There are two ways to upload data for listing in the Search & Match Service:
- manual upload (described below) and
- automatic upload where a connection is established between computer system, so called REST API. The manual for the automatic upload can be found here.
If the data are received they are processed and available for search coordinators and transplant physicians who use the Search & Match Service for search.
This is a technical work instruction, feel free to contact us if you need any support or if you do not understand the work instruction. Our e-mail address is: firstname.lastname@example.org
|PGP||Pretty Good Privacy (PGP) is an encryption programme that provides cryptographic privacy and authentication for data communication|
|XML||Extensible Markup Language, a structued file format|
|API||Application Programming Interface (API): a set of clearly defined methods of communication between various software components|
Issuing Organisation Number (ION) which is provided by ICCBBA to organisations listing in the Search & Match Service
You may lookup IONS in the list of organisations maintained by WMDA
|XSD||XSD defines what elements and attributes may appear in an XML document; annually a new version of the XSD will be released; the current version is: 2.1|
This work instruction describes the manual upload method of an PgP/GpG encrypted XML file through the submission platform.
- Only organisations that have an ION (listing organisations) will be able to upload
- The usernames are your email address that you have requested to be added in our database as Data Uploaders
- Every organisation that is listing only donors or only cord blood units is allowed to have two dedicated accounts. If an organisation is listing both donors and cord blood units, they are allowed to have a maximum of four accounts. Multiple accounts of one organisation share one Workspace, but every user has its own login details.
- The platform is organised in so called 'Workspaces'. This Workspace is a private space for each organisation where files can be uploaded and processing reports become available.
- If your organisation submits data on behalf of other registries then as an uploading organisation you will only see one Workspace where you can upload files for other registry(ies) that you are affiliated with.
- Uploaded files should follow the XML guidelines as described in the Data submission information.
- Files should following the file naming rules as described in the Search & Match Service Data submission information
- XML files larger than 200Mb should be compressed using ZIP (How to compress your file with ZIP can be found here)
- Only files with the .pgp and .gpg extension will be accepted for upload.
- XML files should be encrypted with a public key (How to encrypt a file can be found here)
Accessing the data submission platform
We have 2 variants of the data submission platform :
- staging-dataupload.wmda.info : here organisations can upload their data for testing purposes and check their dataquality, before moving to
- dataupload.wmda.info : here production data is uploaded, which is permitted only after QA inspection by WMDA.
You can access the data submission platform through the web. You can access the web address (or URL) by entering the address: https://staging-dataupload.wmda.info/.
PLEASE NOTE: This platform is still under development. Therefore, you may notice outages, changes to your data, or even find some functions broken and giving errors. These potentially issues are either due to new functional deployments taking place or their being a bug in the software. If you do come across any bugs or defects please do report these as part of any feedback you may have by sending an email to email@example.com.
The premise of giving our listing organisations access to the test site is to allow them to familiarise themselves in advance of this being deployed to production and also start to implement and test their XML files and provide us feedback on any functions that they might wish to enhance or see added to the system.
Logging in for the first time
Before you can access the data upload service, you need to be an authorized user in our system. Currently, the following users are added to the system:
- All users from the old test upload system who helped with the proof of concept consultation
- All people who previously sent a test file by email
- All people who requested access by email
All of these people will receive a welcome email from the data upload service system with instructions how they can access the service.
If you are not a current user and would like to have access to upload your test XML file, please send us an email to firstname.lastname@example.org
To access the system for the first time
- As a new user, you should have received a welcome email that includes a link to the data upload service and instructions to set your password.
- Click on the link and then on the 'Forgot your password?' link.
- Fill out your email address and click on OK. You will now receive an email with a link to reset your password.
- Click on the link, choose your own password, confirm this password and click on the OK button.
- Go to https://staging-dataupload.wmda.info/ to login (Figure 1) If you just have set your password, the system should return you automatically to the login page.
- Within the login page you can optionally change your language by clicking on the flag just besides 'Enter login/password':
- You can also save a bookmark in your browser, e.g. for the data upload service, so that you are immediately directed to the login page rather than having to enter the URL.
- Enter your email address and your password.
- The system defaults to your personalized Workspace, where you will find your organisation Workspace and all other folders like notification and archived folder.
Login screen WMDA data upload service
Change password or forgot password
- Click on the 'Forgot your password?' link and fill out your email address on the password reset page (Figure 2) and click on the 'OK' button. You will then receive an email with a link to reset your password.
- Click on the link and choose your own password, confirm this password and click on the OK button.
Forgot registered email address: If you might have forgotten your e-mail address that was registered for your data upload account, please contact the WMDA office by email via email@example.com
Change password: You can also change your password after you logged into the system.
- To do this, click on your home page on the settings button.
- A drop-down menu will appear and then click on 'My Account'.
- In the next window, click on the button 'change password' in the left bottom corner
- A new smaller window will open. Fill out your old password and your new chosen password and click on OK.
Tip: If you haven’t changed your password for a long time, we recommend that you do so to ensure that your profile is secure. We recommend that you change your password every 6 months.
Figure 2: Forgot your password page
Figure 3a: Screen password reset confirmation
If you attempt to login more than 3 times with incorrect credentials the system for security reasons will ask you to enter a code that appears in an image as shown in Figure 3b.
Figure 3b: Screen after 3 login attempts
Logging off from the service
To close and exit click on the Settings button next to your name on the top left side (Figure 4). This should give you a drop-down menu with 'log out'. Click on 'Log out' and you will be redirected to the login screen.
PLEASE NOTE: Do not simply close your browser; otherwise your unsaved data may be lost.
Figure 4: Logging out of the WMDA data upload service: setting button and dropdown menu
After logging in, you get the screen as shown in Figure 5. On your home page, you can perform the following functions:
Figure 5: Homepage after logging in
- Your name: On the top left corner. This is the name of the user that logged into the system
- Notification indicator: This is the bell that will highlight if you have any new notifications around the status of your uploaded file
- Setting button : This is the menu for functions like - Logout and Updating account details
- Search box: Useful when trying to find files, for example using a specific date
- My Workspace: Your own Workspace named with the ION of your organisation. In conjunction with your Workspace you also see two separate folders called Archives and Reports. For further details on the purpose of these folders please see section around Archive/Reports.
- Recent history of submissions in the middle main pane
PLEASE NOTE: On the left hand side you can see the Workspace for your registry that you have access to. Most organisations will have access to just one space even if you are submitting data on behalf of other registries.
Setting button: when you click on the settings button, you can seen a drop-down menu (Figure 4) with
- My account: In this section you can set an avatar (picture) or your organisations logo and change your password. You can only review the Name and Email address but cant change it. If the name of email address shown within the account section is wrong please contact WMDA via email firstname.lastname@example.org so we can update those details in out CRM database.
- Share and About: These two functions at the moment aren't developed so please refrain from using this.
- Log out: Exit system
Workspace: Within your Workspace you can find the list of uploaded files
When you login for the first time, the Workspace will be empty (Figure 6).
Figure 6: Content of workspace screen
Upload a file
If you wish to upload a new PgP/GpG encrypted XML file into your Workspace in order to process the file, please follow the next steps:
- Click on the Workspace of your organisation.
- Within your Workspace click on the red tab with 'New' and then on the 'Upload' icon at the bottom of the drop-down menu (Figure 7).
- A new screen will open where you can select your file for upload (Figure 8a).
- Click on the red button with 'Pick File'.
- A browser window will open and you can select the file on your computer you would like to upload. Click on Open.
- The file becomes then visible in the browser window and when it is the correct file, click on OK to upload the file to your Workspace.
An alternative method to upload your file to your Workspace is by dragging your file from your desktop to the main middle pane of your Workspace
- Once the upload of the file is completed, you receive a message.
- The file is now ready to be picked-up by the Search & Match Service for further processing. When the file is picked-up by the processing pipeline, a copy of the file is stored in your archives folder. All messages concerning the processing of your file can be found in the Reports folder. The copy of the file and the file with messages have a filename related to the name of the original file in combination with the upload time and user
PLEASE NOTE: The time to upload your file to the system depends on the file size and your internet upload speed.
Figure 7: Upload new file
Figure 8a: Select file for upload screens
You are only allowed to upload files that are encrypted. If you try and upload files that are non PgP/GpG encrypted the system will give you an upload error as shown in figure 8b.
Figure 8b: Only PgP encrypted files allowed
Manage/Update existing uploaded files
After uploading your file, you can still delete the file if it hasn't picked-up by the processing pipeline. Once the file is picked-up, you cannot delete the file anymore or cancel the processing. The system will check for new files every 10 minutes. Therefore, the time that you have left to delete the file can vary.
- Within your Workspace select the file you wish to update/delete and click on the 'Delete' button/tab if you wish to delete file. You can also delete the file by clicking on the file with your right mouse button and select 'Delete' from the drop-down menu.
- The system will warn you to ensure if you really want to delete this file (Figure 9).
- If you click OK the file is deleted and will no longer be processed.
Figure 9: How to delete an uploaded file
This folder contains all of the files that have moved to the pipeline for processing. There is a 10 minutes lag before a file that's been uploaded onto your workspace is picked by the pipeline for processing. Files in the Archive folder can't be deleted. You only have read access to the Archive folder. The file name is changed to indicate the date/time the file was placed in this folder for processing.
PLEASE NOTE: These files are deleted from the folder after 6 months of them being processed. There associated reports too will be deleted from the report folder.
This folder has all of the processed report outcomes of the uploaded file. Once the processing pipeline picked-up the file, it will start with initial validations in a sequence. The sequence is: Decrypting the file > Unzipping the file > XML file structure validation > Data content validation > HLA validation. Only once all of these validations have been completed, the system will provide all the users from the organisation a notification and a report that will indicate the outcome of the file processing. Processing messages are generated and stored in a file in your Reports folder. All messages are collected in one file for each file you uploaded to the system. This is clearly indicated using the same file name with the date/time stamp so users can easily identify the file the report relates to.
PLEASE NOTE: Just like the Archive folder you only have read access to this folder. Also all reports are deleted after 6 months of them being placed in this folder.
Processing report messages
Below are the list of messages that users can expect and the reasons for these messages
***** STILL BEING DRAFTED***
Whilst the uploaded files are being processed users should be reported for the following stages
- Uploaded file successfully - This is a message that users get as part of the standard file upload successfully. Please see section upload a file as part of uploading your file.
- Uploaded file is picked up by pipeline for processing
- Uploaded file processed and report available by the pipeline
Users should be reported for the following scenarios on file level validations
|Scenario||Event stage||Description||Type of message|
|File with wrong filename||The system will reject the file if the file name doesn't conform to the agreed format which is : ION-1234-D.PgP, ION-1234-D.xml.Pgp, ION-1234-D.zip.PgP, ION-1234-C.PgP, ION-1234-C.xml.Pgp, ION-1234-C.zip.PgP.||Rejected - ADD MESSAGE AS PART OF THE REPORT|
|If a user uploads two files consecutively with same file name. Eg ION-1234-D.PgP and ION-1234-D.PgP||In such a scenario the most recently uploaded file is taken through the pipeline, the previous file is deleted and not processed.|
|If a user uploads two files consecutively with different file names. E.g ION-1234-D.PgP and ION-1234-C.PgP||In such a scenario the system will process the two files as separate files.|
|If a user uploads a PgP encrypted file with a invalid key.||Decrypted||In such a scenario the system will not be able to decrypt the file and the pipeline will not be able to process the file.||Rejected - ADD MESSAGE AS PART OF THE REPORT|
|If a user has uploaded a zipped file which isn't an XML||Decompressed||In such a scenario once the system has decrypted the file and finds the file isn't an XML the pipeline will not be able to process the file.||Rejected - ADD MESSAGE AS PART OF THE REPORT|
|If a user has uploaded a file with the file creation time set in the future||XSD file validation||In such a scenario once the system has decrypted the file and finds that the file creation date/time is in the future then the pipeline will not be able to process the file.||Rejected - ADD MESSAGE AS PART OF THE REPORT|
|If a user has uploaded a file with the file creation date and/or time in an incorrect format||XSD file validation||In such a scenario once the system has decrypted the file and finds that the file creation date/time is in an incorrect format then the pipeline will not be able to process the file.||Rejected - ADD MESSAGE AS PART OF THE REPORT|
|If a user has uploaded a file where the listing organisation doesn't match the ION number in the file name||XSD file validation||Rejected - ADD MESSAGE AS PART OF THE REPORT|
|If a user has uploaded a file where the update mode is other than full||XSD file validation||Rejected - ADD MESSAGE AS PART OF THE REPORT|
|If a user has uploaded a file where the file name and content type do not match.||XSD file validation||In such a scenario once the system has decrypted the file and finds that there is a discrepancy in the file name content type and the file content type then the pipeline will not be able to process the file. E.g File name = ION-1234-D.PgP and the Content type = C||Rejected - ADD MESSAGE AS PART OF THE REPORT|
|If a user has uploaded a file that has content type of both donor and cord||XSD file validation||Rejected - ADD MESSAGE AS PART OF THE REPORT|
|If a user has uploaded a file where the file version isn't correct||XSD file validation||Rejected - ADD MESSAGE AS PART OF THE REPORT|
 The specification is available at https://pydio.com/en/docs/references/api/v2#!/File/uploadStream
STANDARD OPERATING PROCEDURE
Data submission protocol
DATE OF ORIGINAL ISSUE:
12 months (This includes the testing process)
ORIGINAL PREPARED BY:
QM REVIEWED BY:
COPY and LOCATION
Master Copy – WMDA Share – DOCxxx
Document Version History
Update (Sprint 3/4)
Release staging version (28-07-2017)
|0.4||Manish Kakkar||Updated post release to staging version (07-08-2017)|