Overview
The Data Upload API provides programmatic access to the ImmPort Data Upload Service. This service includes requests for upload, validation, and status information. This API works as access for posting upload/validation registration requests and acquiring information on the the status of a Batch Upload. The API returns a JSON output by default, except for the documentation request that returns a Zip-file. The HTTP method supported by this API is POST (-X POST) in most cases for this version of this API (exceptions will be noted below).
Tools for communicating with the ImmPort Data Upload API
Many third-party tools can be used for communicating with the API and for visualizing API endpoints.
Examples of tools for communicating with the API:
Tool | Type |
---|---|
Curl | Command line tool |
HTTPie | Command line tool |
Postman REST Client | App for Google Chrome and OS X |
DHC REST Client | Google Chrome extension |
Google Chrome | Google Chrome web browser |
This document will use the curl tool for examples.
API Format
Posting uploads/validation and acquiring information about them in the Data Upload API is accomplished by making calls to the API endpoints.
The HTTP URL that corresponds to the Data Upload API endpoint is specified as follows:
[-X POST] -H "Authorization: bearer $token" [-F Parameterization...] https://immport-upload.niaid.nih.gov:8443/data/upload...
The components of the endpoint may require a POST call [-X POST]
,
-F parameterization [-F Parameterization..]
, or a completion of the endpoint
...
. All this information is presented in the table below. The authorization
token -H "Authorization: bearer $token"
is described Section Sample Request
with Authentication below. Each POST endpoint is parameterized using -F
parameterization, while non-POST endpoints have an inline parameter except for
the workspaces endpoint.
Each Data Upload API endpoint represents a specific batch upload action, for example, data upload, data validation, documentation generation, etc.
In the Examples below, the -F parameter uploadPurpose where it appears below MUST BE as provided and should NOT be modified.
Endpoint | POST | Description | HTTP URL | -F Parameterization |
---|---|---|---|---|
Documentation Generation | No | Generate documenation templates for a specific workspace (WORKSPACE_ID) | https://immport-upload.niaid.nih.gov:8443 /data/upload/documentation /templates/WORKSPACE_ID | |
OffLine File(s) Upload | Yes | Request for an off-line upload; creates upload registration in preparation for receipt of the file | https://immport-upload.niaid.nih.gov:8443 /data/upload/type/offline | -F "workspaceId=WORKSPACE_ID" -F "packageName=PACKAGE_NAME" -F "uploadNotes=UPLOAD_NOTES" -F "uploadPurpose=uploadData" -F "serverName=SERVER_NAME" |
Zip-File Upload | Yes | Request upload of a zip-file; transfers file and creates upload registration and performs upload | https://immport-upload.niaid.nih.gov:8443 /data/upload/type/online | -F "workspaceId=WORKSPACE_ID" -F "packageName=" -F "uploadNotes=UPLOAD_NOTES" -F "uploadPurpose=uploadData" -F "serverName=SERVER_NAME" -F "file=@UPLOAD_ZIP_FILE_PATH_ON_CLIENT" |
Multiple Files Upload (Single File) | Yes | Request upload of a single file; transfers file and creates upload registration and performs upload; Note that single file is specified with the following -F parameter, -F "file=@UPLOAD_FILE_PATH_ON_CLIENT" |
https://immport-upload.niaid.nih.gov:8443 /data/upload/type/online | -F "workspaceId=WORKSPACE_ID" -F "packageName=PACKAGE_NAME" -F "uploadNotes=UPLOAD_NOTES" -F "uploadPurpose=uploadData" -F "serverName=SERVER_NAME" -F "file=@UPLOAD_FILE_PATH_ON_CLIENT" |
Multiple Files Upload (Multiple Files) | Yes | Request upload of a several files; transfers files and creates upload registration and performs upload; Note that each file is specified with the following -F parameter, -F "file=@UPLOAD_FILE_PATH_ON_CLIENT" |
https://immport-upload.niaid.nih.gov:8443 /data/upload/type/online | -F "workspaceId=WORKSPACE_ID" -F "packageName=PACKAGE_NAME" -F "uploadNotes=UPLOAD_NOTES" -F "uploadPurpose=uploadData" -F "serverName=SERVER_NAME" -F "file=@UPLOAD_FILE1_PATH_ON_CLIENT" -F "file=@UPLOAD_FILE_PATH_ON_CLIENT" ... |
Zip-file Upload for Validation | Yes | Zip-file validation is a two step process where the zip-file is uploaded to the server and the upload registration generated and then the validation is requested (see Validation of a File) | https://immport-upload.niaid.nih.gov:8443 /data/upload/type/online | -F "workspaceId=WORKSPACE_ID" -F "packageName=" -F "uploadNotes=UPLOAD_NOTES" -F "uploadPurpose=uploadData" -F "serverName=SERVER_NAME" -F "file=@UPLOAD_ZIP_FILE_PATH_ON_CLIENT" |
Mulitple File Upload for Validation (Single File) | Yes | Request a validation of a single file not as a zip-file package; Note that the single file is specified with the following -F parameter, -F "file=@UPLOAD_FILE_PATH_ON_CLIENT" |
https://immport-upload.niaid.nih.gov:8443 /data/upload/type/online | -F "workspaceId=WORKSPACE_ID" -F "packageName=PACKAGE_NAME" -F "uploadNotes=UPLOAD_NOTES" -F "uploadPurpose=validateData" -F "serverName=SERVER_NAME" -F "file=@UPLOAD_FILE_PATH_ON_CLIENT" |
Mulitple File Upload for Validation (Multiple Files) | Yes | Request upload of several files not as a zip-file package; Note that each file is specified with the following -F parameter, -F "file=@UPLOAD_FILE_PATH_ON_CLIENT" |
https://immport-upload.niaid.nih.gov:8443 /data/upload/type/online | -F "workspaceId=WORKSPACE_ID" -F "packageName=PACKAGE_NAME" -F "uploadNotes=UPLOAD_NOTES" -F "uploadPurpose=validateData" -F "serverName=SERVER_NAME" -F "file=@UPLOAD_FILE1_PATH_ON_CLIENT" -F "file=@UPLOAD_FILE_PATH_ON_CLIENT" ... |
Validation of Upload Ticket | Yes | Validaton of job that is identified by the upload ticket number; Note this endpoint uses the -F parameter, -F "uploadTicketNumber=UPLOAD_TICKET_NUMBER" |
https://immport-upload.niaid.nih.gov:8443 /data/upload/validation | -F "uploadTicketNumber=UPLOAD_TICKET_NUMBER" |
Status of Upload Ticket | No | Return the current status of an upload ticket (UPLOAD_TICKET_NUMBER) | https://immport-upload.niaid.nih.gov:8443 /data/upload/registration /UPLOAD_TICKET_NUMBER/status | |
Summary Information on Upload Ticket | No | On completed jobs (either Completed or Rejected), provide the informaton on the upload ticket (UPLOAD_TICKET_NUMBER) | https://immport-upload.niaid.nih.gov:8443 /data/upload/registration /UPLOAD_TICKET_NUMBER/reports/summary | |
Database Information on Upload Ticket | No | On completed jobs (Completed only) provide database information (UPLOAD_TICKET_NUMBER) | https://immport-upload.niaid.nih.gov:8443 /data/upload/registration /UPLOAD_TICKET_NUMBER /reports/database | |
Set of Workspaces | No | Return the set of workspace(s) on which a user can perform and upload or validation | https://immport-upload.niaid.nih.gov:8443/workspaces |
Documentation Generation Request with Authentication
Authentication
All requests to the Data Query API require authentication. The Data Query API uses tokens for authentication.
Users can obtain tokens by posting to the ImmPort Authentication URL
https://auth.immport.org/auth/token
with a username and password.
This can be done by executing the following curl command:
curl -X POST https://auth.immport.org/auth/token -d username="REPLACE_WITH_USERNAME" -d password="REPLACE_WITH_PASSWORD"
response from the above curl command:
{
"status" : 200,
"token" : "eyJhbGciOiJSUzI1NiIsInR5cCI6IkpXV............"
}
The token returned is a JWT token. (You can go to the JWT token
URL and enter the token got from the above
endpoint. This will give the information that the token contains. The token has
information about the username, roles, permissions for the user.
The token must be used to initiate a API request within 60 secs. After 60 secs the token will be invalid and the user will need to get a new token. But once the call is initiated then the token will be valid throughout the entire api request call and does not become invalid until the response is returned.
Using the Authentication Token
All API requests require authentication. They must include the authentication token as an Authorization: bearer in the custom HTTP header.
In the following example, an authentication token is saved as an environment variable (token) and passed to the HTTP header in the curl command to get back the generated documentation specific to a workspace.
The following is an example of a request to the documentation generation endpoint with a single parameter (WORKSPACE_ID=REPLACE_WITH_WORKSPACE_ID).
#!/bin/bash
export token=`curl -X POST https://auth.immport.org/auth/token -d username="REPLACE_WITH_USERNAME" -d password="REPLACE_WITH_PASSWORD" 2>&1 | fgrep '"token"' | sed -e 's/^.*"token" : "//;s/".*$//'`
curl -k -H "Authorization: bearer $token" https://immport-upload.niaid.nih.gov:8443/data/upload/documentation/templates/REPLACE_WITH_WORKSPACE_ID
Zip-file
https://auth.immport.org/auth/token
with the username and password to get an
authentication token. The fgrep command is used to search the response for a token
and then assign the value of the token to an environment variable named
"token".
The second line is a Non-POST endpoint on the URL
https://immport-upload.niaid.nih.gov:8443/data/upload/documentation/templates/REPLACE_WITH_WORKSPACE_ID
with the parameter REPLACE_WITH_WORKSPACE_ID
. The authentication token ("token") is passed in
the HTTP header as shown.
The response will return zip-file containing the template documentation specific to workspace whose workspace_id = REPLACE_WITH_WORKSPACE_ID.
The above shell script or any code starting with #!/bin/bash can be copied to a .sh file (e.g. documentationGeneration.sh ) and executed at the command prompt of a terminal and the output can be directed to a file. (Please replace the REPLACE_WITH_USERNAME with your username and REPLACE_WITH_PASSWORD with your password.)
./documentationGeneration.sh > ImmportTemplates.REPLACE_WITH_WORKSPACE_ID.zip
OffLine File(s) Upload Request with Authentication
The following is an example of an offline request to upload a zip-file, where several -F parameters are used. Note that the packageName parameter needs to be filled in with the name of the upload (file or directory--in this case a file name). The ticket returned should be in Pending. However, since no file (or directory) provided, the ticket will not be acted upon until a file is deposited on the server in the web drop zone.
#!/bin/bash
export token=`curl -X POST https://auth.immport.org/auth/token -d username="REPLACE_WITH_USERNAME" -d password="REPLACE_WITH_PASSWORD" 2>&1 | fgrep '"token"' | sed -e 's/^.*"token" : "//;s/".*$//'`
curl -k -X POST -H "Authorization: bearer $token" -F "workspaceId=REPLACE_WITH_WORKSPACE_ID" -F "packageName=Test.Fcm_Derived_Data.Comprehensive.zip" -F "uploadNotes=" -F "uploadPurpose=uploadData" -F "serverName=" https://immport-upload.niaid.nih.gov:8443/data/upload/type/offline
{
"uploadTicketNumber" : "testuser_20180523_19546",
"uploadPurpose" : "uploadData",
"workspaceId" : 999999,
"status" : "Pending"
}
https://auth.immport.org/auth/token
with the username and password to get an
authentication token. The fgrep command is used to search the response for a token
and then assign the value of the token to an environment variable named
"token".
The second line is a POST on the URL
https://immport-upload.niaid.nih.gov:8443/data/upload/type/offline
with the -F parameterization. The authentication token ("token") is passed
in the HTTP header as shown. The following -F parameters need values:
workspaceId, and packageName, while uploadNotes, and serverName can have
optional values. The value of uploadPurpose must be what is provided above
as-is.
The response will be a json that provides the upload ticket number (used in information enpoints), the upload purpose, the workspace_id, and the current status of the upload request.
The above shell script or any code starting with #!/bin/bash can be copied to a .sh file (e.g. offlineUploadZipFile.sh) and executed at the command prompt of a terminal and the output can be directed to a file. (Please replace the REPLACE_WITH_USERNAME with your username, and REPLACE_WITH_PASSWORD with your password).
./offlineUploadZipFile.sh > offlineUploadZipFile.json
Zip-File Upload Request with Authentication
The following is an example of an online request to upload a zip-file, where several -F parameters are used. Note that packageName parameter must not have a value.
#!/bin/bash
export token=`curl -X POST https://auth.immport.org/auth/token -d username="REPLACE_WITH_USERNAME" -d password="REPLACE_WITH_PASSWORD" 2>&1 | fgrep '"token"' | sed -e 's/^.*"token" : "//;s/".*$//'`
curl -k -X POST -H "Authorization: bearer $token" -F "workspaceId=REPLACE_WITH_WORKSPACE_ID" -F "packageName=" -F "uploadNotes=" -F "uploadPurpose=uploadData" -F "serverName=" -F "file=@/home/tsmith/Downloads/Test.Fcm_Derived_Data.Comprehensive.zip" https://immport-upload.niaid.nih.gov:8443/data/upload/type/online
{
"uploadTicketNumber" : "testuser_20180523_19544",
"uploadPurpose" : "uploadData",
"workspaceId" : 999999,
"status" : "Pending"
}
https://auth.immport.org/auth/token
with the username and password to get an
authentication token. The fgrep command is used to search the response for a token
and then assign the value of the token to an environment variable named
"token".
The second line is a POST on the URL
https://immport-upload.niaid.nih.gov:8443/data/upload/type/online
with the -F parameterization. The authentication token ("token") is passed
in the HTTP header as shown. The following -F parameters need values:
workspaceId and file (client-path to zip-file), while uploadNotes and serverName
can have optional values. The parameter packageName MUST NOT have a value.
The value of uploadPurpose must be what is provided above as-is.
The response will be a json that provides the upload ticket number (used in information endpoints), the upload purpose, the workspace_id, and the current status of the upload request.
The above shell script or any code starting with #!/bin/bash can be copied to a .sh file (e.g. uploadZipFile.sh) and executed at the command prompt of a terminal and the output can be directed to a file. (Please replace the REPLACE_WITH_USERNAME with your username, and REPLACE_WITH_PASSWORD with your password).
./uploadZipFile.sh > uploadZipFile.json
Multiple Files Upload (Single File) Request with Authentication
The following is an example of an online multiple file upload request with a single file, where several -F parameters are used. Note that packageName parameter MUST HAVE a value.
#!/bin/bash
export token=`curl -X POST https://auth.immport.org/auth/token -d username="REPLACE_WITH_USERNAME" -d password="REPLACE_WITH_PASSWORD" 2>&1 | fgrep '"token"' | sed -e 's/^.*"token" : "//;s/".*$//'`
curl -k -X POST -H "Authorization: bearer $token" -F "workspaceId=REPLACE_WITH_WORKSPACE_ID" -F "packageName=multiPartFilesUploadSingleFile" -F "uploadNotes=" -F "uploadPurpose=uploadData" -F "serverName=" -F "file=@/home/tsmith/Downloads/reagents.flow_cytometry.txt" https://immport-upload.niaid.nih.gov:8443/data/upload/type/online
{
"uploadTicketNumber" : "testuser_20180523_19552",
"uploadPurpose" : "uploadData",
"workspaceId" : 999999,
"status" : "Pending"
}
https://auth.immport.org/auth/token
with the username and password to get an
authentication token. The fgrep command is used to search the response for a token
and then assign the value of the token to an environment variable named
"token".
The second line is a POST on the URL
https://immport-upload.niaid.nih.gov:8443/data/upload/type/online
with the -F parameterization. The authentication token ("token") is passed
in the HTTP header as shown. The following -F parameters need values:
workspaceId, packageName, and file (client-path to single file), while
uploadNotes and serverName can have optional values. The parameter
packageName MUST HAVE a value. The value of uploadPurpose must be what
is provided above as-is.
The response will be a json that provides the upload ticket number (to used in information endpoints), the upload purpose, the workspace_id, and the current status of the upload request.
The above shell script or any code starting with #!/bin/bash can be copied to a .sh file (e.g. uploadSingleFile.sh )and executed at the command prompt of a terminal and the output can be directed to a file. (Please replace the REPLACE_WITH_USERNAME with your username, and REPLACE_WITH_PASSWORD with your password).
./uploadSingleFile.sh > uploadSingleFile.json
Multiple Files Upload (Multiple Files) Request with Authentication
The following is an example of an online multiple file upload request with multipe files, where several -F parameters are used. Note that packageName parameter MUST HAVE a value.
#!/bin/bash
export token=`curl -X POST https://auth.immport.org/auth/token -d username="REPLACE_WITH_USERNAME" -d password="REPLACE_WITH_PASSWORD" 2>&1 | fgrep '"token"' | sed -e 's/^.*"token" : "//;s/".*$//'`
curl -k -X POST -H "Authorization: bearer $token" -F "workspaceId=REPLACE_WITH_WORKSPACE_ID" -F "packageName=multiPartFilesUploadMultipleFiles" -F "uploadNotes=" -F "uploadPurpose=uploadData" -F "serverName=" -F "file=@/home/tsmith/Downloads/test_GE.MA.Affy_study_protocol.txt" -F "file=@/home/tsmith/Downloads/protocols.txt" -F "file=@/home/tsmith/Downloads/cn01adv.txt" -F "file=@/home/tsmith/Downloads/basic_study_design.txt" -F "file=@/home/tsmith/Downloads/MBAA_protocol.txt" https://immport-upload.niaid.nih.gov:8443/data/upload/type/online
{
"uploadTicketNumber" : "testuser_20180523_19553",
"uploadPurpose" : "uploadData",
"workspaceId" : 999999,
"status" : "Pending"
}
https://auth.immport.org/auth/token
with the username and password to get an
authentication token. The fgrep command is used search the response for a token
and then assign the value of the token to an environment variable named
"token".
The second line is a POST on the URL
https://immport-upload.niaid.nih.gov:8443/data/upload/type/online
with the -F parameterization. The authentication token ("token") is passed
in the HTTP header as shown. The following -F parameters need values:
workspaceId, packageName, and files (client-path to multiple files), while
uploadNotes and serverName can have optional values. The parameter
packageName MUST HAVE a value. The value of uploadPurpose must be what
is provided above as-is.
The response will be a json that provides the upload ticket number (to used in information endpoints), the upload purpose, the workspace_id, and the current status of the upload request.
The above shell script or any code starting with #!/bin/bash can be copied to a .sh file (e.g. uploadMultipleFiles.sh )and executed at the command prompt of a terminal and the output can be directed to a file. (Please replace the REPLACE_WITH_USERNAME with your username, and REPLACE_WITH_PASSWORD with your password).
./uploadMultipleFiles.sh > uploadMultipleFiles.json
Zip-file Validation Request with Authentication
The following is an example of validation of a zip-file, where several -F parameters are used. Note that packageName parameter must not have a value. Also, validation is a two endpoint (step) process. The first step is to upload the zip-file to the server and create the ticket, and the second is to request the validation of the zip-file. To obtain the validation report, the user must obtain the database report (See Section Database Report Request with Authentication) using the upload ticket number obtained from the validation request.
Zip-file Upload for Validation with Authentication
#!/bin/bash
export token=`curl -X POST https://auth.immport.org/auth/token -d username="REPLACE_WITH_USERNAME" -d password="REPLACE_WITH_PASSWORD" 2>&1 | fgrep '"token"' | sed -e 's/^.*"token" : "//;s/".*$//'`
curl -k -X POST -H "Authorization: bearer $token" -F "workspaceId=REPLACE_WITH_WORKSPACE_ID" -F "packageName=" -F "uploadNotes=" -F "uploadPurpose=validateData" -F "serverName=" -F "file=@/home/tsmith/Downloads/Test.Fcm_Derived_Data.Comprehensive.zip" https://immport-upload.niaid.nih.gov:8443/data/upload/type/online
{
"uploadTicketNumber" : "testuser_20180523_19543",
"uploadPurpose" : "validateData",
"workspaceId" : 999999,
"status" : "Pending_Validation"
}
https://auth.immport.org/auth/token
with the username and password to get an
authentication token. The fgrep command is used search the response for a token
and then assign the value of the token to an environment variable named
"token".
The second line is a POST on the URL
https://immport-upload.niaid.nih.gov:8443/data/upload/type/online
with the -F parameterization. The authentication token ("token") is passed
in the HTTP header as shown. The following parameters need values: workspaceId
and file (client-path to zip-file), while uploadNotes and serverName can have
optional values. The parameter packageName MUST NOT have a value. The
value of uploadPurpose must be what is provided above as-is.
The response will be a json that provides the upload ticket number (to used in information endpoints), the upload purpose, the workspace_id, and the current status of the validation request.
The above shell script or any code starting with #!/bin/bash can be copied to a .sh file (e.g. validateUploadZipFile.sh )and executed at the command prompt of a terminal and the output can be directed to a file. (Please replace the REPLACE_WITH_USERNAME with your username, and REPLACE_WITH_PASSWORD with your password)
./validateUploadZipFile.sh > validateUploadZipFile.json
Validation of Upload Ticket with Authentication
#!/bin/bash
export token=`curl -X POST https://auth.immport.org/auth/token -d username="REPLACE_WITH_USERNAME" -d password="REPLACE_WITH_PASSWORD" 2>&1 | fgrep '"token"' | sed -e 's/^.*"token" : "//;s/".*$//'`
curl -k -X POST -H "Authorization: bearer $token" -F "uploadTicketNumber=testuser_20180523_19543" https://immport-upload.niaid.nih.gov:8443/data/upload/validation
{
"uploadTicketNumber" : "testuser_20180523_19543",
"status" : "Completed_Validation"
}
https://auth.immport.org/auth/token
with the username and password to get an
authentication token. The fgrep command is used search the response for a token
and then assign the value of the token to an environment variable named
"token".
The second line is a POST on the URL
https://immport-upload.niaid.nih.gov:8443/data/upload/validation
The authentication token ("token") is passed in the HTTP header as shown.
The -F parameter uploadTicketNumber must contain the upload ticket number
obtained from the the upload request response above (Upload Zip File to
Server).
The response will be a json that provides the upload ticket number (to used in information endpoints) and the current status of the validation request.
The above shell script or any code starting with #!/bin/bash can be copied to a .sh file (e.g. validateZipFile.sh )and executed at the command prompt of a terminal and the output can be directed to a file. (Please replace the REPLACE_WITH_USERNAME with your username, and REPLACE_WITH_PASSWORD with your password)
./validateZipFile.sh > validateZipFile.json
Mulitple File Upload for Validation (Single File) Request with Authentication
The following is an example of validation of a single file, where several -F parameters are used. Note that packageName parameter MUST HAVE a value. Also, validation is a two endpoint (step) process. The first step is to upload the zip-file to the server and create the ticket, and the second is to request the validation of the zip-file (See SubSection Validate Validation Request above). To obtain the validation report, the user must obtain the database report (See Section Database Report Request with Authentication) using the upload ticket number obtained from the validation request.
Upload Single File to Server with Authentication
#!/bin/bash
export token=`curl -X POST https://auth.immport.org/auth/token -d username="REPLACE_WITH_USERNAME" -d password="REPLACE_WITH_PASSWORD" 2>&1 | fgrep '"token"' | sed -e 's/^.*"token" : "//;s/".*$//'`
curl -k -X POST -H "Authorization: bearer $token" -F "workspaceId=REPLACE_WITH_WORKSPACE_ID" -F "packageName=multiPartFilesValidateOneFile" -F "uploadNotes=" -F "uploadPurpose=validateData" -F "serverName=" -F "file=@/home/tsmith/Downloads/reagents.flow_cytometry.txt" https://immport-upload.niaid.nih.gov:8443/data/upload/type/online
{
"uploadTicketNumber" : "testuser_20180523_19550",
"uploadPurpose" : "validateData",
"workspaceId" : 999999,
"status" : "Pending_Validation"
}
https://auth.immport.org/auth/token
with the username and password to get an
authentication token. The fgrep command is used search the response for a token
and then assign the value of the token to an environment variable named
"token".
The second line is a POST on the URL
https://immport-upload.niaid.nih.gov:8443/data/upload/type/online
with the -F parameterization. The authentication token ("token") is passed
in the HTTP header as shown. The following parameters need values: workspaceId,
packageName and file (client-path to single file), while uploadNotes and
serverName can have optional values. The parameter packageName MUST HAVE a
value. The value of uploadPurpose must be what is provided above as-is.
The response will be a json that provides the upload ticket number (to used in information endpoints), the upload purpose, the workspace_id, and the current status of the validation request.
The above shell script or any code starting with #!/bin/bash can be copied to a .sh file (e.g. validateUploadSingleFile.sh )and executed at the command prompt of a terminal and the output can be directed to a file. (Please replace the REPLACE_WITH_USERNAME with your username, and REPLACE_WITH_PASSWORD with your password)
./validateUploadSingleFile.sh > validateUploadSingleFile.json
Mulitple File Upload for Validation (Multiple Files) Request with Authentication
The following is an example of validation of a multiple files, where several -F parameters are used. Note that packageName parameter MUST HAVE a value. Also, validation is a two endpoint (step) process. The first step is to upload the zip-file to the server and create the ticket, and the second is to request the validation of the zip-file (See SubSection Validate Validation Request above). To obtain the validation report, the user must obtain the database report (See Section Database Report Request with Authentication) using the upload ticket number obtained from the validation request.
Upload Multiple Files to Server with Authentication
#!/bin/bash
export token=`curl -X POST https://auth.immport.org/auth/token -d username="REPLACE_WITH_USERNAME" -d password="REPLACE_WITH_PASSWORD" 2>&1 | fgrep '"token"' | sed -e 's/^.*"token" : "//;s/".*$//'`
curl -k -X POST -H "Authorization: bearer $token" -F "workspaceId=REPLACE_WITH_WORKSPACE_ID" -F "packageName=multiPartFilesValidateMultipleFiles" -F "uploadNotes=" -F "uploadPurpose=validateData" -F "serverName=" -F "file=@/home/tsmith/Downloads/test_GE.MA.Affy_study_protocol.txt" -F "file=@/home/tsmith/Downloads/protocols.txt" -F "file=@/home/tsmith/Downloads/cn01adv.txt" -F "file=@/home/tsmith/Downloads/basic_study_design.txt" -F "file=@/home/tsmith/Downloads/MBAA_protocol.txt" https://immport-upload.niaid.nih.gov:8443/data/upload/type/online
{
"uploadTicketNumber" : "testuser_20180523_19551",
"uploadPurpose" : "validateData",
"workspaceId" : 999999,
"status" : "Pending_Validation"
}
https://auth.immport.org/auth/token
with the username and password to get an
authentication token. The fgrep command is used search the response for a token
and then assign the value of the token to an environment variable named
"token".
The second line is a POST on the URL
https://immport-upload.niaid.nih.gov:8443/data/upload/type/online
with the -F parameterization. The authentication token ("token") is passed
in the HTTP header as shown. The following parameters need values: workspaceId,
packageName and file (client-path to each of multiple files), while uploadNotes
and serverName can have optional values. The parameter packageName MUST
HAVE a value. The value of uploadPurpose must be what is provided above
as-is.
The response will be a json that provides the upload ticket number (to used in information endpoints), the upload purpose, the workspace_id, and the current status of the validation request.
The above shell script or any code starting with #!/bin/bash can be copied to a .sh file (e.g. validateUploadMultipleFiles.sh )and executed at the command prompt of a terminal and the output can be directed to a file. (Please replace the REPLACE_WITH_USERNAME with your username, and REPLACE_WITH_PASSWORD with your password)
./validateUploadMultipleFiles.sh > validateUploadMultipleFiles.json
Status of Upload Ticket with Authentication
The following is an example of a request for status of an upload ticket number where an inline parameter (UPLOAD_TICKET_NUMBER) is used.
#!/bin/bash
export token=`curl -X POST https://auth.immport.org/auth/token -d username="REPLACE_WITH_USERNAME" -d password="REPLACE_WITH_PASSWORD" 2>&1 | fgrep '"token"' | sed -e 's/^.*"token" : "//;s/".*$//'`
curl -k -H "Authorization: bearer $token" https://immport-upload.niaid.nih.gov:8443/data/upload/registration/testuser_20180523_19544/status
{
"uploadTicketNumber" : "testuser_20180523_19544",
"status" : "Completed"
}
https://auth.immport.org/auth/token
with the username and password to get an
authentication token. The fgrep command is used search the response for a token
and then assign the value of the token to an environment variable named
"token".
The second line is an inline Non-POST URL
/data/upload/registration/testuser_20180523_19544/status
with the inline parameterization, UPLOAD_TICKET_NUMBER. The authentication token
("token") is passed in the HTTP header as shown.
The response will be json that provides the current status of the request.
The above shell script or any code starting with #!/bin/bash can be copied to a .sh file (e.g. uploadStatus.sh )and executed at the command prompt of a terminal and the output can be directed to a file. (Please replace the REPLACE_WITH_USERNAME with your username, and REPLACE_WITH_PASSWORD with your password).
./uploadStatus.sh > uploadStatus.json
Summary Information on Upload Ticket Request with Authentication
The following is an example of a request for summary report status of a validation using an upload ticket number, where an inline parameter (UPLOAD_TICKET_NUMBER) is used.
#!/bin/bash
#########################
### Validation Ticket ###
#########################
export token=`curl -X POST https://auth.immport.org/auth/token -d username="REPLACE_WITH_USERNAME" -d password="REPLACE_WITH_PASSWORD" 2>&1 | fgrep '"token"' | sed -e 's/^.*"token" : "//;s/".*$//'`
curl -k -H "Authorization: bearer $token" https://immport-upload.niaid.nih.gov:8443/data/upload/registration/testuser_20180523_19543/reports/summary
#########################
### Validation Ticket ###
#########################
{
"summary" : {
"uploadRegistrationId" : 19543,
"workspaceName" : "Test Creation Scripts I",
"fileName" : "Test.Fcm_Derived_Data.Comprehensive.zip",
"status" : "Completed_Validation",
"uploadTicketNumber" : "testuser_20180523_19543",
"dateCreated" : "2018-05-23",
"createdBy" : "testuser",
"uploadMethod" : "Secure Web",
"uploadRegistrationResults" : [ {
"uploadRegistrationResultId" : 1101351,
"description" : "server name:client-server",
"errorMessage" : null,
"fileName" : "Test.Fcm_Derived_Data.Comprehensive.zip",
"lineNumber" : null,
"status" : "Completed_Validation",
"uploadTicketNumber" : "testuser_20180523_19543",
"dateCreated" : "2018-05-23",
"createdBy" : "testuser",
"dateLastUpdated" : "2018-05-23",
"lastUpdatedBy" : "testuser"
} ]
},
"uploadTicketNumber" : "testuser_20180523_19543",
"type" : "summary"
}
#!/bin/bash
#####################
### Upload Ticket ###
#####################
export token=`curl -X POST https://auth.immport.org/auth/token -d username="REPLACE_WITH_USERNAME" -d password="REPLACE_WITH_PASSWORD" 2>&1 | fgrep '"token"' | sed -e 's/^.*"token" : "//;s/".*$//'`
curl -k -H "Authorization: bearer $token" https://immport-upload.niaid.nih.gov:8443/data/upload/registration/testuser_20180523_19544/reports/summary
#####################
### Upload Ticket ###
#####################
{
"summary" : {
"uploadRegistrationId" : 19544,
"workspaceName" : "Test Creation Scripts I",
"fileName" : "Test.Fcm_Derived_Data.Comprehensive.zip",
"status" : "Completed",
"uploadTicketNumber" : "testuser_20180523_19544",
"dateCreated" : "2018-05-23",
"createdBy" : "testuser",
"uploadMethod" : "Secure Web",
"uploadRegistrationResults" : [ {
"uploadRegistrationResultId" : 1101260,
"description" : "server name:client-server",
"errorMessage" : null,
"fileName" : "Test.Fcm_Derived_Data.Comprehensive.zip",
"lineNumber" : null,
"status" : "Registered",
"uploadTicketNumber" : "testuser_20180523_19544",
"dateCreated" : "2018-05-23",
"createdBy" : "testuser",
"dateLastUpdated" : "2018-05-23",
"lastUpdatedBy" : "testuser"
}, {
"uploadRegistrationResultId" : 1101261,
"description" : null,
"errorMessage" : null,
"fileName" : "testuser_20180523_19544___Test.Fcm_Derived_Data.Comprehensive.zip",
"lineNumber" : null,
"status" : "Started",
"uploadTicketNumber" : "testuser_20180523_19544",
"dateCreated" : "2018-05-23",
"createdBy" : "testuser",
"dateLastUpdated" : "2018-05-23",
"lastUpdatedBy" : "testuser"
}, {
"uploadRegistrationResultId" : 1101262,
"description" : "Template: protocols.txt, Size:748 bytes",
"errorMessage" : null,
"fileName" : "protocols.txt",
"lineNumber" : null,
"status" : "Parsing",
"uploadTicketNumber" : "testuser_20180523_19544",
"dateCreated" : "2018-05-23",
"createdBy" : "testuser",
"dateLastUpdated" : "2018-05-23",
"lastUpdatedBy" : "testuser"
}, {
"uploadRegistrationResultId" : 1101263,
"description" : "Validation Level = Standard",
"errorMessage" : null,
"fileName" : "protocols.txt",
"lineNumber" : null,
"status" : "Information",
"uploadTicketNumber" : "testuser_20180523_19544",
"dateCreated" : "2018-05-23",
"createdBy" : "testuser",
"dateLastUpdated" : "2018-05-23",
"lastUpdatedBy" : "testuser"
}, {
"uploadRegistrationResultId" : 1101264,
"description" : "Size:748 bytes",
"errorMessage" : null,
"fileName" : "protocols.txt",
"lineNumber" : 3,
"status" : "Stored in:file_info",
"uploadTicketNumber" : "testuser_20180523_19544",
"dateCreated" : "2018-05-23",
"createdBy" : "testuser",
"dateLastUpdated" : "2018-05-23",
"lastUpdatedBy" : "testuser"
}, {
"uploadRegistrationResultId" : 1101265,
"description" : "Size:48046 bytes",
"errorMessage" : null,
"fileName" : "Splenic_B_cell_isolation.pdf",
"lineNumber" : 4,
"status" : "Stored in:protocols",
"uploadTicketNumber" : "testuser_20180523_19544",
"dateCreated" : "2018-05-23",
"createdBy" : "testuser",
"dateLastUpdated" : "2018-05-23",
"lastUpdatedBy" : "testuser"
}, {
"uploadRegistrationResultId" : 1101266,
"description" : "Size:13743 bytes",
"errorMessage" : null,
"fileName" : "Culture_conditions.pdf",
"lineNumber" : 5,
"status" : "Stored in:protocols",
"uploadTicketNumber" : "testuser_20180523_19544",
"dateCreated" : "2018-05-23",
"createdBy" : "testuser",
"dateLastUpdated" : "2018-05-23",
"lastUpdatedBy" : "testuser"
}, {
"uploadRegistrationResultId" : 1101267,
"description" : "Size:18944 bytes",
"errorMessage" : null,
"fileName" : "FlowCytometryProtocol.xls",
"lineNumber" : 6,
"status" : "Stored in:protocols",
"uploadTicketNumber" : "testuser_20180523_19544",
"dateCreated" : "2018-05-23",
"createdBy" : "testuser",
"dateLastUpdated" : "2018-05-23",
"lastUpdatedBy" : "testuser"
}, {
"uploadRegistrationResultId" : 1101268,
"description" : "Size:30 bytes",
"errorMessage" : null,
"fileName" : "example animal study protocol.txt",
"lineNumber" : 7,
"status" : "Stored in:protocols",
"uploadTicketNumber" : "testuser_20180523_19544",
"dateCreated" : "2018-05-23",
"createdBy" : "testuser",
"dateLastUpdated" : "2018-05-23",
"lastUpdatedBy" : "testuser"
}, {
"uploadRegistrationResultId" : 1101269,
"description" : "Template: protocols.txt, Size:748 bytes",
"errorMessage" : null,
"fileName" : "protocols.txt",
"lineNumber" : null,
"status" : "Parsed",
"uploadTicketNumber" : "testuser_20180523_19544",
"dateCreated" : "2018-05-23",
"createdBy" : "testuser",
"dateLastUpdated" : "2018-05-23",
"lastUpdatedBy" : "testuser"
}, {
"uploadRegistrationResultId" : 1101270,
"description" : "Template: reagents.flow_cytometry.txt, Size:1157 bytes",
"errorMessage" : null,
"fileName" : "reagents.flow_cytometry.txt",
"lineNumber" : null,
"status" : "Parsing",
"uploadTicketNumber" : "testuser_20180523_19544",
"dateCreated" : "2018-05-23",
"createdBy" : "testuser",
"dateLastUpdated" : "2018-05-23",
"lastUpdatedBy" : "testuser"
}, {
"uploadRegistrationResultId" : 1101271,
"description" : "Validation Level = Standard",
"errorMessage" : null,
"fileName" : "reagents.flow_cytometry.txt",
"lineNumber" : null,
"status" : "Information",
"uploadTicketNumber" : "testuser_20180523_19544",
"dateCreated" : "2018-05-23",
"createdBy" : "testuser",
"dateLastUpdated" : "2018-05-23",
"lastUpdatedBy" : "testuser"
}, {
"uploadRegistrationResultId" : 1101272,
"description" : "Size:1157 bytes",
"errorMessage" : null,
"fileName" : "reagents.flow_cytometry.txt",
"lineNumber" : 3,
"status" : "Stored in:file_info",
"uploadTicketNumber" : "testuser_20180523_19544",
"dateCreated" : "2018-05-23",
"createdBy" : "testuser",
"dateLastUpdated" : "2018-05-23",
"lastUpdatedBy" : "testuser"
}, {
"uploadRegistrationResultId" : 1101273,
"description" : "Template: reagents.flow_cytometry.txt, Size:1157 bytes",
"errorMessage" : null,
"fileName" : "reagents.flow_cytometry.txt",
"lineNumber" : null,
"status" : "Parsed",
"uploadTicketNumber" : "testuser_20180523_19544",
"dateCreated" : "2018-05-23",
"createdBy" : "testuser",
"dateLastUpdated" : "2018-05-23",
"lastUpdatedBy" : "testuser"
}, {
"uploadRegistrationResultId" : 1101274,
"description" : "Template: reagent_sets.txt, Size:458 bytes",
"errorMessage" : null,
"fileName" : "reagent_sets.txt",
"lineNumber" : null,
"status" : "Parsing",
"uploadTicketNumber" : "testuser_20180523_19544",
"dateCreated" : "2018-05-23",
"createdBy" : "testuser",
"dateLastUpdated" : "2018-05-23",
"lastUpdatedBy" : "testuser"
}, {
"uploadRegistrationResultId" : 1101275,
"description" : "Validation Level = Standard",
"errorMessage" : null,
"fileName" : "reagent_sets.txt",
"lineNumber" : null,
"status" : "Information",
"uploadTicketNumber" : "testuser_20180523_19544",
"dateCreated" : "2018-05-23",
"createdBy" : "testuser",
"dateLastUpdated" : "2018-05-23",
"lastUpdatedBy" : "testuser"
}, {
"uploadRegistrationResultId" : 1101276,
"description" : "Size:458 bytes",
"errorMessage" : null,
"fileName" : "reagent_sets.txt",
"lineNumber" : 3,
"status" : "Stored in:file_info",
"uploadTicketNumber" : "testuser_20180523_19544",
"dateCreated" : "2018-05-23",
"createdBy" : "testuser",
"dateLastUpdated" : "2018-05-23",
"lastUpdatedBy" : "testuser"
}, {
"uploadRegistrationResultId" : 1101277,
"description" : "Template: reagent_sets.txt, Size:458 bytes",
"errorMessage" : null,
"fileName" : "reagent_sets.txt",
"lineNumber" : null,
"status" : "Parsed",
"uploadTicketNumber" : "testuser_20180523_19544",
"dateCreated" : "2018-05-23",
"createdBy" : "testuser",
"dateLastUpdated" : "2018-05-23",
"lastUpdatedBy" : "testuser"
}, {
"uploadRegistrationResultId" : 1101278,
"description" : "Template: treatments.txt, Size:420 bytes",
"errorMessage" : null,
"fileName" : "treatments.txt",
"lineNumber" : null,
"status" : "Parsing",
"uploadTicketNumber" : "testuser_20180523_19544",
"dateCreated" : "2018-05-23",
"createdBy" : "testuser",
"dateLastUpdated" : "2018-05-23",
"lastUpdatedBy" : "testuser"
}, {
"uploadRegistrationResultId" : 1101279,
"description" : "Validation Level = Standard",
"errorMessage" : null,
"fileName" : "treatments.txt",
"lineNumber" : null,
"status" : "Information",
"uploadTicketNumber" : "testuser_20180523_19544",
"dateCreated" : "2018-05-23",
"createdBy" : "testuser",
"dateLastUpdated" : "2018-05-23",
"lastUpdatedBy" : "testuser"
}, {
"uploadRegistrationResultId" : 1101280,
"description" : "Size:420 bytes",
"errorMessage" : null,
"fileName" : "treatments.txt",
"lineNumber" : 3,
"status" : "Stored in:file_info",
"uploadTicketNumber" : "testuser_20180523_19544",
"dateCreated" : "2018-05-23",
"createdBy" : "testuser",
"dateLastUpdated" : "2018-05-23",
"lastUpdatedBy" : "testuser"
}, {
"uploadRegistrationResultId" : 1101281,
"description" : "Template: treatments.txt, Size:420 bytes",
"errorMessage" : null,
"fileName" : "treatments.txt",
"lineNumber" : null,
"status" : "Parsed",
"uploadTicketNumber" : "testuser_20180523_19544",
"dateCreated" : "2018-05-23",
"createdBy" : "testuser",
"dateLastUpdated" : "2018-05-23",
"lastUpdatedBy" : "testuser"
}, {
"uploadRegistrationResultId" : 1101282,
"description" : "Template: basic_study_design.txt, Size:1877 bytes",
"errorMessage" : null,
"fileName" : "basic_study_design.txt",
"lineNumber" : null,
"status" : "Parsing",
"uploadTicketNumber" : "testuser_20180523_19544",
"dateCreated" : "2018-05-23",
"createdBy" : "testuser",
"dateLastUpdated" : "2018-05-23",
"lastUpdatedBy" : "testuser"
}, {
"uploadRegistrationResultId" : 1101283,
"description" : "Validation Level = Standard",
"errorMessage" : null,
"fileName" : "basic_study_design.txt",
"lineNumber" : null,
"status" : "Information",
"uploadTicketNumber" : "testuser_20180523_19544",
"dateCreated" : "2018-05-23",
"createdBy" : "testuser",
"dateLastUpdated" : "2018-05-23",
"lastUpdatedBy" : "testuser"
}, {
"uploadRegistrationResultId" : 1101284,
"description" : "Size:1877 bytes",
"errorMessage" : null,
"fileName" : "basic_study_design.txt",
"lineNumber" : 3,
"status" : "Stored in:file_info",
"uploadTicketNumber" : "testuser_20180523_19544",
"dateCreated" : "2018-05-23",
"createdBy" : "testuser",
"dateLastUpdated" : "2018-05-23",
"lastUpdatedBy" : "testuser"
}, {
"uploadRegistrationResultId" : 1101285,
"description" : "Size:92 bytes",
"errorMessage" : null,
"fileName" : "Information_1.txt",
"lineNumber" : 46,
"status" : "Stored in:study_file",
"uploadTicketNumber" : "testuser_20180523_19544",
"dateCreated" : "2018-05-23",
"createdBy" : "testuser",
"dateLastUpdated" : "2018-05-23",
"lastUpdatedBy" : "testuser"
}, {
"uploadRegistrationResultId" : 1101286,
"description" : "Template: basic_study_design.txt, Size:1877 bytes",
"errorMessage" : null,
"fileName" : "basic_study_design.txt",
"lineNumber" : null,
"status" : "Parsed",
"uploadTicketNumber" : "testuser_20180523_19544",
"dateCreated" : "2018-05-23",
"createdBy" : "testuser",
"dateLastUpdated" : "2018-05-23",
"lastUpdatedBy" : "testuser"
}, {
"uploadRegistrationResultId" : 1101287,
"description" : "Template: subjectsanimal.txt, Size:889 bytes",
"errorMessage" : null,
"fileName" : "subjectsAnimal.txt",
"lineNumber" : null,
"status" : "Parsing",
"uploadTicketNumber" : "testuser_20180523_19544",
"dateCreated" : "2018-05-23",
"createdBy" : "testuser",
"dateLastUpdated" : "2018-05-23",
"lastUpdatedBy" : "testuser"
}, {
"uploadRegistrationResultId" : 1101288,
"description" : "Validation Level = Standard",
"errorMessage" : null,
"fileName" : "subjectsAnimal.txt",
"lineNumber" : null,
"status" : "Information",
"uploadTicketNumber" : "testuser_20180523_19544",
"dateCreated" : "2018-05-23",
"createdBy" : "testuser",
"dateLastUpdated" : "2018-05-23",
"lastUpdatedBy" : "testuser"
}, {
"uploadRegistrationResultId" : 1101289,
"description" : "Size:889 bytes",
"errorMessage" : null,
"fileName" : "subjectsAnimal.txt",
"lineNumber" : 3,
"status" : "Stored in:file_info",
"uploadTicketNumber" : "testuser_20180523_19544",
"dateCreated" : "2018-05-23",
"createdBy" : "testuser",
"dateLastUpdated" : "2018-05-23",
"lastUpdatedBy" : "testuser"
}, {
"uploadRegistrationResultId" : 1101290,
"description" : "Template: subjectsanimal.txt, Size:889 bytes",
"errorMessage" : null,
"fileName" : "subjectsAnimal.txt",
"lineNumber" : null,
"status" : "Parsed",
"uploadTicketNumber" : "testuser_20180523_19544",
"dateCreated" : "2018-05-23",
"createdBy" : "testuser",
"dateLastUpdated" : "2018-05-23",
"lastUpdatedBy" : "testuser"
}, {
"uploadRegistrationResultId" : 1101291,
"description" : "Template: biosamples.txt, Size:1547 bytes",
"errorMessage" : null,
"fileName" : "bioSamples.txt",
"lineNumber" : null,
"status" : "Parsing",
"uploadTicketNumber" : "testuser_20180523_19544",
"dateCreated" : "2018-05-23",
"createdBy" : "testuser",
"dateLastUpdated" : "2018-05-23",
"lastUpdatedBy" : "testuser"
}, {
"uploadRegistrationResultId" : 1101292,
"description" : "Validation Level = Standard",
"errorMessage" : null,
"fileName" : "bioSamples.txt",
"lineNumber" : null,
"status" : "Information",
"uploadTicketNumber" : "testuser_20180523_19544",
"dateCreated" : "2018-05-23",
"createdBy" : "testuser",
"dateLastUpdated" : "2018-05-23",
"lastUpdatedBy" : "testuser"
}, {
"uploadRegistrationResultId" : 1101293,
"description" : "Size:1547 bytes",
"errorMessage" : null,
"fileName" : "bioSamples.txt",
"lineNumber" : 3,
"status" : "Stored in:file_info",
"uploadTicketNumber" : "testuser_20180523_19544",
"dateCreated" : "2018-05-23",
"createdBy" : "testuser",
"dateLastUpdated" : "2018-05-23",
"lastUpdatedBy" : "testuser"
}, {
"uploadRegistrationResultId" : 1101294,
"description" : "Template: biosamples.txt, Size:1547 bytes",
"errorMessage" : null,
"fileName" : "bioSamples.txt",
"lineNumber" : null,
"status" : "Parsed",
"uploadTicketNumber" : "testuser_20180523_19544",
"dateCreated" : "2018-05-23",
"createdBy" : "testuser",
"dateLastUpdated" : "2018-05-23",
"lastUpdatedBy" : "testuser"
}, {
"uploadRegistrationResultId" : 1101295,
"description" : "Template: experiments.txt, Size:545 bytes",
"errorMessage" : null,
"fileName" : "experiments.txt",
"lineNumber" : null,
"status" : "Parsing",
"uploadTicketNumber" : "testuser_20180523_19544",
"dateCreated" : "2018-05-23",
"createdBy" : "testuser",
"dateLastUpdated" : "2018-05-23",
"lastUpdatedBy" : "testuser"
}, {
"uploadRegistrationResultId" : 1101296,
"description" : "Validation Level = Standard",
"errorMessage" : null,
"fileName" : "experiments.txt",
"lineNumber" : null,
"status" : "Information",
"uploadTicketNumber" : "testuser_20180523_19544",
"dateCreated" : "2018-05-23",
"createdBy" : "testuser",
"dateLastUpdated" : "2018-05-23",
"lastUpdatedBy" : "testuser"
}, {
"uploadRegistrationResultId" : 1101297,
"description" : "Size:545 bytes",
"errorMessage" : null,
"fileName" : "experiments.txt",
"lineNumber" : 3,
"status" : "Stored in:file_info",
"uploadTicketNumber" : "testuser_20180523_19544",
"dateCreated" : "2018-05-23",
"createdBy" : "testuser",
"dateLastUpdated" : "2018-05-23",
"lastUpdatedBy" : "testuser"
}, {
"uploadRegistrationResultId" : 1101298,
"description" : "Template: experiments.txt, Size:545 bytes",
"errorMessage" : null,
"fileName" : "experiments.txt",
"lineNumber" : null,
"status" : "Parsed",
"uploadTicketNumber" : "testuser_20180523_19544",
"dateCreated" : "2018-05-23",
"createdBy" : "testuser",
"dateLastUpdated" : "2018-05-23",
"lastUpdatedBy" : "testuser"
}, {
"uploadRegistrationResultId" : 1101299,
"description" : "Template: experimentsamples.flow_cytometry.txt, Size:1038 bytes",
"errorMessage" : null,
"fileName" : "experimentSamples.Flow_Cytometry.txt",
"lineNumber" : null,
"status" : "Parsing",
"uploadTicketNumber" : "testuser_20180523_19544",
"dateCreated" : "2018-05-23",
"createdBy" : "testuser",
"dateLastUpdated" : "2018-05-23",
"lastUpdatedBy" : "testuser"
}, {
"uploadRegistrationResultId" : 1101300,
"description" : "Validation Level = Standard",
"errorMessage" : null,
"fileName" : "experimentSamples.Flow_Cytometry.txt",
"lineNumber" : null,
"status" : "Information",
"uploadTicketNumber" : "testuser_20180523_19544",
"dateCreated" : "2018-05-23",
"createdBy" : "testuser",
"dateLastUpdated" : "2018-05-23",
"lastUpdatedBy" : "testuser"
}, {
"uploadRegistrationResultId" : 1101301,
"description" : "Size:1038 bytes",
"errorMessage" : null,
"fileName" : "experimentSamples.Flow_Cytometry.txt",
"lineNumber" : 2,
"status" : "Stored in:file_info",
"uploadTicketNumber" : "testuser_20180523_19544",
"dateCreated" : "2018-05-23",
"createdBy" : "testuser",
"dateLastUpdated" : "2018-05-23",
"lastUpdatedBy" : "testuser"
}, {
"uploadRegistrationResultId" : 1101302,
"description" : "The combined status for expsample_id (FlowCyt ES 101806_1) and table expsample has values: expsample_required (yes), expsample_user_defined_id (FlowCyt ES 101806_1), and expsample_accession ().",
"errorMessage" : null,
"fileName" : "experimentSamples.Flow_Cytometry.txt",
"lineNumber" : 3,
"status" : "Information",
"uploadTicketNumber" : "testuser_20180523_19544",
"dateCreated" : "2018-05-23",
"createdBy" : "testuser",
"dateLastUpdated" : "2018-05-23",
"lastUpdatedBy" : "testuser"
}, {
"uploadRegistrationResultId" : 1101303,
"description" : "The combined status for biosample_id (Splenic_B-cells_untreated) and table biosample has values: biosample_required (no), biosample_user_defined_id (Splenic_B-cells_untreated), and biosample_accession (BS935311).",
"errorMessage" : null,
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"createdBy" : "testuser",
"dateLastUpdated" : "2018-05-23",
"lastUpdatedBy" : "testuser"
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"createdBy" : "testuser",
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"lastUpdatedBy" : "testuser"
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"status" : "Information",
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"lastUpdatedBy" : "testuser"
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"status" : "Information",
"uploadTicketNumber" : "testuser_20180523_19544",
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"createdBy" : "testuser",
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"lastUpdatedBy" : "testuser"
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"description" : "The value in experiment_study_accession (SDY1897) is assigned to study_accession.",
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"status" : "Information",
"uploadTicketNumber" : "testuser_20180523_19544",
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"createdBy" : "testuser",
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"lastUpdatedBy" : "testuser"
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"errorMessage" : null,
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"createdBy" : "testuser",
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"errorMessage" : null,
"fileName" : "CompensationTube_001.fcs",
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"errorMessage" : null,
"fileName" : "CompensationTube_002.fcs",
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"status" : "Stored in:file_info",
"uploadTicketNumber" : "testuser_20180523_19544",
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"createdBy" : "testuser",
"dateLastUpdated" : "2018-05-23",
"lastUpdatedBy" : "testuser"
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"status" : "Information",
"uploadTicketNumber" : "testuser_20180523_19544",
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"createdBy" : "testuser",
"dateLastUpdated" : "2018-05-23",
"lastUpdatedBy" : "testuser"
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"status" : "Information",
"uploadTicketNumber" : "testuser_20180523_19544",
"dateCreated" : "2018-05-23",
"createdBy" : "testuser",
"dateLastUpdated" : "2018-05-23",
"lastUpdatedBy" : "testuser"
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"description" : "The combined status for experiment_id (FlowCyt Expt) and table experiment has values: experiment_required (no), experiment_user_defined_id (FlowCyt Expt), and experiment_accession (EXP15457).",
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"fileName" : "experimentSamples.Flow_Cytometry.txt",
"lineNumber" : 4,
"status" : "Information",
"uploadTicketNumber" : "testuser_20180523_19544",
"dateCreated" : "2018-05-23",
"createdBy" : "testuser",
"dateLastUpdated" : "2018-05-23",
"lastUpdatedBy" : "testuser"
}, {
"uploadRegistrationResultId" : 1101315,
"description" : "The parent accession biosample_study_accession (SDY1897) was set using the table biosample and biosample_accession (BS935312).",
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"status" : "Information",
"uploadTicketNumber" : "testuser_20180523_19544",
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"createdBy" : "testuser",
"dateLastUpdated" : "2018-05-23",
"lastUpdatedBy" : "testuser"
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"description" : "The parent accession experiment_study_accession (SDY1897) was set using the table experiment and experiment_accession (EXP15457).",
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"fileName" : "experimentSamples.Flow_Cytometry.txt",
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"status" : "Information",
"uploadTicketNumber" : "testuser_20180523_19544",
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"createdBy" : "testuser",
"dateLastUpdated" : "2018-05-23",
"lastUpdatedBy" : "testuser"
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"uploadRegistrationResultId" : 1101317,
"description" : "The value in experiment_study_accession (SDY1897) is assigned to study_accession.",
"errorMessage" : null,
"fileName" : "experimentSamples.Flow_Cytometry.txt",
"lineNumber" : 4,
"status" : "Information",
"uploadTicketNumber" : "testuser_20180523_19544",
"dateCreated" : "2018-05-23",
"createdBy" : "testuser",
"dateLastUpdated" : "2018-05-23",
"lastUpdatedBy" : "testuser"
}, {
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"description" : "Size:201530 bytes",
"errorMessage" : null,
"fileName" : "Specimen_001_Tube_002.fcs",
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"status" : "Stored in:file_info",
"uploadTicketNumber" : "testuser_20180523_19544",
"dateCreated" : "2018-05-23",
"createdBy" : "testuser",
"dateLastUpdated" : "2018-05-23",
"lastUpdatedBy" : "testuser"
}, {
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"description" : "The combined status for expsample_id (FlowCyt ES 101806_3) and table expsample has values: expsample_required (yes), expsample_user_defined_id (FlowCyt ES 101806_3), and expsample_accession ().",
"errorMessage" : null,
"fileName" : "experimentSamples.Flow_Cytometry.txt",
"lineNumber" : 5,
"status" : "Information",
"uploadTicketNumber" : "testuser_20180523_19544",
"dateCreated" : "2018-05-23",
"createdBy" : "testuser",
"dateLastUpdated" : "2018-05-23",
"lastUpdatedBy" : "testuser"
}, {
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"description" : "The combined status for biosample_id (Splenic_B-cells_treated_with_Anti-IgM) and table biosample has values: biosample_required (no), biosample_user_defined_id (Splenic_B-cells_treated_with_Anti-IgM), and biosample_accession (BS935313).",
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"fileName" : "experimentSamples.Flow_Cytometry.txt",
"lineNumber" : 5,
"status" : "Information",
"uploadTicketNumber" : "testuser_20180523_19544",
"dateCreated" : "2018-05-23",
"createdBy" : "testuser",
"dateLastUpdated" : "2018-05-23",
"lastUpdatedBy" : "testuser"
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"description" : "The combined status for experiment_id (FlowCyt Expt) and table experiment has values: experiment_required (no), experiment_user_defined_id (FlowCyt Expt), and experiment_accession (EXP15457).",
"errorMessage" : null,
"fileName" : "experimentSamples.Flow_Cytometry.txt",
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"status" : "Information",
"uploadTicketNumber" : "testuser_20180523_19544",
"dateCreated" : "2018-05-23",
"createdBy" : "testuser",
"dateLastUpdated" : "2018-05-23",
"lastUpdatedBy" : "testuser"
}, {
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"description" : "The parent accession biosample_study_accession (SDY1897) was set using the table biosample and biosample_accession (BS935313).",
"errorMessage" : null,
"fileName" : "experimentSamples.Flow_Cytometry.txt",
"lineNumber" : 5,
"status" : "Information",
"uploadTicketNumber" : "testuser_20180523_19544",
"dateCreated" : "2018-05-23",
"createdBy" : "testuser",
"dateLastUpdated" : "2018-05-23",
"lastUpdatedBy" : "testuser"
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"description" : "The parent accession experiment_study_accession (SDY1897) was set using the table experiment and experiment_accession (EXP15457).",
"errorMessage" : null,
"fileName" : "experimentSamples.Flow_Cytometry.txt",
"lineNumber" : 5,
"status" : "Information",
"uploadTicketNumber" : "testuser_20180523_19544",
"dateCreated" : "2018-05-23",
"createdBy" : "testuser",
"dateLastUpdated" : "2018-05-23",
"lastUpdatedBy" : "testuser"
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"description" : "The value in experiment_study_accession (SDY1897) is assigned to study_accession.",
"errorMessage" : null,
"fileName" : "experimentSamples.Flow_Cytometry.txt",
"lineNumber" : 5,
"status" : "Information",
"uploadTicketNumber" : "testuser_20180523_19544",
"dateCreated" : "2018-05-23",
"createdBy" : "testuser",
"dateLastUpdated" : "2018-05-23",
"lastUpdatedBy" : "testuser"
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"description" : "Size:201529 bytes",
"errorMessage" : null,
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"lineNumber" : 6,
"status" : "Stored in:file_info",
"uploadTicketNumber" : "testuser_20180523_19544",
"dateCreated" : "2018-05-23",
"createdBy" : "testuser",
"dateLastUpdated" : "2018-05-23",
"lastUpdatedBy" : "testuser"
}, {
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"description" : "The combined status for expsample_id (FlowCyt ES 101806_4) and table expsample has values: expsample_required (yes), expsample_user_defined_id (FlowCyt ES 101806_4), and expsample_accession ().",
"errorMessage" : null,
"fileName" : "experimentSamples.Flow_Cytometry.txt",
"lineNumber" : 6,
"status" : "Information",
"uploadTicketNumber" : "testuser_20180523_19544",
"dateCreated" : "2018-05-23",
"createdBy" : "testuser",
"dateLastUpdated" : "2018-05-23",
"lastUpdatedBy" : "testuser"
}, {
"uploadRegistrationResultId" : 1101327,
"description" : "The combined status for biosample_id (Splenic_B-cells_treated_with_BAFF_and_anti-IgM) and table biosample has values: biosample_required (no), biosample_user_defined_id (Splenic_B-cells_treated_with_BAFF_and_anti-IgM), and biosample_accession (BS935314).",
"errorMessage" : null,
"fileName" : "experimentSamples.Flow_Cytometry.txt",
"lineNumber" : 6,
"status" : "Information",
"uploadTicketNumber" : "testuser_20180523_19544",
"dateCreated" : "2018-05-23",
"createdBy" : "testuser",
"dateLastUpdated" : "2018-05-23",
"lastUpdatedBy" : "testuser"
}, {
"uploadRegistrationResultId" : 1101328,
"description" : "The combined status for experiment_id (FlowCyt Expt) and table experiment has values: experiment_required (no), experiment_user_defined_id (FlowCyt Expt), and experiment_accession (EXP15457).",
"errorMessage" : null,
"fileName" : "experimentSamples.Flow_Cytometry.txt",
"lineNumber" : 6,
"status" : "Information",
"uploadTicketNumber" : "testuser_20180523_19544",
"dateCreated" : "2018-05-23",
"createdBy" : "testuser",
"dateLastUpdated" : "2018-05-23",
"lastUpdatedBy" : "testuser"
}, {
"uploadRegistrationResultId" : 1101329,
"description" : "The parent accession biosample_study_accession (SDY1897) was set using the table biosample and biosample_accession (BS935314).",
"errorMessage" : null,
"fileName" : "experimentSamples.Flow_Cytometry.txt",
"lineNumber" : 6,
"status" : "Information",
"uploadTicketNumber" : "testuser_20180523_19544",
"dateCreated" : "2018-05-23",
"createdBy" : "testuser",
"dateLastUpdated" : "2018-05-23",
"lastUpdatedBy" : "testuser"
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"description" : "The parent accession experiment_study_accession (SDY1897) was set using the table experiment and experiment_accession (EXP15457).",
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"fileName" : "experimentSamples.Flow_Cytometry.txt",
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"status" : "Information",
"uploadTicketNumber" : "testuser_20180523_19544",
"dateCreated" : "2018-05-23",
"createdBy" : "testuser",
"dateLastUpdated" : "2018-05-23",
"lastUpdatedBy" : "testuser"
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"description" : "The value in experiment_study_accession (SDY1897) is assigned to study_accession.",
"errorMessage" : null,
"fileName" : "experimentSamples.Flow_Cytometry.txt",
"lineNumber" : 6,
"status" : "Information",
"uploadTicketNumber" : "testuser_20180523_19544",
"dateCreated" : "2018-05-23",
"createdBy" : "testuser",
"dateLastUpdated" : "2018-05-23",
"lastUpdatedBy" : "testuser"
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"description" : "Size:201529 bytes",
"errorMessage" : null,
"fileName" : "Specimen_001_Tube_004.fcs",
"lineNumber" : 6,
"status" : "Stored in:file_info",
"uploadTicketNumber" : "testuser_20180523_19544",
"dateCreated" : "2018-05-23",
"createdBy" : "testuser",
"dateLastUpdated" : "2018-05-23",
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}, {
"uploadRegistrationResultId" : 1101333,
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"fileName" : "experimentSamples.Flow_Cytometry.txt",
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"status" : "Parsed",
"uploadTicketNumber" : "testuser_20180523_19544",
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"lastUpdatedBy" : "testuser"
}, {
"uploadRegistrationResultId" : 1101334,
"description" : "Template: fcm_derived_data.txt, Size:10446 bytes",
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"fileName" : "FCM_derived_data.txt",
"lineNumber" : null,
"status" : "Parsing",
"uploadTicketNumber" : "testuser_20180523_19544",
"dateCreated" : "2018-05-23",
"createdBy" : "testuser",
"dateLastUpdated" : "2018-05-23",
"lastUpdatedBy" : "testuser"
}, {
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"description" : "Validation Level = Standard",
"errorMessage" : null,
"fileName" : "FCM_derived_data.txt",
"lineNumber" : null,
"status" : "Information",
"uploadTicketNumber" : "testuser_20180523_19544",
"dateCreated" : "2018-05-23",
"createdBy" : "testuser",
"dateLastUpdated" : "2018-05-23",
"lastUpdatedBy" : "testuser"
}, {
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"description" : "Size:1149 bytes",
"errorMessage" : null,
"fileName" : "FCM_derived_data.workspace.txt",
"lineNumber" : 75,
"status" : "Stored in:file_info",
"uploadTicketNumber" : "testuser_20180523_19544",
"dateCreated" : "2018-05-23",
"createdBy" : "testuser",
"dateLastUpdated" : "2018-05-23",
"lastUpdatedBy" : "testuser"
}, {
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"errorMessage" : null,
"fileName" : "FCM_derived_data.txt",
"lineNumber" : 4,
"status" : "Information",
"uploadTicketNumber" : "testuser_20180523_19544",
"dateCreated" : "2018-05-23",
"createdBy" : "testuser",
"dateLastUpdated" : "2018-05-23",
"lastUpdatedBy" : "testuser"
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"description" : "\"Gating Definition Reported\" field with value \"CD14lo, HLA-DR+, CD16+\" has a preferred value \"CD14lo, HLADR+, CD16+\" and the preferred value is assigned to the population_defnition_preferred field",
"errorMessage" : null,
"fileName" : "FCM_derived_data.txt",
"lineNumber" : 5,
"status" : "Information",
"uploadTicketNumber" : "testuser_20180523_19544",
"dateCreated" : "2018-05-23",
"createdBy" : "testuser",
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"lastUpdatedBy" : "testuser"
}, {
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"description" : "\"Gating Definition Reported\" field with value \"CD25high CD127LO\" has a preferred value \"IL2RAhigh, CD127LO\" and the preferred value is assigned to the population_defnition_preferred field",
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"fileName" : "FCM_derived_data.txt",
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"status" : "Information",
"uploadTicketNumber" : "testuser_20180523_19544",
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"lastUpdatedBy" : "testuser"
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"errorMessage" : null,
"fileName" : "FCM_derived_data.txt",
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"status" : "Information",
"uploadTicketNumber" : "testuser_20180523_19544",
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"lastUpdatedBy" : "testuser"
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"description" : "\"Gating Definition Reported\" field with value \"CD27++CD38++\" has a preferred value \"CD27++, CD38++\" and the preferred value is assigned to the population_defnition_preferred field",
"errorMessage" : null,
"fileName" : "FCM_derived_data.txt",
"lineNumber" : 37,
"status" : "Information",
"uploadTicketNumber" : "testuser_20180523_19544",
"dateCreated" : "2018-05-23",
"createdBy" : "testuser",
"dateLastUpdated" : "2018-05-23",
"lastUpdatedBy" : "testuser"
}, {
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"description" : "\"Gating Definition Reported\" field with value \"CD3-CD14-CD19+IgD-CD20-CD27+CD38++\" has a preferred value \"CD3-, CD14-, CD19+, IgD-, CD20-, CD27+, CD38++\" and the preferred value is assigned to the population_defnition_preferred field",
"errorMessage" : null,
"fileName" : "FCM_derived_data.txt",
"lineNumber" : 39,
"status" : "Information",
"uploadTicketNumber" : "testuser_20180523_19544",
"dateCreated" : "2018-05-23",
"createdBy" : "testuser",
"dateLastUpdated" : "2018-05-23",
"lastUpdatedBy" : "testuser"
}, {
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"description" : "\"Gating Definition Reported\" field with value \"CD45RA+ Naive\" has a preferred value \"CD45RA+\" and the preferred value is assigned to the population_defnition_preferred field",
"errorMessage" : null,
"fileName" : "FCM_derived_data.txt",
"lineNumber" : 53,
"status" : "Information",
"uploadTicketNumber" : "testuser_20180523_19544",
"dateCreated" : "2018-05-23",
"createdBy" : "testuser",
"dateLastUpdated" : "2018-05-23",
"lastUpdatedBy" : "testuser"
}, {
"uploadRegistrationResultId" : 1101344,
"description" : "\"Gating Definition Reported\" field with value \"CD16+ neutrophil\" has a preferred value \"CD16+\" and the preferred value is assigned to the population_defnition_preferred field",
"errorMessage" : null,
"fileName" : "FCM_derived_data.txt",
"lineNumber" : 55,
"status" : "Information",
"uploadTicketNumber" : "testuser_20180523_19544",
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"createdBy" : "testuser",
"dateLastUpdated" : "2018-05-23",
"lastUpdatedBy" : "testuser"
}, {
"uploadRegistrationResultId" : 1101345,
"description" : "\"Gating Definition Reported\" field with value \"CD16+ granulocyte\" has a preferred value \"CD16+\" and the preferred value is assigned to the population_defnition_preferred field",
"errorMessage" : null,
"fileName" : "FCM_derived_data.txt",
"lineNumber" : 56,
"status" : "Information",
"uploadTicketNumber" : "testuser_20180523_19544",
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"createdBy" : "testuser",
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"lastUpdatedBy" : "testuser"
}, {
"uploadRegistrationResultId" : 1101346,
"description" : "\"Gating Definition Reported\" field with value \"CD16+, CD62L- granulocyte\" has a preferred value \"CD16+, CD62L-\" and the preferred value is assigned to the population_defnition_preferred field",
"errorMessage" : null,
"fileName" : "FCM_derived_data.txt",
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"status" : "Information",
"uploadTicketNumber" : "testuser_20180523_19544",
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"createdBy" : "testuser",
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}, {
"uploadRegistrationResultId" : 1101347,
"description" : "\"Gating Definition Reported\" field with value \"CD14nCD16n_pmo\" has a preferred value \"CD14-, CD16-\" and the preferred value is assigned to the population_defnition_preferred field",
"errorMessage" : null,
"fileName" : "FCM_derived_data.txt",
"lineNumber" : 64,
"status" : "Information",
"uploadTicketNumber" : "testuser_20180523_19544",
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}, {
"uploadRegistrationResultId" : 1101348,
"description" : "\"Gating Definition Reported\" field with value \"CD14pCD16n_pmo\" has a preferred value \"CD14+, CD16-\" and the preferred value is assigned to the population_defnition_preferred field",
"errorMessage" : null,
"fileName" : "FCM_derived_data.txt",
"lineNumber" : 67,
"status" : "Information",
"uploadTicketNumber" : "testuser_20180523_19544",
"dateCreated" : "2018-05-23",
"createdBy" : "testuser",
"dateLastUpdated" : "2018-05-23",
"lastUpdatedBy" : "testuser"
}, {
"uploadRegistrationResultId" : 1101349,
"description" : "Template: fcm_derived_data.txt, Size:10446 bytes",
"errorMessage" : null,
"fileName" : "FCM_derived_data.txt",
"lineNumber" : null,
"status" : "Parsed",
"uploadTicketNumber" : "testuser_20180523_19544",
"dateCreated" : "2018-05-23",
"createdBy" : "testuser",
"dateLastUpdated" : "2018-05-23",
"lastUpdatedBy" : "testuser"
}, {
"uploadRegistrationResultId" : 1101350,
"description" : null,
"errorMessage" : null,
"fileName" : "testuser_20180523_19544___Test.Fcm_Derived_Data.Comprehensive.zip",
"lineNumber" : null,
"status" : "Completed",
"uploadTicketNumber" : "testuser_20180523_19544",
"dateCreated" : "2018-05-23",
"createdBy" : "testuser",
"dateLastUpdated" : "2018-05-23",
"lastUpdatedBy" : "testuser"
} ]
},
"uploadTicketNumber" : "testuser_20180523_19544",
"type" : "summary"
}
https://auth.immport.org/auth/token
with the username and password to get an
authentication token. The fgrep command is used search the response for a token
and then assign the value of the token to an environment variable named
"token".
The second line is an inline Non-POST URL
https://immport-upload.niaid.nih.gov:8443/data/upload/registration/testuser_20180522_19504/reports/summary
with the inline parameterization, UPLOAD_TICKET_NUMBER. The authentication token
("token") is passed in the HTTP header as shown.
The response will be json that provides the summary of the upload request.
The above shell script or any code starting with #!/bin/bash can be copied to a .sh file (e.g. uploadSummaryReport.sh )and executed at the command prompt of a terminal and the output can be directed to a file. (Please replace the REPLACE_WITH_USERNAME with your username, and REPLACE_WITH_PASSWORD with your password).
./uploadSummaryReport.sh > uploadSummaryReport.json
Database Information on Upload Ticket Request with Authentication
The following is an example of a request for the database report for a validation using an upload ticket number where an inline parameter (UPLOAD_TICKET_NUMBER) is used.
#!/bin/bash
#########################
### Validation Ticket ###
#########################
export token=`curl -X POST https://auth.immport.org/auth/token -d username="REPLACE_WITH_USERNAME" -d password="REPLACE_WITH_PASSWORD" 2>&1 | fgrep '"token"' | sed -e 's/^.*"token" : "//;s/".*$//'`
curl -k -H "Authorization: bearer $token" https://immport-upload.niaid.nih.gov:8443/data/upload/registration/testuser_20180523_19543/reports/database
#########################
### Validation Ticket ###
#########################
{
"database" : "The validation report is based on ImmPort workspace (workspace_id = 999999).\nThe validation report was generated on 2018-05-23-14:22:48.\nThe data package file submitted was /home/immport/data/immport-data-upload-server/webupload_drop_zone/testuser_20180523_19543___Test.Fcm_Derived_Data.Comprehensive.zip.\n\nFile Name\tLine Number\tStatus\tError Message\tDescription\nprotocols.txt\t\tParsing\t\tTemplate: protocols.txt, Size:748 bytes\nprotocols.txt\t\tInformation\t\tValidation Level = Standard\nprotocols.txt\t3\tStored in:file_info\t\tSize:748 bytes\nSplenic_B_cell_isolation.pdf\t4\tStored in:protocols\t\tSize:48046 bytes\nCulture_conditions.pdf\t5\tStored in:protocols\t\tSize:13743 bytes\nFlowCytometryProtocol.xls\t6\tStored in:protocols\t\tSize:18944 bytes\nexample animal study protocol.txt\t7\tStored in:protocols\t\tSize:30 bytes\nprotocols.txt\t\tParsed\t\tTemplate: protocols.txt, Size:748 bytes\nreagents.flow_cytometry.txt\t\tParsing\t\tTemplate: reagents.flow_cytometry.txt, Size:1157 bytes\nreagents.flow_cytometry.txt\t\tInformation\t\tValidation Level = Standard\nreagents.flow_cytometry.txt\t3\tStored in:file_info\t\tSize:1157 bytes\nreagents.flow_cytometry.txt\t\tParsed\t\tTemplate: reagents.flow_cytometry.txt, Size:1157 bytes\nreagent_sets.txt\t\tParsing\t\tTemplate: reagent_sets.txt, Size:458 bytes\nreagent_sets.txt\t\tInformation\t\tValidation Level = Standard\nreagent_sets.txt\t3\tStored in:file_info\t\tSize:458 bytes\nreagent_sets.txt\t\tParsed\t\tTemplate: reagent_sets.txt, Size:458 bytes\ntreatments.txt\t\tParsing\t\tTemplate: treatments.txt, Size:420 bytes\ntreatments.txt\t\tInformation\t\tValidation Level = Standard\ntreatments.txt\t3\tStored in:file_info\t\tSize:420 bytes\ntreatments.txt\t\tParsed\t\tTemplate: treatments.txt, Size:420 bytes\nbasic_study_design.txt\t\tParsing\t\tTemplate: basic_study_design.txt, Size:1877 bytes\nbasic_study_design.txt\t\tInformation\t\tValidation Level = Standard\nbasic_study_design.txt\t3\tStored in:file_info\t\tSize:1877 bytes\nInformation_1.txt\t46\tStored in:study_file\t\tSize:92 bytes\nbasic_study_design.txt\t\tParsed\t\tTemplate: basic_study_design.txt, Size:1877 bytes\nsubjectsAnimal.txt\t\tParsing\t\tTemplate: subjectsanimal.txt, Size:889 bytes\nsubjectsAnimal.txt\t\tInformation\t\tValidation Level = Standard\nsubjectsAnimal.txt\t3\tStored in:file_info\t\tSize:889 bytes\nsubjectsAnimal.txt\t\tParsed\t\tTemplate: subjectsanimal.txt, Size:889 bytes\nbioSamples.txt\t\tParsing\t\tTemplate: biosamples.txt, Size:1547 bytes\nbioSamples.txt\t\tInformation\t\tValidation Level = Standard\nbioSamples.txt\t3\tStored in:file_info\t\tSize:1547 bytes\nbioSamples.txt\t\tParsed\t\tTemplate: biosamples.txt, Size:1547 bytes\nexperiments.txt\t\tParsing\t\tTemplate: experiments.txt, Size:545 bytes\nexperiments.txt\t\tInformation\t\tValidation Level = Standard\nexperiments.txt\t3\tStored in:file_info\t\tSize:545 bytes\nexperiments.txt\t\tParsed\t\tTemplate: experiments.txt, Size:545 bytes\nexperimentSamples.Flow_Cytometry.txt\t\tParsing\t\tTemplate: experimentsamples.flow_cytometry.txt, Size:1038 bytes\nexperimentSamples.Flow_Cytometry.txt\t\tInformation\t\tValidation Level = Standard\nexperimentSamples.Flow_Cytometry.txt\t2\tStored in:file_info\t\tSize:1038 bytes\nexperimentSamples.Flow_Cytometry.txt\t3\tInformation\t\tThe combined status for expsample_id (FlowCyt ES 101806_1) and table expsample has values: expsample_required (yes), expsample_user_defined_id (FlowCyt ES 101806_1), and expsample_accession ().\nexperimentSamples.Flow_Cytometry.txt\t3\tInformation\t\tThe combined status for biosample_id (Splenic_B-cells_untreated) and table biosample has values: biosample_required (no), biosample_user_defined_id (Splenic_B-cells_untreated), and biosample_accession (BS1000000071).\nexperimentSamples.Flow_Cytometry.txt\t3\tInformation\t\tThe combined status for experiment_id (FlowCyt Expt) and table experiment has values: experiment_required (no), experiment_user_defined_id (FlowCyt Expt), and experiment_accession (EXP1000000080).\nexperimentSamples.Flow_Cytometry.txt\t3\tInformation\t\tThe parent accession biosample_study_accession (SDY1000000045) was set using the table biosample and biosample_accession (BS1000000071).\nexperimentSamples.Flow_Cytometry.txt\t3\tInformation\t\tThe parent accession experiment_study_accession (SDY1000000045) was set using the table experiment and experiment_accession (EXP1000000080).\nexperimentSamples.Flow_Cytometry.txt\t3\tInformation\t\tThe value in experiment_study_accession (SDY1000000045) is assigned to study_accession.\nSpecimen_001_Tube_001.fcs\t6\tStored in:file_info\t\tSize:201530 bytes\nFCM_derived_data.txt\t6\tStored in:file_info\t\tSize:10446 bytes\nCompensationTube_001.fcs\t6\tStored in:file_info\t\tSize:201631 bytes\nCompensationTube_002.fcs\t6\tStored in:file_info\t\tSize:201631 bytes\nexperimentSamples.Flow_Cytometry.txt\t4\tInformation\t\tThe combined status for expsample_id (FlowCyt ES 101806_2) and table expsample has values: expsample_required (yes), expsample_user_defined_id (FlowCyt ES 101806_2), and expsample_accession ().\nexperimentSamples.Flow_Cytometry.txt\t4\tInformation\t\tThe combined status for biosample_id (Splenic_B-cells_treated_with_BAFF) and table biosample has values: biosample_required (no), biosample_user_defined_id (Splenic_B-cells_treated_with_BAFF), and biosample_accession (BS1000000072).\nexperimentSamples.Flow_Cytometry.txt\t4\tInformation\t\tThe combined status for experiment_id (FlowCyt Expt) and table experiment has values: experiment_required (no), experiment_user_defined_id (FlowCyt Expt), and experiment_accession (EXP1000000080).\nexperimentSamples.Flow_Cytometry.txt\t4\tInformation\t\tThe parent accession biosample_study_accession (SDY1000000045) was set using the table biosample and biosample_accession (BS1000000072).\nexperimentSamples.Flow_Cytometry.txt\t4\tInformation\t\tThe parent accession experiment_study_accession (SDY1000000045) was set using the table experiment and experiment_accession (EXP1000000080).\nexperimentSamples.Flow_Cytometry.txt\t4\tInformation\t\tThe value in experiment_study_accession (SDY1000000045) is assigned to study_accession.\nSpecimen_001_Tube_002.fcs\t6\tStored in:file_info\t\tSize:201530 bytes\nexperimentSamples.Flow_Cytometry.txt\t5\tInformation\t\tThe combined status for expsample_id (FlowCyt ES 101806_3) and table expsample has values: expsample_required (yes), expsample_user_defined_id (FlowCyt ES 101806_3), and expsample_accession ().\nexperimentSamples.Flow_Cytometry.txt\t5\tInformation\t\tThe combined status for biosample_id (Splenic_B-cells_treated_with_Anti-IgM) and table biosample has values: biosample_required (no), biosample_user_defined_id (Splenic_B-cells_treated_with_Anti-IgM), and biosample_accession (BS1000000073).\nexperimentSamples.Flow_Cytometry.txt\t5\tInformation\t\tThe combined status for experiment_id (FlowCyt Expt) and table experiment has values: experiment_required (no), experiment_user_defined_id (FlowCyt Expt), and experiment_accession (EXP1000000080).\nexperimentSamples.Flow_Cytometry.txt\t5\tInformation\t\tThe parent accession biosample_study_accession (SDY1000000045) was set using the table biosample and biosample_accession (BS1000000073).\nexperimentSamples.Flow_Cytometry.txt\t5\tInformation\t\tThe parent accession experiment_study_accession (SDY1000000045) was set using the table experiment and experiment_accession (EXP1000000080).\nexperimentSamples.Flow_Cytometry.txt\t5\tInformation\t\tThe value in experiment_study_accession (SDY1000000045) is assigned to study_accession.\nSpecimen_001_Tube_003.fcs\t6\tStored in:file_info\t\tSize:201529 bytes\nexperimentSamples.Flow_Cytometry.txt\t6\tInformation\t\tThe combined status for expsample_id (FlowCyt ES 101806_4) and table expsample has values: expsample_required (yes), expsample_user_defined_id (FlowCyt ES 101806_4), and expsample_accession ().\nexperimentSamples.Flow_Cytometry.txt\t6\tInformation\t\tThe combined status for biosample_id (Splenic_B-cells_treated_with_BAFF_and_anti-IgM) and table biosample has values: biosample_required (no), biosample_user_defined_id (Splenic_B-cells_treated_with_BAFF_and_anti-IgM), and biosample_accession (BS1000000074).\nexperimentSamples.Flow_Cytometry.txt\t6\tInformation\t\tThe combined status for experiment_id (FlowCyt Expt) and table experiment has values: experiment_required (no), experiment_user_defined_id (FlowCyt Expt), and experiment_accession (EXP1000000080).\nexperimentSamples.Flow_Cytometry.txt\t6\tInformation\t\tThe parent accession biosample_study_accession (SDY1000000045) was set using the table biosample and biosample_accession (BS1000000074).\nexperimentSamples.Flow_Cytometry.txt\t6\tInformation\t\tThe parent accession experiment_study_accession (SDY1000000045) was set using the table experiment and experiment_accession (EXP1000000080).\nexperimentSamples.Flow_Cytometry.txt\t6\tInformation\t\tThe value in experiment_study_accession (SDY1000000045) is assigned to study_accession.\nSpecimen_001_Tube_004.fcs\t6\tStored in:file_info\t\tSize:201529 bytes\nexperimentSamples.Flow_Cytometry.txt\t\tParsed\t\tTemplate: experimentsamples.flow_cytometry.txt, Size:1038 bytes\nFCM_derived_data.txt\t\tParsing\t\tTemplate: fcm_derived_data.txt, Size:10446 bytes\nFCM_derived_data.txt\t\tInformation\t\tValidation Level = Standard\nFCM_derived_data.workspace.txt\t75\tStored in:file_info\t\tSize:1149 bytes\nFCM_derived_data.txt\t4\tInformation\t\t\"Gating Definition Reported\" field with value \"CD14+, HLA-DRhi CD16+\" has a preferred value \"CD14+, HLADRhi, CD16+\" and the preferred value is assigned to the population_defnition_preferred field\nFCM_derived_data.txt\t5\tInformation\t\t\"Gating Definition Reported\" field with value \"CD14lo, HLA-DR+, CD16+\" has a preferred value \"CD14lo, HLADR+, CD16+\" and the preferred value is assigned to the population_defnition_preferred field\nFCM_derived_data.txt\t6\tInformation\t\t\"Gating Definition Reported\" field with value \"CD25high CD127LO\" has a preferred value \"IL2RAhigh, CD127LO\" and the preferred value is assigned to the population_defnition_preferred field\nFCM_derived_data.txt\t36\tInformation\t\t\"Gating Definition Reported\" field with value \"CD14-CD56+CD3++\" has a preferred value \"CD14-, CD56+, CD3++\" and the preferred value is assigned to the population_defnition_preferred field\nFCM_derived_data.txt\t37\tInformation\t\t\"Gating Definition Reported\" field with value \"CD27++CD38++\" has a preferred value \"CD27++, CD38++\" and the preferred value is assigned to the population_defnition_preferred field\nFCM_derived_data.txt\t39\tInformation\t\t\"Gating Definition Reported\" field with value \"CD3-CD14-CD19+IgD-CD20-CD27+CD38++\" has a preferred value \"CD3-, CD14-, CD19+, IgD-, CD20-, CD27+, CD38++\" and the preferred value is assigned to the population_defnition_preferred field\nFCM_derived_data.txt\t53\tInformation\t\t\"Gating Definition Reported\" field with value \"CD45RA+ Naive\" has a preferred value \"CD45RA+\" and the preferred value is assigned to the population_defnition_preferred field\nFCM_derived_data.txt\t55\tInformation\t\t\"Gating Definition Reported\" field with value \"CD16+ neutrophil\" has a preferred value \"CD16+\" and the preferred value is assigned to the population_defnition_preferred field\nFCM_derived_data.txt\t56\tInformation\t\t\"Gating Definition Reported\" field with value \"CD16+ granulocyte\" has a preferred value \"CD16+\" and the preferred value is assigned to the population_defnition_preferred field\nFCM_derived_data.txt\t57\tInformation\t\t\"Gating Definition Reported\" field with value \"CD16+, CD62L- granulocyte\" has a preferred value \"CD16+, CD62L-\" and the preferred value is assigned to the population_defnition_preferred field\nFCM_derived_data.txt\t64\tInformation\t\t\"Gating Definition Reported\" field with value \"CD14nCD16n_pmo\" has a preferred value \"CD14-, CD16-\" and the preferred value is assigned to the population_defnition_preferred field\nFCM_derived_data.txt\t67\tInformation\t\t\"Gating Definition Reported\" field with value \"CD14pCD16n_pmo\" has a preferred value \"CD14+, CD16-\" and the preferred value is assigned to the population_defnition_preferred field\nFCM_derived_data.txt\t\tParsed\t\tTemplate: fcm_derived_data.txt, Size:10446 bytes\nnobody_20180523_1000000001___testuser_20180523_19543___Test.Fcm_Derived_Data.Comprehensive.zip\t\tCompleted\t\t\n",
"uploadTicketNumber" : "testuser_20180523_19543",
"type" : "database"
}
#!/bin/bash
#####################
### Upload Ticket ###
#####################
export token=`curl -X POST https://auth.immport.org/auth/token -d username="REPLACE_WITH_USERNAME" -d password="REPLACE_WITH_PASSWORD" 2>&1 | fgrep '"token"' | sed -e 's/^.*"token" : "//;s/".*$//'`
curl -k -H "Authorization: bearer $token" https://immport-upload.niaid.nih.gov:8443/data/upload/registration/testuser_20180523_19544/reports/database
#####################
### Upload Ticket ###
#####################
{
"database" : "EXPERIMENT DATA UPLOAD REPORT\r\n=============================\r\n\r\nREPORT DATE: 23-MAY-2018 09:50:02\r\nWORKSPACE_ID: 999999 NAME Test Creation Scripts I\r\nSUBMISSION TICKET NUMBER: testuser_20180523_19544\r\nSUBMITTER: user, test s\r\nSUBMITTER USERNAME: testuser\r\nSUBMISSION DATE/TIME: 23-MAY-2018 01:45:45 PM\r\nUPLOAD PACKAGE ZIP FILENAME: Test.Fcm_Derived_Data.Comprehensive.zip\r\nUPLOAD PACKAGE ZIP FILESIZE: 902979\r\nUPLOAD METHOD: Secure Web\r\n\r\n\r\n\r\nFILENAME: experiments.txt Total records: 1\r\n-------------------------------------------------------------\r\nUSER_DEFINED_ID\tEXPERIMENT_ACCESSION\tNAME\tMEASUREMENT_TECHNIQUE\tDESCRIPTION\r\nFlowCyt Expt\tEXP15457\tAnnexin+6 color staining 10/18/06\tFlow Cytometry\tComparison of survival and differentiati\r\n\r\n\r\nFILENAME: experimentSamples.Flow_Cytometry.txt Total records: 4\r\n-------------------------------------------------------------\r\nUSER_DEFINED_ID\tEXPSAMPLE_ACCESSION\tNAME\tRESULT_SCHEMA\tUSER_DEFINED_ID:EXPERIMENT_ACCESSION\r\nFlowCyt ES 101806_1\tES1089595\t-\tFCM\tFlowCyt Expt:EXP15457\r\nFlowCyt ES 101806_2\tES1089596\t-\tFCM\tFlowCyt Expt:EXP15457\r\nFlowCyt ES 101806_3\tES1089597\t-\tFCM\tFlowCyt Expt:EXP15457\r\nFlowCyt ES 101806_4\tES1089598\t-\tFCM\tFlowCyt Expt:EXP15457\r\n\r\n\r\nFILENAME: bioSamples.txt Total records: 5\r\n-------------------------------------------------------------\r\nUSER_DEFINED_ID\tBIOSAMPLE_ACCESSION\tNAME\tDESCRIPTION\tTYPE\tSUBTYPE\r\nSplenic_B-cells\tBS935310\tSplenic B-cells\tB cells from spleen of C57BL/6 WT mice\tRed Blood Cell\tB cells\r\nSplenic_B-cells_untreated\tBS935311\tSplenic_B-cells_untreated\tB cells cultured in media alone for 48hr\tRed Blood Cell\tB cells\r\nSplenic_B-cells_treated_with_BAFF\tBS935312\tSplenic_B-cells_treated_with_BAFF\tB cells cultured in media + BAFF for 48h\tRed Blood Cell\tB cells\r\nSplenic_B-cells_treated_with_Anti-IgM\tBS935313\tSplenic_B-cells_treated_with_Anti-IgM\tB cells cultured in media + anti-IgM for\tRed Blood Cell\tB cells\r\nSplenic_B-cells_treated_with_BAFF_and_anti-IgM\tBS935314\tSplenic_B-cells_treated_with_BAFF_and_anti-IgM\tB cells cultured in media + BAFF + anti-\tRed Blood Cell\tB cells\r\n\r\n\r\nFILENAME: subjectsAnimal.txt Total records: 4\r\n-------------------------------------------------------------\r\nUSER_DEFINED_ID\tSUBJECT_ACCESSION\tDESCRIPTION\tGENDER\tSPECIES\r\ncontrol 1\tSUB182413\t-\tFemale\tMus musculus\r\nvaccinated 1\tSUB182414\t-\tMale\tMus musculus\r\ncontrol 2\tSUB182415\t-\tFemale\tMus musculus\r\nvaccinated 2\tSUB182416\t-\tMale\tMus musculus\r\n\r\n\r\nFILENAME: protocols.txt Total records: 4\r\n-------------------------------------------------------------\r\nUSER_DEFINED_ID\tPROTOCOL_ACCESSION\tFILE_NAME\tPATH\r\nFlowCyt Protocol\tPTL10549\tFlowCytometryProtocol.xls\tworkspace/999999/protocol/FlowCytometryProtocol.PTL10549.xls\r\nexample animal study protocol\tPTL10550\texample animal study protocol.txt\tworkspace/999999/protocol/example animal study protocol.PTL10550.txt\r\nFlowCyt Splenic B cell isolation\tPTL10547\tSplenic_B_cell_isolation.pdf\tworkspace/999999/protocol/Splenic_B_cell_isolation.PTL10547.pdf\r\nFlowCyt Culture conditions\tPTL10548\tCulture_conditions.pdf\tworkspace/999999/protocol/Culture_conditions.PTL10548.pdf\r\n\r\n\r\nFILENAME: basic_study_design.txt Total records: 1\r\n-------------------------------------------------------------\r\nSTUDY_FILE_ACCESSION\tFILE_NAME\tPATH\r\nSFL20719\tInformation_1.txt\tworkspace/999999/study/SDY1897/study_file/Information_1.txt\r\n\r\n\r\nFILENAME: --None-- Total records: 0\r\n-------------------------------------------------------------\r\nSCHEMATIC_ACCESSION\tFILE_NAME\tPATH\r\n\r\n\r\nFILENAME: reagents.flow_cytometry.txt\r\n Total Reagent records: 8\r\n Total Reagent records (Non-Set): 7\r\n Total Reagent records (Set) : 1\r\n Reagent Set information detail : 1 Set(s) containing 7 items\r\n Total Analyte records created : 7\r\n-------------------------------------------------------------\r\nUSER_DEFINED_ID\tREAGENT_ACCESSION\tIS_SET\tname\r\nFlowCyt Annexin V FITC\tESR20959\tN\tAnnexin V\r\nFlowCyt anti CD24 PE\tESR20960\tN\tanti-CD24 antibody\r\nFlowCyt anti IgD bio SA PerCP\tESR20961\tN\tanti-IgD antibody\r\nFlowCyt anti AA4.1 APC\tESR20962\tN\tanti-AA4.1 antibody\r\nFlowCyt anti CD23 PE Cy7\tESR20963\tN\tanti-CD23 antibody\r\nFlowCyt anti CD23 PE CP\tESR20964\tN\tanti-CD19 antibody\r\nFlowCyt anti CD21 Pac blue\tESR20965\tN\tanti-CD21 antibody\r\nFlowCyt Self-made Staining cocktail\tESR20966\tY\thome made reagent\r\n\r\n\r\nLIST OF FILENAME(S) IN PACKAGE Total Files: 22\r\n-------------------------------------------------------------\r\nFILE_STATUS\tFILE_SIZE (BYTES)\tFILE_NAME\tPATH\r\nParsed\t10446\tFCM_derived_data.txt\tworkspace/999999/file_info/template/FCM_derived_data.636567.txt\r\nParsed\t1877\tbasic_study_design.txt\tworkspace/999999/file_info/template/basic_study_design.636561.txt\r\nParsed\t1547\tbioSamples.txt\tworkspace/999999/file_info/template/bioSamples.636563.txt\r\nParsed\t1038\texperimentSamples.Flow_Cytometry.txt\tworkspace/999999/file_info/template/experimentSamples.Flow_Cytometry.636565.txt\r\nParsed\t545\texperiments.txt\tworkspace/999999/file_info/template/experiments.636564.txt\r\nParsed\t748\tprotocols.txt\tworkspace/999999/file_info/template/protocols.636557.txt\r\nParsed\t458\treagent_sets.txt\tworkspace/999999/file_info/template/reagent_sets.636559.txt\r\nParsed\t1157\treagents.flow_cytometry.txt\tworkspace/999999/file_info/template/reagents.flow_cytometry.636558.txt\r\nParsed\t889\tsubjectsAnimal.txt\tworkspace/999999/file_info/template/subjectsAnimal.636562.txt\r\nParsed\t420\ttreatments.txt\tworkspace/999999/file_info/template/treatments.636560.txt\r\nStored in:file_info\t201631\tCompensationTube_001.fcs\tworkspace/999999/study/SDY1897/file_info/60/8/CompensationTube_001.636568.fcs\r\nStored in:file_info\t201631\tCompensationTube_002.fcs\tworkspace/999999/study/SDY1897/file_info/60/9/CompensationTube_002.636569.fcs\r\nStored in:file_info\t1149\tFCM_derived_data.workspace.txt\tworkspace/999999/study/SDY1897/file_info/70/3/FCM_derived_data.workspace.636573.txt\r\nStored in:file_info\t201530\tSpecimen_001_Tube_001.fcs\tworkspace/999999/study/SDY1897/file_info/60/6/Specimen_001_Tube_001.636566.fcs\r\nStored in:file_info\t201530\tSpecimen_001_Tube_002.fcs\tworkspace/999999/study/SDY1897/file_info/70/0/Specimen_001_Tube_002.636570.fcs\r\nStored in:file_info\t201529\tSpecimen_001_Tube_003.fcs\tworkspace/999999/study/SDY1897/file_info/70/1/Specimen_001_Tube_003.636571.fcs\r\nStored in:file_info\t201529\tSpecimen_001_Tube_004.fcs\tworkspace/999999/study/SDY1897/file_info/70/2/Specimen_001_Tube_004.636572.fcs\r\nStored in:protocols\t0\tCulture_conditions.pdf\t-\r\nStored in:protocols\t0\tFlowCytometryProtocol.xls\t-\r\nStored in:protocols\t0\tSplenic_B_cell_isolation.pdf\t-\r\nStored in:protocols\t0\texample animal study protocol.txt\t-\r\nStored in:study_file\t0\tInformation_1.txt\t-\r\n\r\nCount Report (uploadTicketNumber = testuser_20180523_19544):\r\n\r\nupload_registration = 1\r\nupload_registration_result = 91\r\n\r\nWorkspace_2_* Counts\r\nworkspace_2_assessment_panel = 0\r\nworkspace_2_biosample = 5\r\nworkspace_2_control_sample = 0\r\nworkspace_2_experiment = 1\r\nworkspace_2_expsample = 4\r\nworkspace_2_file_info = 17\r\nworkspace_2_lab_test_panel = 0\r\nworkspace_2_protocol = 4\r\nworkspace_2_reagent = 8\r\nworkspace_2_standard_curve = 0\r\nworkspace_2_study = 1\r\nworkspace_2_subject = 4\r\nworkspace_2_treatment = 4\r\n\r\nNon-Study Table Counts\r\nprotocol = 4\r\nreagent = 8\r\nreagent_set_2_reagent = 7\r\ntreatment = 4\r\n\r\nStudy Table Counts\r\nstudy = 1\r\nstudy_2_panel = 8\r\nstudy_2_protocol = 1\r\ncontract_grant_2_study = 0\r\narm_or_cohort = 2\r\ninclusion_exclusion = 2\r\nperiod = 1\r\nplanned_visit = 1\r\nstudy_file = 1\r\nstudy_image = 0\r\nstudy_link = 1\r\nstudy_personnel = 1\r\nstudy_pubmed = 1\r\nadverse_event = 0\r\nassessment_panel = 0\r\nassessment_2_file_info = 0\r\nassessment_component = 0\r\nintervention = 0\r\nlab_test_panel = 0\r\nlab_test_panel_2_protocol = 0\r\nlab_test = 0\r\n\r\nStudy Meta-Data Table Counts\r\nsubject = 4\r\narm_2_subject = 4\r\nbiosample = 5\r\nbiosample_2_treatment = 1\r\nexperiment = 1\r\nexperiment_2_protocol = 3\r\nfile_info = 17\r\nexpsample = 4\r\nexpsample_mbaa_detail = 0\r\nexpsample_public_repository = 0\r\nimmune_exposure = 0\r\nexpsample_2_biosample = 4\r\nexpsample_2_file_info = 14\r\nexpsample_2_reagent = 32\r\nexpsample_2_treatment = 4\r\ncontrol_sample = 0\r\ncontrol_sample_2_file_info = 0\r\nstandard_curve = 0\r\nstandard_curve_2_file_info = 0\r\nfcs_header = 4\r\nfcs_header_marker = 40\r\nfcs_analyzed_result_marker = 383\r\n\r\nResult Table Counts\r\nmbaa_result = 0\r\nfcs_analyzed_result = 73\r\nelisa_result = 0\r\nelispot_result = 0\r\nhai_result = 0\r\nhla_typing_result = 0\r\nkir_typing_result = 0\r\nneut_ab_titer_result = 0\r\npcr_result = 0\r\nrna_seq_result = 0\r\n\r\nOther Non-Upload Table Counts\r\nplanned_visit_2_arm = 0\r\nprotocol_deviation = 0\r\nfcs_header_marker_2_reagent = 0\r\nreference_range = 0\r\nreported_early_termination = 0\r\nstudy_categorization = 0\r\nstudy_data_release = 0\r\nstudy_glossary = 0\r\nsubject_measure_definition = 0\r\nsubject_measure_result = 0\r\n",
"uploadTicketNumber" : "testuser_20180523_19544",
"type" : "database"
}
https://auth.immport.org/auth/token
with the username and password to get an
authentication token. The fgrep command is used search the response for a token
and then assign the value of the token to an environment variable named
"token".
The second line is an inline Non-POST URL
https://immport-upload.niaid.nih.gov:8443/data/upload/registration/testuser_20180522_19504/reports/database
with the inline parameterization UPLOAD_TICKET_NUMBER. The authentication token
("token") is passed in the HTTP header as shown.
The response will be json that provides the database report of the upload request.
The above shell script or any code starting with #!/bin/bash can be copied to a .sh file (e.g. uploadDatabaseport.sh )and executed at the command prompt of a terminal and the output can be directed to a file. (Please replace the REPLACE_WITH_USERNAME with your username, and REPLACE_WITH_PASSWORD with your password).
./uploadDatabaseport.sh > uploadDatabaseport.json
Set of Workspaces Request with Authentication
The following is an example of a request for the set of workspace upon which the user can upload and validate data.
#!/bin/bash
export token=`curl -X POST https://auth.immport.org/auth/token -d username="REPLACE_WITH_USERNAME" -d password="REPLACE_WITH_PASSWORD" 2>&1 | fgrep '"token"' | sed -e 's/^.*"token" : "//;s/".*$//'`
curl -k -H "Authorization: bearer $token" https://immport-upload.niaid.nih.gov:8443/workspaces
{
"workspaces" : [ {
"workspaceId" : 999999,
"name" : "Test Creation Scripts I",
"type" : "PW",
"category" : "LSR",
"dateCreated" : 1524159239000,
"dateLastUpdated" : 1524159239000,
"createdBy" : "tsmith",
"lastUpdatedBy" : "SYSTEM"
}, {
"workspaceId" : 999996,
"name" : "Test Creation Scripts III",
"type" : "PW",
"category" : "LSR",
"dateCreated" : 1524158615000,
"dateLastUpdated" : 1524158615000,
"createdBy" : "tsmith",
"lastUpdatedBy" : "SYSTEM"
}, {
"workspaceId" : 999998,
"name" : "Test Creation Scripts III",
"type" : "PW",
"category" : "LSR",
"dateCreated" : 1524159474000,
"dateLastUpdated" : 1524159474000,
"createdBy" : "tsmith",
"lastUpdatedBy" : "SYSTEM"
}, {
"workspaceId" : 5768,
"name" : "Test Workspace for user testuser",
"type" : "PW",
"category" : "TEST",
"dateCreated" : 1516303125000,
"dateLastUpdated" : 1516303125000,
"createdBy" : "testadmin",
"lastUpdatedBy" : "testadmin"
}, {
"workspaceId" : 5787,
"name" : "test assessments",
"type" : "PW",
"category" : "TEST",
"dateCreated" : 1519228020000,
"dateLastUpdated" : 1519228020000,
"createdBy" : "pattybe",
"lastUpdatedBy" : "pattybe"
} ]
}
https://auth.immport.org/auth/token
with the username and password to get an
authentication token. The fgrep command is used search the response for a token
and then assign the value of the token to an environment variable named
"token".
The second line is a Non-POST URL
https://immport-upload.niaid.nih.gov:8443/workspaces
The authentication token ("token") is passed in the HTTP header as shown.
The response will be json that provides the list of workspaces upon which a user may upload and validate.
The above shell script or any code starting with #!/bin/bash can be copied to a .sh file (e.g. workspaces.sh )and executed at the command prompt of a terminal and the output can be directed to a file. (Please replace the REPLACE_WITH_USERNAME with your username, and REPLACE_WITH_PASSWORD with your password).
./workspaces.sh > workspaces.json