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Leanda Command Line Interface

Project description

Leanda-CLI

Leanda Command Line Interface (CLI) is intended for installation on users computers and will serve as another "client" for Leanda platform.

Quickstart

Install leanda-cli via pip:

pip install leanda

Run help command:

leanda -h

For the next commands you need to set the next environment variables: WEB_API_URL, WEB_STORAGE_API_URL and IDENTITY_SERVER_URL

Login to Leanda:

leanda login -u my_name -p my_password

Get categories list:

leanda categories

Run livesync command:

leanda livesync -l ./leanda-sync-folder

./leanda-sync-folder is a local folder path.

Commands Summary

Command Usage
leanda login Allows to login and store the update session information for an Leanda user.
leanda whoami Check authorization and explore session data.
leanda logout Do logout. Session data is removed.
leanda pwd Identify current Leanda working directory.
leanda cd Change Leanda's current working directory.
leanda ls Browse remote Leanda folder.
leanda rm Allows to remove file or folder.
leanda upload Allows uploading a local file into the BLOB (raw file) store.
leanda download Allows to download an Leanda file.
leanda livesync Two-way synchronization of local folder with the Leanda user's folder.
leanda items Allows to list all items from Leanda using queries.
leanda models Allows to list models from Leanda using queries.
leanda recordsets Allows to list recordsets from Leanda using queries.
leanda train Allows to run Machine Learning command train.
leanda predict Allows to run Machine Learning command predict.
leanda categories Allows to initialize category tree with basic structure.

login

Allows to login and reset session information for an Leanda user.

Parameters for login

-u, --username   your leanda username.
-p, --password   your leanda password
-v, --verbosity  set verbosity level.

Examples:

leanda login -u<user-name> -p<password>
leanda login --verbosity -u<user-name> -p<password>
leanda login -v -u<user-name> -p<password>
leanda login -vv -u<user-name> -p<password>
leanda login -u<user-name> -p
Password:

whoami

Check authorization and explore session data.

Parameters for whoami

-v, --verbosity  set verbosity level.

Examples:

leanda whoami --verbosity
leanda whoami -vv
leanda whoami -vvv

logout

Do logout. Session data is removed.

Parameters for logout

No parameters

Examples:

leanda logout

pwd

Identify current Leanda working directory.

Parameters for pwd

-v, --verbosity  set verbosity level.

Examples:

leanda pwd
leanda pwd --verbosity
leanda pwd -vv
leanda pwd -vvv

ls

Browse remote Leanda folder.

Parameters for ls

container - Remote Leanda user's folder or none for current working folder.
            Leanda user's folder can be choosed by its full id system wide
            or by substring for subfolders in current folder.
            Substring compared to folder name starting from the beggining
            or to folder id ending.
-s, --size - Report page length (default value 10)
-p, --page - Report page number (default value 1)

Examples:

leanda ls c1cc0000-5d8b-0015-e9e3-08d56a8a2e01
leanda ls 2e01
leanda ls -p10
leanda ls -s20 -2

cd

Change Leanda's current working directory.

Parameters for cd

container - Remote Leanda user's folder, none for home  folder or '..' for
            parent folder. Leanda user's folder can be choosed by its full id
            system wide or by substring for subfolders in current folder.
            Substring compared to folder name starting from the beggining
            or to folder id ending.

Examples:

leanda ls
File
    33.mol               Records(  1) Processed  c1cc0000-5d8b-0015-e9e3-08d56a8a2e01
    combined lysomotroph Records( 55) Processed  00160000-ac12-0242-c20e-08d56e29a481

leanda cd 33
leanda cd a481
leanda cd
leanda cd ..
leanda cd c1cc0000-5d8b-0015-e9e3-08d56a8a2e01

rm

Allows to remove file or folder

Parameters for rm

container - Remote Leanda user's folder. Leanda user's folder can be choosed by
            its full id  system wide or by substring for subfolders in current
            folder. Substring compared to folder name starting from the beggining
            or to folder id ending.

Examples:

leanda rm a481
leanda rm abc
leanda rm c1cc0000-5d8b-0015-e9e3-08d56a8a2e01

upload

Allows uploading a local file into the BLOB (raw file) store.

Parameters for upload

container - Remote Leanda user's folder, none for working folder.
            Leanda user's folder can be choosed by its full id system wide
            or by substring for subfolders in current folder.
            Substring compared to folder name starting from the beggining
            or to folder id ending.
-p, --path - path to local file
-n, --name - name for file
-m, --meta - path to model description in json or yaml formats
-v, --verbosity  set verbosity level.

Examples:

leanda upload -p path-to-file
leanda upload -p path-to-file1 -p path-to-file2 -p path-to-file3
leanda upload -p path-to-file -n new-name to file 'filename'
leanda upload -p path-to-file -m path-to-model.json
leanda upload -p path-to-file -m path-to-model.yaml

download

Allows downloading a remote file to local host.

Parameters for download

container - Remote Leanda user's folder, none for working folder.
            Leanda user's folder can be choosed by its full id system wide
            or by substring for subfolders in current folder.
            Substring compared to folder name starting from the beggining
            or to folder id ending.
-o, --output - Path to file or directory to save.
-f, --force - Force overwrite if file exists.

Examples:

leanda upload abc -o path-to-file
leanda upload a481 -f -o path-to-file1
leanda upload c1cc0000-5d8b-0015-e9e3-08d56a8a2e01 -o path-to-file

livesync

Two-way synchronization of local folder with the Leanda user's folder. Comparision between folders based on file names. For more precise comparision see -ul and -ur keys.

 -l, --local-folder - Path to local folder or none for current working directory
 -r, --remote-folder - Remote Leanda user's folder or none for current working folder.
                       Leanda user's folder can be choosed by its full id system wide
                       or by substring for subfolders in current folder. Substring
                       compared to folder name starting from the begining or to
                       folder id ending.
 -ul, --update-local - Compare by name and Leanda file's version
 -ur, --update-remote - Compare by name and last modification time.

Examples:

leanda livesync -l abc -r c1cc0000-5d8b-0015-e9e3-08d56a8a2e01
leanda livesync -l /path/to/folder -f -r 2e01 -ul
leanda livesync -ur

items

Allows to list all items from Leanda using queries.

  -q, --query - Filter models by subquery
  -n, --name  - Filter models by substring
  -s, --short-notation
              - Path to yaml file with list of short notations
                Example - p.radius:MachineLearningModelInfo.Fingerprints.Radius
  -v,--verbosity = 0 
              - Set verbosity level. 
                -v - display query string,
                -vv - display records,
   -f, --format = (json|yaml)
              - Set model verbosity output format

Examples:

leanda items
leanda items -v
leanda items -vv
leanda items -n png
leanda items -q "SubType eq 'Model' and MachineLearningModelInfo.Method eq 'Naive Bayes'"  -vv -f json
leanda items -q "type=Model,prop.chem=MOST_ABUNDANT_MASS,prop.fields=logs"  -s sample_files/short_notations.yaml
leanda items -q "SubType eq 'Model' and MachineLearningModelInfo.Fingerprints.Size gt 200"  -vv -f yaml

models

Allows to list models from Leanda using queries. Same as items, but add preset filter SubType eq 'Model'

Examples:

leanda models
leanda models -v
leanda models -vv
leanda items -n ada
leanda models -q "MachineLearningModelInfo.Method eq 'Naive Bayes'"  -vv -f json
leanda models -q "type=Model,prop.chem=MOST_ABUNDANT_MASS,prop.fields=logs"  -s sample_files/short_notations.yaml
leanda models -q "MachineLearningModelInfo.Fingerprints.Size gt 200"  -vv -f yaml

recordsets

Allows to list recordsets from Leanda using queries. Same as items, but add preset filter SubType eq 'Records'

Examples:

leanda recordsets
leanda recordsets -v
leanda recordsets -vv
leanda recordsets -n combined
leanda recordsets -q "MachineLearningModelInfo.Method eq 'Naive Bayes'"  -vv -f json
leanda recordsets -q "type=Model,prop.chem=MOST_ABUNDANT_MASS,prop.fields=logs"  -s sample_files/short_notations.yaml
leanda recordsets -q "MachineLearningModelInfo.Fingerprints.Size gt 200"  -vv -f yaml

train

Allows to run Machine Learning command train.

  container - Remote Leanda user's folder, none for working folder.
              Leanda user's folder can be choosed by its full id system wide
              or by substring for subfolders in current folder.
              Substring compared to folder name starting from the beggining
              or to folder id ending.
  -m, --meta - Model metadata in json or yaml formats
  -f, --folder-name - Output folder name

Examples:

leanda train 00130000-ac12-0242-0f11-08d58dbc7b8b  -f test1.model -m sample_files/train_sdf_model.yaml
leanda train 08d58dbc7b8b  -f test2.model -m sample_files/train_sdf_model.yaml
leanda train b data_solubility.sdf -f test3.model -m sample_files/train_sdf_model.yaml
leanda train data_solubility.sdf -f test4.model -m sample_files/train_sdf_model.yaml
leanda train data_solu -f test5.model -m sample_files/train_sdf_model.yaml

predict

Allows to run Machine Learning command predict.

 -f - --folder-name - Output folder name
 -m - --model - Leanda model's file id.
 -r - --recordset - Leanda recordsets's file id.

Examples:

leanda predict -f folder.predict -m 7ceef61a-cf7d-41d9-a1f0-19874a2b31e9 -r 000e0000-ac12-0242-36bb-08d585329c5a

categories

Allows to initialize category tree with basic structure.

  -rm, --remove - Remove all categories
  -i, --init    - Initialize categories from categories.json file data

Examples:

leanda categories #get list of categories
leanda categories -rm
leanda categories -i

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