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server.py

Exposed REST API.

protected_route(function)

Protected route function decorator which authenticates requests.

Parameters:

Name Type Description Default
function Callable

Function to decorate, typically routes

 required

Returns:

Type Description
Callable

Function's output if JWT authetication is successful, otherwise return error message
Source code in pharus/server.py 
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def protected_route(function: Callable) -> Callable:
    """
    Protected route function decorator which authenticates requests.

    Args:
        function: Function to decorate, typically routes

    Returns:
        Function's output if JWT authetication is successful, otherwise return error message
    """

    @wraps(function)
    def wrapper(**kwargs):
        try:
            if "database_host" in request.args:
                encoded_jwt = request.headers.get("Authorization").split()[1]
                connect_creds = {
                    "databaseAddress": request.args["database_host"],
                    "username": jwt.decode(
                        encoded_jwt,
                        crypto_serialization.load_der_public_key(
                            b64decode(environ.get("PHARUS_OIDC_PUBLIC_KEY").encode())
                        ),
                        algorithms="RS256",
                        options=dict(verify_aud=False),
                    )[environ.get("PHARUS_OIDC_SUBJECT_KEY")],
                    "password": encoded_jwt,
                }
            else:
                connect_creds = jwt.decode(
                    request.headers.get("Authorization").split()[1],
                    environ["PHARUS_PUBLIC_KEY"],
                    algorithms="RS256",
                )
            connection = dj.Connection(
                host=connect_creds["databaseAddress"],
                user=connect_creds["username"],
                password=connect_creds["password"],
            )
            return function(connection, **kwargs)
        except Exception as e:
            return str(e), 401

    wrapper.__name__ = function.__name__
    return wrapper

api_version()

Handler for /version route.

Returns:

Type Description
str

API version

GET /version

Route to check server health returning the API version.

Example request:
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GET /version HTTP/1.1
Host: fakeservices.datajoint.io
Example response:
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HTTP/1.1 200 OK
Vary: Accept
Content-Type: application/json

{
    "version": "0.8.10"
}
Status Codes
  • 200 OK: No error.
Source code in pharus/server.py 
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@app.route(f"{environ.get('PHARUS_PREFIX', '')}/version", methods=["GET"])
def api_version() -> str:
    """
    Handler for ``/version`` route.

    Returns:
        API version

    ## GET /version

    Route to check server health returning the API version.

    ### Example request:

    ```http
    GET /version HTTP/1.1
    Host: fakeservices.datajoint.io
    ```

    ### Example response:

    ```http
    HTTP/1.1 200 OK
    Vary: Accept
    Content-Type: application/json

    {
        "version": "0.8.10"
    }
    ```

    #### Status Codes
    * 200 OK: No error.
    """
    if request.method in {"GET", "HEAD"}:
        return dict(version=version)

login()

Handler for /login route.

Warning

Currently, this implementation exposes user database credentials as plain text in POST body once and stores it within a bearer token as Base64 encoded for subsequent requests. That is how the server is able to submit queries on user's behalf. Due to this, it is required that remote hosts expose the server only under HTTPS to ensure end-to-end encryption. Sending passwords in plain text over HTTPS in POST request body is common and utilized by companies such as GitHub (2021) and Chase Bank (2021). On server side, there is no caching, logging, or storage of received passwords or tokens and thus available only briefly in memory. This means the primary vulnerable point is client side. Users should be responsible with their passwords and bearer tokens treating them as one-in-the-same. Be aware that if your client system happens to be compromised, a bad actor could monitor your outgoing network requests and capture/log your credentials. However, in such a terrible scenario, a bad actor would not only collect credentials for your DataJoint database but also other sites such as github.com, chase.com, etc. Please be responsible and vigilant with credentials and tokens on client side systems. Improvements to the above strategy is currently being tracked in https://github.com/datajoint/pharus/issues/82.

Returns:

Type Description
dict

Function output is an encoded JWT if successful, otherwise return error message

POST /login

Route to generate an authentication token.

Example request:
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POST /login HTTP/1.1
Host: fakeservices.datajoint.io
Accept: application/json

{
    "databaseAddress": "tutorial-db.datajoint.io",
    "username": "user1",
    "password": "password1"
}
Example successful response:
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HTTP/1.1 200 OK
Vary: Accept
Content-Type: application/json

{
    "jwt": "<token>"
}
Example unexpected response:
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HTTP/1.1 500 Internal Server Error
Vary: Accept
Content-Type: text/plain

400 Bad Request: The browser (or proxy) sent a request that this server could not
    understand.
Response Headers
  • Content-Type: text/plain, application/json
Status Codes
  • 200 OK: No error.
  • 500 Internal Server Error: Unexpected error encountered. Returns the error message as a string.
Source code in pharus/server.py 
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@app.route(f"{environ.get('PHARUS_PREFIX', '')}/login", methods=["POST"])
def login() -> dict:
    """
    Handler for ``/login`` route.

    Warning:
        Currently, this implementation exposes user database credentials as plain text in
        POST body once and stores it within a bearer token as Base64 encoded for
        subsequent requests. That is how the server is able to submit queries on user's
        behalf. Due to this, it is required that remote hosts expose the server only
        under HTTPS to ensure end-to-end encryption. Sending passwords in plain text over
        HTTPS in POST request body is common and utilized by companies such as GitHub
        (2021) and Chase Bank (2021). On server side, there is no caching, logging, or
        storage of received passwords or tokens and thus available only briefly in
        memory. This means the primary vulnerable point is client side. Users should be
        responsible with their passwords and bearer tokens treating them as
        one-in-the-same. Be aware that if your client system happens to be compromised,
        a bad actor could monitor your outgoing network requests and capture/log your
        credentials. However, in such a terrible scenario, a bad actor would not only
        collect credentials for your DataJoint database but also other sites such as
        github.com, chase.com, etc. Please be responsible and vigilant with credentials
        and tokens on client side systems. Improvements to the above strategy is
        currently being tracked in https://github.com/datajoint/pharus/issues/82.

    Returns:
        Function output is an encoded JWT if successful, otherwise return error message

    ## POST /login

    Route to generate an authentication token.

    ### Example request:

    ```http
    POST /login HTTP/1.1
    Host: fakeservices.datajoint.io
    Accept: application/json

    {
        "databaseAddress": "tutorial-db.datajoint.io",
        "username": "user1",
        "password": "password1"
    }
    ```

    ### Example successful response:

    ```http
    HTTP/1.1 200 OK
    Vary: Accept
    Content-Type: application/json

    {
        "jwt": "<token>"
    }
    ```

    ### Example unexpected response:

    ```http
    HTTP/1.1 500 Internal Server Error
    Vary: Accept
    Content-Type: text/plain

    400 Bad Request: The browser (or proxy) sent a request that this server could not
        understand.
    ```

    #### Response Headers
    * Content-Type: text/plain, application/json

    #### Status Codes
    * 200 OK: No error.
    * 500 Internal Server Error: Unexpected error encountered.
        Returns the error message as a string.
    """
    if request.method == "POST":
        # Try to login in with the database connection info, if true then create jwt key
        try:
            if "database_host" in request.args:
                # Oidc token exchange

                body = {
                    "grant_type": "authorization_code",
                    "code": request.args["code"],
                    "code_verifier": environ.get("PHARUS_OIDC_CODE_VERIFIER"),
                    "client_id": environ.get("PHARUS_OIDC_CLIENT_ID"),
                    "redirect_uri": environ.get("PHARUS_OIDC_REDIRECT_URI"),
                }
                headers = {
                    "Content-Type": "application/x-www-form-urlencoded",
                }
                auth = HTTPBasicAuth(
                    environ.get("PHARUS_OIDC_CLIENT_ID"),
                    environ.get("PHARUS_OIDC_CLIENT_SECRET"),
                )
                result = requests.post(
                    environ.get("PHARUS_OIDC_TOKEN_URL"),
                    data=body,
                    headers=headers,
                    auth=auth,
                )
                auth_info = dict(
                    jwt=result.json()["access_token"], id=result.json()["id_token"]
                )
                time.sleep(1)
                connect_creds = {
                    "databaseAddress": request.args["database_host"],
                    "username": jwt.decode(
                        auth_info["jwt"],
                        crypto_serialization.load_der_public_key(
                            b64decode(environ.get("PHARUS_OIDC_PUBLIC_KEY").encode())
                        ),
                        algorithms="RS256",
                        options=dict(verify_aud=False),
                    )[environ.get("PHARUS_OIDC_SUBJECT_KEY")],
                    "password": auth_info["jwt"],
                }
            else:  # Database login
                # Generate JWT key and send it back
                auth_info = dict(
                    jwt=jwt.encode(
                        request.json, environ["PHARUS_PRIVATE_KEY"], algorithm="RS256"
                    )
                )
                connect_creds = request.json
            if connect_creds.keys() < {"databaseAddress", "username", "password"}:
                return dict(error="Invalid Request, check headers and/or json body")
            try:
                dj.Connection(
                    host=connect_creds["databaseAddress"],
                    user=connect_creds["username"],
                    password=connect_creds["password"],
                )
            except pymysql.err.OperationalError as e:
                if (
                    (root_host := environ.get("DJ_HOST"))
                    and (root_user := environ.get("DJ_ROOT_USER"))
                    and (root_password := environ.get("DJ_ROOT_PASS"))
                ):
                    dj.Connection(
                        host=root_host,
                        user=root_user,
                        password=root_password,
                    ).query("FLUSH PRIVILEGES")
                    dj.Connection(
                        host=connect_creds["databaseAddress"],
                        user=connect_creds["username"],
                        password=connect_creds["password"],
                    )
                else:
                    raise e
            return dict(**auth_info)
        except Exception:
            return traceback.format_exc(), 500

schema(connection)

Handler for /schema route.

Parameters:

Name Type Description Default
connection Connection

User's DataJoint connection object

 required

Returns:

Type Description
dict

If successful, then sends back a list of schema names; otherwise, returns an error.

GET /schema

Route to get a list of schemas.

Example request:
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GET /schema HTTP/1.1
Host: fakeservices.datajoint.io
Authorization: Bearer <token>
Example successful response:
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HTTP/1.1 200 OK
Vary: Accept
Content-Type: application/json

{
    "schemaNames": [
        "alpha_company"
    ]
}
Example unexpected response:
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HTTP/1.1 500 Internal Server Error
Vary: Accept
Content-Type: text/plain

400 Bad Request: The browser (or proxy) sent a request that this server could not
    understand.
Request Headers
  • Authorization: Bearer <OAuth2_token>
Response Headers
  • Content-Type: text/plain, application/json
Status Codes
  • 200 OK: No error.
  • 500 Internal Server Error: Unexpected error encountered. Returns the error message as a string.
Source code in pharus/server.py 
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@app.route(f"{environ.get('PHARUS_PREFIX', '')}/schema", methods=["GET"])
@protected_route
def schema(connection: dj.Connection) -> dict:
    """
    Handler for ``/schema`` route.

    Args:
        connection (dj.Connection): User's DataJoint connection object

    Returns:
        If successful, then sends back a list of schema names; otherwise, returns an error.

    ## GET /schema

    Route to get a list of schemas.

    ### Example request:

    ```http
    GET /schema HTTP/1.1
    Host: fakeservices.datajoint.io
    Authorization: Bearer <token>
    ```

    ### Example successful response:

    ```http
    HTTP/1.1 200 OK
    Vary: Accept
    Content-Type: application/json

    {
        "schemaNames": [
            "alpha_company"
        ]
    }
    ```

    ### Example unexpected response:

    ```http
    HTTP/1.1 500 Internal Server Error
    Vary: Accept
    Content-Type: text/plain

    400 Bad Request: The browser (or proxy) sent a request that this server could not
        understand.
    ```

    #### Request Headers
    * Authorization: Bearer <OAuth2_token\>

    #### Response Headers
    * Content-Type: text/plain, application/json

    #### Status Codes
    * 200 OK: No error.
    * 500 Internal Server Error: Unexpected error encountered.
        Returns the error message as a string.
    """

    if request.method in {"GET", "HEAD"}:
        # Get all the schemas
        try:
            schemas_name = _DJConnector._list_schemas(connection)
            return dict(schemaNames=schemas_name)
        except Exception:
            return traceback.format_exc(), 500

table(connection, schema_name)

Handler for /schema/{schema_name}/table route.

Parameters:

Name Type Description Default
connection Connection

User's DataJoint connection object

 required
schema_name str

Schema name.

 required

Returns:

Type Description
dict

If successful, then sends back a list of table names; otherwise, returns an error.

GET /schema/{schema_name}/table

Route to get tables within a schema.

Example request:
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GET /schema/alpha_company/table HTTP/1.1
Host: fakeservices.datajoint.io
Authorization: Bearer <token>
Example successful response:
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HTTP/1.1 200 OK
Vary: Accept
Content-Type: application/json

{
    "tableTypes": {
        "computed": [],
        "imported": [],
        "lookup": [
            "Employee"
        ],
        "manual": [
            "Computer"
        ],
        "part": []
    }
}
Example unexpected response:
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HTTP/1.1 500 Internal Server Error
Vary: Accept
Content-Type: text/plain

400 Bad Request: The browser (or proxy) sent a request that this server could not
    understand.
Query Parameters
  • schema_name: Schema name.
Request Headers
  • Authorization: Bearer <OAuth2_token>
Response Headers
  • Content-Type: text/plain, application/json
Status Codes
  • 200 OK: No error.
  • 500 Internal Server Error: Unexpected error encountered. Returns the error message as a string.
Source code in pharus/server.py 
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@app.route(
    f"{environ.get('PHARUS_PREFIX', '')}/schema/<schema_name>/table", methods=["GET"]
)
@protected_route
def table(
    connection: dj.Connection,
    schema_name: str,
) -> dict:
    """
    Handler for ``/schema/{schema_name}/table`` route.

    Args:
        connection (dj.Connection): User's DataJoint connection object
        schema_name (str): Schema name.

    Returns:
        If successful, then sends back a list of table names; otherwise, returns an error.

    ## GET /schema/{schema_name}/table

    Route to get tables within a schema.

    ### Example request:

    ```http
    GET /schema/alpha_company/table HTTP/1.1
    Host: fakeservices.datajoint.io
    Authorization: Bearer <token>
    ```

    ### Example successful response:

    ```http
    HTTP/1.1 200 OK
    Vary: Accept
    Content-Type: application/json

    {
        "tableTypes": {
            "computed": [],
            "imported": [],
            "lookup": [
                "Employee"
            ],
            "manual": [
                "Computer"
            ],
            "part": []
        }
    }
    ```

    ### Example unexpected response:

    ```http
    HTTP/1.1 500 Internal Server Error
    Vary: Accept
    Content-Type: text/plain

    400 Bad Request: The browser (or proxy) sent a request that this server could not
        understand.
    ```

    #### Query Parameters
    * schema_name: Schema name.

    #### Request Headers
    * Authorization: Bearer <OAuth2_token\>

    #### Response Headers
    * Content-Type: text/plain, application/json

    #### Status Codes
    * 200 OK: No error.
    * 500 Internal Server Error: Unexpected error encountered.
        Returns the error message as a string.
    """
    if request.method in {"GET", "HEAD"}:
        try:
            tables_dict_list = _DJConnector._list_tables(connection, schema_name)
            return dict(tableTypes=tables_dict_list)
        except Exception:
            return traceback.format_exc(), 500

record(connection, schema_name, table_name)

Handler for /schema/{schema_name}/table/{table_name}/record route.

Parameters:

Name Type Description Default
connection Connection

User's DataJoint connection object

 required
schema_name str

Schema name.

 required
table_name str

Table name.

 required

Returns:

Type Description
Union[dict, str, tuple]

If successful, then sends back the desired operation based on the HTTP method; otherwise, returns an error.

GET /schema/{schema_name}/table/{table_name}/record

Route to fetch records.

Example request:
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GET /schema/alpha_company/table/Computer/record?limit=1&page=2&order=computer_id%20DESC&
    restriction=W3siYXR0cmlidXRlTmFtZSI6ICJjb21wdXRlcl9tZW1vcnkiLCAib3BlcmF0aW9uIjogIj49I
    iwgInZhbHVlIjogMTZ9XQo= HTTP/1.1
Host: fakeservices.datajoint.io
Authorization: Bearer <token>
Example successful response:
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HTTP/1.1 200 OK
Vary: Accept
Content-Type: application/json

{
    "recordHeader": [
        "computer_id",
        "computer_serial",
        "computer_brand",
        "computer_built",
        "computer_processor",
        "computer_memory",
        "computer_weight",
        "computer_cost",
        "computer_preowned",
        "computer_purchased",
        "computer_updates",
        "computer_accessories"
    ],
    "records": [
        [
            "4e41491a-86d5-4af7-a013-89bde75528bd",
            "DJS1JA17G",
            "Dell",
            1590364800,
            2.2,
            16,
            4.4,
            "700.99",
            0,
            1603181061,
            null,
            "=BLOB="
        ]
    ],
    "totalCount": 2
}
Example unexpected response:
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HTTP/1.1 500 Internal Server Error
Vary: Accept
Content-Type: text/plain

400 Bad Request: The browser (or proxy) sent a request that this server could
    not understand.
Query Parameters
  • schema_name: Schema name.
  • table_name: Table name.
  • limit: Limit of how many records per page. Defaults to 1000.
  • page: Page requested. Defaults to 1.
  • order: Sort order. Defaults to KEY ASC.
  • restriction: Base64-encoded AND sequence of restrictions. For example, you could restrict as [{"attributeName": "computer_memory", "operation": ">=", "value": 16}] with this param set as W3siYXR0cmlidXRlTmFtZSI6ICJjb21wdXRlcl9tZW1vcnkiLCAib3BlcmF0a W9uIjogIj49IiwgInZhbHVlIjogMTZ9XQo=. Defaults to no restriction.
Request Headers
  • Authorization: Bearer <OAuth2_token>
Response Headers
  • Content-Type: text/plain, application/json
Status Codes
  • 200 OK: No error.
  • 500 Internal Server Error: Unexpected error encountered. Returns the error message as a string.

POST /schema/{schema_name}/table/{table_name}/record

Route to insert a record. Omitted attributes utilize the default if set.

Example request:
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POST /schema/alpha_company/table/Computer/record HTTP/1.1
Host: fakeservices.datajoint.io
Accept: application/json
Authorization: Bearer <token>

{
    "records": [
        {
            "computer_id": "ffffffff-86d5-4af7-a013-89bde75528bd",
            "computer_serial": "ZYXWVEISJ",
            "computer_brand": "HP",
            "computer_built": "2021-01-01",
            "computer_processor": 2.7,
            "computer_memory": 32,
            "computer_weight": 3.7,
            "computer_cost": 599.99,
            "computer_preowned": 0,
            "computer_purchased": "2021-02-01 13:00:00",
            "computer_updates": 0
        }
    ]
}
Example successful response:
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HTTP/1.1 200 OK
Vary: Accept
Content-Type: text/plain

{
    "response": "Insert Successful"
}
Example unexpected response:
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HTTP/1.1 500 Internal Server Error
Vary: Accept
Content-Type: text/plain

400 Bad Request: The browser (or proxy) sent a request that this server could
    not understand.
Request Headers
  • Authorization: Bearer <OAuth2_token>
Response Headers
  • Content-Type: text/plain
Status Codes
  • 200 OK: No error.
  • 500 Internal Server Error: Unexpected error encountered. Returns the error message as a string.

PATCH /schema/{schema_name}/table/{table_name}/record

Route to update a record. Omitted attributes utilize the default if set.

Example request:
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PATCH /schema/alpha_company/table/Computer/record HTTP/1.1
Host: fakeservices.datajoint.io
Accept: application/json
Authorization: Bearer <token>

{
    "records": [
        {
            "computer_id": "ffffffff-86d5-4af7-a013-89bde75528bd",
            "computer_serial": "ZYXWVEISJ",
            "computer_brand": "HP",
            "computer_built": "2021-01-01",
            "computer_processor": 2.7,
            "computer_memory": 32,
            "computer_weight": 3.7,
            "computer_cost": 601.01,
            "computer_preowned": 0,
            "computer_purchased": "2021-02-01 13:00:00",
            "computer_updates": 0
        }
    ]
}
Example successful response:
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HTTP/1.1 200 OK
Vary: Accept
Content-Type: text/plain

{
    "response": "Update Successful"
}
Example unexpected response:
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HTTP/1.1 500 Internal Server Error
Vary: Accept
Content-Type: text/plain

400 Bad Request: The browser (or proxy) sent a request that this server could
    not understand.
Request Headers
  • Authorization: Bearer <OAuth2_token>
Response Headers
  • Content-Type: text/plain
Status Codes
  • 200 OK: No error.
  • 500 Internal Server Error: Unexpected error encountered. Returns the error message as a string.

DELETE /schema/{schema_name}/table/{table_name}/record

Route to delete a specific record.

Example request:
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DELETE /schema/alpha_company/table/Computer/record?cascade=false&restriction=
    W3siYXR0cmlidXRlTmFtZSI6ICJjb21wdXRlcl9tZW1vcnkiLCAib3BlcmF0aW9uIjogIj49IiwgInZhbHVlI
    jogMTZ9XQo= HTTP/1.1
Host: fakeservices.datajoint.io
Authorization: Bearer <token>
Example successful response:
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HTTP/1.1 200 OK
Vary: Accept
Content-Type: text/plain

{
    "response": "Delete Successful"
}
Example conflict response:
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HTTP/1.1 409 Conflict
Vary: Accept
Content-Type: application/json

{
    "error": "IntegrityError",
    "error_msg": "Cannot delete or update a parent row: a foreign key
        constraint fails (`alpha_company`.`#employee`, CONSTRAINT
        `#employee_ibfk_1` FOREIGN KEY (`computer_id`) REFERENCES `computer`
        (`computer_id`) ON DELETE RESTRICT ON UPDATE CASCADE",
    "child_schema": "alpha_company",
    "child_table": "Employee"
}
Example unexpected response:
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HTTP/1.1 500 Internal Server Error
Vary: Accept
Content-Type: text/plain

400 Bad Request: The browser (or proxy) sent a request that this server could
    not understand.
Query Parameters
  • cascade: Enable cascading delete. Accepts true or false. Defaults to false.
  • restriction: Base64-encoded AND sequence of restrictions. For example, you could restrict as [{"attributeName": "computer_memory", "operation": ">=", "value": 16}] with this param set as W3siYXR0cmlidXRlTmFtZSI6ICJjb21wdXRlcl9tZW1vcnkiLCAib3BlcmF0aW9uIjogIj49 IiwgInZhbHVlIjogMTZ9XQo=. Defaults to no restriction.
Request Headers
  • Authorization: Bearer <OAuth2_token>
Response Headers
  • Content-Type: text/plain, application/json
Status Codes
  • 200 OK: No error.
  • 409 Conflict: Attempting to delete a record with dependents while cascade set to false.
  • 500 Internal Server Error: Unexpected error encountered. Returns the error message as a string.
Source code in pharus/server.py 
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@app.route(
    f"{environ.get('PHARUS_PREFIX', '')}/schema/<schema_name>/table/<table_name>/record",
    methods=["GET", "POST", "PATCH", "DELETE"],
)
@protected_route
def record(
    connection: dj.Connection,
    schema_name: str,
    table_name: str,
) -> Union[dict, str, tuple]:
    (
        """
    Handler for ``/schema/{schema_name}/table/{table_name}/record`` route.

    Args:
        connection (dj.Connection): User's DataJoint connection object
        schema_name (str): Schema name.
        table_name (str): Table name.

    Returns:
        If successful, then sends back the desired operation based on the HTTP method;
            otherwise, returns an error.

    ## GET /schema/{schema_name}/table/{table_name}/record

    Route to fetch records.

    ### Example request:

    ```http
    GET /schema/alpha_company/table/Computer/record?limit=1&page=2&order=computer_id%20DESC&
        restriction=W3siYXR0cmlidXRlTmFtZSI6ICJjb21wdXRlcl9tZW1vcnkiLCAib3BlcmF0aW9uIjogIj49I
        iwgInZhbHVlIjogMTZ9XQo= HTTP/1.1
    Host: fakeservices.datajoint.io
    Authorization: Bearer <token>
    ```

    ### Example successful response:

    ```http
    HTTP/1.1 200 OK
    Vary: Accept
    Content-Type: application/json

    {
        "recordHeader": [
            "computer_id",
            "computer_serial",
            "computer_brand",
            "computer_built",
            "computer_processor",
            "computer_memory",
            "computer_weight",
            "computer_cost",
            "computer_preowned",
            "computer_purchased",
            "computer_updates",
            "computer_accessories"
        ],
        "records": [
            [
                "4e41491a-86d5-4af7-a013-89bde75528bd",
                "DJS1JA17G",
                "Dell",
                1590364800,
                2.2,
                16,
                4.4,
                "700.99",
                0,
                1603181061,
                null,
                "=BLOB="
            ]
        ],
        "totalCount": 2
    }
    ```

    ### Example unexpected response:

    ```http
    HTTP/1.1 500 Internal Server Error
    Vary: Accept
    Content-Type: text/plain

    400 Bad Request: The browser (or proxy) sent a request that this server could
        not understand.
    ```

    #### Query Parameters
    * schema_name: Schema name.
    * table_name: Table name.
    * limit: Limit of how many records per page. Defaults to `1000`.
    * page: Page requested. Defaults to `1`.
    * order: Sort order. Defaults to `KEY ASC`.
    * restriction: Base64-encoded `AND` sequence of restrictions. For example, you could
        restrict as `[{"attributeName": "computer_memory", "operation": ">=", "value": 16}]`
        with this param set as `W3siYXR0cmlidXRlTmFtZSI6ICJjb21wdXRlcl9tZW1vcnkiLCAib3BlcmF0a
        W9uIjogIj49IiwgInZhbHVlIjogMTZ9XQo=`. Defaults to no restriction.

    #### Request Headers
    * Authorization: Bearer <OAuth2_token\>

    #### Response Headers
    * Content-Type: text/plain, application/json

    #### Status Codes
    * 200 OK: No error.
    * 500 Internal Server Error: Unexpected error encountered. Returns the error message as a
        string.

    ## POST /schema/{schema_name}/table/{table_name}/record

    Route to insert a record. Omitted attributes utilize the default if set.

    ### Example request:

    ```http
    POST /schema/alpha_company/table/Computer/record HTTP/1.1
    Host: fakeservices.datajoint.io
    Accept: application/json
    Authorization: Bearer <token>

    {
        "records": [
            {
                "computer_id": "ffffffff-86d5-4af7-a013-89bde75528bd",
                "computer_serial": "ZYXWVEISJ",
                "computer_brand": "HP",
                "computer_built": "2021-01-01",
                "computer_processor": 2.7,
                "computer_memory": 32,
                "computer_weight": 3.7,
                "computer_cost": 599.99,
                "computer_preowned": 0,
                "computer_purchased": "2021-02-01 13:00:00",
                "computer_updates": 0
            }
        ]
    }
    ```

    ### Example successful response:

    ```http
    HTTP/1.1 200 OK
    Vary: Accept
    Content-Type: text/plain

    {
        "response": "Insert Successful"
    }
    ```

    ### Example unexpected response:

    ```http
    HTTP/1.1 500 Internal Server Error
    Vary: Accept
    Content-Type: text/plain

    400 Bad Request: The browser (or proxy) sent a request that this server could
        not understand.
    ```

    #### Request Headers
    * Authorization: Bearer <OAuth2_token\>

    #### Response Headers
    * Content-Type: text/plain

    #### Status Codes
    * 200 OK: No error.
    * 500 Internal Server Error: Unexpected error encountered. Returns the error message as a
        string.

    ## PATCH /schema/{schema_name}/table/{table_name}/record

    Route to update a record. Omitted attributes utilize the default if set.

    ### Example request:

    ```http
    PATCH /schema/alpha_company/table/Computer/record HTTP/1.1
    Host: fakeservices.datajoint.io
    Accept: application/json
    Authorization: Bearer <token>

    {
        "records": [
            {
                "computer_id": "ffffffff-86d5-4af7-a013-89bde75528bd",
                "computer_serial": "ZYXWVEISJ",
                "computer_brand": "HP",
                "computer_built": "2021-01-01",
                "computer_processor": 2.7,
                "computer_memory": 32,
                "computer_weight": 3.7,
                "computer_cost": 601.01,
                "computer_preowned": 0,
                "computer_purchased": "2021-02-01 13:00:00",
                "computer_updates": 0
            }
        ]
    }
    ```

    ### Example successful response:

    ```http
    HTTP/1.1 200 OK
    Vary: Accept
    Content-Type: text/plain

    {
        "response": "Update Successful"
    }
    ```

    ### Example unexpected response:

    ```http
    HTTP/1.1 500 Internal Server Error
    Vary: Accept
    Content-Type: text/plain

    400 Bad Request: The browser (or proxy) sent a request that this server could
        not understand.
    ```

    #### Request Headers
    * Authorization: Bearer <OAuth2_token\>

    #### Response Headers
    * Content-Type: text/plain

    #### Status Codes
    * 200 OK: No error.
    * 500 Internal Server Error: Unexpected error encountered. Returns the error message as a
        string.

    ## DELETE /schema/{schema_name}/table/{table_name}/record

    Route to delete a specific record.

    ### Example request:

    ```http
    DELETE /schema/alpha_company/table/Computer/record?cascade=false&restriction=
        W3siYXR0cmlidXRlTmFtZSI6ICJjb21wdXRlcl9tZW1vcnkiLCAib3BlcmF0aW9uIjogIj49IiwgInZhbHVlI
        jogMTZ9XQo= HTTP/1.1
    Host: fakeservices.datajoint.io
    Authorization: Bearer <token>
    ```

    ### Example successful response:

    ```http
    HTTP/1.1 200 OK
    Vary: Accept
    Content-Type: text/plain

    {
        "response": "Delete Successful"
    }
    ```

    ### Example conflict response:

    ```http
    HTTP/1.1 409 Conflict
    Vary: Accept
    Content-Type: application/json

    {
        "error": "IntegrityError",
        "error_msg": "Cannot delete or update a parent row: a foreign key
            constraint fails (`alpha_company`.`#employee`, CONSTRAINT
            `#employee_ibfk_1` FOREIGN KEY (`computer_id`) REFERENCES `computer`
            (`computer_id`) ON DELETE RESTRICT ON UPDATE CASCADE",
        "child_schema": "alpha_company",
        "child_table": "Employee"
    }
    ```

    ### Example unexpected response:

    ```http
    HTTP/1.1 500 Internal Server Error
    Vary: Accept
    Content-Type: text/plain

    400 Bad Request: The browser (or proxy) sent a request that this server could
        not understand.
    ```

    #### Query Parameters
    * cascade: Enable cascading delete. Accepts ``true`` or ``false``. Defaults to
        ``false``.
    * restriction: Base64-encoded ``AND`` sequence of restrictions. For example,
        you could restrict as ``[{"attributeName": "computer_memory", "operation": ">=",
        "value": 16}]`` with this param set as
        ``W3siYXR0cmlidXRlTmFtZSI6ICJjb21wdXRlcl9tZW1vcnkiLCAib3BlcmF0aW9uIjogIj49
        IiwgInZhbHVlIjogMTZ9XQo=``. Defaults to no restriction.

    #### Request Headers
    * Authorization: Bearer <OAuth2_token\>

    #### Response Headers
    * Content-Type: text/plain, application/json

    #### Status Codes
    * 200 OK: No error.
    * 409 Conflict: Attempting to delete a record with dependents while ``cascade``
        set to ``false``.
    * 500 Internal Server Error: Unexpected error encountered. Returns the error message as a
        string.

    """
    )
    if request.method in {"GET", "HEAD"}:
        try:
            schema_virtual_module = dj.VirtualModule(
                schema_name, schema_name, connection=connection
            )

            # Get table object from name
            dj_table = _DJConnector._get_table_object(schema_virtual_module, table_name)

            record_header, table_tuples, total_count = _DJConnector._fetch_records(
                query=dj_table,
                **{
                    k: int(v) for k, v in request.args.items() if k in ("limit", "page")
                },
                **{
                    k: loads(b64decode(v.encode("utf-8")).decode("utf-8"))
                    for k, v in request.args.items()
                    if k == "restriction"
                },
                **{k: v.split(",") for k, v in request.args.items() if k == "order"},
            )
            return dict(
                recordHeader=record_header, records=table_tuples, totalCount=total_count
            )
        except Exception:
            return traceback.format_exc(), 500
    elif request.method == "POST":
        try:
            _DJConnector._insert_tuple(
                connection, schema_name, table_name, request.json["records"]
            )
            return {"response": "Insert Successful"}
        except Exception:
            return traceback.format_exc(), 500
    elif request.method == "PATCH":
        try:
            _DJConnector._update_tuple(
                connection, schema_name, table_name, request.json["records"]
            )
            return {"response": "Update Successful"}
        except Exception:
            return traceback.format_exc(), 500
    elif request.method == "DELETE":
        try:
            _DJConnector._delete_records(
                connection,
                schema_name,
                table_name,
                **{
                    k: loads(b64decode(v.encode("utf-8")).decode("utf-8"))
                    for k, v in request.args.items()
                    if k == "restriction"
                },
                **{
                    k: v.lower() == "true"
                    for k, v in request.args.items()
                    if k == "cascade"
                },
            )
            return {"response": "Delete Successful"}
        except IntegrityError as e:
            match = foreign_key_error_regexp.match(e.args[0])
            return (
                dict(
                    error=e.__class__.__name__,
                    errorMessage=str(e),
                    childSchema=match.group("child").split(".")[0][1:-1],
                    childTable=to_camel_case(match.group("child").split(".")[1][1:-1]),
                ),
                409,
            )
        except Exception:
            return traceback.format_exc(), 500

definition(connection, schema_name, table_name)

Handler for /schema/{schema_name}/table/{table_name}/definition route.

Parameters:

Name Type Description Default
connection Connection

User's DataJoint connection object

 required
schema_name str

Schema name.

 required
table_name str

Table name.

 required

Returns:

Type Description
str

If successful, then sends back the definition for the table; otherwise, returns an error.

GET /schema/{schema_name}/table/{table_name}/definition

Route to get DataJoint table definition.

Example request:
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GET /schema/alpha_company/table/Computer/definition HTTP/1.1
Host: fakeservices.datajoint.io
Authorization: Bearer <token>
Example successful response:
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HTTP/1.1 200 OK
Vary: Accept
Content-Type: text/plain

# Computers that belong to the company
computer_id          : uuid                      # unique id
---
computer_serial="ABC101" : varchar(9)            # manufacturer serial number
computer_brand       : enum('HP','Dell')         # manufacturer brand
computer_built       : date                      # manufactured date
computer_processor   : double                    # processing power in GHz
computer_memory      : int                       # RAM in GB
computer_weight      : float                     # weight in lbs
computer_cost        : decimal(6,2)              # purchased price
computer_preowned    : tinyint                   # purchased as new or used
computer_purchased   : datetime                  # purchased date and time
computer_updates=null : time                     # scheduled daily update timeslot
computer_accessories=null : longblob             # included additional accessories
Example unexpected response:
1
2
3
4
5
6
HTTP/1.1 500 Internal Server Error
Vary: Accept
Content-Type: text/plain

400 Bad Request: The browser (or proxy) sent a request that this server could not
    understand.
Request Headers
  • Authorization: Bearer <OAuth2_token>
Response Headers
  • Content-Type: text/plain
Status Codes
  • 200 OK: No error.
  • 500 Internal Server Error: Unexpected error encountered. Returns the error message as a string.
Source code in pharus/server.py 
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@app.route(
    f"{environ.get('PHARUS_PREFIX', '')}/schema/<schema_name>/table/<table_name>/definition",
    methods=["GET"],
)
@protected_route
def definition(
    connection: dj.Connection,
    schema_name: str,
    table_name: str,
) -> str:
    """
    Handler for ``/schema/{schema_name}/table/{table_name}/definition`` route.

    Args:
        connection (dj.Connection): User's DataJoint connection object
        schema_name (str): Schema name.
        table_name (str): Table name.

    Returns:
        If successful, then sends back the definition for the table; otherwise,
            returns an error.

    ## GET /schema/{schema_name}/table/{table_name}/definition

    Route to get DataJoint table definition.

    ### Example request:

    ```http
    GET /schema/alpha_company/table/Computer/definition HTTP/1.1
    Host: fakeservices.datajoint.io
    Authorization: Bearer <token>
    ```

    ### Example successful response:

    ```http
    HTTP/1.1 200 OK
    Vary: Accept
    Content-Type: text/plain

    # Computers that belong to the company
    computer_id          : uuid                      # unique id
    ---
    computer_serial="ABC101" : varchar(9)            # manufacturer serial number
    computer_brand       : enum('HP','Dell')         # manufacturer brand
    computer_built       : date                      # manufactured date
    computer_processor   : double                    # processing power in GHz
    computer_memory      : int                       # RAM in GB
    computer_weight      : float                     # weight in lbs
    computer_cost        : decimal(6,2)              # purchased price
    computer_preowned    : tinyint                   # purchased as new or used
    computer_purchased   : datetime                  # purchased date and time
    computer_updates=null : time                     # scheduled daily update timeslot
    computer_accessories=null : longblob             # included additional accessories
    ```

    ### Example unexpected response:

    ```http
    HTTP/1.1 500 Internal Server Error
    Vary: Accept
    Content-Type: text/plain

    400 Bad Request: The browser (or proxy) sent a request that this server could not
        understand.
    ```

    #### Request Headers
    * Authorization: Bearer <OAuth2_token\>

    #### Response Headers
    * Content-Type: text/plain

    #### Status Codes
    * 200 OK: No error.
    * 500 Internal Server Error: Unexpected error encountered. Returns the error message as a
        string.
    """

    if request.method in {"GET", "HEAD"}:
        try:
            table_definition = _DJConnector._get_table_definition(
                connection, schema_name, table_name
            )
            return table_definition
        except Exception:
            return traceback.format_exc(), 500

attribute(connection, schema_name, table_name)

Handler for /schema/{schema_name}/table/{table_name}/attribute route.

Parameters:

Name Type Description Default
connection Connection

User's DataJoint connection object

 required
schema_name str

Schema name.

 required
table_name str

Table name.

 required

Returns:

Type Description
dict

If successful, then sends back a dictionary of table attributes; otherwise, returns an error.

GET /schema/{schema_name}/table/{table_name}/attribute

Route to get metadata on table attributes.

Example request:
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GET /schema/alpha_company/table/Computer/attribute HTTP/1.1
Host: fakeservices.datajoint.io
Authorization: Bearer <token>
Example successful response:
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HTTP/1.1 200 OK
Vary: Accept
Content-Type: application/json

{
    "attributeHeader": [
        "name",
        "type",
        "nullable",
        "default",
        "autoincrement"
    ],
    "attributes": {
        "primary": [
            [
                "computer_id",
                "uuid",
                false,
                null,
                false
            ]
        ],
        "secondary": [
            [
                "computer_serial",
                "varchar(9)",
                false,
                ""ABC101"",
                false
            ],
            [
                "computer_brand",
                "enum('HP','Dell')",
                false,
                null,
                false
            ],
            [
                "computer_built",
                "date",
                false,
                null,
                false
            ],
            [
                "computer_processor",
                "double",
                false,
                null,
                false
            ],
            [
                "computer_memory",
                "int",
                false,
                null,
                false
            ],
            [
                "computer_weight",
                "float",
                false,
                null,
                false
            ],
            [
                "computer_cost",
                "decimal(6,2)",
                false,
                null,
                false
            ],
            [
                "computer_preowned",
                "tinyint",
                false,
                null,
                false
            ],
            [
                "computer_purchased",
                "datetime",
                false,
                null,
                false
            ],
            [
                "computer_updates",
                "time",
                true,
                "null",
                false
            ],
            [
                "computer_accessories",
                "longblob",
                true,
                "null",
                false
            ]
        ]
    }
}
Example unexpected response:
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HTTP/1.1 500 Internal Server Error
Vary: Accept
Content-Type: text/plain

400 Bad Request: The browser (or proxy) sent a request that this server could not
    understand.
Request Headers
  • Authorization: Bearer <OAuth2_token>
Response Headers
  • Content-Type: text/plain, application/json
Status Codes
  • 200 OK: No error.
  • 500 Internal Server Error: Unexpected error encountered. Returns the error message as a string.
Source code in pharus/server.py 
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@app.route(
    f"{environ.get('PHARUS_PREFIX', '')}/schema/<schema_name>/table/<table_name>/attribute",
    methods=["GET"],
)
@protected_route
def attribute(
    connection: dj.Connection,
    schema_name: str,
    table_name: str,
) -> dict:
    """
    Handler for ``/schema/{schema_name}/table/{table_name}/attribute`` route.

    Args:
        connection (dj.Connection): User's DataJoint connection object
        schema_name (str): Schema name.
        table_name (str): Table name.

    Returns:
        If successful, then sends back a dictionary of table attributes; otherwise,
            returns an error.

    ## GET /schema/{schema_name}/table/{table_name}/attribute

    Route to get metadata on table attributes.

    ### Example request:

    ```http
    GET /schema/alpha_company/table/Computer/attribute HTTP/1.1
    Host: fakeservices.datajoint.io
    Authorization: Bearer <token>
    ```

    ### Example successful response:

    ```http
    HTTP/1.1 200 OK
    Vary: Accept
    Content-Type: application/json

    {
        "attributeHeader": [
            "name",
            "type",
            "nullable",
            "default",
            "autoincrement"
        ],
        "attributes": {
            "primary": [
                [
                    "computer_id",
                    "uuid",
                    false,
                    null,
                    false
                ]
            ],
            "secondary": [
                [
                    "computer_serial",
                    "varchar(9)",
                    false,
                    ""ABC101"",
                    false
                ],
                [
                    "computer_brand",
                    "enum('HP','Dell')",
                    false,
                    null,
                    false
                ],
                [
                    "computer_built",
                    "date",
                    false,
                    null,
                    false
                ],
                [
                    "computer_processor",
                    "double",
                    false,
                    null,
                    false
                ],
                [
                    "computer_memory",
                    "int",
                    false,
                    null,
                    false
                ],
                [
                    "computer_weight",
                    "float",
                    false,
                    null,
                    false
                ],
                [
                    "computer_cost",
                    "decimal(6,2)",
                    false,
                    null,
                    false
                ],
                [
                    "computer_preowned",
                    "tinyint",
                    false,
                    null,
                    false
                ],
                [
                    "computer_purchased",
                    "datetime",
                    false,
                    null,
                    false
                ],
                [
                    "computer_updates",
                    "time",
                    true,
                    "null",
                    false
                ],
                [
                    "computer_accessories",
                    "longblob",
                    true,
                    "null",
                    false
                ]
            ]
        }
    }
    ```

    ### Example unexpected response:

    ```http
    HTTP/1.1 500 Internal Server Error
    Vary: Accept
    Content-Type: text/plain

    400 Bad Request: The browser (or proxy) sent a request that this server could not
        understand.
    ```

    #### Request Headers
    * Authorization: Bearer <OAuth2_token\>

    #### Response Headers
    * Content-Type: text/plain, application/json

    #### Status Codes
    * 200 OK: No error.
    * 500 Internal Server Error: Unexpected error encountered. Returns the error message as a
        string.
    """

    if request.method in {"GET", "HEAD"}:
        try:
            local_values = locals()
            local_values[schema_name] = dj.VirtualModule(
                schema_name, schema_name, connection=connection
            )

            # Get table object from name
            dj_table = _DJConnector._get_table_object(
                local_values[schema_name], table_name
            )

            attributes_meta = _DJConnector._get_attributes(dj_table)
            return dict(
                attributeHeaders=attributes_meta["attribute_headers"],
                attributes=attributes_meta["attributes"],
            )
        except Exception:
            return traceback.format_exc(), 500

dependency(connection, schema_name, table_name)

Handler for /schema/{schema_name}/table/{table_name}/dependency route.

Parameters:

Name Type Description Default
connection Connection

User's DataJoint connection object

 required
schema_name str

Schema name.

 required
table_name str

Table name.

 required

Returns:

Type Description
dict

If successful, then sends back a list of dependencies; otherwise, returns an error.

GET /schema/{schema_name}/table/{table_name}/dependency

Route to get the metadata in relation to the dependent records associated with a restricted subset of a table.

Example request:
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GET /schema/alpha_company/table/Computer/dependency?restriction=
    W3siYXR0cmlidXRlTmFtZSI6ICJjb21wdXRlcl9tZW1vcnkiLCAib3BlcmF0aW9uIjogIj49IiwgInZ=
    HTTP/1.1
Host: fakeservices.datajoint.io
Authorization: Bearer <token>
Example successful response:
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HTTP/1.1 200 OK
Vary: Accept
Content-Type: application/json

{
    "dependencies": [
        {
            "accessible": true,
            "count": 2,
            "schema": "alpha_company",
            "table": "computer"
        },
        {
            "accessible": true,
            "count": 2,
            "schema": "alpha_company",
            "table": "#employee"
        }
    ]
}
Example unexpected response:
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3
4
5
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HTTP/1.1 500 Internal Server Error
Vary: Accept
Content-Type: text/plain

400 Bad Request: The browser (or proxy) sent a request that this server could not
    understand.
Query Parameters
  • schema_name: Schema name.
  • table_name: Table name.
  • restriction: Base64-encoded AND sequence of restrictions. For example, you could restrict as [{"attributeName": "computer_memory", "operation": ">=", "value": 16}] with this param set as W3siYXR0cmlidXRlTmFtZSI6ICJjb21wdXRlcl9tZW1vcnkiLCAib3BlcmF0aW9uIjogIj49IiwgInZ=. Defaults to no restriction.
Request Headers
  • Authorization: Bearer <OAuth2_token>
Response Headers
  • Content-Type: text/plain, application/json
Status Codes
  • 200 OK: No error.
  • 500 Internal Server Error: Unexpected error encountered. Returns the error message as a string.
Source code in pharus/server.py 
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@app.route(
    f"{environ.get('PHARUS_PREFIX', '')}/schema/<schema_name>/table/<table_name>/dependency",
    methods=["GET"],
)
@protected_route
def dependency(
    connection: dj.Connection,
    schema_name: str,
    table_name: str,
) -> dict:
    (
        """
    Handler for ``/schema/{schema_name}/table/{table_name}/dependency`` route.

    Args:
        connection (dj.Connection): User's DataJoint connection object
        schema_name (str): Schema name.
        table_name (str): Table name.

    Returns:
        If successful, then sends back a list of dependencies; otherwise, returns an error.

    ## GET /schema/{schema_name}/table/{table_name}/dependency

    Route to get the metadata in relation to the dependent records associated with a
        restricted subset of a table.

    ### Example request:

    ```http
    GET /schema/alpha_company/table/Computer/dependency?restriction=
        W3siYXR0cmlidXRlTmFtZSI6ICJjb21wdXRlcl9tZW1vcnkiLCAib3BlcmF0aW9uIjogIj49IiwgInZ=
        HTTP/1.1
    Host: fakeservices.datajoint.io
    Authorization: Bearer <token>
    ```

    ### Example successful response:

    ```http
    HTTP/1.1 200 OK
    Vary: Accept
    Content-Type: application/json

    {
        "dependencies": [
            {
                "accessible": true,
                "count": 2,
                "schema": "alpha_company",
                "table": "computer"
            },
            {
                "accessible": true,
                "count": 2,
                "schema": "alpha_company",
                "table": "#employee"
            }
        ]
    }
    ```

    ### Example unexpected response:

    ```http
    HTTP/1.1 500 Internal Server Error
    Vary: Accept
    Content-Type: text/plain

    400 Bad Request: The browser (or proxy) sent a request that this server could not
        understand.
    ```

    #### Query Parameters
    * schema_name: Schema name.
    * table_name: Table name.
    * restriction: Base64-encoded ``AND`` sequence of restrictions. For example, you could
        restrict as ``[{"attributeName": "computer_memory", "operation": ">=", "value": 16}]``
        with this param set as
        ``W3siYXR0cmlidXRlTmFtZSI6ICJjb21wdXRlcl9tZW1vcnkiLCAib3BlcmF0aW9uIjogIj49IiwgInZ=``.
        Defaults to no restriction.

    #### Request Headers
    * Authorization: Bearer <OAuth2_token\>

    #### Response Headers
    * Content-Type: text/plain, application/json

    #### Status Codes
    * 200 OK: No error.
    * 500 Internal Server Error: Unexpected error encountered. Returns the error message as a
        string.
    """
    )
    if request.method in {"GET", "HEAD"}:
        # Get dependencies
        try:
            dependencies = _DJConnector._record_dependency(
                connection,
                schema_name,
                table_name,
                loads(
                    b64decode(request.args.get("restriction").encode("utf-8")).decode(
                        "utf-8"
                    )
                ),
            )
            return dict(dependencies=dependencies)
        except Exception:
            return traceback.format_exc(), 500

run()

Starts API server.

Source code in pharus/server.py 
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def run():
    """
    Starts API server.
    """
    app.run(host="0.0.0.0", port=environ.get("PHARUS_PORT", 5000), threaded=False)