Module plasmid_assessor.reports

View Source

from datetime import datetime

import os

try:

    import pdf_reports.tools as pdf_tools

    from pdf_reports import (

        add_css_class,

        dataframe_to_html,

        pug_to_html,

        style_table_rows,

        write_report,

    )

    import pandas

    import matplotlib

    REPORT_PKGS_AVAILABLE = True

except ImportError:

    REPORT_PKGS_AVAILABLE = False

from .version import __version__

THIS_PATH = os.path.dirname(os.path.realpath(__file__))

ASSETS_PATH = os.path.join(THIS_PATH, "report_assets")

REPORT_TEMPLATE = os.path.join(ASSETS_PATH, "assessment_report.pug")

STYLESHEET = os.path.join(ASSETS_PATH, "report_style.css")

def end_pug_to_html(template, **context):

    now = datetime.now().strftime("%Y-%m-%d")

    defaults = {

        "sidebar_text": "Generated on %s by EGF's Plasmid assessor (version %s)"

        % (now, __version__),

        "plasma_logo_url": os.path.join(ASSETS_PATH, "imgs", "plasma_logo.png"),

    }

    for k in defaults:

        if k not in context:

            context[k] = defaults[k]

    return pug_to_html(template, **context)

def write_pdf_report(target, assessment):

    """Write an assessment report with a PDF summary.

    **Parameters**

    **target**

    > Path for PDF file.

    **assessment**

    > Assessment instance.

    """

    if not REPORT_PKGS_AVAILABLE:

        raise ImportError(

            "Install extra packages with `pip install plasmid_assessor[report]`"

        )

    assessment.figure_data = pdf_tools.figure_data(assessment.fig, fmt="svg")

    html = end_pug_to_html(REPORT_TEMPLATE, assessment=assessment,)

    write_report(html, target, extra_stylesheets=(STYLESHEET,))

Variables

ASSETS_PATH

REPORT_PKGS_AVAILABLE

REPORT_TEMPLATE

STYLESHEET

THIS_PATH

Functions

end_pug_to_html

def end_pug_to_html(
    template,
    **context
)

View Source

def end_pug_to_html(template, **context):

    now = datetime.now().strftime("%Y-%m-%d")

    defaults = {

        "sidebar_text": "Generated on %s by EGF's Plasmid assessor (version %s)"

        % (now, __version__),

        "plasma_logo_url": os.path.join(ASSETS_PATH, "imgs", "plasma_logo.png"),

    }

    for k in defaults:

        if k not in context:

            context[k] = defaults[k]

    return pug_to_html(template, **context)

write_pdf_report

def write_pdf_report(
    target,
    assessment
)

Write an assessment report with a PDF summary.

Parameters

target

Path for PDF file.

assessment

Assessment instance.

View Source

def write_pdf_report(target, assessment):

    """Write an assessment report with a PDF summary.

    **Parameters**

    **target**

    > Path for PDF file.

    **assessment**

    > Assessment instance.

    """

    if not REPORT_PKGS_AVAILABLE:

        raise ImportError(

            "Install extra packages with `pip install plasmid_assessor[report]`"

        )

    assessment.figure_data = pdf_tools.figure_data(assessment.fig, fmt="svg")

    html = end_pug_to_html(REPORT_TEMPLATE, assessment=assessment,)

    write_report(html, target, extra_stylesheets=(STYLESHEET,))