config.ini.nemo

# site-wide config originally from portal-ui/config.js
[site-wide]
project-abbr=NeMO
api=/api
auth=/api/status
auth-api=/api/status/api
tag=https://github.com/NCI-GDC/portal-ui/releases/tag/1.2.4
fake-auth=False
#ident = desired length of a random alphanumeric string
ident=8
production=False
supported-api=1
version=1.2.4
build-cache-on-first-request=True
subject-excluded-fields=node_type,project_project_name
sample-excluded-fields=node_type,visit_gender
file-excluded-fields=<private>
footer-link-text=NeMO Hub
footer-link=https://portal.nemoarchive.org
google-analytics-enabled=False
google-analytics-id=INSERT-PORTAL-GA-ID-HERE

[navbar]
# Custom external link, else leave empty for logo to link to portal home page
logo-link=
analysis-display=False
analysis-link=https://portal.nemoarchive.org
documentation-display=False
documentation-link=
apps-data-portal-display=True
apps-data-portal-tooltip-text=NeMO Data Portal
apps-data-portal-link=/
apps-api-display=True
apps-api-tooltip-text=NeMO API
apps-api-link=http://github.com/IGS/portal_api
apps-documentation-display=True
apps-documentation-tooltip-text=NeMO Docs
apps-documentation-link=https://github.com/nemoarchive/documentation
apps-legacy-archive-display=False
apps-legacy-archive-tooltip-text=HMP Legacy Archive
apps-legacy-archive-link=http://hmpdacc.org/
apps-website-display=True
apps-website-tooltip-text=NeMO Website
apps-website-link=http://www.nemoarchive.org/
apps-datatransfer-tool-display=True
apps-datatransfer-tool-tooltip-text=NeMO Data Transfer Tool
apps-datatransfer-tool-link=https://github.com/IGS/portal_client
apps-faq-display=True
apps-faq-tooltip-text=NeMO FAQ
apps-faq-link=http://nemoarchive.org/about/index.php
apps-resources-display=True
apps-resources-tooltip-text=NeMO Resources
apps-resources-link=http://nemoarchive.org/resources.php
user-login-link=http://portal.nemoarchive.org/api/login


[home]
page-title=Neuroscience Multi-Omic Data Portal | NeMO
portal-name=Welcome to the NeMO Data Portal
projects-table-title=Go to The Portal Projects Page
projects-table-title-header=Studies by Modality Type
project-external-link=
project-name=

[home-summary-stat-1]
title=Grants
icon=<i class="fa fa-bar-chart data-icon"></i>
data=hc.projectData.aggregations.x_labels.buckets.length

[home-summary-stat-2]
title=Samples
icon=<i class="fa fa-user-o data-icon"></i>
data=hc.caseData.pagination.total

[home-summary-stat-3]
title=Files
icon=<i class="fa fa-folder-open-o data-icon"></i>
data=hc.fileData.pagination.total

[home-summary-stat-4]
title=Modality Type
icon=<span class="icon-gdc-cancer-types project-icon"><span class="path1"></span><span class="path2"></span><span class="path3" style="color: #fff;"></span><span class="path4"></span><span class="path5"></span><span class="path6"></span></span>
data=hc.projectData.pagination.unique_total

[home-example-query-1]
description=Retrieve CEMBA methylomics FASTQ data (demo set)
count-query=MATCH (subject:subject)<-[:extracted_from]-(sample:sample)<-[D:derived_from]-(file:file) WHERE file.format = "FASTQ" AND sample.id = "CEMBA171207_3C" and sample.modality="Methylation" RETURN COUNT(DISTINCT(sample)) as case_count, COUNT(DISTINCT(file)) as file_count
has-cases-link=True
cases-link=/search/c?filters={"content":[{"content":{"field":"file.format","value":["FASTQ"]},"op":"in"},{"content":{"field":"sample.id","value":["CEMBA171207_3C"]},"op":"in"},{"content":{"field":"sample.modality","value":["Methylation"]},"op":"in"}],"op":"and"}
has-files-link=True
files-link=/search/f?filters={"content":[{"content":{"field":"file.format","value":["FASTQ"]},"op":"in"},{"content":{"field":"sample.id","value":["CEMBA171207_3C"]},"op":"in"},{"content":{"field":"sample.modality","value":["Methylation"]},"op":"in"}],"op":"and"}

[home-example-query-2]
description=Retrieve all chromatin FASTQ bundles obtained from mouse samples
count-query=MATCH (subject:subject)<-[:extracted_from]-(sample:sample)<-[D:derived_from]-(file:file) WHERE file.format = "FASTQ" AND sample.organism = "Mouse" AND sample.modality = "Chromatin" RETURN COUNT(DISTINCT(sample)) as case_count, COUNT(DISTINCT(file)) as file_count
has-cases-link=True
cases-link=/search/c?filters={"content":[{"content":{"field":"file.format","value":["FASTQ"]},"op":"in"},{"content":{"field":"sample.organism","value":["Mouse"]},"op":"in"},{"content":{"field":"sample.modality","value":["Chromatin"]},"op":"in"}],"op":"and"}
has-files-link=True
files-link=/search/f?filters={"content":[{"content":{"field":"file.format","value":["FASTQ"]},"op":"in"},{"content":{"field":"sample.organism","value":["Mouse"]},"op":"in"},{"content":{"field":"sample.modality","value":["Chromatin"]},"op":"in"}],"op":"and"}

[home-example-query-3]
description=Retrieve all 10x Chromium 3' v2 sequenced-FASTQ files generated from mouse samples
count-query=MATCH (subject:subject)<-[:extracted_from]-(sample:sample)<-[D:derived_from]-(file:file) WHERE sample.technique = "10x Chromium 3' v2 sequencing" AND subject.project_name = "BICCN" and sample.organism = "Mouse" and file.format = "FASTQ" RETURN COUNT(DISTINCT(sample)) as case_count, COUNT(DISTINCT(file)) as file_count
has-cases-link=True
cases-link=/search/c?filters={"content":[{"content":{"field":"sample.technique","value":["10x Chromium 3' v2 sequencing"]},"op":"in"},{"content":{"field":"subject.project_name","value":["BICCN"]},"op":"in"},{"content":{"field":"sample.organism","value":["Mouse"]},"op":"in"},{"content":{"field":"file.format","value":["FASTQ"]},"op":"in"}],"op":"and"}
has-files-link=True
files-link=/search/f?filters={"content":[{"content":{"field":"sample.technique","value":["10x Chromium 3' v2 sequencing"]},"op":"in"},{"content":{"field":"subject.project_name","value":["BICCN"]},"op":"in"},{"content":{"field":"sample.organism","value":["Mouse"]},"op":"in"},{"content":{"field":"file.format","value":["FASTQ"]},"op":"in"}],"op":"and"}

[projects]
page-title=Projects | NeMO
display-graph-tab=True
study-data-query=MATCH (subject)<-[:extracted_from]-(sample)<-[D:derived_from]-(file) WITH sample.study_name+"_"+sample.organism as study_key, sample.study_name AS study_name, sample.organism as organism, COUNT(DISTINCT(sample)) as _case_count, COUNT(DISTINCT(file)) as _file_count, SUM(file.size) AS _file_size RETURN study_key, study_name, organism, SUM(_case_count) as case_count, SUM(_file_count) as file_count, SUM(_file_size) as file_size
study-sample-count-query=MATCH (subject)<-[:extracted_from]-(sample)<-[D:derived_from]-(file) RETURN sample_study_name+"_"+sample.organism as study_key, sample.study_name AS study_name, COUNT(DISTINCT(sample)) AS sample_count

[projects-table]
title=studies
row-id=study_key
linked-fields=case_count,file_count
default-sort=case_count:desc

[projects-table-heading-1]
name=Grant
id=study_name
# tooltip-text=study_full_name
sortable=True
show=True
draggable=True
col-span=4

[projects-table-heading-2]
name=Organism
id=organism
sortable=True
show=True
draggable=True


[projects-table-heading-3]
name=Samples
id=case_count
sortable=True
show=True
#th-classname is optional
#th-classname=text-right
td-classname=text-right
link-filter-field=sample.study_name

[projects-table-heading-4]
name=Files
id=file_count
sortable=True
show=True
#th-classname is optional
#th-classname=text-right
td-classname=text-right
link-filter-field=sample.study_name

#Default chartconfigs for projects page pie charts
# hover-count-label - Changes the hover. default is 'Files' <study> - <count> <HOVER_COUNT_LABEL>, <file_size stuff> 
# field-filter = field applied to URL when adding a filter
[projects-piechart-config-1]
default-text=Grant
plural-default-text=Grants
hover-count-label=Grant
chart-title=Sample Counts by Grant
grouping-title=Study
filter-key=study_name
field-filter=sample.study_name
display-key=study_name
sort-key=case_count

[projects-piechart-config-2]
default-text=Grant
plural-default-text=Grants
chart-title=File Counts by Grant
grouping-title=File
filter-key=study_name
field-filter=sample.study_name
display-key=study_name
sort-key=file_count

[search]
page-title=Search | NeMO
recalculate-facets=True
#The unique ID property for the sample node
sample-node-id=sample.study_full_name
facets-panel-samples-tab-name=
facets-panel-files-tab-name=
center-panel-samples-tab-name=
center-panel-files-tab-name=
	
#Sets columns for 'samples' table on Search page
[cases-table]
api-row-id-node-type=sample
api-row-id-field=study_full_name
title=Samples
row-id=id
linked-field=sample.sample_id
default-sort=sample.sample_id:asc

[cases-table-heading-1]
name=Sample ID
id=sample.sample_id
show=True
sortable=True

[cases-table-heading-2]
name=Donor ID
id=subject.rand_subject_id
show=True
sortable=False

[cases-table-heading-3]
name=Anatomical Structure
id=sample.anatomical_region
show=True
sortable=False

[cases-table-heading-4]
name=Modality
id=sample.modality
show=True
sortable=True

[cases-table-heading-5]
name=Grant ID
id=sample.study_name
show=True
sortable=False
# tooptip-text is optional
tooltip-text=sample.study_full_name

#[cases-table-heading-6]
#name=Study Full Name
#id=sample.study_full_name
#sortable=True

[files-table]
api-row-id-node-type=file
api-row-id-field=id
title=Files
row-id=file_id
default-sort=file_id:asc
#False = leaves filename unchanged
#True = changes filepath to file_url
rename-filename-absolute-path=False
#Leave blank for default value: "Private data", otherwise specify the string to display for private data
private-data-filename=

[files-table-heading-1]
name=Access
id=file.private_files
show=True
sortable=False

[files-table-heading-2]
name=File UUID
id=file_id
sortable=True
show=False
tooltip-text=file_id
td-classname=id-cell

[files-table-heading-3]
name=File Name
id=file.file_name
sortable=True
show=True
td-classname=id-cell

[files-table-heading-4]
name=Modality
id=file.node_type
sortable=True
show=True

[files-table-heading-5]
name=Data Format
id=file.format
sortable=True
show=True

[files-table-heading-6]
name=Size
id=file.size
sortable=True
show=True
#th-classname is optional
#th-classname=text-right 
td-classname=text-right

[files-table-heading-7]
name=Data Type
id=file.subtype
sortable=True
show=False

# Default config for front-page barchart
# Default body_site query - HMP
[search-barchart-config]
count-query=RETURN DISTINCT PS.grant, VSS.modality, COUNT(DISTINCT(VSS)) as case_count, COUNT(DISTINCT(F)) as file_count ORDER BY file_count DESC
x-axis-labels=PS.grant
x-axis-order-by-count=file_count
data-tooltip-label=VSS.modality
data-tooltip-include-project-id=True
y-axis-scale=log
allow-bar-rotation=True
bar-rotation=rotate(180)
bar-colorscale-data-property=barTip
allow-darker-bar-colors=False
use-custom-color=False
#for the custom color scale, use the colors found in colorbrewer.js (ex. OrRd for orange->red)
custom-color-scale=Set1
#the number of colors you want in the custom scale
custom-color-scale-number=5
# example: reverse OrRd to be red->orange
reverse-custom-color-scale=False


[search-piechart-api]
chart-order=project_name,anatomical_structure,study_name,organism,file_format,modality

[search-piechart-count-queries]
# name the keys using the fields listed in the above [piechart-api]chart-order
# {field}={query}
# {field}_detailed={query_detailed}
project-name=RETURN subject.project_name AS prop, count(subject.project_name) AS counts
project-name-detailed=WITH COUNT(DISTINCT(sample)) as scount, COUNT(DISTINCT(file)) AS fcount, subject.project_name AS prop, SUM(file.size) as tot RETURN prop,scount,fcount,tot
anatomical-structure=RETURN sample.common_ontology AS prop, count(sample.common_ontology) AS counts
anatomical-structure-detailed=WITH COUNT(DISTINCT(sample)) as scount, COUNT(DISTINCT(file)) AS fcount, sample.common_ontology AS prop, SUM(file.size) as tot RETURN prop,scount,fcount,tot
study-name=RETURN sample.study_name AS prop, count(sample.study_name) AS counts
study-name-detailed=WITH COUNT(DISTINCT(sample)) as scount, COUNT(DISTINCT(file)) AS fcount, sample.study_name AS prop, SUM(file.size) as tot RETURN prop,scount,fcount,tot
organism=RETURN sample.organism AS prop, count(sample.organism) AS counts
organism-detailed=WITH COUNT(DISTINCT(sample)) as scount, COUNT(DISTINCT(file)) AS fcount, sample.organism AS prop, SUM(file.size) as tot RETURN prop,scount,fcount,tot
file-format=RETURN file.format AS prop, count(file.format) AS counts
file-format-detailed=WITH COUNT(DISTINCT(sample)) as scount, COUNT(DISTINCT(file)) AS fcount, file.format AS prop, SUM(file.size) as tot RETURN prop,scount,fcount,tot
modality=RETURN file.node_type AS prop, count(file.node_type) AS counts
modality-detailed=WITH COUNT(DISTINCT(sample)) as scount, COUNT(DISTINCT(file)) AS fcount, file.node_type AS prop, SUM(file.size) as tot RETURN prop,scount,fcount,tot


#Default chartconfigs for search page pie charts
[search-piechart-config-1]
default-text=Project
plural-default-text=Projects
chart-title=File Counts by Project
grouping-title=Project
filter-key=subject.project_name
field-filter=subject.project_name

[search-piechart-config-2]
default-text=Anatomical Structure
plural-default-text=Anatomical Structures
chart-title=File Counts by Anatomical Structure
grouping-title=Primary Site
filter-key=sample.common_ontology
field-filter=sample.common_ontology

[search-piechart-config-3]
default-text=Study
plural-default-text=Studies
chart-title=File Counts by Study
grouping-title=Name
filter-key=sample.study_name
field-filter=sample.study_name

[search-piechart-config-4]
default-text=Organism
plural-default-text=Organisms
chart-title=File Counts by Organism
grouping-title=Organism
filter-key=sample.organism
field-filter=sample.organism

[search-piechart-config-5]
default-text=File Format
plural-default-text=File Formats
chart-title=File Counts by File Format
grouping-title=File Format
filter-key=file.format
field-filter=file.format

[search-piechart-config-6]
default-text=Modality
plural-default-text=Modalities
chart-title=File Counts by Modality Type
grouping-title=Modality
filter-key=sample.modality
field-filter=sample.modality

[search-advanced-query-page]
enable-documentation-link=True
documentation-link=https://github.com/nemoarchive/documentation/wiki/Browsing-in-the-NeMO-Portal#advanced-searches-


# /cases page configuration
[cases-page]
page-title=Sample
# sample.id for HMP. sample.study_full_name for NeMO
link-filter-field=sample.study_full_name

[cases-page-summary-table]
# property-names should be formatted: <node_label>_<property>
human-readable=Sample ID,Organism,Library Method,Technique,Modality,Grant,Anatomical Structure
property-names=sample_sample_id,sample_organism,sample_lib_method,sample_technique,sample_modality,sample_study_name,sample_anatomical_region


# /files page configuration
[files-page]
page-title=File
# enable download of the actual data file
enable-download-btn=False
# property-names should be formatted: <node_label>_<property>
[files-page-properties-table]
human-readable=Name,Access,UUID,Data Format,Size,MD5 Checksum
property-names=file_file_name,file_access,file_id,file_format,file_size,file_md5

[files-page-data-information-table]
human-readable=Data Category,Data Type,Project ID
property-names=file_node_type,file_subtype,file_study


[cart]
#list the search-piechart configs to be used for cart page piecharts
piechart-order=search-piechart-config-3,search-piechart-config-4
page-title=Cart | NeMO

enable-study-level-matrices=False
# Neo4j node & property that denote whether the node is a study-level matrix
# For HMBR neo4j: file.study_level = true
study-level-matrix-flag=
# Neo4j node and property that contains the study's name
# For HMBR neo4j: subject.dataset_name = "RISK"
study-name-on-node=


# This requires addition of the multifile_downloader plugin to the api plugins/ directory
enable-download-cart-btn=False
download-cart-text=

# If enabling Terra btn, be sure that [cloud-options]service-name=terra
enable-export-to-terra-btn=True

download-client-link=https://github.com/IGS/NeMO_client
#download-cart-text=Download Files in your Cart directly from the Web Browser.
notes-metadata-text=Please note that each file in a downloaded manifest can be tied to metadata through the sample_id column.
#class for Font-Awesome icon found in the 'Download' button
download-button-icon=fa fa-download
# Select 'Download' or 'Send to Cloud'
download-button-text=Download
# --- For DCPPC ---
# download-manifest-text=Saves manifest file to Amazon S3 bucket. Use the manifest download utility and DCPPC client on a cloud-based VM to comply with NIH data access policy
# download-utility-link=https://github.com/dcppc-phosphorous/manifest-downloader
#comment to remove/exclude unique to DCPPC
# manifest-filename=dcppc_manifest
# metadata-filename=dcppc_manifest_metadata
# --- End DCPPC ---

download-manifest-text=Downloading and analyzing large files can be very resource intensive and so it is recommended to use the NeMO client for this purpose. One can download a manifest file using the button below in order to download their data through the client.
manifest-filename=NeMO_manifest
metadata-filename=NeMO_manifest_metadata
manifest-file-header=file_id\tmd5\tsize\tfiletype\turls\tsample_id\tcomponent_files

[manifest-download-col-1]
col-name=file_id
node-type=file
prop=id

[manifest-download-col-2]
col-name=md5
node-type=file
prop=md5

[manifest-download-col-3]
col-name=size
node-type=file
prop=size

[manifest-download-col-4]
col-name=filetype
node-type=file
prop=format

[manifest-download-col-5]
col-name=urls
node-type=None
prop=urls

[manifest-download-col-6]
col-name=sample_id
node-type=sample
prop=id

[manifest-download-col-7]
col-name=component_files
node-type=None
prop=component_files


[metadata-download-col-1]
col-name=sample_id
node-type=sample
prop=id

[metadata-download-col-2]
col-name=project_id
node-type=subject
prop=id

[metadata-download-col-3]
col-name=sample_anatomical_region
node-type=sample
prop=anatomcial_region

[metadata-download-col-4]
col-name=sample_organism
node-type=sample
prop=organism

[metadata-download-col-5]
col-name=sample_library_method
node-type=sample
prop=lib_method

[metadata-download-col-6]
col-name=sample_modality
node-type=sample
prop=modality

[metadata-download-col-7]
col-name=sample_technique
node-type=sample
prop=technique

[metadata-download-col-8]
col-name=sample_transgenic_line
node-type=sample
prop=transgenic_line

[metadata-download-col-9]
col-name=study_full_name
node-type=sample
prop=study_full_name

[metadata-download-col-10]
col-name=project_name
node-type=subject
prop=project_name

[metadata-download-col-11]
col-name=project_grant
node-type=subject
prop=grant

[metadata-download-col-12]
col-name=project_lab
node-type=subject
prop=lab

[metadata-download-col-13]
col-name=project_organization
node-type=subject
prop=organizations

[cloud-options]
# 'download', 'aws', 'terra'
service-name=terra
# --- AWS settings --- These values are NEVER forwarded to UI
aws-api-key=""
aws-secret-key=""
aws-bucket-name=""
aws-running-on-ec2=False
# --- End AWS ---