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Improve the configuration dictionary for igv.js #18

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Improve the configuration dictionary for igv.js #18

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52626a8
initialized fixing a bug where igv.js can't take a normal configurati…
harrouet Feb 15, 2021
fbcbcee
cleaned the genome dict in the browser configuration - JS side
harrouet Feb 15, 2021
7b930b3
Fixed the generation of the igv browser in the JS side
harrouet Feb 16, 2021
4be7064
Removed all references to **widget_serialization_no_none
harrouet Feb 16, 2021
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13 changes: 6 additions & 7 deletions ipyigv/ipyigv.py
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Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,6 @@

from .options import *

from .utils import widget_serialization_no_none
from ._version import EXTENSION_VERSION

PUBLIC_GENOMES_FILE = os.path.join(os.path.dirname(__file__), 'public_genomes.json')
Expand Down Expand Up @@ -47,23 +46,23 @@ def __init__(self, **kwargs):
# Widget properties are defined as traitlets. Any property tagged with `sync=True`
# is automatically synced to the frontend *any* time it changes in Python.
# It is synced back to Python from the frontend *any* time the model is touched.
genome = InstanceDict(ReferenceGenome).tag(sync=True, **widget_serialization_no_none)
tracks = List(InstanceDict(Track)).tag(sync=True, **widget_serialization_no_none)
genome = InstanceDict(ReferenceGenome).tag(sync=True, **widget_serialization)
tracks = List(InstanceDict(Track)).tag(sync=True, **widget_serialization)
doubleClickDelay = Int(default_value=500).tag(sync=True)
flanking = Int(default_value=1000).tag(sync=True)
genomeList = Unicode(allow_none=True).tag(sync=True, **widget_serialization_no_none) # optional URL
locus = (Unicode() | List(Unicode())).tag(sync=True, **widget_serialization_no_none)
genomeList = Unicode(allow_none=True).tag(sync=True, **widget_serialization) # optional URL
locus = (Unicode() | List(Unicode())).tag(sync=True, **widget_serialization)
minimumBases = Int(default_value=40).tag(sync=True)
queryParametersSupported = Bool(default=False).tag(sync=True)
search = InstanceDict(SearchService, allow_none=True).tag(sync=True, **widget_serialization_no_none)
search = InstanceDict(SearchService, allow_none=True).tag(sync=True, **widget_serialization)
showAllChromosomes = Bool(default_value=True).tag(sync=True)
showAllChromosomeWidget = Bool(default_value=True).tag(sync=True)
showNavigation = Bool(default_value=True).tag(sync=True)
showSVGButton = Bool(default_value=False).tag(sync=True)
showRuler = Bool(default_value=True).tag(sync=True)
showCenterGuide = Bool(default_value=False).tag(sync=True)
# trackDefaults = # missing documentation
roi = List(InstanceDict(AnnotationTrack)).tag(sync=True, **widget_serialization_no_none) # regions of interest
roi = List(InstanceDict(AnnotationTrack)).tag(sync=True, **widget_serialization) # regions of interest
oauthToken = Unicode(allow_none = True).tag(sync=True)
apiKey = Unicode(allow_none = True).tag(sync=True)
clientId = Unicode(allow_none = True).tag(sync=True)
Expand Down
49 changes: 24 additions & 25 deletions ipyigv/options.py
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Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,6 @@
from ipywidgets.widgets.trait_types import Color, InstanceDict
from ipywidgets.widgets import widget

from .utils import widget_serialization_no_none
from ._version import EXTENSION_VERSION


Expand Down Expand Up @@ -143,11 +142,11 @@ class AnnotationTrack(Track):
nameField = Unicode(default_value = 'Name').tag(sync=True)
maxRows = Int (default_value = 500).tag(sync=True)
searchable = Bool(default_value=False).tag(sync=True)
filterTypes = List(Unicode, default_value=['chromosone', 'gene']).tag(sync=True, **widget_serialization_no_none)
filterTypes = List(Unicode, default_value=['chromosone', 'gene']).tag(sync=True, **widget_serialization)
color = Color("rgb(0,0,150)").tag(sync=True)
altColor = Color("rgb(0,0,150)").tag(sync=True)
colorBy = Instance(FieldColors, allow_none=True).tag(sync=True, **widget_serialization_no_none)
roi = List(InstanceDict(Track)).tag(sync=True, **widget_serialization_no_none) # regions of interest
colorBy = Instance(FieldColors, allow_none=True).tag(sync=True, **widget_serialization)
roi = List(InstanceDict(Track)).tag(sync=True, **widget_serialization) # regions of interest


@register
Expand Down Expand Up @@ -175,16 +174,16 @@ class AlignmentTrack(Track):
samplingDepth = Int(100).tag(sync=True)
alignmentRowHeight = Int(14).tag(sync=True)
readgroup = Unicode("RG").tag(sync=True)
sortOption = Instance(SortOption, allow_none=True).tag(sync=True, **widget_serialization_no_none)
sortOption = Instance(SortOption, allow_none=True).tag(sync=True, **widget_serialization)
showSoftClips = Bool(False).tag(sync=True)
showMismatches = Bool(True).tag(sync=True)

# Paired-end and mate-pair coloring options.
pairOrientation = Unicode(allow_none=True).tag(sync=True, **widget_serialization_no_none) # ff, fr, or rf
minFragmentLength = Int(allow_none=True).tag(sync=True, **widget_serialization_no_none)
maxFragmentLength = Int(allow_none=True).tag(sync=True, **widget_serialization_no_none)
pairOrientation = Unicode(allow_none=True).tag(sync=True, **widget_serialization) # ff, fr, or rf
minFragmentLength = Int(allow_none=True).tag(sync=True, **widget_serialization)
maxFragmentLength = Int(allow_none=True).tag(sync=True, **widget_serialization)

roi = List(InstanceDict(Track)).tag(sync=True, **widget_serialization_no_none) # regions of interest
roi = List(InstanceDict(Track)).tag(sync=True, **widget_serialization) # regions of interest


@register
Expand All @@ -203,7 +202,7 @@ class VariantTrack(Track):
squishedCallHeight = Int(1).tag(sync=True)
expandedCallHeight = Int(10).tag(sync=True)

roi = List(InstanceDict(Track)).tag(sync=True, **widget_serialization_no_none) # regions of interest
roi = List(InstanceDict(Track)).tag(sync=True, **widget_serialization) # regions of interest


class Guideline(HasTraits):
Expand All @@ -221,14 +220,14 @@ class WigTrack(Track):

type = Unicode('wig', read_only=True).tag(sync=True)
autoscale = Bool(True).tag(sync=True)
autoscaleGroup = Unicode(allow_none=True).tag(sync=True, **widget_serialization_no_none)
autoscaleGroup = Unicode(allow_none=True).tag(sync=True, **widget_serialization)
min = Int(0).tag(sync=True)
max = Int(allow_none=True).tag(sync=True, **widget_serialization_no_none)
max = Int(allow_none=True).tag(sync=True, **widget_serialization)
color = Color(default_value="rgb(150, 150, 150)").tag(sync=True)
altColor = Color(allow_none=True).tag(sync=True, **widget_serialization_no_none)
guideLines = List(trait=Instance(Guideline), allow_none=True).tag(sync=True, **widget_serialization_no_none)
altColor = Color(allow_none=True).tag(sync=True, **widget_serialization)
guideLines = List(trait=Instance(Guideline), allow_none=True).tag(sync=True, **widget_serialization)

roi = List(InstanceDict(Track)).tag(sync=True, **widget_serialization_no_none) # regions of interest
roi = List(InstanceDict(Track)).tag(sync=True, **widget_serialization) # regions of interest


@register
Expand All @@ -239,11 +238,11 @@ class SegTrack(Track):
"""

type = Unicode('seg', read_only=True).tag(sync=True)
isLog = Bool(allow_none=True).tag(sync=True, **widget_serialization_no_none)
isLog = Bool(allow_none=True).tag(sync=True, **widget_serialization)
displayMode = Unicode("EXPANDED").tag(sync=True) # "EXPANDED", "SQUISHED", or "FILL"
sort = InstanceDict(SortOrder).tag(sync=True, **widget_serialization)

roi = List(InstanceDict(Track)).tag(sync=True, **widget_serialization_no_none) # regions of interest
roi = List(InstanceDict(Track)).tag(sync=True, **widget_serialization) # regions of interest


@register
Expand All @@ -263,19 +262,19 @@ class SpliceJunctionsTrack(Track):
labelMultiMappedReadCount = Bool(True).tag(sync=True)
labelTotalReadCount = Bool(False).tag(sync=True)
labelMotif = Bool(False).tag(sync=True)
labelAnnotatedJunction = Unicode(allow_none=True).tag(sync=True, **widget_serialization_no_none)
labelAnnotatedJunction = Unicode(allow_none=True).tag(sync=True, **widget_serialization)

# Filtering Options
minUniquelyMappedReads = Int(0).tag(sync=True)
minTotalReads = Int(0).tag(sync=True)
maxFractionMultiMappedReads = Int(1).tag(sync=True)
minSplicedAlignmentOverhang = Int(0).tag(sync=True)
hideStrand = Unicode(allow_none=True).tag(sync=True, **widget_serialization_no_none) # None, "+" or "-"
hideStrand = Unicode(allow_none=True).tag(sync=True, **widget_serialization) # None, "+" or "-"
hideAnnotatedJunctions = Bool(False).tag(sync=True)
hideUnannotatedJunctions = Bool(False).tag(sync=True)
hideMotifs = List(Unicode).tag(sync=True, **widget_serialization)

roi = List(InstanceDict(Track)).tag(sync=True, **widget_serialization_no_none) # regions of interest
roi = List(InstanceDict(Track)).tag(sync=True, **widget_serialization) # regions of interest


@register
Expand All @@ -291,9 +290,9 @@ class GwasTrack (Track):
# format = Unicode().tag(sync=True) # 'bed' or 'gwas' - format is already in Track -> validation only
posteriorProbability = Bool(False).tag(sync=True)
dotSize = Int(3).tag(sync=True)
columns = Dict(key_trait=Unicode, value_trait=Int, allow_none=True).tag(sync=True, **widget_serialization_no_none)
columns = Dict(key_trait=Unicode, value_trait=Int, allow_none=True).tag(sync=True, **widget_serialization)

roi = List(InstanceDict(Track)).tag(sync=True, **widget_serialization_no_none) # regions of interest
roi = List(InstanceDict(Track)).tag(sync=True, **widget_serialization) # regions of interest


@register
Expand All @@ -307,7 +306,7 @@ class InteractionTrack (Track):
arcOrientation = Bool(True).tag(sync=True)
thickness = Int(2).tag(sync=True)

roi = List(InstanceDict(Track)).tag(sync=True, **widget_serialization_no_none) # regions of interest
roi = List(InstanceDict(Track)).tag(sync=True, **widget_serialization) # regions of interest


class Exon(HasTraits):
Expand Down Expand Up @@ -357,8 +356,8 @@ class ReferenceGenome(Widget):
indexURL = Unicode(allow_none=True).tag(sync=True)
cytobandURL = Unicode(allow_none=True).tag(sync=True)
aliasURL = Unicode(allow_none=True).tag(sync=True)
indexed = Bool(default_value=False).tag(sync=True)
tracks = List(InstanceDict(Track)).tag(sync=True, **widget_serialization_no_none)
indexed = Bool(allow_none=True, default_value=None).tag(sync=True)
tracks = List(InstanceDict(Track)).tag(sync=True, **widget_serialization)
chromosomeOrder = Unicode(allow_none=True).tag(sync=True)
headers = Dict().tag(sync=True)
wholeGenomeView = Bool(default_value=True).tag(sync=True)
Expand Down
12 changes: 10 additions & 2 deletions ipyigv/utils.py
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Original file line number Diff line number Diff line change
@@ -1,11 +1,19 @@
from ipywidgets import Widget, widget_serialization

def is_json_valid(v):
if v is None:
return False
elif isinstance(v, str):
return (v != "")
else:
return True


def _widget_to_json_no_none(x, obj):
if isinstance(x, dict):
return {k: _widget_to_json_no_none(v, obj) for k, v in x.items() if v is not None}
return {k: _widget_to_json_no_none(v, obj) for k, v in x.items() if v not in (None, "")}
elif isinstance(x, (list, tuple)):
return [_widget_to_json_no_none(v, obj) for v in x if v is not None]
return [_widget_to_json_no_none(v, obj) for v in x if v not in (None, "")]
elif isinstance(x, Widget):
return "IPY_MODEL_" + x.model_id
else:
Expand Down
3 changes: 2 additions & 1 deletion js/package.json
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Expand Up @@ -36,8 +36,9 @@
"@jupyterlab/builder": "^3.0.0",
"css-loader": "^5.0.1",
"rimraf": "^2.6.1",
"schema-utils": "2.6.6",
"style-loader": "^2.0.0",
"webpack": "^4.44.2",
"webpack": "^4.46.0",
"webpack-cli": "^3.1.2"
},
"jupyterlab": {
Expand Down
130 changes: 66 additions & 64 deletions js/src/ipyigv.js
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Expand Up @@ -7,10 +7,6 @@ import '../css/widget.css'

import { MODULE_NAME, MODULE_VERSION } from './version'

// When serialiazing the entire widget state for embedding, only values that
// differ from the defaults will be specified.


export class TrackModel extends widgets.WidgetModel {
defaults () {
return _.extend(super.defaults(), {
Expand All @@ -22,6 +18,21 @@ export class TrackModel extends widgets.WidgetModel {
_view_module_version : MODULE_VERSION,
});
};

// returns a dictionary representing a track which igv.js can take in its configuration
to_dict(include_empty = false) {
let keys = Object.keys(this.attributes).filter(k => !k.startsWith("_"))
// removing empty values unless specified otherwise
.filter(k=> (include_empty || !([null, undefined, ""].includes(this.get(k)))));

var dict = keys.reduce((result, key)=> ({...result, [key]:this.get(key)}), {});

if (keys.includes('roi')) {
dict['roi'] = dict['roi'].map(track => track.to_dict(include_empty));
};
console.log ("Finished generating dictionary from TrackModel", dict);
return dict ;
};
};


Expand All @@ -36,6 +47,23 @@ export class ReferenceGenomeModel extends widgets.WidgetModel {
_view_module_version : MODULE_VERSION,
});
};

// returns a dictionary representing a genome which igv.js can take in its configuration
to_dict(include_empty = false) {
let keys = Object.keys(this.attributes).filter(k => !k.startsWith("_"))
// removing empty values unless specified otherwise
.filter(k=> (include_empty || !([null, undefined, ""].includes(this.get(k)))));

var dict = keys.reduce((result, key)=> ({...result, [key]:this.get(key)}), {});

// special treatment for tracks
if (keys.includes('tracks')) {
let tracks = dict['tracks'];
dict['tracks'] = tracks.map(track=> track.to_dict(include_empty));
};
console.log ("Finished generating dictionary from ReferenceGenomeView", dict);
return dict ;
};
};

ReferenceGenomeModel.serializers = _.extend({
Expand Down Expand Up @@ -71,6 +99,39 @@ export class IgvModel extends widgets.DOMWidgetModel {
this.trigger('search', symbol);
}
};

// returns a dictionary representing a genome which igv.js can take in its configuration
to_dict(include_empty = false) {
var keys = Object.keys(this.attributes).filter(k => !k.startsWith("_"))
// removing the layout attribute -- not related to igv
.filter(k=> (k!='layout'))
// removing empty values unless specified otherwise
.filter(k=> (include_empty || !([null, undefined, ""].includes(this.get(k)))));

var dict = keys.reduce((result, key)=> ({...result, [key]:this.get(key)}), {});

// special treatment for tracks
if (keys.includes('tracks')) {
let tracks = dict['tracks'];
dict['tracks'] = tracks.map(track=> track.to_dict(include_empty));
};

// special treatment for regions of interest
if (keys.includes('roi')) {
let roi = dict['roi'];
dict['roi'] = roi.map(roi=> roi.to_dict(include_empty));
};


// special treatment for genome
if (keys.includes('genome')) { // should always be the case
let genome = dict['genome'];
dict['genome'] = genome.to_dict(include_empty);
};

console.log ("Finished generating dictionary from IgvModel", dict);
return dict ;
};
};

IgvModel.serializers = _.extend({
Expand Down Expand Up @@ -117,58 +178,8 @@ export class IgvBrowser extends widgets.DOMWidgetView {
super.render();

this.igvDiv = document.createElement("div");
var referenceGenome = this.model.get('genome');
var tracks = this.model.get('tracks');
var roi = this.model.get('roi');
var doubleClickDelay = this.model.get('doubleClickDelay');
var flanking = this.model.get('flanking');
var genomeList = this.model.get('genomeList');
var locus = this.model.get('locus');
var minimumBases = this.model.get('minimumBases');
var queryParametersSupported = this.model.get('queryParametersSupported');
var search = this.model.get('search');
var showAllChromosomes = this.model.get('showAllChromosomes');
var showAllChromosomeWidget = this.model.get('showAllChromosomeWidget');
var showNavigation = this.model.get('showNavigation');
var showSVGButton = this.model.get('showSVGButton');
var showRuler = this.model.get('showRuler');
var showCenterGuide = this.model.get('showCenterGuide');
var oauthToken = this.model.get('oauthToken');
var apiKey = this.model.get('apiKey');
var clientId = this.model.get('clientId');


var options = {
reference: referenceGenome,
tracks: tracks,
roi: roi,
doubleClickDelay: doubleClickDelay,
flanking: flanking,
genomeList: genomeList,
locus: locus,
minimumBases: minimumBases,
queryParametersSupported: queryParametersSupported,
showAllChromosomes:showAllChromosomes,
showAllChromosomeWidget: showAllChromosomeWidget,
showNavigation: showNavigation,
showSVGButton: showSVGButton,
showRuler: showRuler,
showCenterGuide: showCenterGuide,
};

if (search) {
options['search']=search
}
if (oauthToken) {
options['oauthToken']=oauthToken
}
if (apiKey) {
options['apiKey']=apiKey
}
if (clientId) {
options['clientId']=clientId
}

var options = this.model.to_dict()
console.log("rendering browser", options);
this.browser = igv.createBrowser(this.igvDiv, options)
.then((browser) => {
Expand Down Expand Up @@ -314,12 +325,3 @@ export class IgvBrowser extends widgets.DOMWidgetView {


}

// module.exports = {
// IgvModel: IgvModel,
// IgvBrowser: IgvBrowser,
// ReferenceGenomeView: ReferenceGenomeView,
// ReferenceGenomeModel: ReferenceGenomeModel,
// TrackView: TrackView,
// TrackModel: TrackModel,
// };
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