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readstore-cli package

readstore module

Provides readstore command line interface

Functions:

Name Description
- configure_list

List configuration settings
- configure

Configure ReadStore CLI
- upload

Upload FASTQ Files
- import_fastq

Import FASTQ Files from Template
- upload_pro_data

Upload Processed Data
- list_fq_datasets

List Datasets
- list_projects

List Projects
- list_pro_data

List Processed Data
- get_fastq_dataset

Get Dataset
- get_project

Get Project
- get_pro_data

Get Processed Data
- create_fastq_dataset

Create Dataset
- create_project

Create Project
- update_fq_dataset

Update Dataset
- update_project

Update Project
- delete_pro_data

Delete Processed Data
- download_fq_dataset_attachment

Download Dataset Attachment
- download_project_attachment

Download Project Attachment
- main

Main function for ReadStore CLI

_get_readstore_client()

Get ReadStore RSClient

Load readstore configuration and generate client Requires READSTORE_CONFIG_FILE global Requires DEFAULT_ENDPOINT_URL Requires DEFAULT_FASTQ_EXTENSIONS Requires DEFAULT_OUTPUT

Raises:

Type Description
ReadStoreError

If no config is found in config file or ENV variables

Returns:

Type Description
RSClient

rsclient.RSClient
Source code in readstore_cli/readstore.py 
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def _get_readstore_client() -> rsclient.RSClient:
    """Get ReadStore RSClient

    Load readstore configuration and generate client
    Requires READSTORE_CONFIG_FILE global
    Requires DEFAULT_ENDPOINT_URL
    Requires DEFAULT_FASTQ_EXTENSIONS
    Requires DEFAULT_OUTPUT

    Raises:
        rsexceptions.ReadStoreError:
            If no config is found in config file or ENV variables

    Returns:
        rsclient.RSClient
    """

    if os.path.isfile(READSTORE_CONFIG_FILE):
        config_params = rsconfig.load_rs_config(filename=READSTORE_CONFIG_FILE)
    else:
        try:
            # Try to load default configuration and environment variables
            config_params = rsconfig.load_rs_config(
                default_endpoint_url=DEFAULT_ENDPOINT_URL,
                default_fastq_extensions=DEFAULT_FASTQ_EXTENSIONS,
                default_output=DEFAULT_OUTPUT,
            )

        except rsexceptions.ReadStoreError as e:
            raise rsexceptions.ReadStoreError(
                e.message + "\n No Configuration File and No ENV Variables Found"
            )

    username, token, endpoint_url, fastq_extensions, output = config_params

    client = rsclient.RSClient(username, token, endpoint_url, output)

    return client

_validate_read_path(fq_file_path)

Check fq_file path

Check if fastq file exists and can be read

Parameters:

Name Type Description Default
fq_file_path str

File to check

 required

Returns:

Name Type Description
bool bool

True if path is valid else False
Source code in readstore_cli/readstore.py 
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def _validate_read_path(fq_file_path: str) -> bool:
    """Check fq_file path

    Check if fastq file exists and can be read

    Args:
        fq_file_path: File to check

    Returns:
        bool: True if path is valid else False
    """

    # Check if file exists
    if not os.path.isfile(fq_file_path):
        sys.stderr.write(
            f"""ReadStore Warning:
            Upload Path of this FASTQ File could not be found: {fq_file_path}\n"""
        )
        return False
    # Check for read permission
    elif not os.access(fq_file_path, os.R_OK):
        sys.stderr.write(f"ReadStore Warning: No Read Permission: {fq_file_path}\n")
        return False
    else:
        return True

configure()

Configure CLI

Write config file for ReadStore CLI

Requires: READSTORE_CONFIG_FILE

Write config file to READSTORE_CONFIG_FILE

Source code in readstore_cli/readstore.py 
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def configure():
    """Configure CLI

    Write config file for ReadStore CLI

    Requires: READSTORE_CONFIG_FILE

    Write config file to READSTORE_CONFIG_FILE

    """

    print("Configuring ReadStore CLI")

    readstore_config_dir = os.path.dirname(READSTORE_CONFIG_FILE)

    os.makedirs(readstore_config_dir, exist_ok=True)

    username = input("ReadStore Username: ")
    token = input("ReadStore Token: ")
    output = input("Default Output Format (json, text, csv): ")

    if output not in OUTPUT_FORMATS:
        sys.stderr.write("ReadStore Error: Invalid Output Format.\n")
        return

    endpoint_url = DEFAULT_ENDPOINT_URL
    fastq_extensions = DEFAULT_FASTQ_EXTENSIONS
    write_config = True

    # Check if config exists, if so, ask to overwrite
    if os.path.isfile(READSTORE_CONFIG_FILE):

        try:
            config = rsconfig.load_rs_config(READSTORE_CONFIG_FILE)
            (
                username_old,
                token_old,
                endpoint_url_old,
                fastq_extensions_old,
                output_format_old,
            ) = config
            write_config = False
            print(f"Config file found at {READSTORE_CONFIG_FILE}")
            overwrite = input("Overwrite? (y/n): ")

            # If not overwrite, don't write config
            if overwrite.lower().strip() == "y":

                endpoint_url = endpoint_url_old
                fastq_extensions = fastq_extensions_old
                rsconfig.write_rs_config(
                    READSTORE_CONFIG_FILE,
                    username,
                    token,
                    endpoint_url,
                    fastq_extensions,
                    output,
                )
                print("Configuration File Updated")
            else:
                print("Abort Configuration")

        except rsexceptions.ReadStoreError:
            # If config file is invalid, overwrite anyway
            sys.stderr.write("Error Setting Configuration\n")

    if write_config:

        rsconfig.write_rs_config(
            READSTORE_CONFIG_FILE,
            username,
            token,
            endpoint_url,
            fastq_extensions,
            output,
        )
        print(f"Created New Configuration File at {READSTORE_CONFIG_FILE}")

configure_list()

List config settings

List user and general client configuration Print in console

Raises: rsexceptions.ReadStoreError

Source code in readstore_cli/readstore.py 
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def configure_list():
    """List config settings

    List user and general client configuration
    Print in console



    Raises: rsexceptions.ReadStoreError
    """

    print("Listing ReadStore Configuration and Credentials")

    if os.path.isfile(READSTORE_CONFIG_FILE):
        try:
            config_params = rsconfig.load_rs_config(READSTORE_CONFIG_FILE)
            username, token, endpoint_url, fastq_extensions, output = config_params

            # For token make last 4 characters visible
            token_hidden = "*" * (len(token) - 4) + token[-4:]

            print(f"Configuration File Found at {READSTORE_CONFIG_FILE}")

            print("[USER]")
            print(f"Username: {username}")
            print(f"Token: {token_hidden}")

            print("[GENERAL]")
            print(f"Endpoint URL: {endpoint_url}")
            print(f"""FASTQ Extensions: {fastq_extensions}""")
            print(f"""Default Output: {output}""")

        except rsexceptions.ReadStoreError as e:
            # If config file is invalid, overwrite anyway
            sys.stderr.write(e.message + "\n")
            sys.stderr.write(
                """Configuration Found, But Corrupted.\n
                             Reset Configuration with "readstore configure"\n"""
            )
    else:
        sys.stderr.write(
            """No Configuration Found.\n
                        Set Configuration with "readstore configure"\n"""
        )

download_fq_dataset_attachment(attachment_name, outpath, dataset_id=None, dataset_name=None)

Download Fastq Dataset Attachment

Parameters:

Name Type Description Default
attachment_name str

Choose attachment to download

 required
outpath str

Set outpath to write file to.

 required
dataset_id int | None

Set dataset id

 None
dataset_name str | None

Set dataset name

 None
Source code in readstore_cli/readstore.py 
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def download_fq_dataset_attachment(
    attachment_name: str,
    outpath: str,
    dataset_id: int | None = None,
    dataset_name: str | None = None,
):
    """Download Fastq Dataset Attachment

    Args:
        attachment_name: Choose attachment to download
        outpath: Set outpath to write file to.
        dataset_id: Set dataset id
        dataset_name: Set dataset name
    """

    if not dataset_id and not dataset_name:
        sys.stderr.write(
            "ReadStore Error: Must Provide Dataset ID (--id) or Name (--name)\n"
        )
        sys.stderr.write("ReadStore Error: Run readstore download -h for help\n")
        return

    # Get ReadStore Client and Validate Connection
    try:
        client = _get_readstore_client()
    except rsexceptions.ReadStoreError as e:
        sys.stderr.write(f"ReadStore Error: {e.message}\n")
        return

    outpath = os.path.abspath(outpath)
    out_dirname = os.path.dirname(outpath)

    # case directory path (e.g. '.' or /home/user/)
    if os.path.isdir(outpath):
        download_path = os.path.join(outpath, attachment_name)
    # case full path is provided, e.g. test.png or /home/user/test.png
    elif os.path.isdir(out_dirname):
        download_path = outpath
    else:
        sys.stderr.write(
            f"ReadStore Error: Output Directory Path Not Found: {outpath}\n"
        )
        return

    try:
        client.download_fq_dataset_attachment(
            attachment_name=attachment_name,
            outpath=download_path,
            dataset_id=dataset_id,
            dataset_name=dataset_name,
        )

        print(f"ReadStore Download: {attachment_name}\nDownloaded to {outpath}")

    except rsexceptions.ReadStoreError as e:
        sys.stderr.write(f"ReadStore Error: {e.message}\n")
        return

download_project_attachment(attachment_name, outpath, project_id=None, project_name=None)

Download Project Attachment

Download attachment file from project defined by project id or project name and download attachment_name

Either project_id and project_name are required

Parameters:

Name Type Description Default
attachment_name str

Choose attachment to download

 required
outpath str

Set outpath to write file to.

 required
project_id int | None

Set project id

 None
project_name str | None

Set project name

 None
Source code in readstore_cli/readstore.py 
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def download_project_attachment(
    attachment_name: str,
    outpath: str,
    project_id: int | None = None,
    project_name: str | None = None,
):
    """Download Project Attachment

    Download attachment file from project defined by project id
    or project name and download attachment_name

    Either project_id and project_name are required

    Args:
        attachment_name: Choose attachment to download
        outpath: Set outpath to write file to.
        project_id: Set project id
        project_name: Set project name
    """

    if not project_id and not project_name:
        sys.stderr.write(
            "ReadStore Error: Must Provide Project ID (--id) or Name (--name)\n"
        )
        sys.stderr.write(
            "ReadStore Error: Run readstore project download -h for help\n"
        )
        return

    # Get ReadStore Client and Validate Connection
    try:
        client = _get_readstore_client()
    except rsexceptions.ReadStoreError as e:
        sys.stderr.write(f"ReadStore Error: {e.message}\n")
        return

    outpath = os.path.abspath(outpath)
    out_dirname = os.path.dirname(outpath)

    # case directory path (e.g. '.' or /home/user/)
    if os.path.isdir(outpath):
        download_path = os.path.join(outpath, attachment_name)
    # case full path is provided, e.g. test.png or /home/user/test.png
    elif os.path.isdir(out_dirname):
        download_path = outpath
    else:
        sys.stderr.write(
            f"ReadStore Error: Output Directory Path Not Found: {outpath}\n"
        )
        return

    try:
        client.download_project_attachment(
            attachment_name=attachment_name,
            outpath=download_path,
            project_id=project_id,
            project_name=project_name,
        )

        print(f"ReadStore Download: {attachment_name}\nDownloaded to {outpath}")

    except rsexceptions.ReadStoreError as e:
        sys.stderr.write(f"ReadStore Error: {e.message}\n")
        return

get_fastq_dataset(dataset_id=None, dataset_name=None, meta=False, attachment=False, pro_data=False, read1=False, read2=False, index1=False, index2=False, read1_path=False, read2_path=False, index1_path=False, index2_path=False, output=None)

Get individual FASTQ dataset

Use arguments to filter and return specific data such as individual reads, metadata or read paths

Parameters:

Name Type Description Default
dataset_id int | None

Filter by Dataset Id. Defaults to None.

 None
dataset_name str | None

Filter by Dataset Name. Defaults to None.

 None
meta bool

Show only metadata.

 False
attachment bool

Show only attachments

 False
read1 bool

Show Read 1 data.

 False
read2 bool

Show Read 2 data.

 False
index1 bool

Show Index 1 data

 False
index2 bool

Show Index 2 data

 False
read1_path bool

Show Read 1 Path

 False
read2_path bool

Show Read 2 Path

 False
index1_path bool

Show Index 1 Path

 False
index2_path bool

Show Index 2 Path

 False
output str | None

Set output format. If none use default from config file

 None
Source code in readstore_cli/readstore.py 
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def get_fastq_dataset(
    dataset_id: int | None = None,
    dataset_name: str | None = None,
    meta: bool = False,
    attachment: bool = False,
    pro_data: bool = False,
    read1: bool = False,
    read2: bool = False,
    index1: bool = False,
    index2: bool = False,
    read1_path: bool = False,
    read2_path: bool = False,
    index1_path: bool = False,
    index2_path: bool = False,
    output: str | None = None,
):
    """Get individual FASTQ dataset

    Use arguments to filter and return specific data
    such as individual reads, metadata or read paths

    Args:
        dataset_id: Filter by Dataset Id. Defaults to None.
        dataset_name: Filter by Dataset Name. Defaults to None.
        meta: Show only metadata.
        attachment: Show only attachments
        read1: Show Read 1 data.
        read2: Show Read 2 data.
        index1: Show Index 1 data
        index2: Show Index 2 data
        read1_path: Show Read 1 Path
        read2_path: Show Read 2 Path
        index1_path: Show Index 1 Path
        index2_path: Show Index 2 Path
        output: Set output format. If none use default from config file
    """

    if not dataset_id and not dataset_name:
        sys.stderr.write(
            "ReadStore Error: Must Provide Dataset ID (--id) or Name (--name)\n"
        )
        sys.stderr.write("ReadStore Error: Run readstore get -h for help\n")
        return

    # Get ReadStore Client and Validate Connection
    try:
        client = _get_readstore_client()
    except rsexceptions.ReadStoreError as e:
        sys.stderr.write(f"ReadStore Error: {e.message}\n")
        return

    if output is None:
        output = client.get_output_format()

    try:
        fq_dataset = client.get_fastq_dataset(dataset_id, dataset_name)

        path = False

        # Check if dataset is empty
        if fq_dataset == {}:
            out_data = {}
        elif meta:
            out_data = fq_dataset.pop("metadata", {})
        elif attachment:
            out_data = fq_dataset.pop("attachments", {})
            out_data = {"name": out_data}
        elif pro_data:
            out_data = fq_dataset.pop("pro_data", {})
            out_data = {"pro_data": out_data}

        # Return individual read files
        elif read1:
            if fq_dataset["fq_file_r1"]:
                out_data = client.get_fq_file(fq_dataset["fq_file_r1"])
            else:
                out_data = {}
        elif read2:
            if fq_dataset["fq_file_r2"]:
                out_data = client.get_fq_file(fq_dataset["fq_file_r2"])
            else:
                out_data = {}
        elif index1:
            if fq_dataset["fq_file_i1"]:
                out_data = client.get_fq_file(fq_dataset["fq_file_i1"])
            else:
                out_data = {}
        elif index2:
            if fq_dataset["fq_file_i2"]:
                out_data = client.get_fq_file(fq_dataset["fq_file_i2"])
            else:
                out_data = {}
        elif read1_path:
            path = True
            if fq_dataset["fq_file_r1"]:
                out_data = client.get_fq_file_upload_path(fq_dataset["fq_file_r1"])
                _ = _validate_read_path(out_data)
            else:
                out_data = ""
        elif read2_path:
            path = True
            if fq_dataset["fq_file_r2"]:
                out_data = client.get_fq_file_upload_path(fq_dataset["fq_file_r2"])
                _ = _validate_read_path(out_data)
            else:
                out_data = ""
        elif index1_path:
            path = True
            if fq_dataset["fq_file_i1"]:
                out_data = client.get_fq_file_upload_path(fq_dataset["fq_file_i1"])
                _ = _validate_read_path(out_data)
            else:
                out_data = ""
        elif index2_path:
            path = True
            if fq_dataset["fq_file_i2"]:
                out_data = client.get_fq_file_upload_path(fq_dataset["fq_file_i2"])
                _ = _validate_read_path(out_data)
            else:
                out_data = ""
        # Return individual read files
        else:
            # Reformat so that all data is in one dict
            out_data = fq_dataset

        if output == "json":
            print(out_data)
        elif output == "text":
            if path:
                print(out_data)
            else:
                header = list(out_data.keys())
                header_str = " | ".join(header)
                print(header_str)

                if attachment:
                    values_str = "\n".join(out_data["name"])
                else:
                    values = [str(out_data[key]) for key in header]
                    values_str = " | ".join(values)
                print(values_str)
        elif output == "csv":
            if path:
                print(out_data)
            else:
                header = list(out_data.keys())
                header_str = ",".join(header)
                print(header_str)

                if attachment:
                    values_str = "\n".join(out_data["name"])
                else:
                    values = [str(out_data[key]) for key in header]
                    values_str = ",".join(values)
                print(values_str)
        else:
            sys.stderr.write("Output Format Not Supported\n")
            return

    except rsexceptions.ReadStoreError as e:
        sys.stderr.write(f"ReadStore Error: {e.message}\n")
        return

get_project(project_id=None, project_name=None, meta=False, attachment=False, output=None)

Get individual Project

Must define project id or name Options to show only meta and attachments

Parameters:

Name Type Description Default
project_id int | None

Set Project ID

 None
project_name str | None

Set Project Name

 None
meta bool

Show only meta data

 False
attachment bool

Show only attachments

 False
output str | None

Set output format. If none use default from config file

 None
Source code in readstore_cli/readstore.py 
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def get_project(
    project_id: int | None = None,
    project_name: str | None = None,
    meta: bool = False,
    attachment: bool = False,
    output: str | None = None,
):
    """Get individual Project

    Must define project id or name
    Options to show only meta and attachments

    Args:
        project_id: Set Project ID
        project_name: Set Project Name
        meta: Show only meta data
        attachment: Show only attachments
        output: Set output format. If none use default from config file
    """

    if not project_id and not project_name:
        sys.stderr.write(
            "ReadStore Error: Must Provide Project ID (--id) or Name (--name)\n"
        )
        sys.stderr.write("ReadStore Error: Run readstore project get -h for help\n")
        return

    # Get ReadStore Client and Validate Connection
    try:
        client = _get_readstore_client()
    except rsexceptions.ReadStoreError as e:
        sys.stderr.write(f"ReadStore Error: {e.message}\n")
        return

    if output is None:
        output = client.get_output_format()

    try:
        project = client.get_project(project_id, project_name)

        project.pop("dataset_metadata_keys", None)

        if meta:
            out_data = project.pop("metadata", {})
        elif attachment:
            out_data = project.pop("attachments", {})
            out_data = {"name": out_data}
        else:
            out_data = project

        if output == "json":
            print(out_data)
        elif output == "text":
            header = list(out_data.keys())
            header_str = " | ".join(header)
            print(header_str)

            if attachment:
                values_str = "\n".join(out_data["name"])
            else:
                values = [str(out_data[key]) for key in header]
                values_str = " | ".join(values)

            print(values_str)
        elif output == "csv":
            header = list(out_data.keys())
            header_str = ",".join(header)
            print(header_str)

            if attachment:
                values_str = "\n".join(out_data["name"])
            else:
                values = [str(out_data[key]) for key in header]
                values_str = ",".join(values)
            print(values_str)
        else:
            sys.stderr.write("Output Format Not Supported\n")
            return

    except rsexceptions.ReadStoreError as e:
        sys.stderr.write(f"ReadStore Error: {e.message}\n")
        return

import_fastq(fastq_template_csv)

Upload fastq files from template

Upload fastq files defined in template csv file Template csv file must have columns: FASTQFileName, ReadType, UploadPath

Parameters:

Name Type Description Default
fastq_template_csv str

Path to fastq template csv

 required

Raises:

Type Description
ReadStoreError

If file is not found or not a csv file
ReadStoreError

If upload path is not found
ReadStoreError

If invalid FASTQ extension
ReadStoreError

If invalid Read Type
Source code in readstore_cli/readstore.py 
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def import_fastq(fastq_template_csv: str):
    """Upload fastq files from template

    Upload fastq files defined in template csv file
    Template csv file must have columns:
    FASTQFileName, ReadType, UploadPath

    Args:
        fastq_template_csv (str): Path to fastq template csv

    Raises:
        rsexceptions.ReadStoreError: If file is not found or not a csv file
        rsecxeptions.ReadStoreError: If upload path is not found
        rsexceptions.ReadStoreError: If invalid FASTQ extension
        rsexceptions.ReadStoreError: If invalid Read Type
    """

    # Get ReadStore Client and Validate Connection
    try:
        client = _get_readstore_client()
    except rsexceptions.ReadStoreError as e:
        sys.stderr.write(f"ReadStore Error: {e.message}\n")
        return

    if not fastq_template_csv.endswith(".csv"):
        sys.stderr.write("ReadStore Error: File is not a .csv file\n")
        return

    if not os.path.isfile(fastq_template_csv):
        sys.stderr.write(f"ReadStore Error: File Not Found: {fastq_template_csv}\n")
        return

    fq_file_names = []
    read_types = []
    upload_paths = []

    with open(fastq_template_csv, "r") as f:
        header = False
        for line in f.readlines():
            line = line.rstrip("\n").split(",")
            if not header:
                header = line
                if not all(
                    e in ["FASTQFileName", "ReadType", "UploadPath"] for e in header
                ):
                    sys.stderr.write(
                        """ReadStore Error: Invalid Template Header.
                        Must be FASTQFileName,ReadType,UploadPath\n"""
                    )
                else:
                    header = True
            else:
                fq_file_name, read_type, upload_path = line

                if not _validate_read_path(upload_path):
                    sys.stderr.write(
                        f"\nReadStore Upload: File Not Found: {upload_path}\n"
                    )

                if not upload_path.endswith(tuple(DEFAULT_FASTQ_EXTENSIONS)):
                    sys.stderr.write(
                        f"\nReadStore Upload: Invalid FASTQ Extension: {upload_path}\n"
                    )

                if read_type not in ["R1", "R2", "I1", "I2"]:
                    sys.stderr.write(
                        f"ReadStore Error: Invalid Read Type for file: {upload_path}\n"
                    )

                if fq_file_name == "":
                    sys.stderr.write(
                        f"ReadStore Error: Invalid Read Type for file: {upload_path}\n"
                    )

                fq_file_names.append(fq_file_name)
                read_types.append(read_type)
                upload_paths.append(upload_path)

    for upload_path, fq_file_name, read_type in zip(
        upload_paths, fq_file_names, read_types
    ):
        print(f"ReadStore Upload: Start {fq_file_name}")
        try:
            client.upload_fastq(upload_path, fq_file_name, read_type)
        except rsexceptions.ReadStoreError as e:
            sys.stderr.write(f"ReadStore Error: {e.message}\n")

list_fq_datasets(project_name=None, project_id=None, role=None, meta=False, attachment=False, pro_data=False, output=None)

List Fastq Datasets

List all Fastq Datasets and Filter by Project Options to show only meta and attachments

Parameters:

Name Type Description Default
project_name str | None

Filter by Project Name

 None
project_id int | None

Filter by Project Id

 None
role str | None

Filter by Owner Role

 None
meta bool

Show metadata

 False
attachment bool

Show attachments

 False
output str | None

Set output format. If none use default from config file

 None
Source code in readstore_cli/readstore.py 
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def list_fq_datasets(
    project_name: str | None = None,
    project_id: int | None = None,
    role: str | None = None,
    meta: bool = False,
    attachment: bool = False,
    pro_data: bool = False,
    output: str | None = None,
):
    """List Fastq Datasets

    List all Fastq Datasets and Filter by Project
    Options to show only meta and attachments

    Args:
        project_name: Filter by Project Name
        project_id: Filter by Project Id
        role: Filter by Owner Role
        meta: Show metadata
        attachment: Show attachments
        output: Set output format. If none use default from config file
    """

    # Get ReadStore Client and Validate Connection
    try:
        client = _get_readstore_client()

    except rsexceptions.ReadStoreError as e:
        sys.stderr.write(f"ReadStore Error: {e.message}\n")
        return

    if output is None:
        output = client.get_output_format()

    try:
        fq_datasets = client.list_fastq_datasets(project_name, project_id, role)

        for fq in fq_datasets:
            if not meta:
                fq.pop("metadata", None)
            if not attachment:
                fq.pop("attachments", None)
            if not pro_data:
                fq.pop("pro_data", None)

        if output == "json":
            print(fq_datasets)
        elif output == "text":
            if len(fq_datasets) > 0:
                header = list(fq_datasets[0].keys())
                header_str = " | ".join(header)
                print(header_str)

                for fq in fq_datasets:
                    values = [str(fq[key]) for key in header]
                    values_str = " | ".join(values)
                    print(values_str)
        elif output == "csv":
            if len(fq_datasets) > 0:
                header = list(fq_datasets[0].keys())
                header_str = ",".join(header)
                print(header_str)

                for fq in fq_datasets:
                    values = [str(fq[key]) for key in header]
                    values_str = ",".join(values)
                    print(values_str)
        else:
            sys.stderr.write("Output Format Not Supported\n")
            return

    except rsexceptions.ReadStoreError as e:
        sys.stderr.write(f"ReadStore Error: {e.message}\n")
        return

list_pro_data(project_id=None, project_name=None, dataset_id=None, dataset_name=None, name=None, data_type=None, meta=False, archived=False, output=None)

List Processed Data

List all Processed Data Filter by Project, Dataset, Data Type, Metadata and Archive

Parameters:

Name Type Description Default
project_name str | None

Filter by Project Name

 None
project_id int | None

Filter by Project ID

 None
dataset_id int | None

Filter by Dataset ID

 None
dataset_name str | None

Filter by Dataset Name

 None
data_type str | None

Filter by Data Type

 None
meta bool

Filter by Metadata

 False
archived bool

Include Archived Data

 False
output str | None

Set output format. If none use default from config file

 None
Source code in readstore_cli/readstore.py 
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def list_pro_data(
    project_id: int | None = None,
    project_name: str | None = None,
    dataset_id: int | None = None,
    dataset_name: str | None = None,
    name: str | None = None,
    data_type: str | None = None,
    meta: bool = False,
    archived: bool = False,
    output: str | None = None,
):
    """List Processed Data

    List all Processed Data
    Filter by Project, Dataset, Data Type, Metadata and Archive

    Args:
        project_name: Filter by Project Name
        project_id: Filter by Project ID
        dataset_id: Filter by Dataset ID
        dataset_name: Filter by Dataset Name
        data_type: Filter by Data Type
        meta: Filter by Metadata
        archived: Include Archived Data
        output: Set output format. If none use default from config file
    """

    # Get ReadStore Client and Validate Connection
    try:
        client = _get_readstore_client()
    except rsexceptions.ReadStoreError as e:
        sys.stderr.write(f"ReadStore Error: {e.message}\n")
        return

    if output is None:
        output = client.get_output_format()

    try:
        pro_data = client.list_pro_data(
            project_id,
            project_name,
            dataset_id,
            dataset_name,
            name,
            data_type,
            archived,
        )

        for p in pro_data:
            if not meta:
                p.pop("metadata", None)

        if output == "json":
            print(pro_data)
        elif output == "text":
            if len(pro_data) > 0:
                header = list(pro_data[0].keys())
                header_str = " | ".join(header)
                print(header_str)

                for p in pro_data:
                    values = [str(p[key]) for key in header]
                    values_str = " | ".join(values)
                    print(values_str)
        elif output == "csv":
            if len(pro_data) > 0:
                header = list(pro_data[0].keys())
                header_str = ",".join(header)
                print(header_str)

                for p in pro_data:
                    values = [str(p[key]) for key in header]
                    values_str = ",".join(values)
                    print(values_str)
        else:
            sys.stderr.write("Output Format Not Supported\n")
            return

    except rsexceptions.ReadStoreError as e:
        sys.stderr.write(f"ReadStore Error: {e.message}\n")
        return

list_projects(role=None, meta=False, attachment=False, output=None)

List Projects

List all Fastq Projects. Options to add metadata and attachments

Role must be in owner, collaborator, creator

Parameters:

Name Type Description Default
role str | None

Filter by Owner Role

 None
meta bool

Show metadata

 False
attachment bool

Show attachments

 False
output str | None

Set output format. If none use default from config file

 None
Source code in readstore_cli/readstore.py 
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def list_projects(
    role: str | None = None,
    meta: bool = False,
    attachment: bool = False,
    output: str | None = None,
):
    """List Projects

    List all Fastq Projects.
    Options to add metadata and attachments

    Role must be in owner, collaborator, creator

    Args:
        role: Filter by Owner Role
        meta: Show metadata
        attachment: Show attachments
        output: Set output format. If none use default from config file
    """

    # Get ReadStore Client and Validate Connection
    try:
        client = _get_readstore_client()
    except rsexceptions.ReadStoreError as e:
        sys.stderr.write(f"ReadStore Error: {e.message}\n")
        return

    if output is None:
        output = client.get_output_format()
    try:
        projects = client.list_projects(role)

        for p in projects:
            p.pop("dataset_metadata_keys", None)
            if not meta:
                p.pop("metadata", None)
            if not attachment:
                p.pop("attachments", None)

        if output == "json":
            print(projects)
        elif output == "text":
            if len(projects) > 0:
                header = list(projects[0].keys())
                header_str = " | ".join(header)
                print(header_str)

                for p in projects:
                    values = [str(p[key]) for key in header]
                    values_str = " | ".join(values)
                    print(values_str)
        elif output == "csv":
            if len(projects) > 0:
                header = list(projects[0].keys())
                header_str = ",".join(header)
                print(header_str)

                for p in projects:
                    values = [str(p[key]) for key in header]
                    values_str = ",".join(values)
                    print(values_str)
        else:
            sys.stderr.write("Output Format Not Supported\n")
            return

    except rsexceptions.ReadStoreError as e:
        sys.stderr.write(f"ReadStore Error: {e.message}\n")
        return

main()

Main function for ReadStore CLI

Source code in readstore_cli/readstore.py 
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def main():
    """
    Main function for ReadStore CLI

    """

    args = parser.parse_args()

    # Keep hierarchy of commands. First check for subparsers.
    if "config_list" in args:
        configure_list()

    elif "config_run" in args:
        configure()

    elif "upload_run" in args:
        upload(fastq_files=args.fastq_files)

    elif "list_fq_run" in args:
        list_fq_datasets(
            project_name=args.project_name,
            project_id=args.project_id,
            role=args.role,
            meta=args.meta,
            attachment=args.attachment,
            pro_data=args.pro_data,
            output=args.output,
        )

    elif "get_fq_run" in args:
        read1 = args.read1
        read2 = args.read2
        index1 = args.index1
        index2 = args.index2
        read1_path = args.read1_path
        read2_path = args.read2_path
        index1_path = args.index1_path
        index2_path = args.index2_path

        meta = args.meta
        attachment = args.attachment
        pro_data = args.pro_data

        if (
            sum([read1,
                 read2,
                 index1,
                 index2,
                 read1_path,
                 read2_path,
                 index1_path,
                 index2_path,
                 meta,
                 attachment,
                 pro_data]) > 1
        ):
            sys.stderr.write(
                """ReadStore Error: Only One Flag Allowed for -r1, -r2,
                             -i1, -i2, -m, -r1p, -r2p, -i1p, -i2p, -m, -a, -pd\n\n"""
            )
            get_fq_parser.print_help()
        else:
            get_fastq_dataset(
                dataset_id=args.id,
                dataset_name=args.name,
                meta=meta,
                attachment=attachment,
                pro_data=pro_data,
                read1=read1,
                read2=read2,
                index1=index1,
                index2=index2,
                read1_path=read1_path,
                read2_path=read2_path,
                index1_path=index1_path,
                index2_path=index2_path,
                output=args.output,
            )

    elif "create_fq_run" in args:

        if args.project_id:
            project_ids = [args.project_id]
        else:
            project_ids = []

        if args.project_name:
            project_names = [args.project_name]
        else:
            project_names = []

        create_fq_dataset(
            name=args.name,
            description=args.description,
            project_ids=project_ids,
            project_names=project_names,
            metadata=args.meta,
        )

    elif "update_fq_run" in args:

        if args.project_id:
            project_ids = [args.project_id]
        else:
            project_ids = None

        if args.project_name:
            project_names = [args.project_name]
        else:
            project_names = None

        update_fq_dataset(
            dataset_id=args.id,
            dataset_name=args.name,
            description=args.description,
            project_ids=project_ids,
            project_names=project_names,
            metadata=args.meta,
        )

    elif "download_run" in args:
        download_fq_dataset_attachment(
            attachment_name=args.attachment,
            outpath=args.outpath,
            dataset_id=args.id,
            dataset_name=args.name,
        )

    elif "dataset_run" in args:
        dataset_parser.print_help()

    elif "list_project_run" in args:
        list_projects(
            role=args.role,
            meta=args.meta,
            attachment=args.attachment,
            output=args.output,
        )

    elif "get_project_run" in args:
        get_project(
            project_id=args.id,
            project_name=args.name,
            meta=args.meta,
            attachment=args.attachment,
            output=args.output,
        )

    elif "create_project_run" in args:
        create_project(name=args.name, description=args.description, metadata=args.meta)

    elif "update_project_run" in args:
        update_project(
            project_id=args.id,
            project_name=args.name,
            description=args.description,
            metadata=args.meta,
        )

    elif "download_project_run" in args:
        download_project_attachment(
            attachment_name=args.attachment,
            outpath=args.outpath,
            project_id=args.id,
            project_name=args.name,
        )

    elif "project_run" in args:
        project_parser.print_help()

    elif "import_fastq_run" in args:
        import_fastq(args.fastq_template[0])

    elif "import_run" in args:
        import_parser.print_help()

    elif "pro_data_upload_run" in args:

        dataset_id = args.dataset_id
        dataset_name = args.dataset_name

        if (not dataset_id) and (not dataset_name):
            sys.stderr.write(
                "ReadStore Error: Must Provide Dataset ID (--did) or Dataset Name (--d) to attach ProData to\n"
            )
            pro_data_parser.print_help()
        else:       
            upload_pro_data(
                name=args.name,
                pro_data_file=args.pro_data_file,
                data_type=args.type,
                description=args.description,
                metadata=args.meta,
                dataset_id=args.dataset_id,
                dataset_name=args.dataset_name,
            )

    elif "pro_data_list_run" in args:
        list_pro_data(
            project_id=args.project_id,
            project_name=args.project_name,
            dataset_id=args.dataset_id,
            dataset_name=args.dataset_name,
            name=args.name,
            data_type=args.type,
            meta=args.meta,
            archived=args.archived,
            output=args.output,
        )

    elif "pro_data_get_run" in args:
        get_pro_data(
            pro_data_id=args.id,
            name=args.name,
            meta=args.meta,
            upload_path=args.upload_path,
            version=args.version,
            dataset_id=args.dataset_id,
            dataset_name=args.dataset_name,
            output=args.output,
        )

    elif "pro_data_delete_run" in args:
        delete_pro_data(
            pro_data_id=args.id,
            name=args.name,
            version=args.version,
            dataset_id=args.dataset_id,
            dataset_name=args.dataset_name,
        )

    elif "pro_data_run" in args:
        pro_data_parser.print_help()

    elif args.version:
        print(f"ReadStore CLI Version: {__version__}")
        sys.exit(0)

    else:
        parser.print_help()

upload(fastq_files)

Upload fastq files

Upload provided files

Check files by extension

Parameters:

Name Type Description Default
fastq_files List[str]

Fastq files to upload

 required
Source code in readstore_cli/readstore.py 
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def upload(fastq_files: List[str]):
    """Upload fastq files

    Upload provided files

    Check files by extension

    Args:
        fastq_files: Fastq files to upload
    """

    # Get ReadStore Client and Validate Connection
    try:
        client = _get_readstore_client()
    except rsexceptions.ReadStoreError as e:
        sys.stderr.write(f"ReadStore Error: {e.message}\n")
        return

    for fq in fastq_files:
        print(f"ReadStore Upload: Start {fq}")

        if not os.path.isfile(fq):
            sys.stderr.write(f"\nReadStore Upload: File Not Found: {fq}\n")
            continue
        elif not fq.endswith(tuple(DEFAULT_FASTQ_EXTENSIONS)):
            sys.stderr.write(f"\nReadStore Upload: Invalid FASTQ Extension: {fq}\n")
        else:
            try:
                client.upload_fastq(fq)
            except rsexceptions.ReadStoreError as e:
                sys.stderr.write(f"ReadStore Error: {e.message}\n")

upload_pro_data(name, pro_data_file, data_type, description, metadata, dataset_id=None, dataset_name=None)

Upload Processed Data

Source code in readstore_cli/readstore.py 
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def upload_pro_data(
    name: str,
    pro_data_file: str,
    data_type: str,
    description: str,
    metadata: str,
    dataset_id: int | None = None,
    dataset_name: str | None = None,
):
    """Upload Processed Data"""

    # Get ReadStore Client and Validate Connection
    try:
        client = _get_readstore_client()
    except rsexceptions.ReadStoreError as e:
        sys.stderr.write(f"ReadStore Error: {e.message}\n")
        return

    fq_dataset = client.get_fastq_dataset(dataset_id, dataset_name)
    if fq_dataset == {}:
        sys.stderr.write("ReadStore Error: Dataset to attach ProData Not Found\n")
        return

    fq_dataset_id = fq_dataset["id"]

    # Convert metadata json string to dict
    try:
        metadata = json.loads(metadata)
    except json.JSONDecodeError:
        sys.stderr.write("ReadStore Error: Invalid Metadata JSON String\n")
        return

    print(f"ReadStore ProData Upload: Start {pro_data_file}")

    try:
        client.upload_pro_data(
            name,
            pro_data_file,
            data_type,
            dataset_id=fq_dataset_id,
            metadata=metadata,
            description=description,
        )

    except rsexceptions.ReadStoreError as e:
        sys.stderr.write(f"ReadStore Error: {e.message}\n")

rsclient module

Provides client for interacting with ReadStore API.

Classes:

Name Description
- RSClient

Provides client for interacting with ReadStore API.

RSClient

A client for interacting with the ReadStore API

Attributes:

Name Type Description
username

ReadStore username
token

ReadStore user token
endpoint

The endpoint URL for the ReadStore API
output_format

The default output format for the client

Methods:

Name Description
_test_server_connection

Validate server URL
_auth_user_token

Validate user and token
validate_charset

Validate charset for query string
validate_metadata

Validate metadata dict
get_output_format

Get Output Format set for client
upload_fastq

Upload Fastq Files
get_fq_file

Get Fastq File
list_fq_files

List Fastq Files
create_fq_file

Create Fastq File
update_fq_file

Update Fastq File
delete_fq_file

Delete Fastq File
get_fq_file_upload_path

Get FASTQ file upload path
list_fastq_datasets

List FASTQ Datasets
get_fastq_dataset

Get FASTQ dataset
create_fastq_dataset

Create Fastq Dataset
update_fastq_dataset

Update Fastq Dataset
delete_fastq_dataset

Delete Fastq Dataset
list_projects

List Projects
get_project

Get Project by id or name
create_project

Create Project
update_project

Update Project
delete_project

Delete Project
download_project_attachment

Download Project Attachments
download_fq_dataset_attachment

Download Fastq Attach
upload_pro_data

Upload Processed Data
list_pro_data

List Processed Data
get_pro_data

Get Processed Data
delete_pro_data

Delete Processed Data
Source code in readstore_cli/rsclient.py 
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class RSClient:
    """
        A client for interacting with the ReadStore API

        Attributes:
            username: ReadStore username
            token: ReadStore user token
            endpoint: The endpoint URL for the ReadStore API
            output_format: The default output format for the client

        Methods:
            _test_server_connection: Validate server URL
            _auth_user_token: Validate user and token
            validate_charset: Validate charset for query string
            validate_metadata: Validate metadata dict
            get_output_format: Get Output Format set for client
            upload_fastq: Upload Fastq Files
            get_fq_file: Get Fastq File
            list_fq_files: List Fastq Files
            create_fq_file: Create Fastq File
            update_fq_file: Update Fastq File
            delete_fq_file: Delete Fastq File
            get_fq_file_upload_path: Get FASTQ file upload  path
            list_fastq_datasets: List FASTQ Datasets
            get_fastq_dataset: Get FASTQ dataset
            create_fastq_dataset: Create Fastq Dataset
            update_fastq_dataset: Update Fastq Dataset
            delete_fastq_dataset: Delete Fastq Dataset
            list_projects: List Projects
            get_project: Get Project by id or name
            create_project: Create Project
            update_project: Update Project
            delete_project: Delete Project
            download_project_attachment: Download Project Attachments
            download_fq_dataset_attachment: Download Fastq Attach
            upload_pro_data: Upload Processed Data
            list_pro_data: List Processed Data
            get_pro_data: Get Processed Data
            delete_pro_data: Delete Processed Data
    """

    REST_API_VERSION = "api_x_v1/"
    USER_AUTH_TOKEN_ENDPOINT = "auth_token/"
    FASTQ_UPLOAD_ENDPOINT = "fq_file_upload/"
    FQ_DATASET_ENDPOINT = "fq_dataset/"
    FQ_FILE_ENDPOINT = "fq_file/"
    FQ_ATTACHMENT_ENDPOINT = "fq_attachment/"
    PROJECT_ENDPOINT = "project/"
    PROJECT_ATTACHMENT_ENDPOINT = "project_attachment/"
    PRO_DATA_ENDPOINT = "pro_data/"

    def __init__(
        self, username: str, token: str, endpoint_url: str, output_format: str
    ):
        """Constructor

        Initialize a new RSClient object

        Args:
            username: ReadStore username
            token: ReadStore user token
            endpoint_url: The endpoint URL for the ReadStore API
            output_format: The default output format for the client

        Raises:
            rsexceptions.ReadStoreError:
                Server Connection to API Failed
            rsexceptions.ReadStoreError:
                User Authentication Failed
        """

        self.username = username
        self.token = token
        self.endpoint = f"{endpoint_url}/{self.REST_API_VERSION}"
        self.output_format = output_format
        self.auth = HTTPBasicAuth(username, token)

        if not self._test_server_connection():
            raise rsexceptions.ReadStoreError(
                f"Server Connection Failed\nEndpoint URL: {self.endpoint}"
            )

        if not self._auth_user_token():
            raise rsexceptions.ReadStoreError(
                f"User Authentication Failed\nUsername: {self.username}"
            )

    def _test_server_connection(self) -> bool:
        """
        Validate server URL

        Returns:
            True if server can be reached else False
        """

        parsed_url = urlparse(self.endpoint)

        if parsed_url.scheme not in ["http", "https"]:
            return False
        else:
            try:
                response = requests.head(self.endpoint)

                if response.status_code == 200:
                    return True
                else:
                    return False
            except requests.exceptions.ConnectionError:
                return False

    def _auth_user_token(self) -> bool:
        """
        Validate user and token

        Returns:
            True if user token is valid else False
        """

        try:
            auth_endpoint = os.path.join(self.endpoint, self.USER_AUTH_TOKEN_ENDPOINT)

            res = requests.post(auth_endpoint, auth=self.auth)

            if res.status_code != 200:
                return False
            else:
                return True

        except requests.exceptions.ConnectionError:
            return False


    def validate_charset(self, query_str: str) -> bool:
        """
        Validate charset for query string

        Args:
            query_str (str): Query string to validate

        Returns:
            bool: 
        """

        allowed = string.digits + string.ascii_lowercase + string.ascii_uppercase + '_-.@'
        allowed = set(allowed)

        return set(query_str) <= allowed


    def get_output_format(self) -> str:
        """
        Get Output Format set for client

        Return:
            str output format
        """

        return self.output_format


    def upload_fastq(self,
                     fastq_path: str,
                     fastq_name: str | None = None,
                     read_type: str | None = None) -> None:
        """Upload Fastq Files

        Upload Fastq files to ReadStore.
        Check if file exists and has read permissions.

        fastq_name: List of Fastq names for files to upload
        read_type: List of read types for files to upload

        Args:
            fastq_path: List of Fastq files to upload
            fastq_name: List of Fastq names for files to upload
            read_types: List of read types for files to upload
            read_types: Must be in ['R1', 'R2', 'I1', 'I2']

        Raises:
            rsexceptions.ReadStoreError: If file not found
            rsexceptions.ReadStoreError: If no read permissions
            rsexceptions.ReadStoreError: If upload URL request failed
        """

        fq_upload_endpoint = os.path.join(self.endpoint, self.FASTQ_UPLOAD_ENDPOINT)

        # Run parallel uploads of fastq files
        fastq_path = os.path.abspath(fastq_path)

        # Make sure file exists and
        if not os.path.exists(fastq_path):
            raise rsexceptions.ReadStoreError(f"File Not Found: {fastq_path}")
        elif not os.access(fastq_path, os.R_OK):
            raise rsexceptions.ReadStoreError(f"No read permissions: {fastq_path}")

        payload = {
            "fq_file_path": fastq_path,
        }

        if not fastq_name is None:
            if fastq_name == "":
                raise rsexceptions.ReadStoreError("Fastq Name Is Empty")
            if not self.validate_charset(fastq_name):
                raise rsexceptions.ReadStoreError("Invalid Fastq Name")
            payload["fq_file_name"] = fastq_name

        if not read_type is None:
            if read_type not in ["R1", "R2", "I1", "I2"]:
                raise rsexceptions.ReadStoreError("Invalid Read Type")
            payload["read_type"] = read_type

        res = requests.post(fq_upload_endpoint, json=payload, auth=self.auth)

        if res.status_code not in [200, 204]:
            res_message = res.json().get("detail", "No Message")
            raise rsexceptions.ReadStoreError(
                f"Upload URL Request Failed: {res_message}"
            )


    def get_fq_file(self, fq_file_id: int) -> Dict:
        """Get Fastq File

        Return Fastq file data by fq_file ID

        Args:
            fq_file_id: ID (pk) of fq_file

        Returns:
            dict with fq file data
        """

        fq_file_endpoint = os.path.join(self.endpoint, self.FQ_FILE_ENDPOINT)


        res = requests.get(fq_file_endpoint + f'{fq_file_id}/',auth=self.auth)

        if res.status_code not in [200, 204]:
            try:
                detail = res.json()
            except:
                detail = "No Message"

            raise rsexceptions.ReadStoreError(f"get_fq_file failed: {detail}")
        else:
            return res.json()[0]


    def list_fq_files(self) -> List[Dict]:
        """List Fastq Files

        List Fastq files in ReadStore

        Returns:
            List of Fastq files
        """

        fq_file_endpoint = os.path.join(self.endpoint, self.FQ_FILE_ENDPOINT)

        res = requests.get(fq_file_endpoint, auth=self.auth)

        if res.status_code not in [200, 204]:
            try:
                detail = res.json()
            except:
                detail = "No Message"

            raise rsexceptions.ReadStoreError(f"list_fq_files failed: {detail}")
        else:
            return res.json()


    def create_fq_file(self,
                       name: str,
                       read_type: str,
                       qc_passed: bool,
                       read_length: int,
                       num_reads: int,
                       size_mb: int,
                       qc_phred_mean: float,
                       qc_phred: dict,
                       upload_path: str,
                       md5_checksum: str,
                       staging: bool,
                       pipeline_version: str) -> dict:

        """Create Fastq File

        Create Fastq file in ReadStore

        Args:
            name: Fastq file name
            read_type: Read type (R1, R2, I1, I2)
            qc_passed: QC Pass
            read_length: Read length
            num_reads: Number of reads
            size_mb: Size in MB
            qc_phred_mean: QC Phred Mean
            qc_phred: QC Phred
            upload_path: Upload Path
            md5_checksum: MD5 Checksum
            staging: Staging
            pipeline_version: Pipeline Version

        Returns:    
            dict: Fastq file data

        Raises:
            rsexceptions.ReadStoreError: If request failed
        """

        fq_file_endpoint = os.path.join(self.endpoint, self.FQ_FILE_ENDPOINT)

        # Define json for post request
        json = {
            "name": name,
            "read_type": read_type,
            "qc_passed": qc_passed,
            "read_length": read_length,
            "num_reads": num_reads,
            "size_mb": size_mb,
            "qc_phred_mean": qc_phred_mean,
            "qc_phred": qc_phred,
            "upload_path": upload_path,
            "md5_checksum": md5_checksum,
            "staging": staging,
            "pipeline_version": pipeline_version
        }

        res = requests.post(fq_file_endpoint, json=json, auth=self.auth)

        if res.status_code != 201:
            try:
                detail = res.json()
            except:
                detail = "No Message"

            raise rsexceptions.ReadStoreError(f"create_fq_file failed: {detail}")
        else:
            return res.json()


    def update_fq_file(self,
                       fq_file_id: int,
                       name: str,
                       read_type: str,
                       qc_passed: bool,
                       read_length: int,
                       num_reads: int,
                       size_mb: int,
                       qc_phred_mean: float,
                       qc_phred: dict,
                       upload_path: str,
                       md5_checksum: str,
                       staging: bool,
                       pipeline_version: str) -> dict:

        """Update Fastq File

        Update Fastq file in ReadStore

        Args:
            fq_file_id: ID of Fastq file
            name: Fastq file name
            read_type: Read type (R1, R2, I1, I2)
            qc_passed: QC Pass
            read_length: Read length
            num_reads: Number of reads
            size_mb: Size in MB
            qc_phred_mean: QC Phred Mean
            qc_phred: QC Phred
            upload_path: Upload Path
            md5_checksum: MD5 Checksum
            staging: Staging
            pipeline_version: Pipeline Version

        Returns:    
            dict: Fastq file data

        Raises:
            rsexceptions.ReadStoreError: If request failed
        """

        fq_file_endpoint = os.path.join(self.endpoint, self.FQ_FILE_ENDPOINT, f'{fq_file_id}/')

        # Define json for post request
        json = {
            "name": name,
            "read_type": read_type,
            "qc_passed": qc_passed,
            "read_length": read_length,
            "num_reads": num_reads,
            "size_mb": size_mb,
            "qc_phred_mean": qc_phred_mean,
            "qc_phred": qc_phred,
            "upload_path": upload_path,
            "md5_checksum": md5_checksum,
            "staging": staging,
            "pipeline_version": pipeline_version
        }

        res = requests.put(fq_file_endpoint, json=json, auth=self.auth)

        if res.status_code != 200:
            try:
                detail = res.json()
            except:
                detail = "No Message"

            raise rsexceptions.ReadStoreError(f"update_fq_file failed: {detail}")
        else:
            return res.json()


    def delete_fq_file(self, fq_file_id: int):
        """Delete Fastq File

        Delete Fastq file in ReadStore

        Args:
            fq_file_id: ID of Fastq file

        Raises:
            rsexceptions.ReadStoreError: If request failed
        """

        fq_file_endpoint = os.path.join(self.endpoint, self.FQ_FILE_ENDPOINT, f'{fq_file_id}/')

        res = requests.delete(fq_file_endpoint, auth=self.auth)

        if not res.status_code in [200, 204]:
            try:
                detail = res.json()
            except:
                detail = "No Message"

            raise rsexceptions.ReadStoreError(f"delete_fq_file failed: {detail}")        


    def get_fq_file_upload_path(self, fq_file_id: int) -> str:
        """Get FASTQ file upload path

        Get upload path for FASTQ file by fq_file ID

        Args:
            fq_file_id: ID (pk) of FASTQ file

        Raises:
            rsexceptions.ReadStoreError: If upload_path is not found

        Returns:
            str: Upload path
        """

        fq_file = self.get_fq_file(fq_file_id)

        if "upload_path" not in fq_file:
            raise rsexceptions.ReadStoreError("upload_path Not Found in FqFile entry")

        upload_path = fq_file.get("upload_path")

        return upload_path

    def list_fastq_datasets(
        self,
        project_name: str | None = None,
        project_id: int | None = None,
        role: str | None = None,
    ) -> List[dict]:
        """
        List FASTQ Datasets

        List FASTQ datasets and filter by project_name, project_id or role.
        Role can be owner, collaborator or creator.

        Args:
            project_name: Filter fq_datasets by project name
            project_id: Filter fq_datasets by project ID
            role: Filter fq_datasets by owner role (owner, collaborator, creator)

        Raises:
            rsexceptions.ReadStoreError if role is not valid
            rsexceptions.ReadStoreError request failed

        Returns:
            List[Dict]: FASTQ datasets in JSON format
        """

        fq_dataset_endpoint = os.path.join(self.endpoint, self.FQ_DATASET_ENDPOINT)

        # Define json for post request
        json = {}

        if role:
            if role.lower() in ["owner", "collaborator", "creator"]:
                json["role"] = role
            else:
                raise rsexceptions.ReadStoreError("Invalid Role")

        if project_name:
            json["project_name"] = project_name
        if project_id:
            json["project_id"] = project_id

        res = requests.get(fq_dataset_endpoint, params=json, auth=self.auth)

        if res.status_code not in [200, 204]:
            raise rsexceptions.ReadStoreError("list_fastq_datasets Failed")
        else:
            return res.json()

    def get_fastq_dataset(
        self,
        dataset_id: int | None = None,
        dataset_name: str | None = None
    ) -> Dict:
        """Get FASTQ dataset

        Get FASTQ dataset by provided dataset_id or dataset_name
        If dataset_name is not unique an error is printed

        Args:
            dataset_id: fq_dataset ID (or pk) to select
            dataset_name: fq_dataset Name to select

        Raises:
            rsexceptions.ReadStoreError: If backend request failed
            rsexceptions.ReadStoreError:
                If multiple datasets found with same name.
                This can occur if datasets with identical name were shared with you.

        Returns:
            Dict: Json Detail response
        """

        fq_dataset_endpoint = os.path.join(self.endpoint, self.FQ_DATASET_ENDPOINT)

        if dataset_id is None and dataset_name is None: 
            raise rsexceptions.ReadStoreError("Dataset ID or Name Required")

        # Define json for post request
        json = {}
        if dataset_id:
            json["id"] = dataset_id
        if dataset_name:
            json["name"] = dataset_name

        res = requests.get(fq_dataset_endpoint, params=json, auth=self.auth)

        # Remove entries not requested
        if res.status_code not in [200, 204]:
            raise rsexceptions.ReadStoreError("get_fastq_dataset Failed")
        else:
            # If no dataset found, return empty dict
            if len(res.json()) == 0:
                return {}
            # If several datasets found, return error
            elif len(res.json()) > 1:
                raise rsexceptions.ReadStoreError(
                    """Multiple Datasets Found.\n
                    This can happen if datasets with identical name were
                    shared with you.\nUse dataset_id to get the correct dataset."""
                )
            else:
                return res.json()[0]

    def create_fastq_dataset(self,
                            name: str,
                            description: str,
                            qc_passed: bool,
                            paired_end: bool,
                            index_read: bool,
                            project_ids: List[int],
                            project_names: List[str],
                            metadata: dict,
                            fq_file_r1_id: int | None,
                            fq_file_r2_id: int | None,
                            fq_file_i1_id: int | None,
                            fq_file_i2_id: int | None) -> dict:

        """Create Fastq Dataset 

        Create Fastq dataset in ReadStore

        Args:
            name: Dataset name
            description: Dataset description
            qc_passed: QC Pass
            paired_end: Paired End
            index_read: Index Read
            project_ids: List of project IDs
            project_names: List of project names
            metadata: Metadata
            fq_file_r1_id: Fastq file R1 ID
            fq_file_r2_id: Fastq file R2 ID
            fq_file_i1_id: Fastq file I1 ID
            fq_file_i2_id: Fastq file I2 ID

        Returns:
            dict: Created Fastq dataset

        Raises:
            rsexceptions.ReadStoreError: If request failed
        """

        fq_dataset_endpoint = os.path.join(self.endpoint, self.FQ_DATASET_ENDPOINT)

        # Define json for post request
        json = {
            "name": name,
            "description": description,
            "qc_passed": qc_passed,
            "paired_end": paired_end,
            "index_read": index_read,
            "project_ids": project_ids,
            "project_names": project_names,
            "metadata": metadata,
            "fq_file_r1": fq_file_r1_id,
            "fq_file_r2": fq_file_r2_id,
            "fq_file_i1": fq_file_i1_id,
            "fq_file_i2": fq_file_i2_id
        }

        res = requests.post(fq_dataset_endpoint, json=json, auth=self.auth)

        if res.status_code != 201:
            try:
                detail = res.json()
            except:
                detail = "No Message"

            raise rsexceptions.ReadStoreError(f"create_fastq_dataset failed: {detail}")
        else:
            return res.json()

    def update_fastq_dataset(self,
                             dataset_id: int,
                             name: str,
                             description: str,
                             qc_passed: bool,
                             paired_end: bool,
                             index_read: bool,
                             project_ids: List[int],
                             project_names: List[str],
                             metadata: dict,
                             fq_file_r1_id: int | None,
                             fq_file_r2_id: int | None,
                             fq_file_i1_id: int | None,
                             fq_file_i2_id: int | None) -> dict:
        """Update Fastq Dataset

        Update Fastq dataset in ReadStore

        Args:
            dataset_id: ID of the dataset to update
            name: Dataset name
            description: Dataset description
            qc_passed: QC Pass
            paired_end: Paired End
            index_read: Index Read
            project_ids: List of project IDs
            project_names: List of project names
            metadata: Metadata
            fq_file_r1_id: Fastq file R1 ID
            fq_file_r2_id: Fastq file R2 ID
            fq_file_i1_id: Fastq file I1 ID
            fq_file_i2_id: Fastq file I2 ID

        Returns:
            dict: Updated Fastq dataset

        Raises:
            rsexceptions.ReadStoreError: If request failed
        """

        fq_dataset_endpoint = os.path.join(self.endpoint, self.FQ_DATASET_ENDPOINT, f'{dataset_id}/')

        # Define json for put request
        json = {
            "name": name,
            "description": description,
            "qc_passed": qc_passed,
            "paired_end": paired_end,
            "index_read": index_read,
            "project_ids": project_ids,
            "project_names": project_names,
            "metadata": metadata,
            "fq_file_r1": fq_file_r1_id,
            "fq_file_r2": fq_file_r2_id,
            "fq_file_i1": fq_file_i1_id,
            "fq_file_i2": fq_file_i2_id
        }

        res = requests.put(fq_dataset_endpoint, json=json, auth=self.auth)

        if res.status_code != 200:
            try:
                detail = res.json()
            except:
                detail = "No Message"

            raise rsexceptions.ReadStoreError(f"update_fastq_dataset failed: {detail}")
        else:
            return res.json()

    def delete_fastq_dataset(self, dataset_id: int):
        """Delete Fastq Dataset

        Delete Fastq dataset in ReadStore

        Args:
            dataset_id: ID of Fastq dataset

        Raises:
            rsexceptions.ReadStoreError: If request failed
        """

        fq_dataset_endpoint = os.path.join(self.endpoint, self.FQ_DATASET_ENDPOINT, f'{dataset_id}/')

        res = requests.delete(fq_dataset_endpoint, auth=self.auth)

        if not res.status_code in [200,204]:
            try:
                detail = res.json()
            except:
                detail = "No Message"

            raise rsexceptions.ReadStoreError(f"delete_fastq_dataset failed: {detail}")


    def list_projects(self, role: str | None = None) -> List[Dict]:
        """List Projects

        List projects and optionally filter by role

        Args:
            role: Owner role to filter (owner, collaborator, creator)

        Raises:
            rsexceptions.ReadStoreError: If role is not valid
            rsexceptions.ReadStoreError: If request failed

        Returns:
            List[Dict]: List of projects
        """

        project_endpoint = os.path.join(self.endpoint, self.PROJECT_ENDPOINT)

        # Define json for post request
        json = {}
        if role:
            if role.lower() in ["owner", "collaborator", "creator"]:
                json["role"] = role
            else:
                raise rsexceptions.ReadStoreError("Invalid Role")

        res = requests.get(project_endpoint, params=json, auth=self.auth)

        if res.status_code not in [200, 204]:
            raise rsexceptions.ReadStoreError("list_projects Failed")
        else:
            return res.json()


    def get_project(
        self,
        project_id: int | None = None,
        project_name: str | None = None
    ) -> Dict:
        """Get Individual Project

        Return project details by project_id or project_name
        If name is duplicated, print error message

        Args:
            project_id: Project ID
            project_name: Project Name

        Raise
            rsexceptions.ReadStoreError: If request failed
            rsexceptions.ReadStoreError: If duplicate names are found

        Returns:
            project detail response
        """

        assert project_id or project_name, "project_id or project_name Required"

        project_endpoint = os.path.join(self.endpoint, self.PROJECT_ENDPOINT)

        # Define json for post request
        json = {"username": self.username, "token": self.token}

        if project_id:
            json["id"] = project_id
        if project_name:
            json["name"] = project_name

        res = requests.get(project_endpoint, params=json, auth=self.auth)

        if res.status_code not in [200, 204]:
            raise rsexceptions.ReadStoreError("get_project Failed")
        else:
            if len(res.json()) == 0:
                return {}
            # If several datasets found, return error
            elif len(res.json()) > 1:
                raise rsexceptions.ReadStoreError(
                    """Multiple Projects Found.\n
                This can happen if Projects with identical name were shared with you.\n
                Use unique Project ID to access the correct dataset."""
                )
            else:
                return res.json()[0]

    def create_project(self,
                       name: str,
                       description: str,
                       metadata: dict,
                       dataset_metadata_keys: List[str]) -> dict:
        """Create Project

        Create a new project in ReadStore

        Args:
            name: Project name
            description: Project description
            metadata: Project metadata
            dataset_metadata_keys: Dataset metadata keys

        Returns:
            dict: Created project data

        Raises:
            rsexceptions.ReadStoreError: If request failed
        """
        project_endpoint = os.path.join(self.endpoint, self.PROJECT_ENDPOINT)

        dataset_metadata_keys = {key: "" for key in dataset_metadata_keys}

        json = {
            "name": name,
            "description": description,
            "metadata": metadata,
            "dataset_metadata_keys": dataset_metadata_keys
        }

        res = requests.post(project_endpoint, json=json, auth=self.auth)

        if res.status_code != 201:
            try:
                detail = res.json()
            except: 
                detail = "No Message"

            raise rsexceptions.ReadStoreError(f"create_project failed: {detail}")
        else:
            return res.json()


    def update_project(self,
                       project_id: int,
                       name: str,
                       description: str,
                       metadata: dict,
                       dataset_metadata_keys: List[str]) -> dict:        
        """Update Project

        Update an existing project in ReadStore

        Args:
            project_id: ID of the project to update
            name: Project name
            description: Project description
            metadata: Project metadata
            dataset_metadata_keys: Dataset metadata keys

        Returns:
            dict: Updated project data

        Raises:
            rsexceptions.ReadStoreError: If request failed
        """
        project_endpoint = os.path.join(self.endpoint, self.PROJECT_ENDPOINT, f'{project_id}/')

        dataset_metadata_keys = {key: "" for key in dataset_metadata_keys}

        json = {
            "name": name,
            "description": description,
            "metadata": metadata,
            "dataset_metadata_keys": dataset_metadata_keys
        }

        res = requests.put(project_endpoint, json=json, auth=self.auth)

        if res.status_code != 200:
            try:
                detail = res.json()
            except:
                detail = "No Message"

            raise rsexceptions.ReadStoreError(f"update_project failed: {detail}")
        else:
            return res.json()


    def delete_project(self, project_id: int):
        """Delete Project

        Delete a project in ReadStore

        Args:
            project_id: ID of the project to delete

        Raises:
            rsexceptions.ReadStoreError: If request failed
        """

        project_endpoint = os.path.join(self.endpoint, self.PROJECT_ENDPOINT, f'{project_id}/')

        res = requests.delete(project_endpoint, auth=self.auth)

        if not res.status_code in [200,204]:
            try:
                detail = res.json()
            except:
                detail = "No Message"

            raise rsexceptions.ReadStoreError(f"delete_project failed: {detail}")


    def download_project_attachment(
        self,
        attachment_name: str,
        outpath: str,
        project_id: int | None = None,
        project_name: str | None = None,
    ):
        """Download Project Attachments

        Download Project Attachment Files to local path

        Args:
            attachment_name: Attachment name
            outpath: Path to write to
            project_id: Id of project
            project_name: Project name.

        Raises:
            rsexceptions.ReadStoreError: Request failed
            rsexceptions.ReadStoreError: Attachment not Found
            rsexceptions.ReadStoreError: Multiple Attachments Found for Project.
        """

        project_attachment_endpoint = os.path.join(
            self.endpoint, self.PROJECT_ATTACHMENT_ENDPOINT
        )

        assert project_id or project_name, \
            "Either project_id or project_name required"

        # Define json for post request
        json = {
            "attachment_name": attachment_name
        }

        if project_id:
            json["project_id"] = project_id
        if project_name:
            json["project_name"] = project_name

        res = requests.get(project_attachment_endpoint, params=json, auth=self.auth)

        if res.status_code not in [200, 204]:
            raise rsexceptions.ReadStoreError("download_project_attachment failed")
        elif len(res.json()) == 0:
            raise rsexceptions.ReadStoreError("Attachment Not Found")
        elif len(res.json()) > 1:
            raise rsexceptions.ReadStoreError(
                """Multiple Attachments Found For Project.
                This can happen if Projects with identical name were shared with you.\n
                Use unique Project ID to access the correct attachment."""
            )
        else:
            attachment = res.json()[0]
            with open(outpath, "wb") as fh:
                fh.write(base64.b64decode(attachment["body"]))


    def download_fq_dataset_attachment(
        self,
        attachment_name: str,
        outpath: str,
        dataset_id: int | None = None,
        dataset_name: str | None = None,
    ):
        """Fastq Attachments

        Download Fastq Attachments

        Args:
            attachment_name: Attachment name
            outpath: Path to write to
            dataset_id: Id of project
            dataset_name: Project name.

        Raises:
            rsexceptions.ReadStoreError: Request failed
            rsexceptions.ReadStoreError: Attachment not Found
            rsexceptions.ReadStoreError: Multiple Attachments Found for Project.
        """

        fq_dataset_endpoint = os.path.join(self.endpoint, self.FQ_ATTACHMENT_ENDPOINT)

        assert dataset_id or dataset_name, "dataset_id or dataset_name required"

        # Define json for post request
        json = {
            "attachment_name": attachment_name,
        }

        if dataset_id:
            json["dataset_id"] = dataset_id
        if dataset_name:
            json["dataset_name"] = dataset_name

        res = requests.get(fq_dataset_endpoint, params=json, auth=self.auth)

        if res.status_code not in [200, 204]:
            raise rsexceptions.ReadStoreError("download_fq_dataset_attachment failed")
        elif len(res.json()) == 0:
            raise rsexceptions.ReadStoreError("Attachment Not Found")
        elif len(res.json()) > 1:
            raise rsexceptions.ReadStoreError(
                """Multiple Attachments Found For Dataset.
                This can happen if Datasets with identical name were shared with you.\n
                Use unique Dataset ID to access the correct attachment."""
            )
        else:
            attachment = res.json()[0]
            with open(outpath, "wb") as fh:
                fh.write(base64.b64decode(attachment["body"]))

    def upload_pro_data(self,
                        name: str,
                        pro_data_path: str,
                        data_type: str,
                        dataset_id: int | None = None,
                        dataset_name: str | None = None,
                        metadata: dict = {},
                        description: str = "") -> None:
        """Upload Processed Data

        Upload Pro Data to ReadStore

        Args:
            pro_data: Pro Data in JSON format

        Raises:
            rsexceptions.ReadStoreError: If upload request failed
        """

        pro_data_endpoint = os.path.join(self.endpoint, self.PRO_DATA_ENDPOINT)

        # Run parallel uploads of fastq files
        pro_data_path = os.path.abspath(pro_data_path)

        # Make sure file exists and
        if not os.path.exists(pro_data_path):
            raise rsexceptions.ReadStoreError(f"File Not Found: {pro_data_path}")
        elif not os.access(pro_data_path, os.R_OK):
            raise rsexceptions.ReadStoreError(f"No read permissions: {pro_data_path}")

        # Define json for post request
        json = {
            "name" : name,
            "data_type": data_type,
            "upload_path": pro_data_path,
            "metadata": metadata,
            "description" : description,
        }

        if dataset_id:
            json['dataset_id'] = dataset_id
        if dataset_name:
            json['dataset_name'] = dataset_name        

        res = requests.post(pro_data_endpoint, json=json, auth=self.auth)

        if res.status_code == 403:
            raise rsexceptions.ReadStoreError(f"Upload ProData Failed: {res.json().get('detail')}")
        elif res.status_code not in [201, 204]:
            raise rsexceptions.ReadStoreError("upload_pro_data failed")


    def list_pro_data(self,
                      project_id: int | None = None,
                      project_name: str | None = None,
                      dataset_id: int | None = None,
                      dataset_name: str | None = None,
                      name: str | None = None,
                      data_type: str | None = None,
                      include_archived: bool = False) -> List[Dict]:
        """List Processed Data

        List Pro Data for Dataset

        Args:
            dataset_id: Dataset ID

        Raises:
            rsexceptions.ReadStoreError: If request failed

        Returns:
            List[Dict]: List of Pro Data
        """

        pro_data_endpoint = os.path.join(self.endpoint, self.PRO_DATA_ENDPOINT)

        # Define json for post request
        json = {
            'project_id': project_id,
            'project_name': project_name,
            'dataset_id': dataset_id,
            'dataset_name': dataset_name,
            'name': name,
            'data_type': data_type
        }

        if not include_archived:
            json['valid'] = True

        res = requests.get(pro_data_endpoint, params=json, auth=self.auth)

        if res.status_code not in [200, 204]:
            raise rsexceptions.ReadStoreError("list_pro_data failed")
        else:
            return res.json()


    def get_pro_data(self,
                    pro_data_id: int | None = None,
                    name: str | None = None,
                    version: int | None = None,
                    dataset_id: int | None = None,
                    dataset_name: str | None = None) -> List[Dict]:   

        """List Processed Data

        List Pro Data for Dataset

        Args:
            dataset_id: Dataset ID

        Raises:
            rsexceptions.ReadStoreError: If request failed

        Returns:
            List[Dict]: List of Pro Data
        """

        if not pro_data_id:
            assert name and (dataset_id or dataset_name), "name and dataset_id or dataset_name required"

        pro_data_endpoint = os.path.join(self.endpoint, self.PRO_DATA_ENDPOINT)

        if not version:
            valid = 'true'
        else:
            valid = 'false'


        # Define json for post request
        json = {
            'dataset_id': dataset_id,
            'dataset_name': dataset_name,
            'name': name,
            'version': version,
            'valid': valid,
            'detail': 'true'
        }

        if pro_data_id:
            res = requests.get(pro_data_endpoint + f'{pro_data_id}/', auth=self.auth)
        else:
            res = requests.get(pro_data_endpoint, params=json, auth=self.auth)

        if res.status_code not in [200, 204]:
            raise rsexceptions.ReadStoreError("list_pro_data failed")
        else:
            if len(res.json()) == 0:
                return {}
            # If several datasets found, return error
            elif len(res.json()) > 1:
                raise rsexceptions.ReadStoreError(
                    """Multiple Projects Found.\n
                This can happen if Projects with identical name were shared with you.\n
                Use unique Project ID to access the correct dataset."""
                )
            else:
                return res.json()[0]

    def delete_pro_data(self,
                        pro_data_id: int | None = None,
                        name: str | None = None,
                        dataset_id: int | None = None,
                        dataset_name: str | None = None,
                        version: int | None = None) -> List[Dict]:   

        """Delete Processed Data

        Delete Pro Data for Dataset

        Args:
            dataset_id: Dataset ID

        Raises:
            rsexceptions.ReadStoreError: If request failed

        Returns:
            List[Dict]: List of Pro Data
        """

        if not pro_data_id:
            assert name and (dataset_id or dataset_name), "name and dataset_id or dataset_name required"

        pro_data_endpoint = os.path.join(self.endpoint, self.PRO_DATA_ENDPOINT)

        # Define json for post request
        json = {
            'dataset_id': dataset_id,
            'dataset_name': dataset_name,
            'name': name,
            'version': version,
        }

        if pro_data_id:
            res = requests.delete(pro_data_endpoint + f'{pro_data_id}/', auth=self.auth)
        else:
            res = requests.delete(pro_data_endpoint, params=json, auth=self.auth)

        if res.status_code == 400:
            detail = res.json().get('detail', 'No Message')
            if detail == 'ProData not found':
                raise rsexceptions.ReadStoreError("ProData not found")
            else:
                raise rsexceptions.ReadStoreError("delete_pro_data failed")
        elif res.status_code == 403:
            raise rsexceptions.ReadStoreError(f"ProData Delete Failed: {res.json().get('detail')}")
        elif res.status_code in [200, 204]:
            return res.json().get('id')
        else:
            raise rsexceptions.ReadStoreError("delete_pro_data failed")

__init__(username, token, endpoint_url, output_format)

Constructor

Initialize a new RSClient object

Parameters:

Name Type Description Default
username str

ReadStore username

 required
token str

ReadStore user token

 required
endpoint_url str

The endpoint URL for the ReadStore API

 required
output_format str

The default output format for the client

 required

Raises:

Type Description
ReadStoreError

Server Connection to API Failed
ReadStoreError

User Authentication Failed
Source code in readstore_cli/rsclient.py 
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def __init__(
    self, username: str, token: str, endpoint_url: str, output_format: str
):
    """Constructor

    Initialize a new RSClient object

    Args:
        username: ReadStore username
        token: ReadStore user token
        endpoint_url: The endpoint URL for the ReadStore API
        output_format: The default output format for the client

    Raises:
        rsexceptions.ReadStoreError:
            Server Connection to API Failed
        rsexceptions.ReadStoreError:
            User Authentication Failed
    """

    self.username = username
    self.token = token
    self.endpoint = f"{endpoint_url}/{self.REST_API_VERSION}"
    self.output_format = output_format
    self.auth = HTTPBasicAuth(username, token)

    if not self._test_server_connection():
        raise rsexceptions.ReadStoreError(
            f"Server Connection Failed\nEndpoint URL: {self.endpoint}"
        )

    if not self._auth_user_token():
        raise rsexceptions.ReadStoreError(
            f"User Authentication Failed\nUsername: {self.username}"
        )

_auth_user_token()

Validate user and token

Returns:

Type Description
bool

True if user token is valid else False
Source code in readstore_cli/rsclient.py 
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def _auth_user_token(self) -> bool:
    """
    Validate user and token

    Returns:
        True if user token is valid else False
    """

    try:
        auth_endpoint = os.path.join(self.endpoint, self.USER_AUTH_TOKEN_ENDPOINT)

        res = requests.post(auth_endpoint, auth=self.auth)

        if res.status_code != 200:
            return False
        else:
            return True

    except requests.exceptions.ConnectionError:
        return False

_test_server_connection()

Validate server URL

Returns:

Type Description
bool

True if server can be reached else False
Source code in readstore_cli/rsclient.py 
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def _test_server_connection(self) -> bool:
    """
    Validate server URL

    Returns:
        True if server can be reached else False
    """

    parsed_url = urlparse(self.endpoint)

    if parsed_url.scheme not in ["http", "https"]:
        return False
    else:
        try:
            response = requests.head(self.endpoint)

            if response.status_code == 200:
                return True
            else:
                return False
        except requests.exceptions.ConnectionError:
            return False

create_fastq_dataset(name, description, qc_passed, paired_end, index_read, project_ids, project_names, metadata, fq_file_r1_id, fq_file_r2_id, fq_file_i1_id, fq_file_i2_id)

Create Fastq Dataset

Create Fastq dataset in ReadStore

Parameters:

Name Type Description Default
name str

Dataset name

 required
description str

Dataset description

 required
qc_passed bool

QC Pass

 required
paired_end bool

Paired End

 required
index_read bool

Index Read

 required
project_ids List[int]

List of project IDs

 required
project_names List[str]

List of project names

 required
metadata dict

Metadata

 required
fq_file_r1_id int | None

Fastq file R1 ID

 required
fq_file_r2_id int | None

Fastq file R2 ID

 required
fq_file_i1_id int | None

Fastq file I1 ID

 required
fq_file_i2_id int | None

Fastq file I2 ID

 required

Returns:

Name Type Description
dict dict

Created Fastq dataset

Raises:

Type Description
ReadStoreError

If request failed
Source code in readstore_cli/rsclient.py 
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def create_fastq_dataset(self,
                        name: str,
                        description: str,
                        qc_passed: bool,
                        paired_end: bool,
                        index_read: bool,
                        project_ids: List[int],
                        project_names: List[str],
                        metadata: dict,
                        fq_file_r1_id: int | None,
                        fq_file_r2_id: int | None,
                        fq_file_i1_id: int | None,
                        fq_file_i2_id: int | None) -> dict:

    """Create Fastq Dataset 

    Create Fastq dataset in ReadStore

    Args:
        name: Dataset name
        description: Dataset description
        qc_passed: QC Pass
        paired_end: Paired End
        index_read: Index Read
        project_ids: List of project IDs
        project_names: List of project names
        metadata: Metadata
        fq_file_r1_id: Fastq file R1 ID
        fq_file_r2_id: Fastq file R2 ID
        fq_file_i1_id: Fastq file I1 ID
        fq_file_i2_id: Fastq file I2 ID

    Returns:
        dict: Created Fastq dataset

    Raises:
        rsexceptions.ReadStoreError: If request failed
    """

    fq_dataset_endpoint = os.path.join(self.endpoint, self.FQ_DATASET_ENDPOINT)

    # Define json for post request
    json = {
        "name": name,
        "description": description,
        "qc_passed": qc_passed,
        "paired_end": paired_end,
        "index_read": index_read,
        "project_ids": project_ids,
        "project_names": project_names,
        "metadata": metadata,
        "fq_file_r1": fq_file_r1_id,
        "fq_file_r2": fq_file_r2_id,
        "fq_file_i1": fq_file_i1_id,
        "fq_file_i2": fq_file_i2_id
    }

    res = requests.post(fq_dataset_endpoint, json=json, auth=self.auth)

    if res.status_code != 201:
        try:
            detail = res.json()
        except:
            detail = "No Message"

        raise rsexceptions.ReadStoreError(f"create_fastq_dataset failed: {detail}")
    else:
        return res.json()

create_fq_file(name, read_type, qc_passed, read_length, num_reads, size_mb, qc_phred_mean, qc_phred, upload_path, md5_checksum, staging, pipeline_version)

Create Fastq File

Create Fastq file in ReadStore

Parameters:

Name Type Description Default
name str

Fastq file name

 required
read_type str

Read type (R1, R2, I1, I2)

 required
qc_passed bool

QC Pass

 required
read_length int

Read length

 required
num_reads int

Number of reads

 required
size_mb int

Size in MB

 required
qc_phred_mean float

QC Phred Mean

 required
qc_phred dict

QC Phred

 required
upload_path str

Upload Path

 required
md5_checksum str

MD5 Checksum

 required
staging bool

Staging

 required
pipeline_version str

Pipeline Version

 required

Returns:

Name Type Description
dict dict

Fastq file data

Raises:

Type Description
ReadStoreError

If request failed
Source code in readstore_cli/rsclient.py 
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def create_fq_file(self,
                   name: str,
                   read_type: str,
                   qc_passed: bool,
                   read_length: int,
                   num_reads: int,
                   size_mb: int,
                   qc_phred_mean: float,
                   qc_phred: dict,
                   upload_path: str,
                   md5_checksum: str,
                   staging: bool,
                   pipeline_version: str) -> dict:

    """Create Fastq File

    Create Fastq file in ReadStore

    Args:
        name: Fastq file name
        read_type: Read type (R1, R2, I1, I2)
        qc_passed: QC Pass
        read_length: Read length
        num_reads: Number of reads
        size_mb: Size in MB
        qc_phred_mean: QC Phred Mean
        qc_phred: QC Phred
        upload_path: Upload Path
        md5_checksum: MD5 Checksum
        staging: Staging
        pipeline_version: Pipeline Version

    Returns:    
        dict: Fastq file data

    Raises:
        rsexceptions.ReadStoreError: If request failed
    """

    fq_file_endpoint = os.path.join(self.endpoint, self.FQ_FILE_ENDPOINT)

    # Define json for post request
    json = {
        "name": name,
        "read_type": read_type,
        "qc_passed": qc_passed,
        "read_length": read_length,
        "num_reads": num_reads,
        "size_mb": size_mb,
        "qc_phred_mean": qc_phred_mean,
        "qc_phred": qc_phred,
        "upload_path": upload_path,
        "md5_checksum": md5_checksum,
        "staging": staging,
        "pipeline_version": pipeline_version
    }

    res = requests.post(fq_file_endpoint, json=json, auth=self.auth)

    if res.status_code != 201:
        try:
            detail = res.json()
        except:
            detail = "No Message"

        raise rsexceptions.ReadStoreError(f"create_fq_file failed: {detail}")
    else:
        return res.json()

create_project(name, description, metadata, dataset_metadata_keys)

Create Project

Create a new project in ReadStore

Parameters:

Name Type Description Default
name str

Project name

 required
description str

Project description

 required
metadata dict

Project metadata

 required
dataset_metadata_keys List[str]

Dataset metadata keys

 required

Returns:

Name Type Description
dict dict

Created project data

Raises:

Type Description
ReadStoreError

If request failed
Source code in readstore_cli/rsclient.py 
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def create_project(self,
                   name: str,
                   description: str,
                   metadata: dict,
                   dataset_metadata_keys: List[str]) -> dict:
    """Create Project

    Create a new project in ReadStore

    Args:
        name: Project name
        description: Project description
        metadata: Project metadata
        dataset_metadata_keys: Dataset metadata keys

    Returns:
        dict: Created project data

    Raises:
        rsexceptions.ReadStoreError: If request failed
    """
    project_endpoint = os.path.join(self.endpoint, self.PROJECT_ENDPOINT)

    dataset_metadata_keys = {key: "" for key in dataset_metadata_keys}

    json = {
        "name": name,
        "description": description,
        "metadata": metadata,
        "dataset_metadata_keys": dataset_metadata_keys
    }

    res = requests.post(project_endpoint, json=json, auth=self.auth)

    if res.status_code != 201:
        try:
            detail = res.json()
        except: 
            detail = "No Message"

        raise rsexceptions.ReadStoreError(f"create_project failed: {detail}")
    else:
        return res.json()

delete_fastq_dataset(dataset_id)

Delete Fastq Dataset

Delete Fastq dataset in ReadStore

Parameters:

Name Type Description Default
dataset_id int

ID of Fastq dataset

 required

Raises:

Type Description
ReadStoreError

If request failed
Source code in readstore_cli/rsclient.py 
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def delete_fastq_dataset(self, dataset_id: int):
    """Delete Fastq Dataset

    Delete Fastq dataset in ReadStore

    Args:
        dataset_id: ID of Fastq dataset

    Raises:
        rsexceptions.ReadStoreError: If request failed
    """

    fq_dataset_endpoint = os.path.join(self.endpoint, self.FQ_DATASET_ENDPOINT, f'{dataset_id}/')

    res = requests.delete(fq_dataset_endpoint, auth=self.auth)

    if not res.status_code in [200,204]:
        try:
            detail = res.json()
        except:
            detail = "No Message"

        raise rsexceptions.ReadStoreError(f"delete_fastq_dataset failed: {detail}")

delete_fq_file(fq_file_id)

Delete Fastq File

Delete Fastq file in ReadStore

Parameters:

Name Type Description Default
fq_file_id int

ID of Fastq file

 required

Raises:

Type Description
ReadStoreError

If request failed
Source code in readstore_cli/rsclient.py 
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def delete_fq_file(self, fq_file_id: int):
    """Delete Fastq File

    Delete Fastq file in ReadStore

    Args:
        fq_file_id: ID of Fastq file

    Raises:
        rsexceptions.ReadStoreError: If request failed
    """

    fq_file_endpoint = os.path.join(self.endpoint, self.FQ_FILE_ENDPOINT, f'{fq_file_id}/')

    res = requests.delete(fq_file_endpoint, auth=self.auth)

    if not res.status_code in [200, 204]:
        try:
            detail = res.json()
        except:
            detail = "No Message"

        raise rsexceptions.ReadStoreError(f"delete_fq_file failed: {detail}")

delete_pro_data(pro_data_id=None, name=None, dataset_id=None, dataset_name=None, version=None)

Delete Processed Data

Delete Pro Data for Dataset

Parameters:

Name Type Description Default
dataset_id int | None

Dataset ID

 None

Raises:

Type Description
ReadStoreError

If request failed

Returns:

Type Description
List[Dict]

List[Dict]: List of Pro Data
Source code in readstore_cli/rsclient.py 
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def delete_pro_data(self,
                    pro_data_id: int | None = None,
                    name: str | None = None,
                    dataset_id: int | None = None,
                    dataset_name: str | None = None,
                    version: int | None = None) -> List[Dict]:   

    """Delete Processed Data

    Delete Pro Data for Dataset

    Args:
        dataset_id: Dataset ID

    Raises:
        rsexceptions.ReadStoreError: If request failed

    Returns:
        List[Dict]: List of Pro Data
    """

    if not pro_data_id:
        assert name and (dataset_id or dataset_name), "name and dataset_id or dataset_name required"

    pro_data_endpoint = os.path.join(self.endpoint, self.PRO_DATA_ENDPOINT)

    # Define json for post request
    json = {
        'dataset_id': dataset_id,
        'dataset_name': dataset_name,
        'name': name,
        'version': version,
    }

    if pro_data_id:
        res = requests.delete(pro_data_endpoint + f'{pro_data_id}/', auth=self.auth)
    else:
        res = requests.delete(pro_data_endpoint, params=json, auth=self.auth)

    if res.status_code == 400:
        detail = res.json().get('detail', 'No Message')
        if detail == 'ProData not found':
            raise rsexceptions.ReadStoreError("ProData not found")
        else:
            raise rsexceptions.ReadStoreError("delete_pro_data failed")
    elif res.status_code == 403:
        raise rsexceptions.ReadStoreError(f"ProData Delete Failed: {res.json().get('detail')}")
    elif res.status_code in [200, 204]:
        return res.json().get('id')
    else:
        raise rsexceptions.ReadStoreError("delete_pro_data failed")

delete_project(project_id)

Delete Project

Delete a project in ReadStore

Parameters:

Name Type Description Default
project_id int

ID of the project to delete

 required

Raises:

Type Description
ReadStoreError

If request failed
Source code in readstore_cli/rsclient.py 
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def delete_project(self, project_id: int):
    """Delete Project

    Delete a project in ReadStore

    Args:
        project_id: ID of the project to delete

    Raises:
        rsexceptions.ReadStoreError: If request failed
    """

    project_endpoint = os.path.join(self.endpoint, self.PROJECT_ENDPOINT, f'{project_id}/')

    res = requests.delete(project_endpoint, auth=self.auth)

    if not res.status_code in [200,204]:
        try:
            detail = res.json()
        except:
            detail = "No Message"

        raise rsexceptions.ReadStoreError(f"delete_project failed: {detail}")

download_fq_dataset_attachment(attachment_name, outpath, dataset_id=None, dataset_name=None)

Fastq Attachments

Download Fastq Attachments

Parameters:

Name Type Description Default
attachment_name str

Attachment name

 required
outpath str

Path to write to

 required
dataset_id int | None

Id of project

 None
dataset_name str | None

Project name.

 None

Raises:

Type Description
ReadStoreError

Request failed
ReadStoreError

Attachment not Found
ReadStoreError

Multiple Attachments Found for Project.
Source code in readstore_cli/rsclient.py 
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def download_fq_dataset_attachment(
    self,
    attachment_name: str,
    outpath: str,
    dataset_id: int | None = None,
    dataset_name: str | None = None,
):
    """Fastq Attachments

    Download Fastq Attachments

    Args:
        attachment_name: Attachment name
        outpath: Path to write to
        dataset_id: Id of project
        dataset_name: Project name.

    Raises:
        rsexceptions.ReadStoreError: Request failed
        rsexceptions.ReadStoreError: Attachment not Found
        rsexceptions.ReadStoreError: Multiple Attachments Found for Project.
    """

    fq_dataset_endpoint = os.path.join(self.endpoint, self.FQ_ATTACHMENT_ENDPOINT)

    assert dataset_id or dataset_name, "dataset_id or dataset_name required"

    # Define json for post request
    json = {
        "attachment_name": attachment_name,
    }

    if dataset_id:
        json["dataset_id"] = dataset_id
    if dataset_name:
        json["dataset_name"] = dataset_name

    res = requests.get(fq_dataset_endpoint, params=json, auth=self.auth)

    if res.status_code not in [200, 204]:
        raise rsexceptions.ReadStoreError("download_fq_dataset_attachment failed")
    elif len(res.json()) == 0:
        raise rsexceptions.ReadStoreError("Attachment Not Found")
    elif len(res.json()) > 1:
        raise rsexceptions.ReadStoreError(
            """Multiple Attachments Found For Dataset.
            This can happen if Datasets with identical name were shared with you.\n
            Use unique Dataset ID to access the correct attachment."""
        )
    else:
        attachment = res.json()[0]
        with open(outpath, "wb") as fh:
            fh.write(base64.b64decode(attachment["body"]))

download_project_attachment(attachment_name, outpath, project_id=None, project_name=None)

Download Project Attachments

Download Project Attachment Files to local path

Parameters:

Name Type Description Default
attachment_name str

Attachment name

 required
outpath str

Path to write to

 required
project_id int | None

Id of project

 None
project_name str | None

Project name.

 None

Raises:

Type Description
ReadStoreError

Request failed
ReadStoreError

Attachment not Found
ReadStoreError

Multiple Attachments Found for Project.
Source code in readstore_cli/rsclient.py 
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def download_project_attachment(
    self,
    attachment_name: str,
    outpath: str,
    project_id: int | None = None,
    project_name: str | None = None,
):
    """Download Project Attachments

    Download Project Attachment Files to local path

    Args:
        attachment_name: Attachment name
        outpath: Path to write to
        project_id: Id of project
        project_name: Project name.

    Raises:
        rsexceptions.ReadStoreError: Request failed
        rsexceptions.ReadStoreError: Attachment not Found
        rsexceptions.ReadStoreError: Multiple Attachments Found for Project.
    """

    project_attachment_endpoint = os.path.join(
        self.endpoint, self.PROJECT_ATTACHMENT_ENDPOINT
    )

    assert project_id or project_name, \
        "Either project_id or project_name required"

    # Define json for post request
    json = {
        "attachment_name": attachment_name
    }

    if project_id:
        json["project_id"] = project_id
    if project_name:
        json["project_name"] = project_name

    res = requests.get(project_attachment_endpoint, params=json, auth=self.auth)

    if res.status_code not in [200, 204]:
        raise rsexceptions.ReadStoreError("download_project_attachment failed")
    elif len(res.json()) == 0:
        raise rsexceptions.ReadStoreError("Attachment Not Found")
    elif len(res.json()) > 1:
        raise rsexceptions.ReadStoreError(
            """Multiple Attachments Found For Project.
            This can happen if Projects with identical name were shared with you.\n
            Use unique Project ID to access the correct attachment."""
        )
    else:
        attachment = res.json()[0]
        with open(outpath, "wb") as fh:
            fh.write(base64.b64decode(attachment["body"]))

get_fastq_dataset(dataset_id=None, dataset_name=None)

Get FASTQ dataset

Get FASTQ dataset by provided dataset_id or dataset_name If dataset_name is not unique an error is printed

Parameters:

Name Type Description Default
dataset_id int | None

fq_dataset ID (or pk) to select

 None
dataset_name str | None

fq_dataset Name to select

 None

Raises:

Type Description
ReadStoreError

If backend request failed
ReadStoreError

If multiple datasets found with same name. This can occur if datasets with identical name were shared with you.

Returns:

Name Type Description
Dict Dict

Json Detail response
Source code in readstore_cli/rsclient.py 
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def get_fastq_dataset(
    self,
    dataset_id: int | None = None,
    dataset_name: str | None = None
) -> Dict:
    """Get FASTQ dataset

    Get FASTQ dataset by provided dataset_id or dataset_name
    If dataset_name is not unique an error is printed

    Args:
        dataset_id: fq_dataset ID (or pk) to select
        dataset_name: fq_dataset Name to select

    Raises:
        rsexceptions.ReadStoreError: If backend request failed
        rsexceptions.ReadStoreError:
            If multiple datasets found with same name.
            This can occur if datasets with identical name were shared with you.

    Returns:
        Dict: Json Detail response
    """

    fq_dataset_endpoint = os.path.join(self.endpoint, self.FQ_DATASET_ENDPOINT)

    if dataset_id is None and dataset_name is None: 
        raise rsexceptions.ReadStoreError("Dataset ID or Name Required")

    # Define json for post request
    json = {}
    if dataset_id:
        json["id"] = dataset_id
    if dataset_name:
        json["name"] = dataset_name

    res = requests.get(fq_dataset_endpoint, params=json, auth=self.auth)

    # Remove entries not requested
    if res.status_code not in [200, 204]:
        raise rsexceptions.ReadStoreError("get_fastq_dataset Failed")
    else:
        # If no dataset found, return empty dict
        if len(res.json()) == 0:
            return {}
        # If several datasets found, return error
        elif len(res.json()) > 1:
            raise rsexceptions.ReadStoreError(
                """Multiple Datasets Found.\n
                This can happen if datasets with identical name were
                shared with you.\nUse dataset_id to get the correct dataset."""
            )
        else:
            return res.json()[0]

get_fq_file(fq_file_id)

Get Fastq File

Return Fastq file data by fq_file ID

Parameters:

Name Type Description Default
fq_file_id int

ID (pk) of fq_file

 required

Returns:

Type Description
Dict

dict with fq file data
Source code in readstore_cli/rsclient.py 
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def get_fq_file(self, fq_file_id: int) -> Dict:
    """Get Fastq File

    Return Fastq file data by fq_file ID

    Args:
        fq_file_id: ID (pk) of fq_file

    Returns:
        dict with fq file data
    """

    fq_file_endpoint = os.path.join(self.endpoint, self.FQ_FILE_ENDPOINT)


    res = requests.get(fq_file_endpoint + f'{fq_file_id}/',auth=self.auth)

    if res.status_code not in [200, 204]:
        try:
            detail = res.json()
        except:
            detail = "No Message"

        raise rsexceptions.ReadStoreError(f"get_fq_file failed: {detail}")
    else:
        return res.json()[0]

get_fq_file_upload_path(fq_file_id)

Get FASTQ file upload path

Get upload path for FASTQ file by fq_file ID

Parameters:

Name Type Description Default
fq_file_id int

ID (pk) of FASTQ file

 required

Raises:

Type Description
ReadStoreError

If upload_path is not found

Returns:

Name Type Description
str str

Upload path
Source code in readstore_cli/rsclient.py 
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def get_fq_file_upload_path(self, fq_file_id: int) -> str:
    """Get FASTQ file upload path

    Get upload path for FASTQ file by fq_file ID

    Args:
        fq_file_id: ID (pk) of FASTQ file

    Raises:
        rsexceptions.ReadStoreError: If upload_path is not found

    Returns:
        str: Upload path
    """

    fq_file = self.get_fq_file(fq_file_id)

    if "upload_path" not in fq_file:
        raise rsexceptions.ReadStoreError("upload_path Not Found in FqFile entry")

    upload_path = fq_file.get("upload_path")

    return upload_path

get_output_format()

Get Output Format set for client

Return

str output format

Source code in readstore_cli/rsclient.py 
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def get_output_format(self) -> str:
    """
    Get Output Format set for client

    Return:
        str output format
    """

    return self.output_format

get_pro_data(pro_data_id=None, name=None, version=None, dataset_id=None, dataset_name=None)

List Processed Data

List Pro Data for Dataset

Parameters:

Name Type Description Default
dataset_id int | None

Dataset ID

 None

Raises:

Type Description
ReadStoreError

If request failed

Returns:

Type Description
List[Dict]

List[Dict]: List of Pro Data
Source code in readstore_cli/rsclient.py 
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def get_pro_data(self,
                pro_data_id: int | None = None,
                name: str | None = None,
                version: int | None = None,
                dataset_id: int | None = None,
                dataset_name: str | None = None) -> List[Dict]:   

    """List Processed Data

    List Pro Data for Dataset

    Args:
        dataset_id: Dataset ID

    Raises:
        rsexceptions.ReadStoreError: If request failed

    Returns:
        List[Dict]: List of Pro Data
    """

    if not pro_data_id:
        assert name and (dataset_id or dataset_name), "name and dataset_id or dataset_name required"

    pro_data_endpoint = os.path.join(self.endpoint, self.PRO_DATA_ENDPOINT)

    if not version:
        valid = 'true'
    else:
        valid = 'false'


    # Define json for post request
    json = {
        'dataset_id': dataset_id,
        'dataset_name': dataset_name,
        'name': name,
        'version': version,
        'valid': valid,
        'detail': 'true'
    }

    if pro_data_id:
        res = requests.get(pro_data_endpoint + f'{pro_data_id}/', auth=self.auth)
    else:
        res = requests.get(pro_data_endpoint, params=json, auth=self.auth)

    if res.status_code not in [200, 204]:
        raise rsexceptions.ReadStoreError("list_pro_data failed")
    else:
        if len(res.json()) == 0:
            return {}
        # If several datasets found, return error
        elif len(res.json()) > 1:
            raise rsexceptions.ReadStoreError(
                """Multiple Projects Found.\n
            This can happen if Projects with identical name were shared with you.\n
            Use unique Project ID to access the correct dataset."""
            )
        else:
            return res.json()[0]

get_project(project_id=None, project_name=None)

Get Individual Project

Return project details by project_id or project_name If name is duplicated, print error message

Parameters:

Name Type Description Default
project_id int | None

Project ID

 None
project_name str | None

Project Name

 None

Raise rsexceptions.ReadStoreError: If request failed rsexceptions.ReadStoreError: If duplicate names are found

Returns:

Type Description
Dict

project detail response
Source code in readstore_cli/rsclient.py 
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def get_project(
    self,
    project_id: int | None = None,
    project_name: str | None = None
) -> Dict:
    """Get Individual Project

    Return project details by project_id or project_name
    If name is duplicated, print error message

    Args:
        project_id: Project ID
        project_name: Project Name

    Raise
        rsexceptions.ReadStoreError: If request failed
        rsexceptions.ReadStoreError: If duplicate names are found

    Returns:
        project detail response
    """

    assert project_id or project_name, "project_id or project_name Required"

    project_endpoint = os.path.join(self.endpoint, self.PROJECT_ENDPOINT)

    # Define json for post request
    json = {"username": self.username, "token": self.token}

    if project_id:
        json["id"] = project_id
    if project_name:
        json["name"] = project_name

    res = requests.get(project_endpoint, params=json, auth=self.auth)

    if res.status_code not in [200, 204]:
        raise rsexceptions.ReadStoreError("get_project Failed")
    else:
        if len(res.json()) == 0:
            return {}
        # If several datasets found, return error
        elif len(res.json()) > 1:
            raise rsexceptions.ReadStoreError(
                """Multiple Projects Found.\n
            This can happen if Projects with identical name were shared with you.\n
            Use unique Project ID to access the correct dataset."""
            )
        else:
            return res.json()[0]

list_fastq_datasets(project_name=None, project_id=None, role=None)

List FASTQ Datasets

List FASTQ datasets and filter by project_name, project_id or role. Role can be owner, collaborator or creator.

Parameters:

Name Type Description Default
project_name str | None

Filter fq_datasets by project name

 None
project_id int | None

Filter fq_datasets by project ID

 None
role str | None

Filter fq_datasets by owner role (owner, collaborator, creator)

 None

Returns:

Type Description
List[dict]

List[Dict]: FASTQ datasets in JSON format
Source code in readstore_cli/rsclient.py 
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def list_fastq_datasets(
    self,
    project_name: str | None = None,
    project_id: int | None = None,
    role: str | None = None,
) -> List[dict]:
    """
    List FASTQ Datasets

    List FASTQ datasets and filter by project_name, project_id or role.
    Role can be owner, collaborator or creator.

    Args:
        project_name: Filter fq_datasets by project name
        project_id: Filter fq_datasets by project ID
        role: Filter fq_datasets by owner role (owner, collaborator, creator)

    Raises:
        rsexceptions.ReadStoreError if role is not valid
        rsexceptions.ReadStoreError request failed

    Returns:
        List[Dict]: FASTQ datasets in JSON format
    """

    fq_dataset_endpoint = os.path.join(self.endpoint, self.FQ_DATASET_ENDPOINT)

    # Define json for post request
    json = {}

    if role:
        if role.lower() in ["owner", "collaborator", "creator"]:
            json["role"] = role
        else:
            raise rsexceptions.ReadStoreError("Invalid Role")

    if project_name:
        json["project_name"] = project_name
    if project_id:
        json["project_id"] = project_id

    res = requests.get(fq_dataset_endpoint, params=json, auth=self.auth)

    if res.status_code not in [200, 204]:
        raise rsexceptions.ReadStoreError("list_fastq_datasets Failed")
    else:
        return res.json()

list_fq_files()

List Fastq Files

List Fastq files in ReadStore

Returns:

Type Description
List[Dict]

List of Fastq files
Source code in readstore_cli/rsclient.py 
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def list_fq_files(self) -> List[Dict]:
    """List Fastq Files

    List Fastq files in ReadStore

    Returns:
        List of Fastq files
    """

    fq_file_endpoint = os.path.join(self.endpoint, self.FQ_FILE_ENDPOINT)

    res = requests.get(fq_file_endpoint, auth=self.auth)

    if res.status_code not in [200, 204]:
        try:
            detail = res.json()
        except:
            detail = "No Message"

        raise rsexceptions.ReadStoreError(f"list_fq_files failed: {detail}")
    else:
        return res.json()

list_pro_data(project_id=None, project_name=None, dataset_id=None, dataset_name=None, name=None, data_type=None, include_archived=False)

List Processed Data

List Pro Data for Dataset

Parameters:

Name Type Description Default
dataset_id int | None

Dataset ID

 None

Raises:

Type Description
ReadStoreError

If request failed

Returns:

Type Description
List[Dict]

List[Dict]: List of Pro Data
Source code in readstore_cli/rsclient.py 
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def list_pro_data(self,
                  project_id: int | None = None,
                  project_name: str | None = None,
                  dataset_id: int | None = None,
                  dataset_name: str | None = None,
                  name: str | None = None,
                  data_type: str | None = None,
                  include_archived: bool = False) -> List[Dict]:
    """List Processed Data

    List Pro Data for Dataset

    Args:
        dataset_id: Dataset ID

    Raises:
        rsexceptions.ReadStoreError: If request failed

    Returns:
        List[Dict]: List of Pro Data
    """

    pro_data_endpoint = os.path.join(self.endpoint, self.PRO_DATA_ENDPOINT)

    # Define json for post request
    json = {
        'project_id': project_id,
        'project_name': project_name,
        'dataset_id': dataset_id,
        'dataset_name': dataset_name,
        'name': name,
        'data_type': data_type
    }

    if not include_archived:
        json['valid'] = True

    res = requests.get(pro_data_endpoint, params=json, auth=self.auth)

    if res.status_code not in [200, 204]:
        raise rsexceptions.ReadStoreError("list_pro_data failed")
    else:
        return res.json()

list_projects(role=None)

List Projects

List projects and optionally filter by role

Parameters:

Name Type Description Default
role str | None

Owner role to filter (owner, collaborator, creator)

 None

Raises:

Type Description
ReadStoreError

If role is not valid
ReadStoreError

If request failed

Returns:

Type Description
List[Dict]

List[Dict]: List of projects
Source code in readstore_cli/rsclient.py 
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def list_projects(self, role: str | None = None) -> List[Dict]:
    """List Projects

    List projects and optionally filter by role

    Args:
        role: Owner role to filter (owner, collaborator, creator)

    Raises:
        rsexceptions.ReadStoreError: If role is not valid
        rsexceptions.ReadStoreError: If request failed

    Returns:
        List[Dict]: List of projects
    """

    project_endpoint = os.path.join(self.endpoint, self.PROJECT_ENDPOINT)

    # Define json for post request
    json = {}
    if role:
        if role.lower() in ["owner", "collaborator", "creator"]:
            json["role"] = role
        else:
            raise rsexceptions.ReadStoreError("Invalid Role")

    res = requests.get(project_endpoint, params=json, auth=self.auth)

    if res.status_code not in [200, 204]:
        raise rsexceptions.ReadStoreError("list_projects Failed")
    else:
        return res.json()

update_fastq_dataset(dataset_id, name, description, qc_passed, paired_end, index_read, project_ids, project_names, metadata, fq_file_r1_id, fq_file_r2_id, fq_file_i1_id, fq_file_i2_id)

Update Fastq Dataset

Update Fastq dataset in ReadStore

Parameters:

Name Type Description Default
dataset_id int

ID of the dataset to update

 required
name str

Dataset name

 required
description str

Dataset description

 required
qc_passed bool

QC Pass

 required
paired_end bool

Paired End

 required
index_read bool

Index Read

 required
project_ids List[int]

List of project IDs

 required
project_names List[str]

List of project names

 required
metadata dict

Metadata

 required
fq_file_r1_id int | None

Fastq file R1 ID

 required
fq_file_r2_id int | None

Fastq file R2 ID

 required
fq_file_i1_id int | None

Fastq file I1 ID

 required
fq_file_i2_id int | None

Fastq file I2 ID

 required

Returns:

Name Type Description
dict dict

Updated Fastq dataset

Raises:

Type Description
ReadStoreError

If request failed
Source code in readstore_cli/rsclient.py 
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def update_fastq_dataset(self,
                         dataset_id: int,
                         name: str,
                         description: str,
                         qc_passed: bool,
                         paired_end: bool,
                         index_read: bool,
                         project_ids: List[int],
                         project_names: List[str],
                         metadata: dict,
                         fq_file_r1_id: int | None,
                         fq_file_r2_id: int | None,
                         fq_file_i1_id: int | None,
                         fq_file_i2_id: int | None) -> dict:
    """Update Fastq Dataset

    Update Fastq dataset in ReadStore

    Args:
        dataset_id: ID of the dataset to update
        name: Dataset name
        description: Dataset description
        qc_passed: QC Pass
        paired_end: Paired End
        index_read: Index Read
        project_ids: List of project IDs
        project_names: List of project names
        metadata: Metadata
        fq_file_r1_id: Fastq file R1 ID
        fq_file_r2_id: Fastq file R2 ID
        fq_file_i1_id: Fastq file I1 ID
        fq_file_i2_id: Fastq file I2 ID

    Returns:
        dict: Updated Fastq dataset

    Raises:
        rsexceptions.ReadStoreError: If request failed
    """

    fq_dataset_endpoint = os.path.join(self.endpoint, self.FQ_DATASET_ENDPOINT, f'{dataset_id}/')

    # Define json for put request
    json = {
        "name": name,
        "description": description,
        "qc_passed": qc_passed,
        "paired_end": paired_end,
        "index_read": index_read,
        "project_ids": project_ids,
        "project_names": project_names,
        "metadata": metadata,
        "fq_file_r1": fq_file_r1_id,
        "fq_file_r2": fq_file_r2_id,
        "fq_file_i1": fq_file_i1_id,
        "fq_file_i2": fq_file_i2_id
    }

    res = requests.put(fq_dataset_endpoint, json=json, auth=self.auth)

    if res.status_code != 200:
        try:
            detail = res.json()
        except:
            detail = "No Message"

        raise rsexceptions.ReadStoreError(f"update_fastq_dataset failed: {detail}")
    else:
        return res.json()

update_fq_file(fq_file_id, name, read_type, qc_passed, read_length, num_reads, size_mb, qc_phred_mean, qc_phred, upload_path, md5_checksum, staging, pipeline_version)

Update Fastq File

Update Fastq file in ReadStore

Parameters:

Name Type Description Default
fq_file_id int

ID of Fastq file

 required
name str

Fastq file name

 required
read_type str

Read type (R1, R2, I1, I2)

 required
qc_passed bool

QC Pass

 required
read_length int

Read length

 required
num_reads int

Number of reads

 required
size_mb int

Size in MB

 required
qc_phred_mean float

QC Phred Mean

 required
qc_phred dict

QC Phred

 required
upload_path str

Upload Path

 required
md5_checksum str

MD5 Checksum

 required
staging bool

Staging

 required
pipeline_version str

Pipeline Version

 required

Returns:

Name Type Description
dict dict

Fastq file data

Raises:

Type Description
ReadStoreError

If request failed
Source code in readstore_cli/rsclient.py 
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def update_fq_file(self,
                   fq_file_id: int,
                   name: str,
                   read_type: str,
                   qc_passed: bool,
                   read_length: int,
                   num_reads: int,
                   size_mb: int,
                   qc_phred_mean: float,
                   qc_phred: dict,
                   upload_path: str,
                   md5_checksum: str,
                   staging: bool,
                   pipeline_version: str) -> dict:

    """Update Fastq File

    Update Fastq file in ReadStore

    Args:
        fq_file_id: ID of Fastq file
        name: Fastq file name
        read_type: Read type (R1, R2, I1, I2)
        qc_passed: QC Pass
        read_length: Read length
        num_reads: Number of reads
        size_mb: Size in MB
        qc_phred_mean: QC Phred Mean
        qc_phred: QC Phred
        upload_path: Upload Path
        md5_checksum: MD5 Checksum
        staging: Staging
        pipeline_version: Pipeline Version

    Returns:    
        dict: Fastq file data

    Raises:
        rsexceptions.ReadStoreError: If request failed
    """

    fq_file_endpoint = os.path.join(self.endpoint, self.FQ_FILE_ENDPOINT, f'{fq_file_id}/')

    # Define json for post request
    json = {
        "name": name,
        "read_type": read_type,
        "qc_passed": qc_passed,
        "read_length": read_length,
        "num_reads": num_reads,
        "size_mb": size_mb,
        "qc_phred_mean": qc_phred_mean,
        "qc_phred": qc_phred,
        "upload_path": upload_path,
        "md5_checksum": md5_checksum,
        "staging": staging,
        "pipeline_version": pipeline_version
    }

    res = requests.put(fq_file_endpoint, json=json, auth=self.auth)

    if res.status_code != 200:
        try:
            detail = res.json()
        except:
            detail = "No Message"

        raise rsexceptions.ReadStoreError(f"update_fq_file failed: {detail}")
    else:
        return res.json()

update_project(project_id, name, description, metadata, dataset_metadata_keys)

Update Project

Update an existing project in ReadStore

Parameters:

Name Type Description Default
project_id int

ID of the project to update

 required
name str

Project name

 required
description str

Project description

 required
metadata dict

Project metadata

 required
dataset_metadata_keys List[str]

Dataset metadata keys

 required

Returns:

Name Type Description
dict dict

Updated project data

Raises:

Type Description
ReadStoreError

If request failed
Source code in readstore_cli/rsclient.py 
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def update_project(self,
                   project_id: int,
                   name: str,
                   description: str,
                   metadata: dict,
                   dataset_metadata_keys: List[str]) -> dict:        
    """Update Project

    Update an existing project in ReadStore

    Args:
        project_id: ID of the project to update
        name: Project name
        description: Project description
        metadata: Project metadata
        dataset_metadata_keys: Dataset metadata keys

    Returns:
        dict: Updated project data

    Raises:
        rsexceptions.ReadStoreError: If request failed
    """
    project_endpoint = os.path.join(self.endpoint, self.PROJECT_ENDPOINT, f'{project_id}/')

    dataset_metadata_keys = {key: "" for key in dataset_metadata_keys}

    json = {
        "name": name,
        "description": description,
        "metadata": metadata,
        "dataset_metadata_keys": dataset_metadata_keys
    }

    res = requests.put(project_endpoint, json=json, auth=self.auth)

    if res.status_code != 200:
        try:
            detail = res.json()
        except:
            detail = "No Message"

        raise rsexceptions.ReadStoreError(f"update_project failed: {detail}")
    else:
        return res.json()

upload_fastq(fastq_path, fastq_name=None, read_type=None)

Upload Fastq Files

Upload Fastq files to ReadStore. Check if file exists and has read permissions.

fastq_name: List of Fastq names for files to upload read_type: List of read types for files to upload

Parameters:

Name Type Description Default
fastq_path str

List of Fastq files to upload

 required
fastq_name str | None

List of Fastq names for files to upload

 None
read_types

List of read types for files to upload

 required
read_types

Must be in ['R1', 'R2', 'I1', 'I2']

 required

Raises:

Type Description
ReadStoreError

If file not found
ReadStoreError

If no read permissions
ReadStoreError

If upload URL request failed
Source code in readstore_cli/rsclient.py 
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def upload_fastq(self,
                 fastq_path: str,
                 fastq_name: str | None = None,
                 read_type: str | None = None) -> None:
    """Upload Fastq Files

    Upload Fastq files to ReadStore.
    Check if file exists and has read permissions.

    fastq_name: List of Fastq names for files to upload
    read_type: List of read types for files to upload

    Args:
        fastq_path: List of Fastq files to upload
        fastq_name: List of Fastq names for files to upload
        read_types: List of read types for files to upload
        read_types: Must be in ['R1', 'R2', 'I1', 'I2']

    Raises:
        rsexceptions.ReadStoreError: If file not found
        rsexceptions.ReadStoreError: If no read permissions
        rsexceptions.ReadStoreError: If upload URL request failed
    """

    fq_upload_endpoint = os.path.join(self.endpoint, self.FASTQ_UPLOAD_ENDPOINT)

    # Run parallel uploads of fastq files
    fastq_path = os.path.abspath(fastq_path)

    # Make sure file exists and
    if not os.path.exists(fastq_path):
        raise rsexceptions.ReadStoreError(f"File Not Found: {fastq_path}")
    elif not os.access(fastq_path, os.R_OK):
        raise rsexceptions.ReadStoreError(f"No read permissions: {fastq_path}")

    payload = {
        "fq_file_path": fastq_path,
    }

    if not fastq_name is None:
        if fastq_name == "":
            raise rsexceptions.ReadStoreError("Fastq Name Is Empty")
        if not self.validate_charset(fastq_name):
            raise rsexceptions.ReadStoreError("Invalid Fastq Name")
        payload["fq_file_name"] = fastq_name

    if not read_type is None:
        if read_type not in ["R1", "R2", "I1", "I2"]:
            raise rsexceptions.ReadStoreError("Invalid Read Type")
        payload["read_type"] = read_type

    res = requests.post(fq_upload_endpoint, json=payload, auth=self.auth)

    if res.status_code not in [200, 204]:
        res_message = res.json().get("detail", "No Message")
        raise rsexceptions.ReadStoreError(
            f"Upload URL Request Failed: {res_message}"
        )

upload_pro_data(name, pro_data_path, data_type, dataset_id=None, dataset_name=None, metadata={}, description='')

Upload Processed Data

Upload Pro Data to ReadStore

Parameters:

Name Type Description Default
pro_data

Pro Data in JSON format

 required

Raises:

Type Description
ReadStoreError

If upload request failed
Source code in readstore_cli/rsclient.py 
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def upload_pro_data(self,
                    name: str,
                    pro_data_path: str,
                    data_type: str,
                    dataset_id: int | None = None,
                    dataset_name: str | None = None,
                    metadata: dict = {},
                    description: str = "") -> None:
    """Upload Processed Data

    Upload Pro Data to ReadStore

    Args:
        pro_data: Pro Data in JSON format

    Raises:
        rsexceptions.ReadStoreError: If upload request failed
    """

    pro_data_endpoint = os.path.join(self.endpoint, self.PRO_DATA_ENDPOINT)

    # Run parallel uploads of fastq files
    pro_data_path = os.path.abspath(pro_data_path)

    # Make sure file exists and
    if not os.path.exists(pro_data_path):
        raise rsexceptions.ReadStoreError(f"File Not Found: {pro_data_path}")
    elif not os.access(pro_data_path, os.R_OK):
        raise rsexceptions.ReadStoreError(f"No read permissions: {pro_data_path}")

    # Define json for post request
    json = {
        "name" : name,
        "data_type": data_type,
        "upload_path": pro_data_path,
        "metadata": metadata,
        "description" : description,
    }

    if dataset_id:
        json['dataset_id'] = dataset_id
    if dataset_name:
        json['dataset_name'] = dataset_name        

    res = requests.post(pro_data_endpoint, json=json, auth=self.auth)

    if res.status_code == 403:
        raise rsexceptions.ReadStoreError(f"Upload ProData Failed: {res.json().get('detail')}")
    elif res.status_code not in [201, 204]:
        raise rsexceptions.ReadStoreError("upload_pro_data failed")

validate_charset(query_str)

Validate charset for query string

Parameters:

Name Type Description Default
query_str str

Query string to validate

 required

Returns:

Name Type Description
bool bool
Source code in readstore_cli/rsclient.py 
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def validate_charset(self, query_str: str) -> bool:
    """
    Validate charset for query string

    Args:
        query_str (str): Query string to validate

    Returns:
        bool: 
    """

    allowed = string.digits + string.ascii_lowercase + string.ascii_uppercase + '_-.@'
    allowed = set(allowed)

    return set(query_str) <= allowed

rsexceptions module

ReadStoreError

Bases: Exception

Base class for ReadStoreError exceptions.

Source code in readstore_cli/rsexceptions.py 
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class ReadStoreError(Exception):
    """Base class for ReadStoreError exceptions."""
    def __init__(self, message: str):
        super().__init__(message)
        self.message = message