Upload files¶

This page describes how to upload files to the Deep Origin data hub, and assign them to individual cells.

Upload a file to the data hub¶

To upload a file to the Deep Origin data hub, run the following commands:

CLIPython

deeporigin data upload /path/to/test.fasta

This will upload the file to your data hub, but the file will not yet be assigned to any database or cell. An example response is shown below:

╭──────────────────┬──────────────────────────────╮
│ Property         │ Value                        │
├──────────────────┼──────────────────────────────┤
│ name             │ test.fasta                   │
│ contentType      │ data/fasta                   │
│ contentLength    │ 554588                       │
│ id               │ _file:36ufKT2Sej22coSEOizpK  │
│ status           │ ready                        │
│ uri              │ s3://foo                     │
│ dateCreated      │ 2024-06-18T14:48:33.501Z     │
│ dateUpdated      │ 2024-06-18T14:48:33.501Z     │
│ createdByUserDrn │ levins@deeporigin.com        │
╰──────────────────┴──────────────────────────────╯

JSON output with --json

JSON output can be requested by adding --json, and allows you to pipe out to a JSON processor like jq:

deeporigin upload /path/to/test.fasta | jq

{
  "name": "test.fasta",
  "contentType": "data/fasta",
  "contentLength": 554588,
  "id": "_file:36ufKT2Sej22coSEOizpK",
  "status": "ready",
  "uri": "s3://foo",
  "dateCreated": "2024-06-18T14:51:43.876Z",
  "dateUpdated": "2024-06-18T14:51:43.876Z",
  "createdByUserDrn": "levins@deeporigin.com"
}

from deeporigin.data_hub import api
api.upload_file("/path/to/file.fasta")

This will upload the file to your data hub. An example is shown below:

{
    "name": "file.fasta",
    "contentType": "data/foo",
    "contentLength": 55454688,
    "id": "_file:6Hdhyc3t8xZ6pmyCrQy1t",
    "status": "ready",
    "uri": "s3://data.<org-name>/_file:6Hdhyc3t8xZ6pmyCrQy1t",
    "dateCreated": "2024-06-18T14:18:37.409Z",
    "dateUpdated": "2024-06-18T14:18:37.409Z",
    "createdByUserDrn": "haldane@deeporigin.com",
}

Upload a file to an existing row¶

To upload a file and assign it to a cell in an existing row, run the following commands:

CLIPython

deeporigin data upload /path/to/test.fasta \
    --column <column_id> \
    --database <database_id> \
    --row <row_id>

from deeporigin.data_hub import api
api.upload_file("/path/to/file.fasta")

To assign an uploaded file to a cell in an existing row, run the assign_files_to_cell function:

    api.assign_files_to_cell(
    file_ids=["_file:6Hdhyc3t8xZ6pmyCrQy1t"],
    database_id="db-dna",
    column_id="base_sequence_file",
    row_id="row-id",
)

Upload a file to a new row of a database¶

To upload a file and assign it to a column in a new row, run the following commands:

CLIPython

deeporigin data upload /path/to/test.fasta \
    --column <column_id> \
    --database <database_id>

This omits the --row parameter, which would create a new row in the database.

First, upload a file to your data hub by running:

from deeporigin.data_hub import api
api.upload_file("/path/to/file.fasta")

Second, assign the file to a new row by running:

api.assign_files_to_cell(
    file_ids=["_file:6Hdhyc3t8xZ6pmyCrQy1t"],
    database_id="db-dna",
    column_id="base_sequence_file",
)