BisQue is a web-based platform designed to provide researchers with organizational and quantitative analysis tools for 5D image data. Users can extend BisQue by implementing containerized ML workflows.

Vision Research Lab @ UCSB

Last update: Nov 29, 2022

Related tags

Deep Learning python threejs machine-learning bioinformatics computer-vision deep-learning image-processing medical-imaging cloud-computing segmentation

Overview

BisQue is a web-based platform specifically designed to provide researchers with organizational and quantitative analysis tools for up to 5D image data. Users can extend BisQue by creating their own modules that take advantage of cutting edge machine learning algorithms. BisQue’s extensibility stems from two core concepts: flexible metadata facility and an open web-based architecture. Together these empower researchers to create, develop and share novel multimodal data analyses.

Features

Bisque is free and open-source
Flexible textual and graphical annotations
Cloud scalability: PBs of images, millions of annotations
Distributed storage: local, iRODS, S3
Integrated image analysis, high-throughput with Condor
Analysis in MATLAB, Python, Java+ImageJ
100+ biological image formats
Very large 5D images (100+ GB)

Documentation

BisQue Documentation

The official documentation covers the BisQue cloud service running live at UCSB, module development for the platform, and the BQAPI. If you have any questions, feel free to reach out. We will be continuously updating the documentation so check back often for updates!

Papers using BisQue

Latypov, M.I., Khan, A., Lang, C.A. et al. Integr Mater Manuf Innov (2019) 8: 52. https://doi.org/10.1007/s40192-019-00128-5
Polonsky, A.T., Lang, C.A., Kvilekval, K.G. et al. Integr Mater Manuf Innov (2019) 8: 37. https://doi.org/10.1007/s40192-019-00126-7
Kvilekval K, Fedorov D, Obara B, Singh A, Manjunath BS. Bisque: a platform for bioimage analysis and management. Bioinformatics. 2010 Feb 15;26(4):544-52. doi: 10.1093/bioinformatics/btp699. Epub 2009 Dec 22. PMID: 20031971.

Team

Amil Khan (BisQue Team)
Satish Kumar (BisQue Team)
Mike Goebel

Built With

Docker
ExtJS (UI)
Imaris Convert (Image Service)
OpenSlide (Image Service)
Bio-Formats (Image Service)
FFMpeg (Image Service)
libTIFF (Image Service)
TurboGears (backend)
SQLAlchemy (backend)

Acknowledgments

NSF SI2-SSI No.1664172, NSF MCB Grant No. 1715544

License

Comments

TurboGears 2.3.0b2
TurboGears 2.3.0b2

This is the second upgrade in the process. If you have any questions, tag @amilworks on here. Current Version: TurboGears2==2.2.0 Upgrade Version: TurboGears2==2.3.0b2

As you are going through, check off what Step you completed to make it easier for us to help, and for you to feel accomplished.

Getting Started

Step 1. Clone the Repo

GOAL

[x] Start by cloning the branch from this current repo

git clone -b tg-upgrade --single-branch https://github.com/UCSB-VRL/bisqueUCSB.git

cd tg-upgrade and you should see a folder structure like this

. ├── boot ├── builder ├── COPYRIGHT ├── DOCKER-BUILD_LOG.md ├── Dockerfile.caffe.xenial ├── DOCKER-RUN_LOG.md ├── entry.sh ├── LICENSE ├── Makefile ├── modules ├── README.md ├── requirements.txt ├── run-bisque.sh ├── source ├── sources.list ├── start-bisque.sh └── virtualenv.sh 4 directories, 13 files

Step 2. Verify Everything Works

GOAL

[x] Establish a baseline that BisQue works on your local system before changing anything.

You have two choices to verify that the repo is working.

Option 1. Pull the Latest Docker Build (Recommended)

The repo is rebuilt and pushed automatically after a successful push/merge on GitHub. Download the latest image by running the following command:

docker pull amilworks/bisque-tg2-upgrade:git

You can run this image to verify BisQue is working and able to run locally on your system by running:

docker run -itp 8080:8080 --name bqdev-tg2 amilworks/bisque-tg2-upgrade:git

You should see BisQue on http://localhost:8080/ in your browser. If not, paste the logs below and we will take a look.

Option 2. Build the Image

Building the image from scratch is what you will end up doing throughout the upgrade process. Luckily, we automated it to where you run a Makefile.

make bisque05-caffe-xenial

If you vim Makefile, you will see it's a series of basic commands. I suggest you Edit this file and --tag the image something different and update the version you are upgrading instead of amilworks/bisque05-caffe-xenial:flour-tg2.2. You can leave it but it's kind of long. Once the build is done, verify that BisQue comes up on your local system just as above:

docker run -itp 8080:8080 --name bqdev-tg2 amilworks/bisque-tg2-upgrade:git

You should see BisQue on http://localhost:8080/ in your browser. If not, paste both the Build and Run Logs below and we will take a look.

Step 3. Make Changes/Break Stuff

GOAL

[ ] Upgrade TurboGears to TurboGears2==2.3.0b2, fix problems that arise, document changes.

Create a new branch Creating a new branch will enable you to make changes, nuke your own branch over and over again, and maintain a clean copy of the original branch when you need to start fresh for the millionth time.

git checkout -b [name_of_your_new_branch]

Open source/requirements.txt with your favorite editor (hopefully Vim). Change the version to the one you are assigned, and save the file.

Here is the link to the line you will update.

TurboGears2==2.2 # <--- Update Version TurboMail==3.0.3 WebError==0.10.3 WebFlash==0.1a9 WebHelpers==1.3 WebOb==1.1.1 # <--- Potential Update Needed, Check Build Logs

Push to GitHub You made changes and you want to have version control. Push your new branch and changes to GitHub by running:

git push -u origin [name_of_your_new_branch]

Step 4. Build and Run!

GOAL

[ ] Build and run your changes, fix any dependency issues, document changes, rebuild if necessary (most likely unless you are super lucky), trust the process, and always ask for help if you get stuck!

Once you made your changes, make sure you cd .. out of source/ and are back to the tree view displayed above. You should see a file called Makefile. You can Edit this file as mentioned in Option 2. or simply run the following command to build the image with your updated TurboGears2.

make bisque05-caffe-xenial

While its building, make sure that there are no errors during the pip installs. Typically errors are skipped over in favor of a successful build. I know, right?

Next, once the build is finished, run the image and verify BisQue comes up on your local system:

docker run -itp 8080:8080 --name bqdev-tg2 amilworks/bisque-tg2-upgrade:git

NOTE: There might be other packages that need updating when upgrading to different TurboGears2 versions. Sometimes there will be an error raised with the version required, or it simply will not run and you will have to do a logsdump here and we will have to sift through it together to track the failed step(s).

If everything is successful, push your branch to GitHub if you have not already, file a pull request, and pat yourself on the back. Job well done. We will review it and test it on our production-like setup and give feedback if any issues arise.

Post Upgrade

Use this issue to document any issues you faced during the upgrade process. Log dumps can be thrown here as well. Try to use the code syntax for large blocks of code so we can easily read through it. Otherwise, go crazy.

[x] What broke, if anything? Just a simple list will suffice.

[ ] Were there any files significantly changed or that requires significant attention?

[ ] Can we move forward to the next upgrade?

[ ] Any blockers now or that you foresee?

dependencies no-issue-activity
opened by amilworks 16
TurboGears==2.2.1
TurboGears 2.2.1

This is the second upgrade in the process. If you have any questions, tag @amilworks on here. Current Version: TurboGears2==2.2.0 Upgrade Version: TurboGears2==2.2.1

As you are going through, check off what Step you completed to make it easier for us to help, and for you to feel accomplished.

Getting Started

Step 1. Clone the Repo

GOAL

[ ] Start by cloning the branch from this current repo

git clone -b tg-upgrade --single-branch https://github.com/UCSB-VRL/bisqueUCSB.git

cd tg-upgrade and you should see a folder structure like this

. ├── boot ├── builder ├── COPYRIGHT ├── DOCKER-BUILD_LOG.md ├── Dockerfile.caffe.xenial ├── DOCKER-RUN_LOG.md ├── entry.sh ├── LICENSE ├── Makefile ├── modules ├── README.md ├── requirements.txt ├── run-bisque.sh ├── source ├── sources.list ├── start-bisque.sh └── virtualenv.sh 4 directories, 13 files

Step 2. Verify Everything Works

GOAL

[ ] Establish a baseline that BisQue works on your local system before changing anything.

You have two choices to verify that the repo is working.

Option 1. Pull the Latest Docker Build (Recommended)

The repo is rebuilt and pushed automatically after a successful push/merge on GitHub. Download the latest image by running the following command:

docker pull amilworks/bisque-tg2-upgrade:git

You can run this image to verify BisQue is working and able to run locally on your system by running:

docker run -itp 8080:8080 --name bqdev-tg2 amilworks/bisque-tg2-upgrade:git

You should see BisQue on http://localhost:8080/ in your browser. If not, paste the logs below and we will take a look.

Option 2. Build the Image

Building the image from scratch is what you will end up doing throughout the upgrade process. Luckily, we automated it to where you run a Makefile.

make bisque05-caffe-xenial

If you vim Makefile, you will see it's a series of basic commands. I suggest you Edit this file and --tag the image something different and update the version you are upgrading instead of amilworks/bisque05-caffe-xenial:flour-tg2.2. You can leave it but it's kind of long. Once the build is done, verify that BisQue comes up on your local system just as above:

docker run -itp 8080:8080 --name bqdev-tg2 amilworks/bisque-tg2-upgrade:git

You should see BisQue on http://localhost:8080/ in your browser. If not, paste both the Build and Run Logs below and we will take a look.

Step 3. Make Changes/Break Stuff

GOAL

[ ] Upgrade TurboGears to TurboGears2==2.2.1, fix problems that arise, document changes.

Create a new branch Creating a new branch will enable you to make changes, nuke your own branch over and over again, and maintain a clean copy of the original branch when you need to start fresh for the millionth time.

git checkout -b [name_of_your_new_branch]

Open source/requirements.txt with your favorite editor (hopefully Vim). Change the version to the one you are assigned, and save the file.

Here is the link to the line you will update.

TurboGears2==2.2 # <--- Update Version TurboMail==3.0.3 WebError==0.10.3 WebFlash==0.1a9 WebHelpers==1.3 WebOb==1.1.1 # <--- Potential Update Needed, Check Build Logs

Push to GitHub You made changes and you want to have version control. Push your new branch and changes to GitHub by running:

git push -u origin [name_of_your_new_branch]

Step 4. Build and Run!

GOAL

[ ] Build and run your changes, fix any dependency issues, document changes, rebuild if necessary (most likely unless you are super lucky), trust the process, and always ask for help if you get stuck!

Once you made your changes, make sure you cd .. out of source/ and are back to the tree view displayed above. You should see a file called Makefile. You can Edit this file as mentioned in Option 2. or simply run the following command to build the image with your updated TurboGears2.

make bisque05-caffe-xenial

While its building, make sure that there are no errors during the pip installs. Typically errors are skipped over in favor of a successful build. I know, right?

Next, once the build is finished, run the image and verify BisQue comes up on your local system:

docker run -itp 8080:8080 --name bqdev-tg2 amilworks/bisque-tg2-upgrade:git

NOTE: There might be other packages that need updating when upgrading to different TurboGears2 versions. Sometimes there will be an error raised with the version required, or it simply will not run and you will have to do a logsdump here and we will have to sift through it together to track the failed step(s).

If everything is successful, push your branch to GitHub if you have not already, file a pull request, and pat yourself on the back. Job well done. We will review it and test it on our production-like setup and give feedback if any issues arise.

Post Upgrade

Use this issue to document any issues you faced during the upgrade process. Log dumps can be thrown here as well. Try to use the code syntax for large blocks of code so we can easily read through it. Otherwise, go crazy.

[x] What broke, if anything? Just a simple list will suffice.

[ ] Were there any files significantly changed or that requires significant attention?

[ ] Can we move forward to the next upgrade?

[ ] Any blockers now or that you foresee?

dependencies no-issue-activity
opened by amilworks 13
TurboGears 2.2.2
TurboGears 2.2.2

This is the second upgrade in the process. If you have any questions, tag @amilworks on here. Current Version: TurboGears2==2.2.0 Upgrade Version: TurboGears2==2.2.2

As you are going through, check off what Step you completed to make it easier for us to help, and for you to feel accomplished.

Getting Started

Step 1. Clone the Repo

GOAL

[x] Start by cloning the branch from this current repo

git clone -b tg-upgrade --single-branch https://github.com/UCSB-VRL/bisqueUCSB.git

cd tg-upgrade and you should see a folder structure like this

. ├── boot ├── builder ├── COPYRIGHT ├── DOCKER-BUILD_LOG.md ├── Dockerfile.caffe.xenial ├── DOCKER-RUN_LOG.md ├── entry.sh ├── LICENSE ├── Makefile ├── modules ├── README.md ├── requirements.txt ├── run-bisque.sh ├── source ├── sources.list ├── start-bisque.sh └── virtualenv.sh 4 directories, 13 files

Step 2. Verify Everything Works

GOAL

[ ] Establish a baseline that BisQue works on your local system before changing anything.

You have two choices to verify that the repo is working.

Option 1. Pull the Latest Docker Build (Recommended)

The repo is rebuilt and pushed automatically after a successful push/merge on GitHub. Download the latest image by running the following command:

docker pull amilworks/bisque-tg2-upgrade:git

You can run this image to verify BisQue is working and able to run locally on your system by running:

docker run -itp 8080:8080 --name bqdev-tg2 amilworks/bisque-tg2-upgrade:git

You should see BisQue on http://localhost:8080/ in your browser. If not, paste the logs below and we will take a look.

Option 2. Build the Image

Building the image from scratch is what you will end up doing throughout the upgrade process. Luckily, we automated it to where you run a Makefile.

make bisque05-caffe-xenial

If you vim Makefile, you will see it's a series of basic commands. I suggest you Edit this file and --tag the image something different and update the version you are upgrading instead of amilworks/bisque05-caffe-xenial:flour-tg2.2. You can leave it but it's kind of long. Once the build is done, verify that BisQue comes up on your local system just as above:

docker run -itp 8080:8080 --name bqdev-tg2 amilworks/bisque-tg2-upgrade:git

You should see BisQue on http://localhost:8080/ in your browser. If not, paste both the Build and Run Logs below and we will take a look.

Step 3. Make Changes/Break Stuff

GOAL

[ ] Upgrade TurboGears to TurboGears2==2.2.2, fix problems that arise, document changes.

Create a new branch Creating a new branch will enable you to make changes, nuke your own branch over and over again, and maintain a clean copy of the original branch when you need to start fresh for the millionth time.

git checkout -b [name_of_your_new_branch]

Open source/requirements.txt with your favorite editor (hopefully Vim). Change the version to the one you are assigned, and save the file.

Here is the link to the line you will update.

TurboGears2==2.2 # <--- Update Version TurboMail==3.0.3 WebError==0.10.3 WebFlash==0.1a9 WebHelpers==1.3 WebOb==1.1.1 # <--- Potential Update Needed, Check Build Logs

Push to GitHub You made changes and you want to have version control. Push your new branch and changes to GitHub by running:

git push -u origin [name_of_your_new_branch]

Step 4. Build and Run!

GOAL

[ ] Build and run your changes, fix any dependency issues, document changes, rebuild if necessary (most likely unless you are super lucky), trust the process, and always ask for help if you get stuck!

Once you made your changes, make sure you cd .. out of source/ and are back to the tree view displayed above. You should see a file called Makefile. You can Edit this file as mentioned in Option 2. or simply run the following command to build the image with your updated TurboGears2.

make bisque05-caffe-xenial

While its building, make sure that there are no errors during the pip installs. Typically errors are skipped over in favor of a successful build. I know, right?

Next, once the build is finished, run the image and verify BisQue comes up on your local system:

docker run -itp 8080:8080 --name bqdev-tg2 amilworks/bisque-tg2-upgrade:git

NOTE: There might be other packages that need updating when upgrading to different TurboGears2 versions. Sometimes there will be an error raised with the version required, or it simply will not run and you will have to do a logsdump here and we will have to sift through it together to track the failed step(s).

If everything is successful, push your branch to GitHub if you have not already, file a pull request, and pat yourself on the back. Job well done. We will review it and test it on our production-like setup and give feedback if any issues arise.

Post Upgrade

Use this issue to document any issues you faced during the upgrade process. Log dumps can be thrown here as well. Try to use the code syntax for large blocks of code so we can easily read through it. Otherwise, go crazy.

[x] What broke, if anything? Just a simple list will suffice.

[ ] Were there any files significantly changed or that requires significant attention?

[ ] Can we move forward to the next upgrade?

[ ] Any blockers now or that you foresee?

dependencies no-issue-activity
opened by amilworks 4
Bump waitress from 0.8.8 to 2.1.1 in /source
Bumps waitress from 0.8.8 to 2.1.1.

Release notes

Sourced from waitress's releases.

v2.1.1

No release notes provided.

v2.1.0

No release notes provided.

v2.1.0b0

No release notes provided.

v2.0.0

No release notes provided.

v2.0.0b1

No release notes provided.

v2.0.0b0

No release notes provided.

v1.4.4

No release notes provided.

v1.4.3

No release notes provided.

v1.4.2

No release notes provided.

v1.4.1

No release notes provided.

v1.4.0

No release notes provided.

v1.3.1

No release notes provided.

v1.3.0

No release notes provided.

v1.3.0b0

No release notes provided.

v1.2.1

No release notes provided.

v1.2.0

No release notes provided.

v1.1.0

https://pypi.org/project/waitress/1.1.0/

... (truncated)

Changelog

Sourced from waitress's changelog.

2.1.1

Security Bugfix

- Waitress now validates that chunked encoding extensions are valid, and don't contain invalid characters that are not allowed. They are still skipped/not processed, but if they contain invalid data we no longer continue in and return a 400 Bad Request. This stops potential HTTP desync/HTTP request smuggling. Thanks to Zhang Zeyu for reporting this issue. See https://github.com/Pylons/waitress/security/advisories/GHSA-4f7p-27jc-3c36 Waitress now validates that the chunk length is only valid hex digits when parsing chunked encoding, and values such as 0x01 and +01 are no longer supported. This stops potential HTTP desync/HTTP request smuggling. Thanks to Zhang Zeyu for reporting this issue. See https://github.com/Pylons/waitress/security/advisories/GHSA-4f7p-27jc-3c36 Waitress now validates that the Content-Length sent by a remote contains only digits in accordance with RFC7230 and will return a 400 Bad Request when the Content-Length header contains invalid data, such as +10 which would previously get parsed as 10 and accepted. This stops potential HTTP desync/HTTP request smuggling Thanks to Zhang Zeyu for reporting this issue. See https://github.com/Pylons/waitress/security/advisories/GHSA-4f7p-27jc-3c36 2.1.0
Python Version Support

Python 3.6 is no longer supported by Waitress

Python 3.10 is fully supported by Waitress

Bugfix

- ``wsgi.file_wrapper`` now sets the ``seekable``, ``seek``, and ``tell`` attributes from the underlying file if the underlying file is seekable. This allows WSGI middleware to implement things like range requests for example See Pylons/waitress#359 and Pylons/waitress#363 In Python 3 OSError is no longer subscriptable, this caused failures on Windows attempting to loop to find an socket that would work for use in the trigger.
</tr></table>

... (truncated)

Commits

9e0b8c8 Merge pull request from GHSA-4f7p-27jc-3c36

b28c9e8 Prep for 2.1.1

bd22869 Remove extraneous calls to .strip() in Chunked Encoding

d9bdfa0 Validate chunk size in Chunked Encoding are HEXDIG

d032a66 Error when receiving back Chunk Extension

884bed1 Update tests to remove invalid chunked encoding chunk-size

1f6059f Be more strict in parsing Content-Length

e75b0d9 Add new regular expressions for Chunked Encoding

22c0394 Merge pull request #367 from Pylons/fixup/collect-wasyncore-tests

dc15d9f Make sure to collect all wasyncore tests

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You can disable automated security fix PRs for this repo from the Security Alerts page.

dependencies no-pr-activity
opened by dependabot[bot] 2
Services Error Fix
Finally the /services Error is Fixed

Huge thanks to @michael-goebel for finding and fixing the /services issue that came up while upgrading from turbogears2==2.1.5 --> turbogears2==2.2. The current way to test is simply by rebuilding the BisQue image and deploying it locally to verify that the issue is resolved. A few questions are:

@michael-goebel How did you build and test the image? Can we just build the image as usual or did you make changes to the Dockerfile and/or in other build scripts that we need to account for?

Do we have any existing unit tests that we can use to verify the changes? Basically, if we push this to production, we don't want other things breaking that could have been caught earlier on by writing a 5-liner unit test.

There's 55 files that are changed. Are we merging all of these files or are there specific ones we should merge?

I will review the changes and make comments if necessary. Having a second pair of eyes and another person that can test the changes on their local setup would be useful. Maybe @satish1901 or @ASMIftekhar <3

Python 3 Branch

Also, @satish1901 which branch is the one you cleaned up with the Python 3 source code? This merge needs to be changed to the branch with the Python 3 source code. We can test Mike's changes on Python 2.7 but soon thereafter this needs to be tested on Python 3.
bug dependencies
opened by amilworks 2
TurboGears 2.3.0b1
TurboGears 2.3.0b1

This is the second upgrade in the process. If you have any questions, tag @amilworks on here. Current Version: TurboGears2==2.2.0 Upgrade Version: TurboGears2==2.3.0b1

As you are going through, check off what Step you completed to make it easier for us to help, and for you to feel accomplished.

Getting Started

Step 1. Clone the Repo

GOAL

[x] Start by cloning the branch from this current repo

git clone -b tg-upgrade --single-branch https://github.com/UCSB-VRL/bisqueUCSB.git

cd tg-upgrade and you should see a folder structure like this

. ├── boot ├── builder ├── COPYRIGHT ├── DOCKER-BUILD_LOG.md ├── Dockerfile.caffe.xenial ├── DOCKER-RUN_LOG.md ├── entry.sh ├── LICENSE ├── Makefile ├── modules ├── README.md ├── requirements.txt ├── run-bisque.sh ├── source ├── sources.list ├── start-bisque.sh └── virtualenv.sh 4 directories, 13 files

Step 2. Verify Everything Works

GOAL

[x] Establish a baseline that BisQue works on your local system before changing anything.

You have two choices to verify that the repo is working.

Option 1. Pull the Latest Docker Build (Recommended)

The repo is rebuilt and pushed automatically after a successful push/merge on GitHub. Download the latest image by running the following command:

docker pull amilworks/bisque-tg2-upgrade:git

You can run this image to verify BisQue is working and able to run locally on your system by running:

docker run -itp 8080:8080 --name bqdev-tg2 amilworks/bisque-tg2-upgrade:git

You should see BisQue on http://localhost:8080/ in your browser. If not, paste the logs below and we will take a look.

Option 2. Build the Image

Building the image from scratch is what you will end up doing throughout the upgrade process. Luckily, we automated it to where you run a Makefile.

make bisque05-caffe-xenial

If you vim Makefile, you will see it's a series of basic commands. I suggest you Edit this file and --tag the image something different and update the version you are upgrading instead of amilworks/bisque05-caffe-xenial:flour-tg2.2. You can leave it but it's kind of long. Once the build is done, verify that BisQue comes up on your local system just as above:

docker run -itp 8080:8080 --name bqdev-tg2 amilworks/bisque-tg2-upgrade:git

You should see BisQue on http://localhost:8080/ in your browser. If not, paste both the Build and Run Logs below and we will take a look.

Step 3. Make Changes/Break Stuff

GOAL

[ ] Upgrade TurboGears to `TurboGears2==2.3.0b1', fix problems that arise, document changes.

Create a new branch Creating a new branch will enable you to make changes, nuke your own branch over and over again, and maintain a clean copy of the original branch when you need to start fresh for the millionth time.

git checkout -b [name_of_your_new_branch]

Open source/requirements.txt with your favorite editor (hopefully Vim). Change the version to the one you are assigned, and save the file.

Here is the link to the line you will update.

TurboGears2==2.2 # <--- Update Version TurboMail==3.0.3 WebError==0.10.3 WebFlash==0.1a9 WebHelpers==1.3 WebOb==1.1.1 # <--- Potential Update Needed, Check Build Logs

Push to GitHub You made changes and you want to have version control. Push your new branch and changes to GitHub by running:

git push -u origin [name_of_your_new_branch]

Step 4. Build and Run!

GOAL

[ ] Build and run your changes, fix any dependency issues, document changes, rebuild if necessary (most likely unless you are super lucky), trust the process, and always ask for help if you get stuck!

Once you made your changes, make sure you cd .. out of source/ and are back to the tree view displayed above. You should see a file called Makefile. You can Edit this file as mentioned in Option 2. or simply run the following command to build the image with your updated TurboGears2.

make bisque05-caffe-xenial

While its building, make sure that there are no errors during the pip installs. Typically errors are skipped over in favor of a successful build. I know, right?

Next, once the build is finished, run the image and verify BisQue comes up on your local system:

docker run -itp 8080:8080 --name bqdev-tg2 amilworks/bisque-tg2-upgrade:git

NOTE: There might be other packages that need updating when upgrading to different TurboGears2 versions. Sometimes there will be an error raised with the version required, or it simply will not run and you will have to do a logsdump here and we will have to sift through it together to track the failed step(s).

If everything is successful, push your branch to GitHub if you have not already, file a pull request, and pat yourself on the back. Job well done. We will review it and test it on our production-like setup and give feedback if any issues arise.

Post Upgrade

Use this issue to document any issues you faced during the upgrade process. Log dumps can be thrown here as well. Try to use the code syntax for large blocks of code so we can easily read through it. Otherwise, go crazy.

[x] What broke, if anything? Just a simple list will suffice.

[ ] Were there any files significantly changed or that requires significant attention?

[ ] Can we move forward to the next upgrade?

[ ] Any blockers now or that you foresee?

dependencies no-issue-activity
opened by amilworks 2
TG Upgrade---TurboGears2==2.2.0
TurboGears 2.2.0

As a first step in the upgrade process, we will shoot for incremental upgrades of TG2 and document any issues faced.

Current Version: TurboGears2==2.1.5 Upgrade Version: TurboGears2==2.2.0

Post Upgrade

Use this issue to document any issues you faced during the upgrade process. Log dumps can be thrown here as well. Try to use the code syntax for large blocks of code so we can easily read through it. Otherwise, go crazy.

What broke, if anything? Just a simple list will suffice.

Were there any files significantly changed or that requires significant attention?

Can we move forward to the next upgrade?

Any blockers now or that you foresee?

dependencies
opened by amilworks 2
Image file renaming not working
I have uploaded a file,

made it publicly accessible

Opened the image and tried to rename it using the button on the top right corner

Changes are not being reflected

We need to find the root cause of this issue. Not sure what's happening in the backend.

Thanks, Chandrakanth.
no-issue-activity
opened by chandrakanth-gudavalli 1
Delete operation not working (in some scenarios)
Description: Unable to delete the files that belong to a datasets

Steps to Recreate:

Upload two images and add to a dataset.

Navigate to that dataset

Click on an image and click delete button (on top left corner)

You should see a pop up saying Resource deleted successfully! You will be redirected to your BISQUE homepage.

But the file is not getting deleted. It is still sitting inside the dataset

Note: There is no issue in deleting the files that do NOT belong to a dataset.

Thanks.
bug good first issue no-issue-activity
opened by chandrakanth-gudavalli 1
bqapi tutorial - file upload and file download
Jupyter notebooks to guide users on using bqapi for file upload and file download.

Potential TODOs:

Functionality to upload folder/dataset

Functionality to download folder/dataset

Clear documentation on several response codes
opened by chandrakanth-gudavalli 1
Provide default inputs to modules

It would be really helpful for the first time users of Bisque to have a default inputs show up automatically, when the user clicks on buttons like Select an Image or Select file (while working on Bisque modules).

Current state: User have to manually investigate About/Help tab to figure out the appropriate input format (.png or .tif or .xyz). It would be great to have appropriate inputs, to be selected, show up automatically. So users cannot get an actual sense of each module as they do not have access to first-good sample input.

Posting this here. But this could be a change to module generator repository.
enhancement no-issue-activity

opened by chandrakanth-gudavalli 1

Releases(v1.0.1)

v1.0.1(Apr 17, 2022)
Minor Release

This release is mostly comprised of bug fixes and uploading missing files. For further information on the changes we made for the Dockerfile, please check out the merged request below.

What's Changed

Added BASE Dockerfile by @amilworks in https://github.com/UCSB-VRL/bisqueUCSB/pull/43

Run BisQue using Docker

Download

Ensure you have the latest release by first running the following pull command:

docker pull amilworks/bisque-module-dev:git

Run the BisQue Docker Container

To run the docker version of BisQue locally, start a bisque server on the host port 8080:

docker run --name bisque --rm -p 8080:8080 amilworks/bisque-module-dev:git

and point your browser at http://localhost:8080. You should see a BisQue homepage similar to the one on bisque.ece.ucsb.edu. If you do not see the homepage, check to make sure that port 8080 is not being used by another container or application and that you have correctly mapped the ports using -p 8080:8080, where -p is short for port.

Full Changelog: https://github.com/UCSB-VRL/bisqueUCSB/compare/v1.0.0...v1.0.1
Source code(tar.gz)
Source code(zip)
v1.0.0(Mar 24, 2022)
BisQue2

We have moved to v1.0.0! This new release brings a new module backend that is powered by the powerful Argo Workflow Engine and a new storage backend that creates an iRODS user and a Minio S3 bucket for that user. We have also cleaned up our Dockerfile to make it easier to build and develop for BisQue.

Features

Argo Workflows for running modules in BisQue

iRODS as main storage backend

Automatic iRODS user creation

Minio S3 bucket for each user to facilitate hyperscale deep learning training

Enabled OpenID

Easier builds for BisQue developers with new Multi-stage Dockerfile

Run BisQue using Docker

Download

Ensure you have the latest release by first running the following pull command:

docker pull amilworks/bisque-module-dev:git

Intro: BisQue Docker Container

Run the BisQue Docker Container

To run the docker version of BisQue locally, start a bisque server on the host port 8080:

docker run --name bisque --rm -p 8080:8080 amilworks/bisque-module-dev:git

and point your browser at http://localhost:8080. You should see a BisQue homepage similar to the one on bisque.ece.ucsb.edu. If you do not see the homepage, check to make sure that port 8080 is not being used by another container or application and that you have correctly mapped the ports using -p 8080:8080, where -p is short for port.

Full Changelog: https://github.com/UCSB-VRL/bisqueUCSB/compare/v0.7...v1.0.0
Source code(tar.gz)
Source code(zip)
v0.7(Mar 24, 2021)
This release focused on deploying Two New Modules to the BisQue platform. The work was in conjunction with UC Riverside's Electrical and Computer Engineering Department. We also have updated the NPH prediction module.

We have also updated our documentation which is always an ever growing compilation of BisQue goodness. Fell free to file an issue if there are missing details, extra clarification needed, or an example you feel would be useful to the BisQue community. Documentation Link: https://ucsb-vrl.github.io/bisqueUCSB/

New Modules

Cell Segmentation 2D

This module implements watershed segmentation in 2D for cell segmentation of Arabidopsis thaliana. The module takes as input a TIFF image with a z-stack and outputs the segmented image in a TIFF z-stack, respectively.

Enhanced Reconstruction

This module implements a latent space quantization model that generates an enhanced z-stack given a noisy input of Arabidopsis thaliana. For more details, take a look at the paper Deep Quantized Representation for Enhanced Reconstruction. Paper Link: https://vcg.ece.ucr.edu/sites/g/files/rcwecm2661/files/2020-05/ISBI2020_CellEnhancement.pdf

Updated Modules

NPH Prediction

We have updated this module to output 7 classes and the trained model has been retrained with new data. This work is in conjunction with UC Irvine. There will be more updates to this module in the coming months so stay tuned!

Source code(tar.gz)
Source code(zip)
v0.6.2(Aug 28, 2020)
This release updates the codebase to reflect a better overall structure for build, test, and deployment pipelines.

Main Changes:

Updated code structure

Fixed broken dependencies

Added Dockerfile for build state

Source code(tar.gz)
Source code(zip)
v0.6(Jun 29, 2020)
June 2020: BisQue v0.6

We are bringing a small list of updates for this version that include TWO new modules, an updated image converter to better handle TIFF files and various bug fixes. A full detailed list can be found below!

This release includes

NPH Prediction Module

CellECT 2.0 Module

Updated Image Converter

Minor bug fixes

Code clean-up

Removal of deprecated files

UI Improvements

Source code(tar.gz)
Source code(zip)