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Als portal #170

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d4848b8
add portalversion bean properties for ALS portal
preetisi May 29, 2018
79eeebb
merge conflict resolved and add code for als portal to config
preetisi May 31, 2018
68d4817
Images for ALS portal added
dkjang Jun 11, 2018
7f86bff
mrege master - resolve conflicts
preetisi Jun 12, 2018
a06ca55
Merge branch 'als_portal' of https://github.com/broadinstitute/dig-di…
preetisi Jun 12, 2018
273e8c4
changes for als portal
preetisi Jun 12, 2018
bb61b08
als image- DK
preetisi Jun 13, 2018
b2a3af7
add neurological category
preetisi Jun 14, 2018
5dc1996
adding als portal grails link
preetisi Jun 18, 2018
01423bf
ALS-specific modifications
mariacos Jun 19, 2018
9fda4fd
Merge branch 'als_portal' of github.com:broadinstitute/dig-diabetes-p…
mariacos Jun 19, 2018
93623f3
title and heading name for als
preetisi Jun 19, 2018
f20ca65
merge conflict resolved
preetisi Jun 19, 2018
145a60b
working on data pages
mariacos Jul 5, 2018
f558b72
added translation and data page for ALS 2016 exome sequencing
mariacos Jul 5, 2018
923c18b
Merge branch 'als_portal' of github.com:broadinstitute/dig-diabetes-p…
mariacos Jul 5, 2018
31297cb
removed forward slash from dataset name
mariacos Jul 5, 2018
d16fbd5
nearest gene column replaced by gene, add filter in showVariantforAGe…
preetisi Jul 19, 2018
7dac790
updated ALS dataset translations
mariacos Jul 19, 2018
b314f4e
added page for ExSeq_ALS2018
mariacos Jul 19, 2018
6454851
added page for GWAS_ALS2016meta
mariacos Jul 19, 2018
ace5940
enabled ALS data pages
mariacos Jul 19, 2018
1754e59
added ALS dataset descriptions
mariacos Jul 20, 2018
a5a3c8d
created page for ALS exome 2018
mariacos Jul 20, 2018
00d1a2c
added ALS dataset descriptions
mariacos Jul 20, 2018
c59d435
edited page for ALS exome 2018
mariacos Jul 20, 2018
42c3d8f
edited ALS 2016 GWAS LMM data page
mariacos Jul 20, 2018
54013be
edited ALS 2016 GWAS meta data page
mariacos Jul 20, 2018
efd8a16
deleted unnecessary data page
mariacos Jul 20, 2018
f17e248
Merge branch 'als_portal' of https://github.com/broadinstitute/dig-di…
preetisi Aug 1, 2018
10cbd63
add AC filters for ALS
preetisi Aug 16, 2018
5859697
Merge branch 'als_portal' of https://github.com/broadinstitute/dig-di…
preetisi Aug 16, 2018
ba38c3a
change the default function to exeq
preetisi Aug 22, 2018
43903a8
add the AC filter and add the ACA_PH/ACU_PH filters
preetisi Aug 22, 2018
4f964fb
fix the typo in function name
preetisi Aug 22, 2018
e49d7fc
Code for portal title changed.
dkjang Aug 23, 2018
969c6cd
add more cproperty - not working
preetisi Sep 4, 2018
e90520d
edited error message text
mariacos Nov 20, 2018
82f2d1e
added ALS blogID
mariacos Nov 20, 2018
14c0bc8
updated ALS dataset names
mariacos Nov 20, 2018
1aa5cad
updated ALS dataset names
mariacos Nov 20, 2018
7539939
updated ALS dataset namesgrails-app/views/informational/data/_GWAS_AL…
mariacos Nov 20, 2018
2f8e8cb
updated ALS dataset names
mariacos Nov 20, 2018
14f6f5e
added ALS blogID
mariacos Nov 20, 2018
b931622
customized ALSKP home page
mariacos Nov 20, 2018
ac7760b
customized ALSKP home page
mariacos Nov 20, 2018
7c959a2
updating ALS dataset names
mariacos Nov 20, 2018
e98b59f
ALSKP about page
mariacos Nov 20, 2018
bd7519f
editing ALSKP policies
mariacos Nov 20, 2018
fa38227
editing ALSKP policies
mariacos Nov 20, 2018
95d01d3
ALSKP content
mariacos Nov 20, 2018
8a45294
ALS portal content
mariacos Nov 21, 2018
f93da64
corrected typo in dataset name
mariacos Nov 27, 2018
5f5aa16
remove secret key
preetisi Dec 6, 2018
60bfa0a
add sift and polyphen scrore
preetisi Dec 10, 2018
a442081
update the dataset name
preetisi Dec 12, 2018
76838b4
add ACA_PH and ACU_PH columns to the gene table
preetisi Dec 18, 2018
b3bc3b9
add het and hom counts to the gene page
preetisi Dec 18, 2018
24e137d
added translation
mariacos Jan 3, 2019
4d1f45b
added translation
mariacos Jan 4, 2019
249979c
add case plus control AC
preetisi Jan 15, 2019
6ae0f34
initial version for adding pProperties to function variantSearchInfo …
preetisi Jan 16, 2019
70f9d31
added translations for CADD
mariacos Jan 17, 2019
7c3037c
changes for ALS
preetisi Jan 23, 2019
a8102ad
editing interface text
mariacos Jan 23, 2019
3ad6feb
editing interface text
mariacos Jan 23, 2019
8af7a7a
editing interface text
mariacos Jan 23, 2019
854aab7
editing interface text
mariacos Jan 23, 2019
c445d3f
added link to sleep portal
mariacos Jan 23, 2019
d5491fe
added link to sleep portal
mariacos Jan 23, 2019
606704b
added SDKP link to home page
mariacos Jan 23, 2019
6184f8a
fixes for adding dproperties
preetisi Jan 24, 2019
4f081b6
Merge branch 'als_portal' of https://github.com/broadinstitute/dig-di…
preetisi Jan 24, 2019
cd92ad2
removed link to T2D portal data page
mariacos Jan 24, 2019
d61ff61
fix the url
preetisi Jan 25, 2019
f806d1b
Merge branch 'als_portal' of https://github.com/broadinstitute/dig-di…
preetisi Jan 25, 2019
4b1bcbb
added translation for HOM
mariacos Jan 25, 2019
83d8992
Merge branch 'als_portal' of github.com:broadinstitute/dig-diabetes-p…
mariacos Jan 25, 2019
88cb446
disable modify button
preetisi Jan 25, 2019
3cd9237
edited home page text
mariacos Jan 28, 2019
41614d4
changes in the gene table as requested by Sali
preetisi Jan 29, 2019
0d41bfc
Merge branch 'als_portal' of https://github.com/broadinstitute/dig-di…
preetisi Jan 29, 2019
e9d16df
adding analytics for ALSKP
mariacos Jan 29, 2019
cface41
adding analytics for ALSKP
mariacos Jan 29, 2019
1e60bc0
adding FAQ page
mariacos Jan 29, 2019
f6d77e0
updating ALSKP content
mariacos Jan 29, 2019
8c842d6
updating ALSKP content
mariacos Jan 29, 2019
6997cd8
updating ALSKP content
mariacos Jan 29, 2019
700e84f
updating ALSKP content
mariacos Jan 29, 2019
0123d7a
working on ALSKP FAQ page
mariacos Jan 30, 2019
5a5b44c
renamed ALSKP FAQ page
mariacos Jan 30, 2019
0256ef3
added FAQ page
mariacos Jan 30, 2019
7b859b8
ALS portal content
mariacos Jan 30, 2019
d446b0b
adding link to FAQ page
mariacos Jan 30, 2019
b3dd63d
editing ALSKP FAQ page
mariacos Jan 30, 2019
3a1f147
adding link to ALSKP FAQ page
mariacos Jan 30, 2019
74d1dd4
add het, maf columns for als dataset
preetisi Jan 30, 2019
cb1991e
Merge branch 'als_portal' of https://github.com/broadinstitute/dig-di…
preetisi Jan 30, 2019
1ca05ab
added link to FAQ
mariacos Jan 30, 2019
5384f87
Merge branch 'als_portal' of github.com:broadinstitute/dig-diabetes-p…
mariacos Jan 30, 2019
a04dd14
added ALSKP production URL to list
mariacos Jan 30, 2019
a46587b
edited alskp URL
mariacos Jan 30, 2019
69eecf4
edited translation of MAF_PH
mariacos Jan 31, 2019
84fd606
added link to T2DKP
mariacos Jan 31, 2019
9328518
added link to KPN website
mariacos Jan 31, 2019
d5a0e2f
updated citation
mariacos Feb 1, 2019
3f6027c
fix the url for dotClickLink
preetisi Feb 7, 2019
d9f9282
fix the url
preetisi Feb 7, 2019
4974be6
changes for OAuth
preetisi Feb 26, 2019
0511b79
changed default KB to QA
mariacos Feb 26, 2019
6b7c42f
get only mdv specific metadata
preetisi Mar 8, 2019
637716a
changes for manhattan -page - dropdown fixed
preetisi Feb 20, 2020
824fa00
fix the refreshing of manhattan plot and table after selecting a new …
preetisi Feb 26, 2020
2a3ef96
reduce the limit to 500
preetisi Feb 26, 2020
010c716
remove the keys
preetisi Feb 26, 2020
8f21ace
text edits requested by Sali
mariacos Mar 6, 2020
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64 changes: 60 additions & 4 deletions grails-app/conf/Config.groovy
Original file line number Diff line number Diff line change
Expand Up @@ -290,9 +290,17 @@ environments {

// grails.serverURL = "http://stroke-qasrvr-1.us-east-1.elasticbeanstalk.com"


// grails.serverURL = "http://www.type2diabetesgenetics.org"

// grails.serverURL = "http://www.type2diabetesgenetics.org"

// grails.serverURL = "http://variant2function.org"


// grails.serverURL = "http://variant2function.org"
grails.serverURL = "http://demo52k.us-east-1.elasticbeanstalk.com"
// grails.serverURL = "http://demo52k.us-east-1.elasticbeanstalk.com"

// grails.serverURL = "http://ci-env.elasticbeanstalk.com"
// grails.serverURL = "http://type2diabetes-dev.elasticbeanstalk.com"
// grails.serverURL = "http://type2diabetesgen-qasrvr.elasticbeanstalk.com"
Expand All @@ -312,8 +320,12 @@ environments {
// grails.serverURL = "http://strokeprodnew.us-east-1.elasticbeanstalk.com"

// grails.serverURL = "http://broadcvdi.org" // CVDKP (MI portal) production
// grails.serverURL = "http://mi-qasrvr.us-east-1.elasticbeanstalk.com" // CVDKP (MI portal) test site
// grails.serverURL = "http://miprodportal.us-east-1.elasticbeanstalk.com"

// grails.serverURL = "http://mi-qasrvr.us-east-1.elasticbeanstalk.com"// CVDKP (MI portal) test site

grails.serverURL = "http://alsportal.us-east-1.elasticbeanstalk.com"

// grails.serverURL = "http://miprodportal.us-east-1.elasticbeanstalk.com"
// grails.serverURL = "http://miprod-env.us-east-1.elasticbeanstalk.com"

// grails.serverURL = "http://sleepportal-prodsrvr.us-east-1.elasticbeanstalk.com"
Expand Down Expand Up @@ -561,7 +573,9 @@ grails.plugin.springsecurity.userLookup.authorityJoinClassName = 'org.broadinsti
grails.plugin.springsecurity.authority.className = 'org.broadinstitute.mpg.people.Role'


portal.type.override = "t2d" // options are "t2d", "stroke", "mi", "ibd", "epilepsy", or "sleep". What is the portal type for all nonsystem users?


portal.type.override = "als" // options are "t2d", "stroke", "mi", "ibd", "epilepsy", or "sleep". What is the portal type for all nonsystem users?


portal.data.versionDesignator = [ new PortalVersionBean("t2d", // label for this portal type
Expand Down Expand Up @@ -706,13 +720,49 @@ portal.data.versionDesignator = [ new PortalVersionBean("t2d", // label for
1,
1
),
new PortalVersionBean("als",
"ALS",
"mdv60",
"ALS", // make sure your default phenotype exists in your default data set
"ExSeq_ALS2018_eu_mdv60",// used to pick a default data set for a gene query
["8_Genic_enhancer","9_Active_enhancer_1","10_Active_enhancer_2","11_Weak_enhancer"],
["8_Genic_enhancer","9_Active_enhancer_1","10_Active_enhancer_2","11_Weak_enhancer"],
["AnteriorCaudate"],
["PSYCHIATRIC", "NEUROLOGICAL"], // most important phenotype group name
[],
"[1,2]",
"GWAS_IBDGenomics_eu_mdv80",
"images/als/front_als_logo_2018.svg",
"portal.ALS.header.tagline",
[],
["SOD1"],
[],
["chr14:35,907,000-36,400,000"],
"images/als/front_als_banner_2018.png",
"",
"images/als/als_header_logo.svg",
"images/menu_bg_2017_5.png",
"false",
"",
"",
'2854182648437419920',
0,
1,
0,
1,
0,
0,0,0,
0,
0
),
new PortalVersionBean("epilepsy",
"Epilepsy",
"mdv100",
"GGE", // make sure your default phenotype exists in your default data set
"ExSeq_Epi25k_mdv100",// used to pick a default data set for a gene query
["8_Genic_enhancer","9_Active_enhancer_1","10_Active_enhancer_2","11_Weak_enhancer"],
["8_Genic_enhancer","9_Active_enhancer_1","10_Active_enhancer_2","11_Weak_enhancer"],

["AnteriorCaudate"],
["PSYCHIATRIC"], // most important phenotype group name
[],
Expand All @@ -722,6 +772,7 @@ portal.data.versionDesignator = [ new PortalVersionBean("t2d", // label for
"portal.epilepsy.header.tagline",
[],
["CDKL5"],

[],
["chr14:35,907,000-36,400,000"],
"images/epilepsy/front_epilepsy_bg_2018.png",
Expand All @@ -732,6 +783,7 @@ portal.data.versionDesignator = [ new PortalVersionBean("t2d", // label for
"",
"",
'5414069947481666863',

0,
1,
0,
Expand All @@ -741,6 +793,8 @@ portal.data.versionDesignator = [ new PortalVersionBean("t2d", // label for
0,
0
),


new PortalVersionBean("sleep",
"Sleep",
"mdv110",
Expand Down Expand Up @@ -777,3 +831,5 @@ portal.data.versionDesignator = [ new PortalVersionBean("t2d", // label for
0
)
]


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