Purpose

Upload and download files in Data Manager can be done using various mechanisms :

Web-based interface at https://sandbox-datamanager.wmda.info (please note the URL for production is https://datamanager.wmda.info )
REST API, using commands like cURL, or libraries like Restsharp

This document describes the Data Manager mechanism via the REST API method, where users can upload a PGP encrypted file.

Please do read https://ec.haxx.se/usingcurl-netrc.html on the use of Bearer Token if you plan to automate these procedures.

# example use:
curl --netrc-file mycredentialsfile https://xyz.com

# the mycredentialsfile contains :
machine <xyz.com> login <johndoe@xyz.com> password <uf9873o^9ufwa>

Request credential

First time request

Update credential because of expiration

Using the REST API

There are many ways by using different programming languages to execute API requests. WMDA provide an example by using curl for educational purpose.

To get more knowledge for usage of curl, we recommend member to read the doc for curl https://ec.haxx.se/usingcurl-netrc.html.

There are 2 steps

Step 1: Request the credential which can be used to generate the Bear Token

Step 2: Test to use the API in WMDA Data Manager swagger: https://brave-forest-04a379103.azurestaticapps.net/?urls.primaryName=Data%20Manager%20Data%20Exchange%20API#/

Step 3: Implement the API.

If you are already familiar with the API implementation, then you can skip Step 2, and test from your own implementation.

In case the upload succeeded, an XML response with meta information of the upload is generated. You may use this for own logging purposes. For more info you can read the full API specification.

URL
SERVER URL	Staging system: https://san-dataupload.wmda.info Production system: https://dataupload.wmda.info
URI	/api/v2/io/ION1234/ Explanations: Please refer to the file naming convention. This is stated as : For XML format: The files are marked with ION numbers ( ION-1234-D or ION-1234-C) The ION number is the unique ION number of an organisation sending the file. The D give the information that it is a donor file and the C give the information that it is a cord blood file
METHOD	PUT
Full URL path example	For donor for organization with ION-1234, the full path is as below: https://staging-dataupload.wmda.info/api/v2/io/ION1234/ION-1234-D.gpg
HEADER	Authorization and Content-Type are required, the other ones are optional
Authorization	basic
Content-Type	application/octet-stream (when your file < 128K) multipart/form-data (when your file >128K) From 27 Oct 2022 , Content-Type is required. See our suggestion below in "Upload".
cX-Rename-If-Exists	true

Server name should be https://staging-dataupload.wmda.info
For production you will need https://dataupload.wmda.info

SAMPLE Request

First test the connection by using the right path and fetching the metadata : it should result in a response 200 OK.

Look carefully at the path : here we use ion0999, that should be replaced by your ION.
You may notice that we add the filename to the path: depending on the library you may need to add that

Search & Match Service > Data Manager: How to automate data upload/download with REST API? > image2018-3-30 10:5:0.png

Upload

Now we know the path is correct and we can do an upload using cURL:

Below is the invalid to deploy, currently it is still available in PRODUCTION till production maintenance. But not available any more in STAGING dataupload.

curl -i -X PUT -H "Authorization:Basic d21.....uZT=="   -T "./test.pgp"  'https://staging-dataupload.wmda.info/api/v2/io/ION0999/'

Below are suggestions with more secure headers:

The curl script needs update to upload in STAGING from Oct, 27th, 2022 after maintenance/update . And the new suggested script can be used in PRODUCTION as well. So we strongly suggest API users to update, then there will be less stress after PRODUCTION update/maintenance.
For registries use other script, please test in STAGING as well, and adjust with the Content-Type if not used before. We noticed that the uploaded file format can be binary or with info to identify it is PGP/GPG MESSAGE. And for PGP/GPG MESSAGE format, there are more solutions.

Suggestion 1:

For all the files, script as below is suggested for file larger than 128K.

curl -i -X PUT -H "Authorization:Basic d21.....uZT==" -H "Content-Type: multipart/form-data" --data-binary "@/path/to/file/ION-0999-D.gpg"  "https://staging-dataupload.wmda.info/api/v2/io/ION0999/" -H "X-File-Name:ION-0999-D.gpg"

curl -i -X PUT -H "Authorization:Basic d21.....uZT==" -H "Content-Type: multipart/form-data" --data-binary "@c:/path/to/file/ION-0999-D.gpg"  "https://staging-dataupload.wmda.info/api/v2/io/ION0999/" -H "X-File-Name:ION-0999-D.gpg"

Suggestion 2:

For files that encrypted and identified as PGP/GPG MESSAGE (open the encrypted file and you can see this info), then -F and -H options also work. -F already included "Content-Type: multipart/form-data", so no need to provide it any more.

For binary file, extra header information will be added to the content of the file when file is uploaded, and then it can not be decrypted any more, so please use suggestion 1 to upload.

curl -i -X PUT -H "Authorization:Basic d21.....uZT==" -F "file="@/path/to/file/ION-0999-D.gpg" "https://staging-dataupload.wmda.info/api/v2/io/ION0999/" -H "X-File-Name:ION-0999-D.gpg"

curl -i -X PUT -H "Authorization:Basic d21.....uZT==" -F "file="@c:/path/to/file/ION-0999-D.gpg" "https://staging-dataupload.wmda.info/api/v2/io/ION0999/" -H "X-File-Name:ION-0999-D.gpg"

Download

Download reports

You may use the API also to fetch your reports . Unfortunately, it is not one line cmd, and need 2 steps.

1.Fetch the files list and get the file names.

Use the following curl and endpoint to fetch an array with filedescriptors: url should use double quote or no quote in windows env:

curl -H "Authorization:Basic d21.....uZT==" https://staging-dataupload.wmda.info/api/v2/fs/reports-ion0999/?children=f

You will get the result in xml format, and you can get json format, use the cmd below:

curl -H "Authorization:Basic d21.....uZT==" https://staging-dataupload.wmda.info/api/v2/fs/reports-ion0999/?children=f&format=json

2. Fetch all the reports or the one you need.

Note, you need to use "io" instead of "fs" in the path.

curl -O GET -H "Authorization:Basic d21.....uZT==" 'https://staging-dataupload.wmda.info/api/v2/io/reports-ion0999/$filename' -o '$filename.txt'

In windows cmd, the -o dose not work, and the cmd is as below:

curl -H "Authorization:Basic d21.....uZT==" https://staging-dataupload.wmda.info/api/v2/io/reports-ion0999/$filename > $filename.txt

Download archived files

Download archived files will be the same as download reports. And 2 steps as above are needed.

The example URL for archive folder is as below:

https://staging-dataupload.wmda.info/api/v2/fs/archive-ion0999/?children=f

In RESTLET :

Search & Match Service > Data Manager: How to automate data upload/download with REST API? > image2017-10-12 12:58:44.png

Click on Code to get raw CURL syntax:

Search & Match Service > Data Manager: How to automate data upload/download with REST API? > image2017-10-12 13:2:15.png

Response should be 200:

Search & Match Service > Data Manager: How to automate data upload/download with REST API? > image2017-10-12 12:58:44.png

Download full dataset

For those registries that are permitted to use the full dataset the statement below will fetch that. Please change the ION workspace to match your ION.

curl -O GET -H "Authorization:Basic .............." 'https://dataupload.wmda.info/api/v2/io/downloads/ION1804/bmdw4data.zip.gpg' -o 'wmda_data_v22.zip.gpg'

In windows cmd, the -o dose not work, and the cmd is as below:

curl -H "Authorization:Basic .............." "https://dataupload.wmda.info/api/v2/io/downloads/ION1804/bmdw4data.zip.gpg" > wmda_data_v22.zip.gpg

We noticed sometimes the download maybe terminated because of some temp network limitation, and the "-C -" option can be used to continue the download.
-v is for more details of the track info

curl -v -H "Authorization:Basic .............." -o 'wmda_data_v22.zip.gpg' -C - 'https://dataupload.wmda.info/api/v2/io/downloads/ION1804/wmda_data_v22.zip.gpg'

FAQ

Question : My report states : File could not be processed due to a file decryption error, when using the API upload? Why?

Answer :

The Dataupload's API endpoint /io streams file(s) directly to the workspace. We have detected that premature file pickups may occur and attempt to move/delete files while content is still being appended or processed. We have taken actions to reduce this behaviour by decreasing the frequency for file pickup which in turn does lower the chance for premature pick. We have also implemented gpg error validation to check integrity based on its messages.

Note: Files are picked from the workspaces for processing every 10 minutes. And file will only picked up if it is not updated for 5 mins.

Some key messages:

Known internal gpg messages for corrupted files during API uploads: "invalid packet", "invalid encoding" and "failed".
Report message that uploader users would receive in case of corrupted gpg file upload: File could not be processed due to a file decryption error. Please make sure file is properly encrypted.

For more information please contact WMDA support team.