Files [GET, POST, DELETE]

API calls related to file objects:

Retrieve

Create

Delete

Retrieve

Return a single file

GET /api/v1/vaults/<vault_id>/files/<file_id>

Note: The contents are base64 encoded

 

Example 

curl -H "X-CDD-Token: $TOKEN" -X GET "https://app.collaborativedrug.com/api/v1/vaults/<vault_id>/files/<file_id>"

Returns:

{
  "id": 1069448031,
  "class": "uploaded file",
  "name": "tmp.txt",
  "mime_type":
  {
    "synonyms": [],
    "symbol": "text",
    "string": "text/plain",
    "hash": -1147906696977776415
  },
  "character_set": "US-ASCII",
  "contents": "VGhpcyBpcyBhIGZpbGUK"
}

Following this up with:

echo VGhpcyBpcyBhIGZpbGUK | base64 -D

Returns:

This is a file

Note: "This is a file" is the actual content of this text file

 

Create

Attach a file to an object (Run, Molecule, Protocol or ELN entry)

POST /api/v1/vaults/<vault_id>/files

 

Example (adding a file to a Protocol Run)

curl -H "X-CDD-Token: $TOKEN" -X POST --form "file=@C:\files\<file_name>" --form "resource_class=run" --form "resource_id=<run_id>" "https://app.collaborativedrug.com/api/v1/vaults/<vault_id>/files"

Returns:

{
   "id": "1069448044"
   "name": "<file_name>"
}

 Note: Additional allowed values for resource_class are "molecule", "protocol" and "eln_entry".

 

Example (adding a file to an ELN Entry)

curl -H "X-CDD-Token: $TOKEN" -X POST --form "file=@C:\files\<file_name>" --form "resource_class=eln_entry" --form "resource_id=<eln_entry_id>" "https://app.collaborativedrug.com/api/v1/vaults/<vault_id>/files"

Returns:

{
   "id": "7395612976"
   "name": "<file_name>"
}

 Note: To add a file into an ELN entry, the entry must already exist. ELN Entries can be created (by Vault Administrators only) using the POST eln/entries API call.

 

Attach a file to a Molecule/Batch field or a Protocol Readout Row

There is a 2-step API workflow available now to programmatically attach files to Molecule/Batch fields and to Protocol readouts.

 

The first step involves using the POST Files API end point to send a file to the CDD Vault server. This step returns an internal file id that must be used in a 2nd API call to attach this file to the desired field/readout.

 

Step 1
The 1st API call used is POST /api/v1/vaults/<vault_id>/files which returns JSON containing the internal file id.

{
"id": 20167608,
"name": "FlowCyto.png",
"expires_at": "2023-10-13"
}

 

Helpful Hint: The JSON also includes an “expires_at” date indicating when the file you just sent to the CDD Vault server will no longer exist if it’s not subsequently attached to a field/readout.

 

Step 2

The next API call should attach the file to the desired field/readout. This step uses the PUT Molecules, PUT Batches or PUT Readout_Rows end points.

PUT /api/v1/vaults/<vault_id>/molecules

PUT /api/v1/vaults/<vault_id>/batches

PUT /api/v1/vaults/<vault_id>/readout_rows

 

Example (adding a file to a Batch field)

As an example, if the file just POSTed needs to be attached to an existing Batch field, use this API call:

PUT https://app.collaborativedrug.com/api/v1/vaults/<vault_id>/batches/<batch_id>

And pass JSON like this:

{"batch_fields":
        {"DataFile": 20167608}
}

 

Example (adding a file to an existing Readout Row)

As another example, if the file just POSTed needs to be attached to an existing Protocol readout row, use this API call:

PUT https://app.collaborativedrug.com/api/v1/vaults/<vault_id>/readout_rows/<readout_row_id>

And pass JSON like this:

{"readouts":
       {"1146750": {"value": "20167608"}}
}

 

Delete

Delete a file attachment

DELETE /api/v1/vaults/<vault_id>/files/<file_id>

Deletes a single file.

 

Example  

curl -H "X-CDD-Token: $TOKEN" -X DELETE "https://app.collaborativedrug.com/api/v1/vaults/<vault_id>/files/<file_id>"

Returns:

{
      "message": "File with ID <file_id> has been destroyed"
}