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ST
ga4gh-arraymap
Commits
6853e4a2
Commit
6853e4a2
authored
Jun 16, 2016
by
Severine Duvaud
Browse files
Do not allow minLength and maxLength to be compliant with 0.3
parent
a632d519
Changes
3
Hide whitespace changes
Inline
Side-by-side
app/node-app/arraymap-beacon/v0.3/beacon-query.js
View file @
6853e4a2
...
...
@@ -94,6 +94,8 @@ function checkPreconditions(params) {
};
}
// Do not allow minLength and maxLength to be compliant with 0.3
/*
if (params.minlength && !Number(params.minlength)) {
return {
hasError: true,
...
...
@@ -106,7 +108,7 @@ function checkPreconditions(params) {
hasError: true,
msg: "max length not a number"
};
}
}
*/
//TODO add additional checks
...
...
@@ -142,6 +144,8 @@ function buildMongoQuery(params) {
var
position
=
parseInt
(
params
.
start
);
// Do not allow minLength and maxLength to be compliant with 0.3
/*
if(params.alternateBases == 'DEL') {
var minLength = params.minlength ? parseInt(params.minlength) : 0;
...
...
@@ -151,7 +155,7 @@ function buildMongoQuery(params) {
minLength = 1;
}
}
}
*/
var
andConditions
=
[];
var
orConditions
=
[];
...
...
@@ -180,6 +184,8 @@ function buildMongoQuery(params) {
//elem match element
var
condElemMatch
=
condition
[
convertedReference
][
'
$elemMatch
'
];
// Do not allow minLength and maxLength to be compliant with 0.3
/*
if (minLength > 0) { //There is a minLength
if (maxLength > 0) { //There is always a minLenght, if there is a max length specified (see code above)
condElemMatch.SEGSIZE = { $gte: minLength,$lte: maxLength } // min. and max lengths
...
...
@@ -189,9 +195,10 @@ function buildMongoQuery(params) {
condElemMatch.SEGSTART = position; // exact position
}
}else { //If there is a position specific
*/
condElemMatch
.
SEGSTOP
=
{
$gte
:
position
};
condElemMatch
.
SEGSTART
=
{
$lte
:
position
};
}
//
}
andConditions
.
push
(
condition
);
if
(
orConditions
.
length
>
0
)
{
...
...
@@ -219,7 +226,9 @@ function buildMongoQuery(params) {
function
checkResultAndGetResponse
(
params
,
datasets
)
{
var
length
=
0
;
// Do not allow minLength and maxLength to be compliant with 0.3
// var length = 0;
/*
if (typeof params.minlength != undefined && params.minlength != null && params.minlength != '')
{
length = parseInt(params.minlength);
...
...
@@ -233,7 +242,7 @@ function checkResultAndGetResponse(params, datasets) {
{
maxLength = parseInt(params.maxlength);
}
*/
var
responses
=
[];
// The query returns only datasets for which there is at least one sample with at least one matching SEGMENT...
...
...
@@ -305,9 +314,12 @@ function checkResultAndGetResponse(params, datasets) {
"
start
"
:
params
.
start
,
"
assemblyId
"
:
params
.
assemblyId
,
"
datasetIds
"
:
params
.
datasetIds
,
"
alternateBases
"
:
params
.
alternateBases
,
"
alternateBases
"
:
params
.
alternateBases
// Do not allow minLength and maxLength to be compliant with 0.3
/*
"length": length,
"maxlength": maxLength
*/
};
// BeaconAlleleResponse
...
...
app/node-app/public/js/index.js
View file @
6853e4a2
...
...
@@ -22,9 +22,12 @@ arrayMap.controller('BeaconController', ['$scope', '$location', function ($scope
"
start
"
:
34439881
,
"
assemblyId
"
:
"
GRCh38
"
,
"
datasetIds
"
:
"
8070/3
"
,
"
alternateBases
"
:
"
DEL
"
,
"
alternateBases
"
:
"
DEL
"
// Do not allow minLength and maxLength to be compliant with 0.3
/*
"minlength": '',
"maxlength": ''
*/
};
...
...
@@ -41,9 +44,12 @@ arrayMap.controller('BeaconController', ['$scope', '$location', function ($scope
"
&start=
"
+
conf
.
start
+
"
&assemblyId=
"
+
conf
.
assemblyId
+
"
&datasetIds=
"
+
conf
.
datasetIds
+
((
conf
.
alternateBases
===
""
)
?
"
all
"
:
"
&alternateBases=
"
+
conf
.
alternateBases
)
+
((
conf
.
alternateBases
===
""
)
?
"
all
"
:
"
&alternateBases=
"
+
conf
.
alternateBases
);
// Do not allow minLength and maxLength to be compliant with 0.3
/*
((conf.minlength === '') ? "" : "&minlength=" + conf.minlength) +
((conf.maxlength === '') ? "" : "&maxlength=" + conf.maxlength);
*/
};
$scope
.
getInfoUrl
=
function
()
{
...
...
app/node-app/public/partials/beacon-home.html
View file @
6853e4a2
...
...
@@ -47,6 +47,8 @@
</select>
</div>
</div>
<!-- Do not allow minLength and maxLength to be compliant with 0.3
<div class="form-group">
<label for="minlength" class="col-sm-2 control-label">Minimal length</label>
<div class="col-sm-4">
...
...
@@ -59,7 +61,7 @@
<div class="col-sm-4">
<input type="text" class="form-control" id="maxlength" ng-model="config.maxlength" placeholder="Max bases for the selected chromosome">
</div>
</div>
</div>
-->
<div
class=
"form-group"
>
<div
class=
"col-sm-offset-2 col-sm-8"
>
...
...
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