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burtonrj / CytoPy

A data-centric flow/mass cytometry automated analysis framework
https://cytopy.readthedocs.io/en/latest/
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Issues with saving new project to local database #32

Closed connorcall closed 2 years ago

connorcall commented 2 years ago

Hi, I'm trying to develop a new flow data analysis protocol using CytoPy, but I seem to be having troubles getting a project successfully set up. I am going through the tutorials and I can set up a local database and project, but then if I try to save, I get a timeout error every time.

Are there stipulations on what types of connections are needed to form databases? All I have so far is:

from cytopy.data import setup,project

setup.global_init("test")

newproject = project.Project(project_id = 'testproj',data_directory = "/Users/connorcall/Desktop/testdata") newproject.save()

and I get the following error: ServerSelectionTimeoutError: localhost:27017: [Errno 61] Connection refused, Timeout: 30s, Topology Description: <TopologyDescription id: 62a7abb9c1f069dabb0789b8, topology_type: Single, servers: [<ServerDescription ('localhost', 27017) server_type: Unknown, rtt: None, error=AutoReconnect('localhost:27017: [Errno 61] Connection refused')>]>

Thanks for any help you can offer!

jfgonsalves commented 2 years ago

Hi there, are you using the Docker image or manual install?

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On 14 Jun 2022, at 7:41 am, connorcall @.***> wrote:

 Hi, I'm trying to develop a new flow data analysis protocol using CytoPy, but I seem to be having troubles getting a project successfully set up. I am going through the tutorials and I can set up a local database and project, but then if I try to save, I get a timeout error every time.

Are there stipulations on what types of connections are needed to form databases? All I have so far is:

from cytopy.data import setup,project

setup.global_init("test")

newproject = project.Project(project_id = 'testproj',data_directory = "/Users/connorcall/Desktop/testdata") newproject.save()

and I get the following error: ServerSelectionTimeoutError: localhost:27017: [Errno 61] Connection refused, Timeout: 30s, Topology Description: <TopologyDescription id: 62a7abb9c1f069dabb0789b8, topology_type: Single, servers: [<ServerDescription ('localhost', 27017) server_type: Unknown, rtt: None, error=AutoReconnect('localhost:27017: [Errno 61] Connection refused')>]>

Thanks for any help you can offer!

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connorcall commented 2 years ago

I did a manual install and set up a new conda enviornment.

jfgonsalves commented 2 years ago

Okay, did you install MongoDB with Homebrew? (I’m assuming you are on a Mac judging by your Home folder structure?).

On 14 Jun 2022, at 7:51 am, connorcall @.***> wrote:

 I did a manual install and set up a new conda enviornment.

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connorcall commented 2 years ago

ah, I found out there was an error in the MongoDB install. Thank you for your help!

leeanapeters commented 2 years ago

Hi, I am also experiencing the same issue coupled with some issues with the install itself through docker.

In particular I am not sure if it is normal for the docker compose to take so long (24 hours post compose command) and to output this text in the teminal

cytopy-mongodb-1 | {"t":{"$date":"2022-06-17T15:32:49.824+00:00"},"s":"I", "c":"STORAGE", "id":22430, "ctx":"WTCheckpointThread","msg":"WiredTiger message","attr":{"message":"[1655479969:824679][1:0x7f803626a700], WT_SESSION.checkpoint: [WT_VERB_CHECKPOINT_PROGRESS] saving checkpoint snapshot min: 1136, snapshot max: 1136 snapshot count: 0, oldest timestamp: (0, 0) , meta checkpoint timestamp: (0, 0)"}}

I tried to execute the database commands through the container (opened in terminal through docker desktop in windows)

Any help would be much appreciated!

Leeana

jfgonsalves commented 2 years ago

Are you using the default Dockercompose file?

Maybe try use the latest version of of MongoDB rather than the old image that the compose file requests.

Change "4.4-bionic" to "latest"

leeanapeters commented 2 years ago

I do have 4.4 bionic so I will try that, thank you!

From: Filipe Gonsalves @.> Sent: Friday, June 17, 2022 10:48 PM To: burtonrj/CytoPy @.> Cc: Peters,Leeana D @.>; Comment @.> Subject: Re: [burtonrj/CytoPy] Issues with saving new project to local database (Issue #32)

[External Email]

Are you using the default Dockercompose file?

Maybe try use the latest version of of MongoDB rather than the old image that the compose file requests.

Change "4.4-bionic" to "latest"

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