overture_song
song-1.4.0
Introduction
What is SONG?
Features
Data Submission Workflow
Projects Using SONG
Getting Started
Tutorial using a CLI with Docker for SONG
Tutorial using the Python SDK with SONG
Play with the REST API from your browser
Deploy SONG to Production
License
User Access
DACO Authentication
OAuth2 Authorization
SCORE Client
Installation
Configuration
Usage
Deploying a SONG Server in Production
Prerequisites
Official Releases
Installation
Configuration
Server
Database
Running as a Service
Linux (SysV)
Docker for SONG
Introduction
What is Docker for SONG?
Important Features
Bonus Features
Microservice Architecture
Prerequisites
Mandatory
Optional
Getting Docker for SONG
Find the Latest Official Release Tag
Download
Download ZIP
Download TAR.GZ
Download using GIT
Build and Run
Configuration
Tutorial
Stage 1: SONG Upload
Stage 2: SONG Saving and Manifest Generation
Stage 3: SCORE Upload
Stage 4: SONG Publish
Issues
License
Supported SDKs
SONG Python SDK
Prerequisites
Installation
Configuration
Tutorial
Configuration
Create a Study
Create a Simple Payload
Use a Custom AnalysisId
Upload the Payload
Check the Status of the Upload
Save the Analysis
Observe the UNPUBLISHED Analysis
Generate the Manifest
Upload the Object Files
Publish the Analysis
Observe the PUBLISHED Analysis
Reference
client
entities
model
rest
tools
utils
validation
Frequently Asked Questions
How can I find the latest official release via command line?
overture_song
Docs
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Index
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B
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C
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D
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E
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F
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G
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H
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I
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L
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M
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N
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O
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P
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R
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S
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T
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U
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V
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W
A
access token
add_entry() (overture_song.model.Manifest method)
add_info() (overture_song.entities.Metadata method)
aligned (overture_song.entities.SequencingRead attribute)
alignmentTool (overture_song.entities.SequencingRead attribute)
analysis
Analysis (class in overture_song.entities)
analysisId (overture_song.entities.Analysis attribute)
(overture_song.entities.File attribute)
(overture_song.entities.SequencingRead attribute)
(overture_song.entities.VariantCall attribute)
(overture_song.tools.SimplePayloadBuilder attribute)
analysisState (overture_song.entities.Analysis attribute)
analysisType (overture_song.entities.SequencingReadAnalysis attribute)
(overture_song.entities.VariantCallAnalysis attribute)
Api (class in overture_song.client)
ApiConfig (class in overture_song.model)
B
base_on_sample() (overture_song.entities.CompositeEntity class method)
BatchUploader (class in overture_song.tools)
build() (overture_song.utils.Builder method)
Builder (class in overture_song.utils)
builder() (overture_song.entities.Analysis class method)
(overture_song.entities.SequencingRead class method)
C
check_dir() (in module overture_song.utils)
check_file() (in module overture_song.utils)
check_is_alive() (overture_song.client.Api method)
check_song_state() (in module overture_song.utils)
check_state() (in module overture_song.utils)
check_type() (in module overture_song.utils)
check_upload_status() (overture_song.client.UploadClient method)
collaboratory
CompositeEntity (class in overture_song.entities)
config (overture_song.client.Api attribute)
cononical id
convert_to_url_param_list() (in module overture_song.utils)
create() (overture_song.client.StudyClient method)
(overture_song.entities.CompositeEntity class method)
(overture_song.entities.Donor class method)
(overture_song.entities.File class method)
(overture_song.entities.Sample class method)
(overture_song.entities.SequencingRead class method)
(overture_song.entities.SequencingReadAnalysis class method)
(overture_song.entities.Specimen class method)
(overture_song.entities.Study class method)
(overture_song.entities.VariantCall class method)
(overture_song.entities.VariantCallAnalysis class method)
create_dir() (in module overture_song.utils)
create_from_raw() (overture_song.entities.Study class method)
create_manifest() (overture_song.client.ManifestClient method)
create_manifest_entry() (overture_song.model.ManifestEntry class method)
create_song_error() (overture_song.model.SongError class method)
D
DataField (class in overture_song.validation)
debug (overture_song.model.ApiConfig attribute)
default_value() (in module overture_song.utils)
description (overture_song.entities.Study attribute)
display() (overture_song.utils.GenericObjectType method)
donor
Donor (class in overture_song.entities)
donor (overture_song.entities.CompositeEntity attribute)
donorGender (overture_song.entities.Donor attribute)
donorId (overture_song.entities.Donor attribute)
(overture_song.entities.Specimen attribute)
donorSubmitterId (overture_song.entities.Donor attribute)
E
Endpoints (class in overture_song.client)
Entity (class in overture_song.entities)
Experiment (class in overture_song.entities)
experiment (overture_song.entities.SequencingReadAnalysis attribute)
(overture_song.entities.VariantCallAnalysis attribute)
F
file
File (class in overture_song.entities)
file (overture_song.entities.Analysis attribute)
fileAccess (overture_song.entities.File attribute)
(overture_song.model.FileUpdateRequest attribute)
fileMd5sum (overture_song.entities.File attribute)
(overture_song.model.FileUpdateRequest attribute)
fileName (overture_song.entities.File attribute)
fileSize (overture_song.entities.File attribute)
(overture_song.model.FileUpdateRequest attribute)
fileType (overture_song.entities.File attribute)
FileUpdateRequest (class in overture_song.model)
FileUploadClient (class in overture_song.tools)
FileUploadState (class in overture_song.tools)
from_json() (overture_song.entities.Analysis class method)
G
GenericObjectType (class in overture_song.utils)
get() (overture_song.rest.Rest method)
get_all_files() (overture_song.tools.BatchUploader method)
get_all_studies() (overture_song.client.Api method)
(overture_song.client.Endpoints method)
get_analysis() (overture_song.client.Api method)
(overture_song.client.Endpoints method)
get_analysis_files() (overture_song.client.Api method)
(overture_song.client.Endpoints method)
get_entire_study() (overture_song.client.Api method)
(overture_song.client.Endpoints method)
get_field_names() (overture_song.model.SongError class method)
get_file() (overture_song.tools.BatchUploader method)
get_files() (overture_song.tools.BatchUploader method)
get_json_header() (overture_song.rest.HeaderGenerator method)
get_optional_field() (in module overture_song.utils)
get_plain_header() (overture_song.rest.HeaderGenerator method)
get_required_field() (in module overture_song.utils)
get_schema() (overture_song.client.Api method)
(overture_song.client.Endpoints method)
get_studies() (overture_song.tools.BatchUploader method)
get_study() (overture_song.client.Api method)
(overture_song.client.Endpoints method)
get_with_params() (overture_song.rest.Rest method)
H
has() (overture_song.client.StudyClient method)
HeaderGenerator (class in overture_song.rest)
I
ICGC
icgc-storage-client
id_search() (overture_song.client.Api method)
(overture_song.client.Endpoints method)
info (overture_song.entities.Metadata attribute)
(overture_song.model.FileUpdateRequest attribute)
info_search() (overture_song.client.Api method)
(overture_song.client.Endpoints method)
insertSize (overture_song.entities.SequencingRead attribute)
intercept_response() (in module overture_song.rest)
is_alive() (overture_song.client.Api method)
(overture_song.client.Endpoints method)
is_empty() (overture_song.utils.Stack method)
is_song_error() (overture_song.model.SongError class method)
L
libraryStrategy (overture_song.entities.SequencingRead attribute)
list_schemas() (overture_song.client.Api method)
(overture_song.client.Endpoints method)
M
Manifest (class in overture_song.model)
ManifestClient (class in overture_song.client)
ManifestEntry (class in overture_song.model)
matchedNormalSampleSubmitterId (overture_song.entities.VariantCall attribute)
metadata
Metadata (class in overture_song.entities)
N
name (overture_song.entities.Study attribute)
non_null() (in module overture_song.validation)
NOT_UPLOADED (overture_song.tools.FileUploadState attribute)
O
objectId (overture_song.entities.File attribute)
objectize() (in module overture_song.utils)
ObjectRest (class in overture_song.rest)
organization (overture_song.entities.Study attribute)
overture-stack
overture_song (module)
overture_song.client (module)
overture_song.entities (module)
overture_song.model (module)
overture_song.rest (module)
overture_song.tools (module)
overture_song.utils (module)
overture_song.validation (module)
P
pairedEnd (overture_song.entities.SequencingRead attribute)
payload
peek() (overture_song.utils.Stack method)
pop() (overture_song.utils.Stack method)
post() (overture_song.rest.Rest method)
print_upload_states() (overture_song.tools.BatchUploader method)
publish
publish() (overture_song.client.Api method)
(overture_song.client.Endpoints method)
(overture_song.client.UploadClient method)
(overture_song.tools.FileUploadClient method)
publish_all() (overture_song.tools.BatchUploader method)
PUBLISH_ERROR (overture_song.tools.FileUploadState attribute)
PUBLISHED (overture_song.tools.FileUploadState attribute)
push() (overture_song.utils.Stack method)
put() (overture_song.rest.Rest method)
R
read() (overture_song.client.StudyClient method)
referenceGenome (overture_song.entities.SequencingRead attribute)
repeat() (in module overture_song.utils)
Rest (class in overture_song.rest)
S
sample
Sample (class in overture_song.entities)
sample (overture_song.entities.Analysis attribute)
sampleId (overture_song.entities.Sample attribute)
sampleSubmitterId (overture_song.entities.Sample attribute)
sampleType (overture_song.entities.Sample attribute)
save
save() (overture_song.client.Api method)
(overture_song.client.UploadClient method)
(overture_song.tools.FileUploadClient method)
save_all() (overture_song.tools.BatchUploader method)
save_by_id() (overture_song.client.Endpoints method)
SAVE_ERROR (overture_song.tools.FileUploadState attribute)
save_study() (overture_song.client.Api method)
(overture_song.client.Endpoints method)
SAVED (overture_song.tools.FileUploadState attribute)
SequencingRead (class in overture_song.entities)
SequencingReadAnalysis (class in overture_song.entities)
ServerErrors (class in overture_song.model)
set_info() (overture_song.entities.Metadata method)
setup_output_file_path() (in module overture_song.utils)
SimplePayloadBuilder (class in overture_song.tools)
size() (overture_song.utils.Stack method)
SongClientException
SongError
specimen
Specimen (class in overture_song.entities)
specimen (overture_song.entities.CompositeEntity attribute)
specimenClass (overture_song.entities.Specimen attribute)
specimenId (overture_song.entities.Sample attribute)
(overture_song.entities.Specimen attribute)
specimenSubmitterId (overture_song.entities.Specimen attribute)
specimenType (overture_song.entities.Specimen attribute)
Stack (class in overture_song.utils)
status() (overture_song.client.Api method)
(overture_song.client.Endpoints method)
status_all() (overture_song.tools.BatchUploader method)
STATUS_ERROR (overture_song.tools.FileUploadState attribute)
study
Study (class in overture_song.entities)
study (overture_song.entities.Analysis attribute)
STUDY_ID_DOES_NOT_EXIST (overture_song.model.ServerErrors attribute)
StudyClient (class in overture_song.client)
studyId (overture_song.entities.Donor attribute)
(overture_song.entities.File attribute)
(overture_song.entities.Study attribute)
submit
SUBMITTED (overture_song.tools.FileUploadState attribute)
submitter id
suppress() (overture_song.client.Api method)
(overture_song.client.Endpoints method)
T
tab_repeat() (in module overture_song.utils)
to_dict() (overture_song.entities.Entity method)
(overture_song.tools.SimplePayloadBuilder method)
(overture_song.utils.GenericObjectType method)
to_generic_object() (in module overture_song.utils)
to_json() (overture_song.entities.Entity method)
to_pretty_json_string() (in module overture_song.utils)
to_pretty_string() (overture_song.utils.GenericObjectType method)
U
UNKNOWN_ERROR (overture_song.tools.FileUploadState attribute)
unpublish() (overture_song.client.Api method)
(overture_song.client.Endpoints method)
update_file() (overture_song.client.Api method)
(overture_song.client.Endpoints method)
update_status() (overture_song.tools.FileUploadClient method)
upload
upload() (overture_song.client.Api method)
(overture_song.client.Endpoints method)
(overture_song.tools.FileUploadClient method)
upload_all() (overture_song.tools.BatchUploader method)
UPLOAD_ERROR (overture_song.tools.FileUploadState attribute)
upload_file() (overture_song.client.UploadClient method)
UploadClient (class in overture_song.client)
V
Validatable (class in overture_song.validation)
validate() (overture_song.entities.CompositeEntity method)
(overture_song.entities.Donor method)
(overture_song.entities.File method)
(overture_song.entities.Sample method)
(overture_song.entities.SequencingRead method)
(overture_song.entities.SequencingReadAnalysis method)
(overture_song.entities.Specimen method)
(overture_song.entities.Study method)
(overture_song.entities.VariantCall method)
(overture_song.entities.VariantCallAnalysis method)
(overture_song.validation.DataField method)
(overture_song.validation.Validatable method)
VALIDATED (overture_song.tools.FileUploadState attribute)
validation (class in overture_song.validation)
VALIDATION_ERROR (overture_song.tools.FileUploadState attribute)
VariantCall (class in overture_song.entities)
VariantCallAnalysis (class in overture_song.entities)
variantCallingTool (overture_song.entities.VariantCall attribute)
W
whitespace_repeat() (in module overture_song.utils)
write() (overture_song.model.Manifest method)
write_manifest() (overture_song.client.ManifestClient method)
write_object() (in module overture_song.utils)
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v: song-1.4.0
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