Workflow REST API service: specific query that retrieves all the workflows from certain user

[Sue Tairaku]

Hello,

I am a student from The University of Queensland and I am developing a Kepler add-on in order to integrate it with myExperiment as my Thesis topic. During my development, I need to get a myExperiment service that can retrieve all the workflows uploaded by a given user. Is this type of service available? I have tried using the search suggestion in the REST API webpage but none of them seems to bring the response I need.

I would appreciate your help about this concern. In case there is not service available for this specific search, please let me know.

Kind Regards,

Sue Tairaku.

[Finn Bacall]

Hi Sue,

You can access this information through the users API. See:
http://wiki.myexperiment.org/index.php/Developer:UsersResource#Read_user
and the "Elements for user" section at the bottom.

For example, for user with ID 666:
http://www.myexperiment.org/user.xml?id=666&elements=workflows

You can then query the individual workflow URLs.

Cheers,

Finn

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[Sue Tairaku]

Hello Finn,

Thank you so much for your reply. It is very useful, however, I am trying to get the user id now.

I have implemented the simple session cookie authentication and I thought that by a GET request to http://www.myexperiment.org/whoami.xml with my cookie, I will get the user of the authenticated session, but it doesn't work. I am not sure how I can insert session inputs to whoami page.

Can you give me any advise of how I could get the user information by grating username and password? I am using Java Jersey's libraries.

Thank you so much in advance.

Kind Regards!

Sue

On Thu, Mar 9, 2017 at 10:11 PM, Finn Bacall <finn....@manchester.ac.uk> wrote:

Hi Sue,

You can access this information through the users API. See:
http://wiki.myexperiment.org/index.php/Developer:UsersResource#Read_user
and the "Elements for user" section at the bottom.

For example, for user with ID 666:
http://www.myexperiment.org/user.xml?id=666&elements=workflows

You can then query the individual workflow URLs.

Cheers,

Finn

On 09/03/2017 11:44, Sue Tairaku wrote:

Hello,

I am a student from The University of Queensland and I am developing a Kepler add-on in order to integrate it with myExperiment as my Thesis topic. During my development, I need to get a myExperiment service that can retrieve all the workflows uploaded by a given user. Is this type of service available? I have tried using the search suggestion in the REST API webpage but none of them seems to bring the response I need.

I would appreciate your help about this concern. In case there is not service available for this specific search, please let me know.

Kind Regards,

Sue Tairaku.

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[Sue Tairaku]

Dear MyExperiment Group,

Thank you all for your support. I really appreciate it. I have one more question about Content-types.

Since I am developing a Add-On for Kepler, I want to send MyExperiment with Kepler workflows. Right now I am testing my POST request by trying to create a workflow from my application, however, I get error 400 with reason: Content type matches more than one registered content type. I understand that, as a content-type I must send the mime-type registered at http://www.myexperiment.org/type.xml?id=14 which is the type specified for Kepler. However, I realized that that mime-type, indeed, is not unique for Kepler since other content-types have the same mime-type.

How can I resolve this error? In case my add-on wants to send workflows with content-type Kepler, what should I specified as content-type? In case I am making a mistake by grabbing all the mime-types from each http://www.myexperiment.org/types.xml (which is what I did), I will really appreciate to have the list of real mime-types, otherwise, what information is expected to be sent for each of the registered content-types.

I will really appreciate your support.

Thank you in advance,

Sue

On Thu, Mar 9, 2017 at 10:11 PM, Finn Bacall <finn....@manchester.ac.uk> wrote:

Hi Sue,

You can access this information through the users API. See:
http://wiki.myexperiment.org/index.php/Developer:UsersResource#Read_user
and the "Elements for user" section at the bottom.

For example, for user with ID 666:
http://www.myexperiment.org/user.xml?id=666&elements=workflows

You can then query the individual workflow URLs.

Cheers,

Finn

On 09/03/2017 11:44, Sue Tairaku wrote:

Hello,

I am a student from The University of Queensland and I am developing a Kepler add-on in order to integrate it with myExperiment as my Thesis topic. During my development, I need to get a myExperiment service that can retrieve all the workflows uploaded by a given user. Is this type of service available? I have tried using the search suggestion in the REST API webpage but none of them seems to bring the response I need.

I would appreciate your help about this concern. In case there is not service available for this specific search, please let me know.

Kind Regards,

Sue Tairaku.

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[Finn Bacall]

Hi,

Have you seen this page in the wiki? http://wiki.myexperiment.org/index.php/Developer:SessionCookie

I'm not too familiar with the library you are using, but it seems to work via curl. Can you tell me what errors you are getting?

Alternatively, you could use HTTP Basic authentication and supply the username and password with every request.

Cheers,

Finn

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[Finn Bacall]

Hi Sue,

Instead of using MIME type, e.g:

    <content-type>application/octet-stream</content-type>

you can specify the type by using the content type's name:

    <type>Kepler</type>

Apologies, API documentation doesn't really make this clear.

Hope this helps,

Finn

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[Sue Tairaku]

Hello Finn,

Thank you so much for your support. Indeed, I implemented the HTTP Basic and is working now. Also, the content-type, I changed it to type and finally I can POST to myExperiment.

Again, thank you so much for your fast replies, I really appreciate it.

Warm regards!

Sue

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[Sue Tairaku]

Hello Finn,

I have another issue about MyExperiment integration. I now can create workflows and upload them from my application. The service responses successfully to my requests and this process just work smoothly. However, every time I upload a workflow, no matter which content-type I send when I download the workflow content from myExperiment, it always gives me a .txt format.

I was wondering if you may have an idea of why this happens, if it could be an issue from my request (even though the service recognizes it as a good request), I will appreciate if you can give me any hints on what to improve. I am currently sending the workflow content encrypted with base64. It doesn't matter if I transform the whole XML content into a String or I attached an XML file and encrypted, I always get a .txt when the workflow I uploaded is downloaded.

Hope this makes sense.

Thank you again for your constant support.

Warm regards,

Sue

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[Sue Tairaku]

Hello Finn,

I have another issue about MyExperiment integration. I now can create workflows and upload them from my application. The service responses successfully to my requests and this process just work smoothly. However, every time I upload a workflow, no matter which content-type I send when I download the workflow content from myExperiment, it always gives me a .txt format.

I was wondering if you may have an idea of why this happens, if it could be an issue from my request (even though the service recognizes it as a good request), I will appreciate if you can give me any hints on what to improve. I am currently sending the workflow content encrypted with base64. It doesn't matter if I transform the whole XML content into a String or I attached an XML file and encrypted, I always get a .txt when the workflow I uploaded is downloaded.

Hope this makes sense.

Thank you again for your constant support.

Warm regards,

Sue

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[Finn Bacall]

Hi Sue,

Can you send me a link to one of the workflows that is displaying this behaviour?

(You might need to edit the privacy settings so I can see it)

Thanks,

Finn

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[Sue Tairaku]

Hello Finn,

Thank you for your help!. Here is a link of an example of my workflows uploaded from my add-on: https://www.myexperiment.org/workflows/4968.html

Thank you in advance!

Cheers

Sue

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[Finn Bacall]

Hi,

There doesn't seem to be a way to set the filename/file extension through the API, unfortunately.

Will your Kepler workflows always have the same file extension?

I think I can set a default file extension for Kepler workflows.

Finn

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[Sue Tairaku]

Hi Finn,

At the moment I am working with XML extension.  Would be amazing you can set that for me.

Thank you so much!

Cheers

Sue

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[Finn Bacall]

I've deployed this on http://sandbox.myexperiment.org

Could you test your client using this server?

If everything is OK I will deploy it on the main server.

Thanks,

Finn

[Sue Tairaku]

Hi Finn,

It works! Now I can download an XML. I tested your change at Sandbox. This is the URL: http://sandbox.myexperiment.org/workflows/3403.html.

Another question, do you know why the image that I upload are displayed with a color filter? For example, the image of the attached workflow has a green filter over the original image.

Thank you for your constant help.

Cheers!

Sue

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[Finn Bacall]

Cool, I will update the main server sometime today.

What format are you using for the image? myExperiment converts uploaded images into JPEGs, so there may be an issue with how it converts whichever format you are using.

Cheers,

Finn

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[Sue Tairaku]

Hello Finn,

I am using .png images. Would you recommend me to limit my app for using just jpeg images? 

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[Finn Bacall]

Are you sure you are using PNGs?

The image for http://sandbox.myexperiment.org/workflows/3403.html appears to be a JPEG, unless it was converted before being stored somehow (usually images are stored in their raw form and converted afterwards).

Have you noticed the strange image appearance on any of your other workflows or just that one?

Could you see if you get the same problem if you upload through the web interface?

Thanks,

Finn

PS. I have updated myexperiment.org with the file extension fix.

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[Sue Tairaku]

Hello Finn,

I have noticed that strange color image in every test I did. Both, at the Production and Sandbox services. 

When I upload directly from MyExperiment I don't get that color filter.

Cheers!

Sue

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[Finn Bacall]

Hi Sue,

I've been looking into this and can't seem to reproduce it: http://sandbox.myexperiment.org/workflows/3410.html

Could it be the code you are using in your client to serialize the image into Base64?

You could try decoding the Base64 and writing it back to a file, and seeing if the image is discoloured on your computer.

Cheers,

Finn

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[Sue Tairaku]

Hi Finn,

Thank you for let me know. I'll check my encoding as you suggest.

On the other hand, I was checking myExperiment PUT service because we want to give Kepler users the chance to create and update workflows from Kepler and upload/update directly to myExperiment, however, I have seen that PUT service doesn't allow to update workflow content. Is it possible to implement it? We wish to have the chance to update workflow content and image preview.

Let me know if that is possible.

Thank you again for your constant support.

Kind regards,

Sue

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[Finn Bacall]

Hi,

It does support updating the content/image. I'm not sure what the docs say because the wiki seems to be down for me!

You can update a workflow in the same way as creating, but change the POST to a PUT and specify "?id=workflow-id-here" in the URL.

I just tested this on sandbox via curl: http://sandbox.myexperiment.org/workflows/3410.html

Cheers,

Finn

[Don Cruickshank]

Hi,

 

Yes, the machine that hosts the wiki is down at the moment I'm afraid. I hope to have an update on that later today.

 

Regards,

Don.

[Sue Tairaku]

Hi Finn,

Thanks for the clarification. I'll try your suggestion and let you know how it goes.

Cheers!

Sue

[Don Cruickshank]

Just to add that you can still get to the document via archive.org for now:

 

https://web-beta.archive.org/web/20160712204629/http://wiki.myexperiment.org/index.php/Developer:API

 

Regards,

Don.

[Sue Tairaku]

Thanks Don, I really appreciate that link, I need that information to make progress.

Kind regards,

Sue

[Sue Tairaku]

Hello!

I haven't  been in contact with you for a while but I am glad to say that thanks to your help, my Integration between Kepler and MyExperiment is already working :)

I have been doing some fixes and I was sent a list of licenses but they are not working correctly. I wanted to validate with you which is the real list of licenses that could be used with My Experiment. Unfortunately, the REST API web page is still down and I cannot check on my own. This is the list I have so far:

• Creative Commons by Attribution (CC BY)
  
• Creative Commons By Attribution-ShareAlike 4.0 International (CC BY-SA 4.0)
  
• Creative Commons By Attribution-Noncommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)
  
• BSD license 3.0
  
• GPL license 3.0
  
• MIT license
  
• Apache License 2.0
  

Please, let me know the correct nomenclature to use for each of these license types due to using them exactly as they are displayed, I am getting errors.

Thank you for your constant support.

Cheers!

Sue

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[Finn Bacall]

Hi Sue,

Glad to hear your client is working!

Apologies for the REST API docs site being down, I'll try and chase that up.

Regarding licenses, check out this API endpoint:
http://www.myexperiment.org/licenses.xml?elements=unique-name,title

"unique-name" is the identifier that you need to use in the workflow XML.

Those licenses most likely won't change, so you can probably hard code them into your client or cache them.

Cheers,

Finn

[Don Cruickshank]

Hi Sue, Finn,

 

I've just talked to the systems programmer responsible for the migration of the wiki and he has prioritized it now.

 

Regards,

Don.

 

From: myexperimen...@googlegroups.com [mailto:myexperimen...@googlegroups.com] On Behalf Of Finn Bacall
Sent: 18 May 2017 09:56
To: myexperimen...@googlegroups.com
Subject: Re: [myexperiment-developers] Workflow REST API service: specific query that retrieves all the workflows from certain user

 

Hi Sue,

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[Finn Bacall]

Cheers, Don

I think when it's back up and running, it's probably worth me creating a "mirror" of the API docs in the myExperiment github wiki thing: https://github.com/myExperiment/myExperiment/wiki

Finn

[Don Cruickshank]

Hi Finn,

 

The wiki is now back up.

 

I agree - an API mirror on GitHub wiki pages sounds like a good idea!

[Finn Bacall]

Great!

Thanks for sorting this out,

Finn

[Sue Tairaku]

Hello Finn,

Thanks again for helping me out all this time. My thesis project with MyExperiment is almost done and so far, it is a success. We are hoping to see my add-on integrated with Kepler in the near future so users could use MyExperiment within Kepler.

I have a requirement to add these licenses types to MyExperiment since these are commonly used in Kepler. Let me know if this is possible. Here is the list:

• Creative Commons by Attribution (CC-BY)
  
• Creative Commons By Attribution-ShareAlike 4.0 International (BY-SA-4.0)
  
• Creative Commons By Attribution-Noncommercial-ShareAlike 4.0 International (BY-NC-SA-4.0)
  
• BSD license 3.0 (BSD-3.0)
  
• GPL license 3.0 (GLP-3.0)
  

About the specific name for the licenses (CC-BY, BY-SA-4.0, etc...), they are suggestions. I have checked the current licenses types and I think they don't duplicate the existent ones. If this could be done, let me know so I could add these licenses to my programming as well. In the past, I asked you if they were available but, since they are not, I currently get an error status when I use them.

Thank you again for your support,

Cheers

Sue

 

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[Finn Bacall]

Hi,

I've added them with some minor tweaks to the unique-names to make them consistant with the current licenses.

See: https://www.myexperiment.org/licenses.xml?elements=unique-name,title,url

Cheers!

Finn

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[Sue Tairaku]

Hello Finn,

Thank you so much for your support!

Cheers!

Sue

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