[SVCS-86] Add Papaya Renderer for Dicom and NifTi Files #265

TomBaxter · 2017-06-16T13:47:01Z

Purpose:

Create renderer for NifTI images. (.nii)

Collateral

Supports .nii.gz (NifTi files are commonly saved with .gz)
Supports .dcm (DICOM images)

Changes:

Create papaya renderer in /mfr/extensions/papaya
Relies on https://github.com/rii-mango/Papaya
Copies file to render to /mfr/extensions/papaya/static/data to make available to papaya.js
NiFTI files are often saved as .nii.gz by convention. I've added a facility to handle file extensions with an additional extension, such as compression.
At the beginning of each render files older then 5 minutes will be deleted.
Added a test.

Side effects

Some rendered file data will temporarily exist in mfr/extensions/papaya/static/data

Notes

I created PR for our use case...
rii-mango/Papaya#101
Which was accepted as of Papaya release build-1430
Use papaya.js and papaya.css from /Papaya-build-1430/release/current/standard/

We should keep an eye on this project...
https://github.com/FNNDSC/ami
We may want to switch to it in the future.

Tickets

https://openscience.atlassian.net/browse/SVCS-86

cslzchen

@TomBaxter A few thoughts and suggestions, thanks.

The papaya.js is super huge. Is there a way that it is loaded as a package or at least from a script tag which retrieves the content from a trusted third party domain or maybe our CDN domain (still in progress I think) that holds all the scripts/resources. Similar for the papaya.css though it is small. Update: it seems that including JS locally is how the way we built the MFR at the beginning. In the future we will have a package manager for JS. For now, it looks good.
The project you mentioned now support Nifti1but still not .nii.gz or the .dcm. Is this worth trying?
Formfr/extensions/papaya/static/data, does the temporary files only exist during file rendering? When are they cleaned? Don't want this to take up server memory.

TomBaxter · 2017-10-17T20:17:17Z

@cslzchen

OK
I don't think so. The Dicom files are the files that are in demand.
The temporary files are removed at the beginning of each run of the renderer.

cslzchen

First pass done 🎆 with a few questions and suggestions. Back to you @TomBaxter .

cslzchen · 2017-10-24T20:22:18Z

tests/extensions/papaya/test_renderer.py

+
+    def test_render_papaya(self, renderer, metadata, assets_url):
+        body = renderer.render()
+        print(body)


Remove this.

cslzchen · 2017-10-24T20:31:54Z

tests/extensions/papaya/test_renderer.py

+    return PapayaRenderer(metadata, file_path, url, assets_url, export_url)
+
+
+class TestPapayaRenderer:


Can we expand the tests to cover at least valid and invalid files:

Valid files

If there are any potential version issues/differences, we should include them as well.

Invalid/Corrupted files that may throw exceptions during opening, parsing, rendering, e.t.c.

We should be able to handle exceptions and return a relevant error message.

This applies to all three types. (Dicom, Compressed and Uncompressed NifTi).

Added tests for other two file extensions. However, not that interesting as this only tests the python rendering of the HTML. I don't believe there is a way to test the javascript from pytest. Therefore, didn't bother adding an Invalid/Corrupted test.

You are right. This is the render instead of the exporter. No need for the invalid files.

cslzchen · 2017-10-24T20:43:32Z

mfr/extensions/papaya/render.py

+        for data_file in os.listdir(self.data_dir):
+            if data_file == '.gitignore':
+                continue
+            if (time.time() - os.path.getctime(self.data_dir + data_file)) >= self.data_old:


Can we make this a general util method for checking file time expiration for MFR in general?

cslzchen · 2017-10-24T20:45:01Z

mfr/extensions/papaya/static/data/.gitignore

+# Ignore everything in this directory
+*
+# Except this file
+!.gitignore


We should ignore the directory and all its sub directories and contents instead of having such a .gitignore. In this way, no need to check:

if data_file == '.gitignore': continue

Not sure what you're getting at here. In any case, the .gitignore was for my convenience while developing. Removing it.

For example, here is a directory /repo/level_1/level_2/level_3/. If you want to ignore all files in level_3/, instead of having a level3/.gitignore you can use a level2/.gitignore or even a repo level one that ignores everything in the directory level3/.

Travis failed, which reminded me of why I had the .gitignore. In addition to it being handy during development, I also need it to create and check in the empty directory mfr/extensions/papaya/static/data/

👍 I will locally test it again today before sending this to PCR.

cslzchen · 2017-10-24T20:47:49Z

mfr/extensions/papaya/render.py

+class PapayaRenderer(extension.BaseRenderer):
+
+    data_dir = settings.DATA_DIR
+    data_old = settings.DATA_OLD


How about data_exp and DATA_EXP for expiration?

Yeah, OLD doesn't really fit. But EXP doesn't either. Went with TTL (Time To Live).

cslzchen · 2017-10-24T20:50:47Z

mfr/extensions/papaya/render.py

+        ]).get_template('viewer.mako')
+
+    def render(self):
+        self.remove_old_files()


Does this mean the temporary files for rendering will get stuck here all the time? Each time users try to render a file, the old ones gets removed but new ones are created.

Yes, that is correct.

Not sure how much this will impact prod memory. MFR and WB pods constantly run out of space though. I will leave this for Phase 2 Review.

cslzchen · 2017-10-24T21:05:14Z

mfr/extensions/papaya/static/papaya.css

@@ -0,0 +1 @@
+.papaya{width:90%;height:90%;margin:25px auto;background-color:black;font-family:sans-serif}.papaya:before{position:relative;content:"Papaya requires JavaScript...";display:block;top:45%;color:red;margin:0 auto;font-size:18px;font-family:sans-serif}.papaya-fullscreen{height:100%}.papaya-toolbar{text-align:left;box-sizing:content-box;position:relative}.papaya-toolbar ul{margin:0;list-style:none}.papaya-toolbar input[type=file]{text-align:right;display:none}.papaya-kiosk-controls{position:relative;margin:5px auto;list-style:none;-webkit-touch-callout:none;-webkit-user-select:none;-khtml-user-select:none;-moz-user-select:none;-ms-user-select:none;user-select:none}.papaya-kiosk-controls ul{list-style:none}.papaya-kiosk-controls button{-webkit-appearance:none;border-radius:0;-webkit-border-radius:0;font-size:14px;height:25px;background-color:lightgray}.papaya-control-increment{-webkit-appearance:none;border-radius:0;-webkit-border-radius:0;font-size:14px;height:25px;width:25px;text-align:center;vertical-align:middle;padding:0;margin-left:auto;margin-right:auto;line-height:16px;box-sizing:border-box;font-family:"Courier New",Courier,monospace}.papaya-main-increment{-webkit-appearance:none;border-radius:0;-webkit-border-radius:0;font-size:14px;height:25px;width:25px;text-align:center;font-family:"Courier New",Courier,monospace;background-color:lightgray;vertical-align:middle;padding:0;margin-left:auto;margin-right:auto;box-sizing:border-box;outline:0}.papaya-main-decrement{-webkit-appearance:none;border-radius:0;-webkit-border-radius:0;font-size:14px;height:25px;width:25px;text-align:center;font-family:"Courier New",Courier,monospace;background-color:lightgray;vertical-align:middle;padding:0;margin-left:auto;margin-right:auto;box-sizing:border-box;outline:0}.papaya-main-swap{-webkit-appearance:none;border-radius:0;-webkit-border-radius:0;font-size:14px;height:25px;background-color:lightgray;outline:0}.papaya-main-goto-center{-webkit-appearance:none;border-radius:0;-webkit-border-radius:0;font-size:14px;height:25px;background-color:lightgray;outline:0}.papaya-main-goto-origin{-webkit-appearance:none;border-radius:0;-webkit-border-radius:0;font-size:14px;height:25px;background-color:lightgray;outline:0}.papaya-slider-slice{padding:0 5px;display:inline}.papaya-slider-slice span{font-size:14px;font-family:sans-serif;vertical-align:middle}.papaya-slider-slice button{-webkit-appearance:none;border-radius:0;-webkit-border-radius:0;vertical-align:middle;font-size:14px;height:25px;background-color:lightgray}.papaya-controlbar-label{color:#000}.papaya-menu{width:220px;background:#222;z-index:100;position:absolute;border:solid 2px darkgray;padding:4px;margin:0}.papaya-menu li{font-size:12px;font-family:sans-serif;padding:4px 2px;color:#b5cbd3;cursor:pointer;list-style-type:none}.papaya-menu-label{font-size:14px;font-family:sans-serif;font-weight:bold;padding:2px 8px;cursor:pointer;vertical-align:text-bottom}.papaya-menu-titlebar{font-size:16px;font-family:sans-serif;padding:3px 8px 0 8px;cursor:default;vertical-align:text-bottom;color:white}.papaya-menu-icon{margin-left:5px}.papaya-menu-icon img{box-sizing:content-box}.papaya-menu-hovering{background-color:#444}.papaya-menu-spacer{height:8px}.papaya-menu-unselectable{-moz-user-select:-moz-none;-khtml-user-select:none;-webkit-user-select:none;-ms-user-select:none;user-select:none;-webkit-user-drag:none;user-drag:none}.papaya-menu-button-hovering{background-color:#DDD}.papaya-menu-filechooser{cursor:pointer;width:200px;display:inline-block;font-weight:normal}.papaya-menu-input{width:38px;margin-right:5px;color:black}li .papaya-menu-slider{vertical-align:middle;text-align:center;display:inline;width:120px;padding:0;margin:0}.papaya-dialog{min-width:400px;max-width:500px;height:500px;background:#222;position:absolute;z-index:100;border:solid 2px darkgray;padding:6px;font-size:14px;font-family:sans-serif;color:#b5cbd3;box-sizing:content-box;line-height:1.45}.papaya-dialog-content{margin:20px;height:415px;color:#dedede;overflow:auto;-ms-overflow-style:-ms-autohiding-scrollbar}.papaya-dialog-content-nowrap{white-space:nowrap}.papaya-dialog-content table{margin:0 auto}.papaya-dialog-content-label{text-align:right;padding:5px;color:#b5cbd3}.papaya-dialog-content-control{text-align:left;padding:5px}.papaya-dialog-content-help{text-align:right;padding:5px;color:lightgray;font-size:12px}.papaya-dialog-title{color:#b5cbd3;font-weight:bold;font-size:16px}.papaya-dialog-button{text-align:right;box-sizing:content-box;height:22px}.papaya-dialog-button button{box-sizing:content-box;color:black;font-size:11px}.papaya-dialog-background{position:fixed;top:0;left:0;background-color:#fff;width:100%;height:100%;opacity:.5}.papaya-dialog-stopscroll{height:100%;overflow:hidden}.checkForJS{width:90%;height:90%;margin:25px auto;background-color:black}.checkForJS:before{position:relative;content:"Papaya requires JavaScript...";display:block;top:45%;color:red;margin:0 auto;font-size:18px;font-family:sans-serif;text-align:center}.papaya-utils-unsupported{width:90%;height:90%;margin:25px auto;background-color:black}.papaya-utils-unsupported-message{position:relative;display:block;top:45%;color:red;margin:0 auto;font-size:18px;font-family:sans-serif;text-align:center}.papaya-viewer{line-height:1;font-family:sans-serif}.papaya-viewer div,.papaya-viewer canvas{margin:0;padding:0;border:0;font:inherit;font-size:100%;vertical-align:baseline;font-family:sans-serif}.papaya-viewer canvas{cursor:crosshair}


Add an empty line at the end of the file.

This file was copied straight from GitHub. I'm not knowledgeable about CSS, are you sure that is the right thing to do?

I am not sure. It is GitHub that complains. No need to change.

cslzchen · 2017-10-24T21:09:09Z

mfr/extensions/papaya/static/papaya.js

@@ -0,0 +1,2105 @@
+var PAPAYA_BUILD_NUM="1430",papayaLoadableImages=[];


There are several different version of released code. Is this the smallest file that covers our need. (e.g. If their minimal version has what we need, we can use that one (1K+) instead of this (2K+).

I think that is a question for product team. I demoed, and they appeared to like the added functionality.

coveralls · 2017-11-07T18:19:18Z

Coverage increased (+0.6%) to 64.458% when pulling e723f4c on TomBaxter:feature/svcs-86 into ee122ff on CenterForOpenScience:develop.

Add customization to papaya library to disallow opening of new files from user desktop. Consulted with Product Team. They determined that it would be confusing and possibly dangerous to allow opening of files from user desktop, when they might confuse it with the WaterButler repository. Used a custom built papaya.js built on https://github.com/TomBaxter/Papaya/tree/feature/noNewFiles I have sent them a PR, hopefully they bite. rii-mango/Papaya#101

cslzchen · 2017-11-17T16:14:00Z

There is an "entrypoints" test that needs to be updated if you add new file types. Don't worry about it and I will have it along with my PR.

…cs-86 [SVCS-86] Add Papaya Renderer for Dicom and NifTi Files

[#SVCS-86]

coveralls · 2017-11-20T16:40:53Z

Coverage increased (+0.5%) to 68.47% when pulling 6937fee on TomBaxter:feature/svcs-86 into 8bb2dd4 on CenterForOpenScience:develop.

[SVCS-86] Papaya Render

[#SVCS-86]

coveralls · 2017-11-21T22:47:14Z

Coverage increased (+0.7%) to 68.726% when pulling c834abf on TomBaxter:feature/svcs-86 into 8bb2dd4 on CenterForOpenScience:develop.

cslzchen

Looks good and works as expected. 🎆 🎆 Move to PCR.

@felliott @TomBaxter
There is one issue for Phase 2 on removing old files.

Temporary files are generated during rendering. It never gets deleted automatically. The solution in this PR is to remove old files in the temp directory at the beginning of each rendering. Here is a few concerns:

There is always old files there.
If more than one person try to render a file (and both try to clean the old files), only one of them will grab the lock while others hanging? Not able to tigger this locally but might be an issue on staging (less likely) and prod (likely).

Suggestions: we schedule a periodic task in celery to clean them?

TomBaxter · 2017-11-22T15:16:17Z

Keep in mind that the files MFR downloads get named with a UUID, so overlap is extremely unlikely.

TomBaxter · 2017-11-22T15:40:08Z

After discussing with @cslzchen , I understand his concern is that if two renderers try to delete a file that one will error since the other would have already deleted the file. An idea for handling this could be to simply handle the OSError exception with a try/except/pass .

TomBaxter · 2018-01-15T14:41:57Z

mfr/extensions/papaya/static/README-papaya.txt

@@ -0,0 +1,7 @@
+Currently using a custom built papaya.js with option to remove the ability to open new files from the users desktop.


TODO: Remove this file. PR was accepted and we are no longer using custom build.

🎉 Nicely done!

cslzchen

As mentioned, the PR that customized the JS lib has been accepted. This ticket and PR should be updated to reflect the changes. Please rebase and fix conflicts along the way. h/t to @TomBaxter and I will take over.

TomBaxter changed the title ~~[WIP] Add papaya renderer for nifti files.~~ [RFR] [SVCS-86] Add papaya renderer for nifti files. Jun 28, 2017

cslzchen requested changes Oct 5, 2017

View reviewed changes

cslzchen added the Code Review label Oct 12, 2017

cslzchen changed the title ~~[RFR] [SVCS-86] Add papaya renderer for nifti files.~~ [SVCS-86] Add Papaya Renderer for NifTi Files Oct 12, 2017

TomBaxter changed the title ~~[SVCS-86] Add Papaya Renderer for NifTi Files~~ [SVCS-86] Add Papaya Renderer for Dicom and NifTi Files Oct 17, 2017

cslzchen requested changes Oct 24, 2017

View reviewed changes

TomBaxter added 2 commits November 17, 2017 10:46

Fix test

ba45d59

cslzchen added a commit to cslzchen/modular-file-renderer that referenced this pull request Nov 17, 2017

Merge pull request CenterForOpenScience#265 from TomBaxter/feature/sv…

666e8bd

…cs-86 [SVCS-86] Add Papaya Renderer for Dicom and NifTi Files

CR update - minor - additional tests

6937fee

[#SVCS-86]

cslzchen and others added 3 commits November 21, 2017 10:22

Clean up code and respond to CR.

0dbe5d5

Merge pull request #1 from cslzchen/feature/papaya-renderer

eccfbd8

[SVCS-86] Papaya Render

Minor use new file_ext utility

c834abf

[#SVCS-86]

cslzchen approved these changes Nov 22, 2017

View reviewed changes

cslzchen added Final Review and removed Code Review labels Nov 22, 2017

TomBaxter commented Jan 15, 2018

View reviewed changes

felliott mentioned this pull request Jan 25, 2018

Render medical images #5

Open

cslzchen requested changes Jun 18, 2018

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cslzchen added Add'l Dev and removed Final Review labels Jun 18, 2018

cslzchen self-assigned this Jun 18, 2018

felliott unassigned cslzchen Jul 30, 2018

		return PapayaRenderer(metadata, file_path, url, assets_url, export_url)


		class TestPapayaRenderer:

		@@ -0,0 +1 @@
		.papaya{width:90%;height:90%;margin:25px auto;background-color:black;font-family:sans-serif}.papaya:before{position:relative;content:"Papaya requires JavaScript...";display:block;top:45%;color:red;margin:0 auto;font-size:18px;font-family:sans-serif}.papaya-fullscreen{height:100%}.papaya-toolbar{text-align:left;box-sizing:content-box;position:relative}.papaya-toolbar ul{margin:0;list-style:none}.papaya-toolbar input[type=file]{text-align:right;display:none}.papaya-kiosk-controls{position:relative;margin:5px auto;list-style:none;-webkit-touch-callout:none;-webkit-user-select:none;-khtml-user-select:none;-moz-user-select:none;-ms-user-select:none;user-select:none}.papaya-kiosk-controls ul{list-style:none}.papaya-kiosk-controls button{-webkit-appearance:none;border-radius:0;-webkit-border-radius:0;font-size:14px;height:25px;background-color:lightgray}.papaya-control-increment{-webkit-appearance:none;border-radius:0;-webkit-border-radius:0;font-size:14px;height:25px;width:25px;text-align:center;vertical-align:middle;padding:0;margin-left:auto;margin-right:auto;line-height:16px;box-sizing:border-box;font-family:"Courier New",Courier,monospace}.papaya-main-increment{-webkit-appearance:none;border-radius:0;-webkit-border-radius:0;font-size:14px;height:25px;width:25px;text-align:center;font-family:"Courier New",Courier,monospace;background-color:lightgray;vertical-align:middle;padding:0;margin-left:auto;margin-right:auto;box-sizing:border-box;outline:0}.papaya-main-decrement{-webkit-appearance:none;border-radius:0;-webkit-border-radius:0;font-size:14px;height:25px;width:25px;text-align:center;font-family:"Courier New",Courier,monospace;background-color:lightgray;vertical-align:middle;padding:0;margin-left:auto;margin-right:auto;box-sizing:border-box;outline:0}.papaya-main-swap{-webkit-appearance:none;border-radius:0;-webkit-border-radius:0;font-size:14px;height:25px;background-color:lightgray;outline:0}.papaya-main-goto-center{-webkit-appearance:none;border-radius:0;-webkit-border-radius:0;font-size:14px;height:25px;background-color:lightgray;outline:0}.papaya-main-goto-origin{-webkit-appearance:none;border-radius:0;-webkit-border-radius:0;font-size:14px;height:25px;background-color:lightgray;outline:0}.papaya-slider-slice{padding:0 5px;display:inline}.papaya-slider-slice span{font-size:14px;font-family:sans-serif;vertical-align:middle}.papaya-slider-slice button{-webkit-appearance:none;border-radius:0;-webkit-border-radius:0;vertical-align:middle;font-size:14px;height:25px;background-color:lightgray}.papaya-controlbar-label{color:#000}.papaya-menu{width:220px;background:#222;z-index:100;position:absolute;border:solid 2px darkgray;padding:4px;margin:0}.papaya-menu li{font-size:12px;font-family:sans-serif;padding:4px 2px;color:#b5cbd3;cursor:pointer;list-style-type:none}.papaya-menu-label{font-size:14px;font-family:sans-serif;font-weight:bold;padding:2px 8px;cursor:pointer;vertical-align:text-bottom}.papaya-menu-titlebar{font-size:16px;font-family:sans-serif;padding:3px 8px 0 8px;cursor:default;vertical-align:text-bottom;color:white}.papaya-menu-icon{margin-left:5px}.papaya-menu-icon img{box-sizing:content-box}.papaya-menu-hovering{background-color:#444}.papaya-menu-spacer{height:8px}.papaya-menu-unselectable{-moz-user-select:-moz-none;-khtml-user-select:none;-webkit-user-select:none;-ms-user-select:none;user-select:none;-webkit-user-drag:none;user-drag:none}.papaya-menu-button-hovering{background-color:#DDD}.papaya-menu-filechooser{cursor:pointer;width:200px;display:inline-block;font-weight:normal}.papaya-menu-input{width:38px;margin-right:5px;color:black}li .papaya-menu-slider{vertical-align:middle;text-align:center;display:inline;width:120px;padding:0;margin:0}.papaya-dialog{min-width:400px;max-width:500px;height:500px;background:#222;position:absolute;z-index:100;border:solid 2px darkgray;padding:6px;font-size:14px;font-family:sans-serif;color:#b5cbd3;box-sizing:content-box;line-height:1.45}.papaya-dialog-content{margin:20px;height:415px;color:#dedede;overflow:auto;-ms-overflow-style:-ms-autohiding-scrollbar}.papaya-dialog-content-nowrap{white-space:nowrap}.papaya-dialog-content table{margin:0 auto}.papaya-dialog-content-label{text-align:right;padding:5px;color:#b5cbd3}.papaya-dialog-content-control{text-align:left;padding:5px}.papaya-dialog-content-help{text-align:right;padding:5px;color:lightgray;font-size:12px}.papaya-dialog-title{color:#b5cbd3;font-weight:bold;font-size:16px}.papaya-dialog-button{text-align:right;box-sizing:content-box;height:22px}.papaya-dialog-button button{box-sizing:content-box;color:black;font-size:11px}.papaya-dialog-background{position:fixed;top:0;left:0;background-color:#fff;width:100%;height:100%;opacity:.5}.papaya-dialog-stopscroll{height:100%;overflow:hidden}.checkForJS{width:90%;height:90%;margin:25px auto;background-color:black}.checkForJS:before{position:relative;content:"Papaya requires JavaScript...";display:block;top:45%;color:red;margin:0 auto;font-size:18px;font-family:sans-serif;text-align:center}.papaya-utils-unsupported{width:90%;height:90%;margin:25px auto;background-color:black}.papaya-utils-unsupported-message{position:relative;display:block;top:45%;color:red;margin:0 auto;font-size:18px;font-family:sans-serif;text-align:center}.papaya-viewer{line-height:1;font-family:sans-serif}.papaya-viewer div,.papaya-viewer canvas{margin:0;padding:0;border:0;font:inherit;font-size:100%;vertical-align:baseline;font-family:sans-serif}.papaya-viewer canvas{cursor:crosshair}

		@@ -0,0 +1,2105 @@
		var PAPAYA_BUILD_NUM="1430",papayaLoadableImages=[];

		@@ -0,0 +1,7 @@
		Currently using a custom built papaya.js with option to remove the ability to open new files from the users desktop.

[SVCS-86] Add Papaya Renderer for Dicom and NifTi Files #265

Are you sure you want to change the base?

[SVCS-86] Add Papaya Renderer for Dicom and NifTi Files #265

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TomBaxter commented Jun 16, 2017 • edited by cslzchen Loading

Purpose:

Collateral

Changes:

Side effects

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TomBaxter commented Jun 16, 2017 •

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cslzchen Nov 6, 2017 •

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coveralls commented Nov 7, 2017 •

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coveralls commented Nov 20, 2017 •

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coveralls commented Nov 21, 2017 •

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cslzchen left a comment •

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