camicroscope / distro Goto Github PK

https://developers.googleblog.com/2021/08/gsi-jsweb-deprecation.html

due in 2023. Got some errors when trying (unexplained 403s), revisit later.

To Reproduce
Steps to reproduce the behavior:

1. Click on the Draw tool icon
2. Form for the name and note typing appears

Just for a moment before form for the name and note typing appears you can see the drop-down menu for color selection. It could not be accessed because it is immediately overlapped by the form.

Expected behavior
Ability to access the drop-down menu and select color for the area.

Screenshots
If applicable, add screenshots to help explain your problem.

As noted in #65, our image loading is not at all intuitive. Let's automate this as much as possible.

I took a quick look at caMicroscope distro but I am not able to ignore a thing that why load slider image option is on completely different page instead it could have been shown in the same table page.

It would be time saving and useful if load slide option can be added to table page itself.

that is, we need to handle logouts from both OUR and EXTERNAL identity providers without too much code duplication

To Reproduce
Steps to reproduce the behavior:

1. Select Draw tool
2. Type name
3. Select area on the picture
4. Type note
5. No Save button

Expected behavior
Either area should be automatically saved or Save button should appear

Screenshots

Note
Everything is working as expected if you firstly type name and note and select area only after that.

I've issued these commands:

git clone https://github.com/camicroscope/Distro.git
cd Distro/
docker-compose -f caMicroscope.yml up

which appear to work okay. This leaves me with this:

Everything look good so far

Then when i go to: http://haeckel.case.edu:4010/apps/loader/loader.html

I see a landing page, cool

clicking on load image page, i select a local image, and click upload, but see this:

ca-security | {"__statusCode":400,"err":"BAD REQUEST","type":"proxy error"}
ca-security | { Error: write ECONNRESET
ca-security |     at WriteWrap.afterWrite [as oncomplete] (net.js:868:14) errno: 'ECONNRESET', code: 'ECONNRESET', syscall: 'write' }
ca-security | [HPM] Error occurred while trying to proxy request upload/continue/KOY25R9L4D from haeckel.case.edu:4010 to http://ca-load:4000 (ECONNRESET) (https://nodejs.org/api/errors.html#errors_common_system_errors)
ca-security | Error: write ECONNRESET
ca-security |     at WriteWrap.afterWrite [as oncomplete] (net.js:868:14)
ca-security | public check false
ca-security | [HPM] Proxy created: /  ->  http://ca-load:4000
ca-security | 6990556
ca-security | {"__statusCode":400,"err":"BAD REQUEST","type":"proxy error"}
ca-security | { Error: write ECONNRESET
ca-security |     at WriteWrap.afterWrite [as oncomplete] (net.js:868:14) errno: 'ECONNRESET', code: 'ECONNRESET', syscall: 'write' }
ca-security | [HPM] Error occurred while trying to proxy request upload/continue/KOY25R9L4D from haeckel.case.edu:4010 to http://ca-load:4000 (ECONNRESET) (https://nodejs.org/api/errors.html#errors_common_system_errors)
ca-security | Error: write ECONNRESET
ca-security |     at WriteWrap.afterWrite [as oncomplete] (net.js:868:14)
ca-security | public check false

A number of times. No file is ultimately uploaded

going to:

http://haeckel.case.edu:4010/apps/table.html

produces the message "No data Found .... x _x"

I have confirmed this exact behavior on 2 different machines. both are ubuntu 16.04

Any ideas?

but distro uses camicroscope-imageloader. This means loading fails.

For pathdb and for caracal, add ability to select fork, in addition to branch

Consider use of another CI platform.

Bug Descriptions
Created the credentials from the linked guide and edited the client id in config/login.html. I also edited config/add_users.js to add a new admin user and uncommented the line to insert into the db.

When run I'm getting the following error

Further it seems like it successfully signs in via the Google-sign in but then produces an error stating "User not found" and redirects to the User Signup page.

Currently I'm unsure where the client secret key needs to be added and if the mongo db update is working to add the new user as an admin since I also see a BulkWriteError from mongo in the logs.

Desktop (please complete the following information):

• OS: macOS Monterey
• Safari

Is it possible to run the software without requiring an identity provider?

If not are there any instructions for running with e.g. a keycloak container to allow setting up a simple test environment without needing a google account?

Is your feature request related to a problem? Please describe.
caMicroscope needs, at the least, a good access control system. This is complicated by having two middleware agents (bindaas and security). This would allow us to have a centralized caMicroscope setup. Then, as long as we keep everything stateless, we can scale on microservice rather than project.

Describe the solution you'd like
Late last year, caboodle (https://github.com/camicroscope/caboodle) was born. It's still a baby, so let's revisit it, test it thoroughly, make required changes to the ui, and release it.

I've assigned this to myself since it's kind of big and touches everything.

Docker image was created with the develop.yml. Now i am simply trying to upload a svs file but it is giving me the following error.

Upgrade Mongo upgrade from 3.6 to 4.2

TODO:

• Do all of the routes/queries/features work on the backend?
• Do we need to update the indices or default insertions?
• Will a user need to anything to keep data

@ebremer @nanli-emory

re #1351

It'd be nice to have an agreed-upon set of rules that could be used to automatically or semi-automatically applied on LightGraphs.

In 1351, I ended up using JuliaFormatter with the following rules:
indent = 4, margin = 100, always_for_in = true, whitespace_typedefs = true, whitespace_ops_in_indices = false, remove_extra_newlines = true

However, some other changes needed to be made after the fact; namely, re-adding the semicolon in the last line of src/shortestpaths13/bellman-ford.jl, fixing each of the trait functions which were more than one statement (see sbromberger/LightGraphs.jl@cc0b755), and making the inline functions one line (see sbromberger/LightGraphs.jl@2e66207).

see https://hub.docker.com/u/camicroscope; claims 5 months ago

Describe the bug
I've been trying to get caMicroscope running on my local docker-compose setup and have run into an issue when attempting to upload images to get started with testing.

I downloaded an example ndpi file from the openslide website:
http://openslide.cs.cmu.edu/download/openslide-testdata/Hamamatsu/CMU-1.ndpi
This slide opens fine in Nanoborb and also

To Reproduce
Steps to reproduce the behavior:

1. Launch caMicroscope using the unmodified develop.yml from the Distro repo.
2. Download: http://openslide.cs.cmu.edu/download/openslide-testdata/Hamamatsu/CMU-1.ndpi
3. Upload CMU-1.ndpi from your local PC.
4. Wait until upload is complete.
5. Click Finish Upload
6. Click Check
   At that point there is an error thrown in the browser console:
   loader.js:69 Uncaught (in promise) TypeError: Cannot set property 'innerHTML' of undefined
   at loader.js:69
7. No file appears in the list of slides page.

Expected behavior
Should be able to upload slides :-D
Actually the bulk upload option with the single slide does work.

Desktop (please complete the following information):

• OS: Windows 10
• Browser Chrome
• Version 85

Is your feature request related to a problem? Please describe.
No admins are present at startup, and using the UI, an admin account is needed to add an admin account.

Describe the solution you'd like
something to add a single user-provided email as an admin without using mongo

Describe alternatives you've considered
Instruct users to edit the user seed to add their own user.

Steps to reproduce the behavior:
Based on #206, I'm using docker-compose -f develop.yml build --no-cache loader to build the containers.

Expected behavior
The ca-iip restarting, exiting, and restarting, and exiting. The error message shown in the screenshot would come up each time.

Desktop

• OS: Venture 13.4
• Browser: Chrome
• Version: Version 114.0.5735.106 (Official Build) (arm64)

Additional
I also want to start contributing to camicroscope. based on the current caMicroscope.yml file being out of date, how should i go about starting my contributions using the develop.yml?

Thanks so much!

Since different deployments have different feature support (can users upload images, app name/download/grant info, etc) we should have a simple way to configure each deployment. I'm considering expanding the config.ini system I have going on camicroscope/Security, but open to suggestions

This has been reported a few times, so it needs its own issue.
May consider un-disabling the mongo logs in prod deployments, since mongo's exit with 100 is pretty cryptic, but that's just a start.
Relates to docker-library/mongo#154

I simply ran the docker commad docker-compose -f caMicroscope.yml up which failed with the folllowing error message. Can someone please help me on this.

remove georoutes if we're not doing that index. Add index back if we are.

After installation (current Distro, installation with docker compose), I need to log in. The proposed way is using the google-account. However, this does not work.
There is the "error 400". Based on the google page, there is a problem with the authentication solution used on the webpage?

Looking for other ways of adding users, I found in the documentation a solution with an add_user-file; which does not exist?
Do I have to write it? And if so, which fields are required?

Describe the bug
I tried to install the Distro-version from GitHub with docker compose. But it exists with some error code, I do not understand.
For testing, I have used a clean and new linux system, twice.

To Reproduce

1. I have downloaded the Distro from GitHub
2. I started the installation with docker-compose -f dh_caMicroscope.yml up
3. There is the following error:

Creating network "distro_default" with the default driver
Pulling mongo (mongo:4.2-bionic)...
4.2-bionic: Pulling from library/mongo
456d651ccb27: Pull complete
0d873b46166f: Pull complete
b700537f311e: Pull complete
8ba0f53e4854: Pull complete
80b58c92c83f: Pull complete
f4ed2f74d01b: Pull complete
0a2bd86063a1: Pull complete
9d3479b42a1a: Pull complete
59e7441cc47f: Pull complete
Digest: sha256:b9633e6eb4ff0b96ab48a14e0b3792bb185a5daa3ea4c83b69e0bec2a8f5379a
Status: Downloaded newer image for mongo:4.2-bionic
Pulling back (camicroscope/caracal:latest)...
latest: Pulling from camicroscope/caracal
fa1690ae9228: Pull complete
2e799f213a71: Pull complete
83086ca62414: Pull complete
83fd155f6c91: Pull complete
71f84117b593: Pull complete
3b0d74d5e595: Pull complete
2663b58c5f3c: Pull complete
cfd4e70f8767: Pull complete
f1649ad9b855: Pull complete
a6f29a811e51: Pull complete
dbf6e08966fb: Pull complete
Digest: sha256:d32d2ad6e51e3069a706c8112f1d03d2d7aa0431c4db1dd4a2a3ded59f303b5f
Status: Downloaded newer image for camicroscope/caracal:latest
Pulling iip (camicroscope/iipimage:latest)...
latest: Pulling from camicroscope/iipimage
d519e2592276: Pulling fs layer
d22d2dfcfa9c: Pulling fs layer
b3afe92c540b: Pulling fs layer
f132eb32600c: Pulling fs layer
656eed345341: Pulling fs layer
d997a5b00862: Pulling fs layer
ce1a16d57185: Pulling fs layer
e9dccd3e9305: Pulling fs layer
aa944791aaff: Pulling fs layer
cbda0eed89e4: Pulling fs layer
f3ac8c6696a1: Pull complete
6d5c0609bf72: Pull complete
7f3f4e19709b: Pull complete
ad5706679bdd: Pull complete
29cab59db9cd: Pull complete
1b62486b3399: Pull complete
0e1c109062c2: Pull complete
be6e5f2ea5d3: Pull complete
d1c79b973fac: Pull complete
7af66d892f09: Pull complete
914f9ce178a0: Pull complete
8f2e3273d3d0: Pull complete
35ee6dcf95b0: Pull complete
ffe2fd0e000f: Pull complete
94b64151fccc: Pull complete
7efeff70c246: Pull complete
d976816aa311: Pull complete
72fd4d475a96: Pull complete
51b3ffa03cab: Pull complete
1014c1f41d2c: Pull complete
ba761b93afcc: Pull complete
d9454aad60f1: Pull complete
2d9dbc6fd99e: Pull complete
8e9a76dca507: Pull complete
3c4055694229: Pull complete
2f2c1aefbd04: Pull complete
ae8b2a79ed36: Pull complete
4fd8460f80d9: Pull complete
e537ba43b279: Pull complete
Digest: sha256:0d4bdc55e5fd77f992ab1d1bb44c570b9d587255a3ca955c050caad37dcc979c
Status: Downloaded newer image for camicroscope/iipimage:latest
Pulling loader (camicroscope/slideloader:latest)...
latest: Pulling from camicroscope/slideloader
092586df9206: Pull complete
ef599477fae0: Pull complete
4530c6472b5d: Pull complete
d34d61487075: Pull complete
87fc2710b63f: Pull complete
f142141aaad3: Pull complete
12eb19f5f2be: Pull complete
d34466b69a2a: Pull complete
fd8a0746ef83: Pull complete
b9b92267804c: Pull complete
1bb86f6ffd2d: Pull complete
513a8c6698db: Pull complete
307b5b83655c: Pull complete
ef7f501267da: Pull complete
63f5bed8872f: Pull complete
85e39ac47182: Pull complete
bee7e3f8cb13: Pull complete
1739564bb1c5: Pull complete
ce80f8bd8fa7: Pull complete
07501b932e7b: Pull complete
8f2046c0eea2: Pull complete
8c0e32917d16: Pull complete
aa0a77d81757: Pull complete
Digest: sha256:0b42150b5be5b4d070c6eeade5c58db98a4e677f1376c03704f39b4b72b98b4e
Status: Downloaded newer image for camicroscope/slideloader:latest
Creating ca-load ... done
Creating ca-iip ... done
Creating ca-mongo ... done
Creating ca-back ... done
Creating ca-idx ... done
Attaching to ca-iip, ca-mongo, ca-load, ca-back, ca-idx
ca-idx | /usr/local/bin/docker-entrypoint.sh: line 418: /config/run_idx.sh: No such file or directory
ca-load | [2023-02-19 11:49:49 +0000] [7] [INFO] Starting gunicorn 20.0.4
ca-load | [2023-02-19 11:49:49 +0000] [7] [INFO] Listening at: http://0.0.0.0:4000 (7)
ca-load | [2023-02-19 11:49:49 +0000] [7] [INFO] Using worker: sync
ca-load | [2023-02-19 11:49:49 +0000] [10] [INFO] Booting worker with pid: 10
ca-load | [2023-02-19 11:49:49 +0000] [11] [INFO] Booting worker with pid: 11
ca-load | [2023-02-19 11:49:49 +0000] [12] [INFO] Booting worker with pid: 12
ca-load | [2023-02-19 11:49:49 +0000] [13] [INFO] Booting worker with pid: 13
ca-mongo | 2023-02-19T11:49:48.860+0000 I CONTROL [main] Automatically disabling TLS 1.0, to force-enable TLS 1.0 specify --sslDisabledProtocols 'none'
ca-mongo | 2023-02-19T11:49:48.864+0000 W ASIO [main] No TransportLayer configured during NetworkInterface startup
ca-mongo | 2023-02-19T11:49:48.864+0000 I CONTROL [initandlisten] MongoDB starting : pid=1 port=27017 dbpath=/data/db 64-bit host=1db79c011754
ca-mongo | 2023-02-19T11:49:48.864+0000 I CONTROL [initandlisten] db version v4.2.23
ca-mongo | 2023-02-19T11:49:48.864+0000 I CONTROL [initandlisten] git version: f4e6602d3a4c5b22e9d8bcf0722d0afd0ec01ea2
ca-mongo | 2023-02-19T11:49:48.864+0000 I CONTROL [initandlisten] OpenSSL version: OpenSSL 1.1.1 11 Sep 2018
ca-mongo | 2023-02-19T11:49:48.864+0000 I CONTROL [initandlisten] allocator: tcmalloc
ca-mongo | 2023-02-19T11:49:48.864+0000 I CONTROL [initandlisten] modules: none
ca-mongo | 2023-02-19T11:49:48.864+0000 I CONTROL [initandlisten] build environment:
ca-mongo | 2023-02-19T11:49:48.864+0000 I CONTROL [initandlisten] distmod: ubuntu1804
ca-mongo | 2023-02-19T11:49:48.864+0000 I CONTROL [initandlisten] distarch: x86_64
ca-mongo | 2023-02-19T11:49:48.864+0000 I CONTROL [initandlisten] target_arch: x86_64
ca-mongo | 2023-02-19T11:49:48.864+0000 I CONTROL [initandlisten] options: { net: { bindIp: "*" } }
ca-mongo | 2023-02-19T11:49:48.865+0000 I STORAGE [initandlisten]
ca-mongo | 2023-02-19T11:49:48.865+0000 I STORAGE [initandlisten] ** WARNING: Using the XFS filesystem is strongly recommended with the WiredTiger storage engine
ca-mongo | 2023-02-19T11:49:48.865+0000 I STORAGE [initandlisten] ** See http://dochub.mongodb.org/core/prodnotes-filesystem
ca-mongo | 2023-02-19T11:49:48.866+0000 I STORAGE [initandlisten] wiredtiger_open config: create,cache_size=3468M,cache_overflow=(file_max=0M),session_max=33000,eviction=(threads_min=4,threads_max=4),config_base=false,statistics=(fast),log=(enabled=true,archive=true,path=journal,compressor=snappy),file_manager=(close_idle_time=100000,close_scan_interval=10,close_handle_minimum=250),statistics_log=(wait=0),verbose=[recovery_progress,checkpoint_progress],
ca-mongo | 2023-02-19T11:49:49.896+0000 I STORAGE [initandlisten] WiredTiger message [1676807389:896650][1:0x7f147a9cbb00], txn-recover: Set global recovery timestamp: (0, 0)
ca-mongo | 2023-02-19T11:49:49.941+0000 I RECOVERY [initandlisten] WiredTiger recoveryTimestamp. Ts: Timestamp(0, 0)
ca-mongo | 2023-02-19T11:49:50.082+0000 I STORAGE [initandlisten] Timestamp monitor starting
ca-mongo | 2023-02-19T11:49:50.189+0000 I CONTROL [initandlisten]
ca-mongo | 2023-02-19T11:49:50.189+0000 I CONTROL [initandlisten] ** WARNING: Access control is not enabled for the database.
ca-mongo | 2023-02-19T11:49:50.189+0000 I CONTROL [initandlisten] ** Read and write access to data and configuration is unrestricted.
ca-mongo | 2023-02-19T11:49:50.189+0000 I CONTROL [initandlisten]
ca-mongo | 2023-02-19T11:49:50.196+0000 I STORAGE [initandlisten] createCollection: admin.system.version with provided UUID: 06888b0d-15ff-4337-8a61-ee26f8b4dd0b and options: { uuid: UUID("06888b0d-15ff-4337-8a61-ee26f8b4dd0b") }
ca-mongo | 2023-02-19T11:49:50.263+0000 I INDEX [initandlisten] index build: done building index id on ns admin.system.version
ca-mongo | 2023-02-19T11:49:50.263+0000 I COMMAND [initandlisten] setting featureCompatibilityVersion to 4.2
ca-mongo | 2023-02-19T11:49:50.264+0000 I STORAGE [initandlisten] Flow Control is enabled on this deployment.
ca-mongo | 2023-02-19T11:49:50.264+0000 I STORAGE [initandlisten] createCollection: local.startup_log with generated UUID: 48415917-8462-4661-8518-fa1699db7289 and options: { capped: true, size: 10485760 }
ca-mongo | 2023-02-19T11:49:50.333+0000 I INDEX [initandlisten] index build: done building index id on ns local.startup_log
ca-mongo | 2023-02-19T11:49:50.334+0000 I FTDC [initandlisten] Initializing full-time diagnostic data capture with directory '/data/db/diagnostic.data'
ca-mongo | 2023-02-19T11:49:50.337+0000 I CONTROL [LogicalSessionCacheReap] Sessions collection is not set up; waiting until next sessions reap interval: config.system.sessions does not exist
ca-mongo | 2023-02-19T11:49:50.337+0000 I NETWORK [listener] Listening on /tmp/mongodb-27017.sock
ca-mongo | 2023-02-19T11:49:50.337+0000 I NETWORK [listener] Listening on 0.0.0.0
ca-mongo | 2023-02-19T11:49:50.337+0000 I NETWORK [listener] waiting for connections on port 27017
ca-mongo | 2023-02-19T11:49:50.337+0000 I STORAGE [LogicalSessionCacheRefresh] createCollection: config.system.sessions with provided UUID: 26709a37-d3d4-4eb4-9418-7175e9465f0a and options: { uuid: UUID("26709a37-d3d4-4eb4-9418-7175e9465f0a") }
ca-mongo | 2023-02-19T11:49:50.510+0000 I INDEX [LogicalSessionCacheRefresh] index build: done building index id on ns config.system.sessions
ca-mongo | 2023-02-19T11:49:50.608+0000 I INDEX [LogicalSessionCacheRefresh] index build: starting on config.system.sessions properties: { v: 2, key: { lastUse: 1 }, name: "lsidTTLIndex", ns: "config.system.sessions", expireAfterSeconds: 1800 } using method: Hybrid
ca-mongo | 2023-02-19T11:49:50.608+0000 I INDEX [LogicalSessionCacheRefresh] build may temporarily use up to 200 megabytes of RAM
ca-mongo | 2023-02-19T11:49:50.608+0000 I INDEX [LogicalSessionCacheRefresh] index build: collection scan done. scanned 0 total records in 0 seconds
ca-mongo | 2023-02-19T11:49:50.609+0000 I INDEX [LogicalSessionCacheRefresh] index build: inserted 0 keys from external sorter into index in 0 seconds
ca-mongo | 2023-02-19T11:49:50.625+0000 I INDEX [LogicalSessionCacheRefresh] index build: done building index lsidTTLIndex on ns config.system.sessions
ca-mongo | 2023-02-19T11:49:50.631+0000 I COMMAND [LogicalSessionCacheRefresh] command config.system.sessions command: createIndexes { createIndexes: "system.sessions", indexes: [ { key: { lastUse: 1 }, name: "lsidTTLIndex", expireAfterSeconds: 1800 } ], $db: "config" } numYields:0 reslen:114 locks:{ ParallelBatchWriterMode: { acquireCount: { r: 2 } }, ReplicationStateTransition: { acquireCount: { w: 3 } }, Global: { acquireCount: { r: 1, w: 2 } }, Database: { acquireCount: { r: 1, w: 2, W: 1 } }, Collection: { acquireCount: { r: 4, w: 1, R: 1, W: 2 } }, Mutex: { acquireCount: { r: 3 } } } flowControl:{ acquireCount: 1, timeAcquiringMicros: 1 } storage:{} protocol:op_msg 293ms
ca-back | prikey does not exist
ca-back | pubkey does not exist
ca-idx exited with code 127
ca-back | 2023-02-19 11:49:51.333783: I tensorflow/core/platform/cpu_feature_guard.cc:142] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA
ca-back | 2023-02-19 11:49:51.355351: I tensorflow/core/platform/profile_utils/cpu_utils.cc:94] CPU Frequency: 2399995000 Hz
ca-back | 2023-02-19 11:49:51.355829: I tensorflow/compiler/xla/service/service.cc:168] XLA service 0x5b9fe80 initialized for platform Host (this does not guarantee that XLA will be used). Devices:
ca-back | 2023-02-19 11:49:51.355891: I tensorflow/compiler/xla/service/service.cc:176] StreamExecutor device (0): Host, Default Version
ca-back | handler named "updateMarksLabel" not found (rule 23 handler 0)
ca-back exited with code 1

All images from these slides table are not working https://wolf.cci.emory.edu//camic_org/apps/table.html.

Describe the bug
In Nanoborb, after open the .svs file, there will be a toolbar on the left-top on the website, and there is a "draw" on the toolbar.

In nanoborb, this tool can be successfully used to draw lines but in the server of caMicroscope (after hosted setup) will show errors: for more options, balabala... and then nothing will change no lines can be drawn.

A clear and concise description of what the bug is.

To Reproduce
Steps to reproduce the behavior:

1. Do the hosted setup in Linux (mine is Ubuntu)
2. Input command: "docker-compose -f development.yml up" under the directory: Distro
3. Open the website: the ip address + 4010 and then get into the website
4. Then upload a .svs file onto the server
5. Open this file on server
6. Use the draw tool in the toolbox
7. See error
   My browser is google chrome which has an error:
   Uncaught TypeError: Cannot read property 'style' of undefined
   at MouseEvent.annotationOn (uicallbacks.js:411)
   at MouseEvent. (uicallbacks.js:295)

Expected behavior
I hope the draw tool in server just appears the same function like Nanoborb

Screenshots

Desktop (please complete the following information):

• OS: Windows 10, SSH with Ubuntu
• Browser google chrome version 83.0.4103.97

Additional context
In Windows Edge, it even cannot open the website! thus I wonder if it is the error with Browser!

the jwt_keys/make_keys.sh script doesn't seem to work on windows. can we make something which does?

Describe the bug
When building the application with docker-compose -f caMicroscope.yml up, it fails with the below error :

Building iip
ERROR: error fetching: fatal: unable to find remote helper for 'https'
: exit status 128

I am using docker-compose version 1.25.4 build unkown, Docker version 18.09.9, build 1752eb3.

To Reproduce
Steps to reproduce the behavior:

1. Clone this repository
2. Inside the repository folder, open your terminal
3. Run docker-compose -f caMicroscope.yml up (using sudo privilidges)

Expected behavior
The application should run at http://localhost:4010

Desktop (please complete the following information):

• OS: Ubuntu 18.04 LTS

Add system requirements for different scales, and report on it, preferably per-service.

Is your feature request related to a problem? Please describe.
Frequently, users/administrators are interested in a summary of data in the database.

Describe the solution you'd like
A simple page that answers some questions about items, mostly at the slide level.
Questions such as - how many images have at least one annotation associated with them? one heatmap?
This may be able to be done in browser, but there's no issue with requesting/making more data endpoints if needed.

Hi! I am Tingyuan (Leon).
Thank you for previous discussionissue #204, it inspired me a lot.

By running develop.yml , I successfully sign up a temporary account.

I also tried the other two potential methods, however, as @catweis said, they do not work.

The followings are my tries on these two methods:

• For the way of manually adding account in mongo database, I successfully added a new account data in the local database called 'camic'. But no matter how I restart or rebuild the service, it still shows that "User not added".
  

Log:

• For the way of temporarily disabling security check, I did not found develop.yml under Caracal, but I did found there were config related with security check in .env file that was copied and renamed from .env.example.
  

I tried modifying both DISABLE_SEC and ALLOW_PUBLIC to value of true, and made sure configs in .env were run by re-executing setup_script.sh under Caracal, but it still did not worked.

In short, for now, it seems like running develop.yml is the only way to access the system.

I know it is very likely that there is something wrong with my operations, so I will be extremely happy if anyone could point me in the right direction! Thank you so much!

Originally posted by @CoToYo in #204 (comment)

Describe the bug
After creating a directory to clone caMicroscope into, I received this error:

ERROR: A service can not depend on itself: mongo

To Reproduce
These were the steps I took:

cd $HOME
mkdir -v camicroscope
cd camicroscope
git clone [email protected]:camicroscope/Distro.git
docker-compose -f caMicroscope.yml up

Expected behavior
I am expecting a smooth start of the installation. A quick solution is to change the following in the caMicroscope.yml-file:

# this part of the code is wrong - 'ERROR: A service can not depend on itself: mongo'
#    depends_on:
#      - mongo

One can't reference a service to itself.

Screenshots
n/a

Desktop (please complete the following information):

• OS: macOS Monterey, v12.5
• home-brew:

brew config
HOMEBREW_VERSION: 3.5.7
ORIGIN: https://github.com/Homebrew/brew
HEAD: ce8ef89ec0cfe875c48c3a83a843af9074c05930
Last commit: 4 days ago
Core tap ORIGIN: https://github.com/Homebrew/homebrew-core
Core tap HEAD: 2745e4f9b1473f148ce8d8e9aeb779f204c25541
Core tap last commit: 4 hours ago
Core tap branch: master
HOMEBREW_PREFIX: /usr/local
HOMEBREW_CASK_OPTS: []
HOMEBREW_DISPLAY: /private/tmp/com.apple.launchd.EQK4w2iKJT/org.xquartz:0
HOMEBREW_MAKE_JOBS: 8
Homebrew Ruby: 2.6.8 => /System/Library/Frameworks/Ruby.framework/Versions/2.6/usr/bin/ruby
CPU: octa-core 64-bit kabylake
Clang: 13.1.6 build 1316
Git: 2.37.1 => /usr/local/bin/git
Curl: 7.79.1 => /usr/bin/curl
macOS: 12.5-x86_64
CLT: 13.4.0.0.1.1651278267
Xcode: 13.4.1

Smartphone (please complete the following information):
n/r

Additional context
none

Is your feature request related to a problem? Please describe.
The current color scheme for the heatmaps are often useful, but may not be conveyant or visible in all contexts

Describe the solution you'd like
Addition of a mechanism to let a user define a heatmap color function (takes in the value(s) for a patch, outputs a color)

Describe alternatives you've considered
Different possible options include just adding presets, use of a single color gradient, etc.
Could also include taking in multiple fields to make a color (at simplest, imagine variables a,b,c -> r,g,b)

While using caMicroscope a lack of menu bar always bugs me. I feel if there were a navigation bar for all the sections of the web app it would be more user friendly.
Possible Solution:
adding a menu bar to facilitate easy navigation

@birm would you assign this issue to me?

Add meaningful heatmap, annotation, and segmentation to a public slide, and add them all to this distro.

Avoid bad documents (missing required fields) in the DB.

Service 'back' failed to build: toomanyrequests: You have reached your pull rate limit. You may increase the limit by authenticating and upgrading: https://www.docker.com/increase-rate-limit

See, for example, https://travis-ci.org/github/camicroscope/Distro/builds/761490524

Describe the bug
Only .svs slides can be uploaded but .tiff slides cannot be uploaded which is wired because not only in caMicroscope but also in Nanoborb, the .tiff slides cannot be uploaded.

However, in the guide in Nanoborb, it recommends that .tiff slides can be uploaded and CMU.tiff is shown as the sample file.

Hi all, I have some questions towards the Distro local usage.
Setup:
I clone the Distro directory and run the container of Distro using command docker-compose -f caMicroscope.yml up as suggested and go to localhost:4010
Questions:

1. When I try to post an Image, I select a sample image from my local disk, click Finish Upload, Check without seeing error messages. When I click Post and wait for a few seconds, there comes an error message as shown in screen shot.
   
   I checked the directory "Distro/images" and found the newly created sample2.svs file (Which is not there before I hit the post).
   Not sure if these messages are expected when run the app locally.

2. After posting the image file as described above, when I go to "app/table.html", there is no image loaded and here is the screen shot. I think there might be something unexpcted happening in my case but I don't know why.
   

Describe the bug
When running docker-compose on develop.yml and camicroscope.yml, the command exits with error since additional_links.json file was deleted in a previous commit.

A good solution would be to either comment out/delete the lines importing the additional_links.json file in the yml files.

To Reproduce
Steps to reproduce the behavior:

1. Open Distro on develop
2. Run docker-compose develop.yml up or docker-compose camicroscope.yml up
3. See error (similar to the one shown in the attached screenshot).

Expected behavior
The containers should be up and running successfully.

Screenshots
The error ->

Desktop:

• OS: Ubuntu 20.04
• Browser: Firefox
• Version: 88.0.1 (64-bit)

After observation, I guess, this entire software uses js to make not only the front end but also the back end?

The question is, If I choose the preset label tool in the tool bar and choose the Tumor, Positive, 2000. Then I draw and drag on the slide, then annotation will be saved in the mongoDB. AND, what functions will be called in this process? Which files will be used?

Is your feature request related to a problem? Please describe.
Aperio also has a geometric annotation format, analogous to caMicroscope's "marks" (extended geoJson). It would be nice to convert between these formats.

Describe the solution you'd like
The lightest touch is the best, so there's kind of a priority list for implementations. From "best" to "worst":

• Using javascript in browser, not requiring a new microservice
• Using wasm or similar in browser, not requring a new microservice (preferred less due to slight preference to keep a single language as possible)
• Extending an existing service (maybe iip or security middleware?)
• Addition of a new microservice

Additional context
We can probably get a few sample annotations in aperio's format upon request.

So people can use or generate data, let's describe all of the data that camicroscope interacts with, especially annotations and heatmaps.

We need a working and easy kubernetes config. Kompose alone has been insufficient so far.

Rotate logs so they don't become too big