug(organism.scientificName)];	90✔
124	var assemblies = organism.assemblies;	90✔
125	var resolution = ideo.config.resolution;	90✔
126
127	if (accession !== assemblies.default) {	90✔
128	bandFileName.push(accession);	8✔
129	}
130	if (	90✔
131	taxid === '9606' &&	230!
132	(accession in assemblies === 'false' &&
133	Object.values(assemblies).includes(config.assembly) \|\|
134	(resolution !== '' && resolution !== 850))
135	) {
136	bandFileName.push(resolution);	4✔
137	}
138
139	bandFileName = bandFileName.join('-');	90✔
140
141	var fullyBandedTaxids = ['9606', '10090', '10116'];	90✔
142	if (fullyBandedTaxids.includes(taxid) && !ideo.config.showFullyBanded) {	90✔
143	bandFileName += '-no-bands';	14✔
144	}
145
146	bandFileName += '.json';	90✔
147
148	return bandFileName;	90✔
149	}
150
151	function getBandFileNames(taxid, bandFileNames, ideo) {
152	var organism, assemblies, accession, bandFileName,
153	config = ideo.config;	90✔
154
155	organism = ideo.organisms[taxid];	90✔
156
157	if (!config.assembly) ideo.config.assembly = 'default';	90✔
158
159	assemblies = organism.assemblies;	90✔
160
161	if (ideo.assemblyIsAccession()) {	90✔
162	accession = config.assembly;	2✔
163	} else {
164	accession = assemblies[config.assembly];	88✔
165	}
166
167	bandFileName = getBandFileName(taxid, accession, ideo);	90✔
168	var isCustomOrganism = taxid === '-1';	90✔
169
170	if (taxid in ideo.organismsWithBands \|\| isCustomOrganism) {	90✔
171	bandFileNames[taxid] = bandFileName;	89✔
172	}
173	return bandFileNames;	90✔
174	}
175
176	function prepareContainer(taxid, bandFileNames, t0, ideo) {
177
178	if (shouldFetchBands(bandFileNames, taxid, ideo)) {	90✔
179	return fetchBands(bandFileNames, taxid, t0, ideo).then(function() {	89✔
180	return ideo.processBandData(taxid);	89✔
181	});
182	} else {
183	return new Promise(function(resolve) {	1✔
184	ideo.processBandData(taxid);	1✔
185	resolve([taxid, undefined]);	1✔
186	});
187	}
188	}
189
190	function initializeTaxids(ideo) {
191	return new Promise(function(resolve) {	84✔
192	var organism = ideo.config.organism;	84✔
193	if (typeof organism === 'number') {	84✔
194	// 'organism' is a taxid, e.g. 9606
195	ideo.getOrganismFromEutils(organism, function() {	1✔
196	ideo.getTaxids(resolve);	1✔
197	});
198	} else {
199	ideo.getTaxids(resolve);	83✔
200	}
201
202	});
203	}
204
205	function getBandsAndPrepareContainer(taxids, t0, ideo) {
206	var bandFileNames, i, taxid,
207	promises = [];	84✔
208
209	bandFileNames = {};	84✔
210	for (taxid in organismMetadata) {	84✔
211	bandFileNames[taxid] = '';	2,520✔
212	}
213
214	for (i = 0; i < taxids.length; i++) {	84✔
215	taxid = String(taxids[i]);	90✔
216	bandFileNames = getBandFileNames(taxid, bandFileNames, ideo);	90✔
217	promises.push(prepareContainer(taxid, bandFileNames, t0, ideo));	90✔
218	}
219
220	Promise.all(promises).then(function(taxidsAndBandsArrays) {	84✔
221	var taxidAndBandsArray, taxid, bandsArray;
222
223	for (i = 0; i < taxidsAndBandsArrays.length; i++) {	84✔
224	taxidAndBandsArray = taxidsAndBandsArrays[i];	90✔
225	taxid = taxidAndBandsArray[0];	90✔
226	bandsArray = taxidAndBandsArray[1];	90✔
227
228	if ('bandsArray' in ideo === false) {	90✔
229	ideo.bandsArray = {};	84✔
230	}
231
232	ideo.bandsArray[taxid] = bandsArray;	90✔
233	}
234	ideo.writeContainer(t0);	84✔
235	});
236	}
237
238	/**
239	* Initializes an ideogram.
240	* Sets some high-level properties based on instance configuration,
241	* fetches band and annotation data if needed, and
242	* writes an SVG element to the document to contain the ideogram
243	*/
244	// Prevents race condition when init is called multiple times in
245	// quick succession.
246	// See https://github.com/eweitz/ideogram/pull/154.
247	var ideoNext = {};	1✔
248	var ideoQueued = {};	1✔
249	var ideoWait = {};	1✔
250
251	function init(ideo) {
252	ideo = ideo \|\| this;	84✔
253	var containerId = ideo.config.container;	84✔
254
255	if (ideoWait[containerId]) {	84!
256	ideoQueued[containerId] = true;	×
257	ideoNext[containerId] = ideo;	×
258	} else {
259	ideoWait[containerId] = true;	84✔
260	initializeTaxids(ideo)	84✔
261	.then(function(taxids) {
262
263	var taxid = taxids[0];	84✔
264	ideo.config.taxid = taxid;	84✔
265	ideo.config.taxids = taxids;	84✔
266
267	ideo.organismScientificName =	84✔
268	ideo.getScientificName(ideo.config.taxid);
269
270	var t0 = new Date().getTime();	84✔
271	getBandsAndPrepareContainer(taxids, t0, ideo);	84✔
272
273	ideoWait[containerId] = false;	84✔
274	if (ideoQueued[containerId]) {	84!
275	ideoQueued[containerId] = false;	×
276	init(ideoNext[containerId]);	×
277	}
278	});
279	}
280	}
281
282	export {
283	configure, initDrawChromosomes, handleRotateOnClick,
284	onLoad, init, finishInit, writeContainer
285	};

eweitz / ideogram / 2118

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