__author__ = "Johannes Köster"
__copyright__ = "Copyright 2022, Johannes Köster"
__email__ = "johannes.koester@uni-due.de"
__license__ = "MIT"
import os
import sys
import mimetypes
import base64
import textwrap
import datetime
import io
import uuid
import json
import time
import shutil
import subprocess as sp
import itertools
import csv
from collections import namedtuple, defaultdict
from itertools import accumulate, chain
import urllib.parse
import hashlib
from zipfile import ZipFile, ZIP_DEFLATED
from pathlib import Path
import requests
from docutils.parsers.rst.directives.images import Image, Figure
from docutils.parsers.rst import directives
from docutils.core import publish_file, publish_parts
from snakemake import script, wrapper, notebook
from snakemake.utils import format
from snakemake.logging import logger
from snakemake.io import (
is_callable,
is_flagged,
get_flag_value,
glob_wildcards,
Wildcards,
apply_wildcards,
contains_wildcard,
)
from snakemake.exceptions import InputFunctionException, WorkflowError
from snakemake.script import Snakemake
from snakemake import __version__
from snakemake.common import (
get_input_function_aux_params,
is_local_file,
num_if_possible,
lazy_property,
)
from snakemake import logging
from snakemake.report import data
from snakemake.report.rulegraph_spec import rulegraph_spec
[docs]class EmbeddedMixin(object):
"""
Replaces the URI of a directive with a base64-encoded version.
Useful for embedding images/figures in reports.
"""
[docs] def run(self):
"""
Image.run() handles most of the
"""
result = Image.run(self)
reference = directives.uri(self.arguments[0])
self.options["uri"] = data_uri_from_file(reference)
return result
# Create (and register) new image:: and figure:: directives that use a base64
# data URI instead of pointing to a filename.
[docs]class EmbeddedImage(Image, EmbeddedMixin):
pass
directives.register_directive("embeddedimage", EmbeddedImage)
directives.register_directive("embeddedfigure", EmbeddedFigure)
[docs]def data_uri(data, filename, encoding="utf8", mime="text/plain"):
"""Craft a base64 data URI from file with proper encoding and mimetype."""
data = base64.b64encode(data)
uri = "data:{mime};charset={charset};filename={filename};base64,{data}" "".format(
filename=filename, mime=mime, charset=encoding, data=data.decode("utf-8")
)
return uri
[docs]def mime_from_file(file):
mime, encoding = mimetypes.guess_type(file)
if mime is None:
mime = "text/plain"
logger.info(
"Could not detect mimetype for {}, assuming " "text/plain.".format(file)
)
return mime, encoding
[docs]def data_uri_from_file(file, defaultenc="utf8"):
"""Craft a base64 data URI from file with proper encoding and mimetype."""
if isinstance(file, Path):
file = str(file)
mime, encoding = mime_from_file(file)
if encoding is None:
encoding = defaultenc
with open(file, "rb") as f:
return data_uri(f.read(), os.path.basename(file), encoding, mime)
[docs]def report(
text,
path,
stylesheet=None,
defaultenc="utf8",
template=None,
metadata=None,
**files,
):
if stylesheet is None:
os.path.join(os.path.dirname(__file__), "report.css")
outmime, _ = mimetypes.guess_type(path)
if outmime != "text/html":
raise ValueError("Path to report output has to be an HTML file.")
definitions = textwrap.dedent(
"""
.. role:: raw-html(raw)
:format: html
"""
)
metadata = textwrap.dedent(
"""
.. container::
:name: metadata
{metadata}{date}
"""
).format(
metadata=metadata + " | " if metadata else "",
date=datetime.date.today().isoformat(),
)
text = format(textwrap.dedent(text), stepout=3)
attachments = []
if files:
attachments = [
textwrap.dedent(
"""
.. container::
:name: attachments
"""
)
]
for name, _files in sorted(files.items()):
if not isinstance(_files, list):
_files = [_files]
links = []
for file in sorted(_files):
data = data_uri_from_file(file)
links.append(
':raw-html:`<a href="{data}" download="{filename}" draggable="true">{filename}</a>`'.format(
data=data, filename=os.path.basename(file)
)
)
links = "\n\n ".join(links)
attachments.append(
"""
.. container::
:name: {name}
{name}:
{links}
""".format(
name=name, links=links
)
)
text = definitions + text + "\n\n" + "\n\n".join(attachments) + metadata
overrides = dict()
if template is not None:
overrides["template"] = template
if stylesheet is not None:
overrides["stylesheet_path"] = stylesheet
html = open(path, "w")
publish_file(
source=io.StringIO(text),
destination=html,
writer_name="html",
settings_overrides=overrides,
)
[docs]def expand_report_argument(item, wildcards, job):
if is_callable(item):
aux_params = get_input_function_aux_params(item, {"params": job.params})
try:
item = item(wildcards, **aux_params)
except Exception as e:
raise InputFunctionException(e, rule=job.rule, wildcards=wildcards)
if isinstance(item, str):
try:
return apply_wildcards(item, wildcards)
except AttributeError as e:
raise WorkflowError("Failed to resolve wildcards.", e, rule=job.rule)
else:
return item
[docs]class Category:
def __init__(self, name, wildcards, job):
if name is None:
name = "Other"
self.is_other = True
else:
self.is_other = False
name = expand_report_argument(name, wildcards, job)
self.name = name
h = hashlib.sha256()
h.update(name.encode())
self.id = h.hexdigest()
def __eq__(self, other):
return self.name.__eq__(other.name)
def __hash__(self):
return self.name.__hash__()
def __lt__(self, other):
if self.name == "other":
return False
return self.name.__lt__(other.name)
[docs]def render_iofile(iofile):
if is_callable(iofile):
return "<function>"
else:
return str(iofile)
[docs]class RuleRecord:
def __init__(self, job, job_rec):
import yaml
self.name = job_rec.rule
self._rule = job.rule
self.container_img_url = job_rec.container_img_url
self.conda_env = None
self._conda_env_raw = None
if job_rec.conda_env:
self._conda_env_raw = base64.b64decode(job_rec.conda_env).decode()
self.conda_env = yaml.load(self._conda_env_raw, Loader=yaml.Loader)
self.n_jobs = 1
self.id = uuid.uuid4()
@lazy_property
def code(self):
try:
from pygments.lexers import get_lexer_by_name
from pygments.formatters import HtmlFormatter
from pygments import highlight
import pygments.util
except ImportError:
raise WorkflowError(
"Python package pygments must be installed to create reports."
)
sources, language = None, None
if self._rule.shellcmd is not None:
sources = [self._rule.shellcmd]
language = "bash"
elif self._rule.script is not None and not contains_wildcard(self._rule.script):
logger.info("Loading script code for rule {}".format(self.name))
_, source, language, _ = script.get_source(
self._rule.script, self._rule.workflow.sourcecache, self._rule.basedir
)
sources = [source]
elif self._rule.wrapper is not None and not contains_wildcard(
self._rule.wrapper
):
logger.info("Loading wrapper code for rule {}".format(self.name))
_, source, language, _ = script.get_source(
wrapper.get_script(
self._rule.wrapper,
self._rule.workflow.sourcecache,
prefix=self._rule.workflow.wrapper_prefix,
),
self._rule.workflow.sourcecache,
)
sources = [source]
elif self._rule.notebook is not None and not contains_wildcard(
self._rule.notebook
):
_, source, language, _ = script.get_source(
self._rule.notebook,
self._rule.workflow.sourcecache,
self._rule.basedir,
)
language = language.split("_")[1]
sources = notebook.get_cell_sources(source)
else:
# A run directive. There is no easy way yet to obtain
# the actual uncompiled source code.
sources = []
language = "python"
try:
lexer = get_lexer_by_name(language)
highlighted = highlight(
"\n\n".join(sources),
lexer,
HtmlFormatter(linenos=True, cssclass="source", wrapcode=True),
)
return highlighted
except pygments.util.ClassNotFound:
return [
'<pre class="source"><code>{}</code></pre>'.format(source)
for source in sources
]
[docs] def add(self, job_rec):
self.n_jobs += 1
@property
def output(self):
return [render_iofile(f) for f in self._rule.output]
@property
def input(self):
return [render_iofile(f) for f in self._rule.input]
def __eq__(self, other):
return (
self.name == other.name
and self.conda_env == other.conda_env
and self.container_img_url == other.container_img_url
)
[docs]class ConfigfileRecord:
def __init__(self, configfile):
self.path = Path(configfile)
[docs] def code(self):
try:
from pygments.lexers import get_lexer_by_name
from pygments.formatters import HtmlFormatter
from pygments import highlight
except ImportError:
raise WorkflowError(
"Python package pygments must be installed to create reports."
)
file_ext = self.path.suffix
if file_ext in (".yml", ".yaml"):
language = "yaml"
elif file_ext == ".json":
language = "json"
else:
raise ValueError(
"Config file extension {} is not supported - must be YAML or JSON".format(
file_ext
)
)
lexer = get_lexer_by_name(language)
return highlight(
self.path.read_text(),
lexer,
HtmlFormatter(linenos=True, cssclass="source", wrapcode=True),
)
[docs]class JobRecord:
def __init__(self):
self.job = None
self.rule = None
self.starttime = sys.maxsize
self.endtime = 0
self.output = []
self.conda_env_file = None
self.container_img_url = None
[docs]class FileRecord:
def __init__(
self,
path,
job,
caption,
env,
category,
workflow,
wildcards_overwrite=None,
mode_embedded=True,
aux_files=None,
name_overwrite=None,
labels=None,
):
self.labels = labels
self.name_overwrite = name_overwrite
self.mode_embedded = mode_embedded
self.path = path
self.target = os.path.basename(path)
self.size = os.path.getsize(self.path)
self.size_mb = f"{self.size / 1e6:.2g} MB"
logger.info(f"Adding {self.name} ({self.size_mb}).")
self.raw_caption = caption
self.mime, _ = mime_from_file(self.path)
self.workflow = workflow
h = hashlib.sha256()
h.update(path.encode())
self.id = h.hexdigest()
self.job = job
self._wildcards = (
job.wildcards if wildcards_overwrite is None else wildcards_overwrite
)
self.wildcards = logging.format_wildcards(self._wildcards)
self.params = (
logging.format_dict(job.params).replace("\n", r"\n").replace('"', r"\"")
)
self.category = category
self.aux_files = aux_files or []
self.data_uri = self._data_uri()
def _data_uri(self):
if self.mode_embedded:
return data_uri_from_file(self.path)
else:
return os.path.join("data/raw", self.id, self.filename)
[docs] def render(self, env, rst_links, categories, files):
if self.raw_caption is not None:
try:
from jinja2 import Template
except ImportError as e:
raise WorkflowError(
"Python package jinja2 must be installed to create reports."
)
job = self.job
snakemake = Snakemake(
job.input,
job.output,
job.params,
self._wildcards,
job.threads,
job.resources,
job.log,
job.dag.workflow.config,
job.rule.name,
None,
)
try:
caption = (
self.workflow.sourcecache.open(self.raw_caption).read() + rst_links
)
caption = env.from_string(caption).render(
snakemake=snakemake, categories=categories, files=files
)
self.caption = publish_parts(caption, writer_name="html")["body"]
except Exception as e:
raise WorkflowError(
"Error loading caption file {} of output marked for report.".format(
self.raw_caption.get_path_or_uri()
),
e,
)
@property
def is_img(self):
web_safe = {
"image/gif",
"image/jpeg",
"image/png",
"image/svg+xml",
"application/pdf",
}
return self.mime in web_safe
@property
def is_text(self):
return self.is_table or self.mime == "text/plain"
@property
def is_table(self):
return self.mime in {"text/csv", "text/tab-separated-values"}
@property
def is_vega(self):
return (
self.mime == "application/json"
and self.path.endswith(".vl.json")
or self.path.endswith(".vg.json")
)
@property
def icon(self):
if self.is_img:
return "image"
elif self.is_text:
return "file-text"
else:
return "file"
@property
def name(self):
if self.name_overwrite:
return self.name_overwrite
return os.path.basename(self.path)
@property
def filename(self):
return os.path.basename(self.path)
[docs]def get_resource_as_string(path_or_uri):
if is_local_file(path_or_uri):
return open(Path(__file__).parent / "template" / path_or_uri).read()
else:
r = requests.get(path_or_uri)
if r.status_code == requests.codes.ok:
return r.text
raise WorkflowError(
"Failed to download resource needed for " "report: {}".format(path_or_uri)
)
[docs]def expand_labels(labels, wildcards, job):
if labels is None:
return None
labels = expand_report_argument(labels, wildcards, job)
if not isinstance(labels, dict) or not all(
isinstance(col, str) for col in labels.values()
):
raise WorkflowError(
"Expected dict of strings as labels argument given to report flag.",
rule=job.rule,
)
return {
name: expand_report_argument(col, wildcards, job)
for name, col in labels.items()
}
[docs]def auto_report(dag, path, stylesheet=None):
try:
from jinja2 import Template, Environment, PackageLoader, UndefinedError
except ImportError as e:
raise WorkflowError(
"Python package jinja2 must be installed to create reports."
)
mode_embedded = True
if path.endswith(".zip"):
mode_embedded = False
elif not path.endswith(".html"):
raise WorkflowError("Report file does not end with .html or .zip")
custom_stylesheet = None
if stylesheet is not None:
try:
with open(stylesheet) as s:
custom_stylesheet = s.read()
except (Exception, BaseException) as e:
raise WorkflowError("Unable to read custom report stylesheet.", e)
logger.info("Creating report...")
env = Environment(
loader=PackageLoader("snakemake", "report/template"),
trim_blocks=True,
lstrip_blocks=True,
)
env.filters["get_resource_as_string"] = get_resource_as_string
persistence = dag.workflow.persistence
results = defaultdict(lambda: defaultdict(list))
records = defaultdict(JobRecord)
recorded_files = set()
for job in dag.jobs:
for f in itertools.chain(job.expanded_output, job.input):
if is_flagged(f, "report") and f not in recorded_files:
if not f.exists:
raise WorkflowError(
"File {} marked for report but does " "not exist.".format(f)
)
report_obj = get_flag_value(f, "report")
def register_file(
f, wildcards_overwrite=None, aux_files=None, name_overwrite=None
):
wildcards = wildcards_overwrite or job.wildcards
category = Category(
report_obj.category, wildcards=wildcards, job=job
)
subcategory = Category(
report_obj.subcategory, wildcards=wildcards, job=job
)
labels = expand_labels(report_obj.labels, wildcards, job)
results[category][subcategory].append(
FileRecord(
f,
job,
report_obj.caption,
env,
category,
dag.workflow,
wildcards_overwrite=wildcards_overwrite,
mode_embedded=mode_embedded,
aux_files=aux_files,
name_overwrite=name_overwrite,
labels=labels,
)
)
recorded_files.add(f)
if os.path.isfile(f):
register_file(f)
elif os.path.isdir(f):
if report_obj.htmlindex:
if mode_embedded:
raise WorkflowError(
"Directory marked for report specifies htmlindex. "
"This is unsupported when requesting a pure HTML report. "
"Please use store as zip instead (--report report.zip)."
)
aux_files = []
index_found = False
for root, dirs, files in os.walk(f):
for name in files:
if name != ".snakemake_timestamp":
filepath = os.path.join(root, name)
if (
os.path.relpath(filepath, f)
!= report_obj.htmlindex
):
aux_files.append(filepath)
else:
index_found = True
if not index_found:
raise WorkflowError(
"Given htmlindex {} not found in directory "
"marked for report".format(report_obj.htmlindex)
)
register_file(
os.path.join(f, report_obj.htmlindex),
aux_files=aux_files,
name_overwrite="{}.html".format(os.path.basename(f)),
)
elif report_obj.patterns:
if not isinstance(report_obj.patterns, list):
raise WorkflowError(
"Invalid patterns given for report. Must be list.",
rule=job.rule,
)
for pattern in report_obj.patterns:
pattern = os.path.join(f, pattern)
wildcards = glob_wildcards(pattern)._asdict()
names = wildcards.keys()
for w in zip(*wildcards.values()):
w = dict(zip(names, w))
w.update(job.wildcards_dict)
w = Wildcards(fromdict=w)
f = apply_wildcards(pattern, w)
register_file(f, wildcards_overwrite=w)
else:
raise WorkflowError(
"Directory marked for report but neither file patterns "
"given via patterns=[...], nor htmlindex given. "
"See report documentation.",
rule=job.rule,
)
for f in job.expanded_output:
meta = persistence.metadata(f)
if not meta:
logger.warning(
"Missing metadata for file {}. Maybe metadata "
"was deleted or it was created using an older "
"version of Snakemake. This is a non critical "
"warning.".format(f)
)
continue
def get_time(rectime, metatime, sel_func):
if metatime is None:
return rectime
return sel_func(metatime, rectime)
try:
job_hash = meta["job_hash"]
rule = meta["rule"]
rec = records[(job_hash, rule)]
rec.rule = rule
rec.job = job
rec.starttime = get_time(rec.starttime, meta["starttime"], min)
rec.endtime = get_time(rec.endtime, meta["endtime"], max)
rec.conda_env_file = None
rec.conda_env = meta["conda_env"]
rec.container_img_url = meta["container_img_url"]
rec.output.append(f)
except KeyError as e:
logger.warning(
"Metadata for file {} was created with a too "
"old Snakemake version.".format(f)
)
for subcats in results.values():
for catresults in subcats.values():
catresults.sort(key=lambda res: res.name)
# prepare runtimes
runtimes = [
{"rule": rec.rule, "runtime": rec.endtime - rec.starttime}
for rec in sorted(records.values(), key=lambda rec: rec.rule)
]
def get_datetime(rectime):
try:
return datetime.datetime.fromtimestamp(rectime).isoformat()
except OSError:
return None
# prepare end times
timeline = [
{
"rule": rec.rule,
"starttime": get_datetime(rec.starttime),
"endtime": get_datetime(rec.endtime),
}
for rec in sorted(records.values(), key=lambda rec: rec.rule)
]
# prepare per-rule information
rules = defaultdict(list)
for rec in records.values():
rule = RuleRecord(rec.job, rec)
if rec.rule not in rules:
rules[rec.rule].append(rule)
else:
merged = False
for other in rules[rec.rule]:
if rule == other:
other.add(rec)
merged = True
break
if not merged:
rules[rec.rule].append(rule)
# In theory there could be more than one rule with the same name kept from above.
# For now, we just keep the first.
rules = {rulename: items[0] for rulename, items in rules.items()}
# rulegraph
rulegraph, xmax, ymax = rulegraph_spec(dag)
# configfiles
configfiles = [ConfigfileRecord(f) for f in dag.workflow.configfiles]
seen = set()
files = [
seen.add(res.target) or res
for cat in results.values()
for subcat in cat.values()
for res in subcat
if res.target not in seen
]
rst_links = textwrap.dedent(
"""
.. _Workflow: javascript:show_panel('workflow')
.. _Statistics: javascript:show_panel('statistics')
{% for cat, catresults in categories|dictsort %}
.. _{{ cat.name }}: javascript:app.showCategory('{{ cat.name|urlencode }}')
{% endfor %}
{% for res in files %}
.. _{{ res.target }}: javascript:app.showResultInfo('{{ res.path|urlencode }}')
{% endfor %}
"""
)
for cat, subcats in results.items():
for subcat, catresults in subcats.items():
for res in catresults:
res.render(env, rst_links, results, files)
# global description
text = ""
if dag.workflow.report_text:
with dag.workflow.sourcecache.open(dag.workflow.report_text) as f:
class Snakemake:
config = dag.workflow.config
text = f.read() + rst_links
try:
text = publish_parts(
env.from_string(text).render(
snakemake=Snakemake, categories=results, files=files
),
writer_name="html",
)["body"]
except UndefinedError as e:
raise WorkflowError(
"Error rendering global report caption {}:".format(
dag.workflow.report_text.get_path_or_uri()
),
e,
)
# record time
now = "{} {}".format(datetime.datetime.now().ctime(), time.tzname[0])
results_size = sum(
res.size
for cat in results.values()
for subcat in cat.values()
for res in subcat
)
try:
from pygments.formatters import HtmlFormatter
except ImportError:
raise WorkflowError(
"Python package pygments must be installed to create reports."
)
categories = data.render_categories(results)
rendered_results = data.render_results(results)
rulegraph = data.render_rulegraph(
rulegraph["nodes"], rulegraph["links"], rulegraph["links_direct"]
)
rules = data.render_rules(rules)
runtimes = data.render_runtimes(runtimes)
timeline = data.render_timeline(timeline)
template = env.get_template("index.html.jinja2")
logger.info("Downloading resources and rendering HTML.")
rendered = template.render(
results=rendered_results,
categories=categories,
rulegraph=rulegraph,
rules=rules,
workflow_desc=json.dumps(text),
runtimes=runtimes,
timeline=timeline,
pygments_css=HtmlFormatter(style="stata-dark").get_style_defs(".source"),
custom_stylesheet=custom_stylesheet,
logo=data_uri_from_file(Path(__file__).parent / "template" / "logo.svg"),
now=now,
version=__version__.split("+")[0],
)
# TODO look into supporting .WARC format, also see (https://webrecorder.io)
if not mode_embedded:
with ZipFile(path, compression=ZIP_DEFLATED, mode="w") as zipout:
folder = Path(Path(path).stem)
# store results in data folder
for subcats in results.values():
for catresults in subcats.values():
for result in catresults:
# write raw data
zipout.write(result.path, str(folder.joinpath(result.data_uri)))
# write aux files
parent = folder.joinpath(result.data_uri).parent
for aux_path in result.aux_files:
# print(aux_path, parent, str(parent.joinpath(os.path.relpath(aux_path, os.path.dirname(result.path)))))
zipout.write(
aux_path,
str(
parent.joinpath(
os.path.relpath(
aux_path, os.path.dirname(result.path)
)
)
),
)
# write report html
zipout.writestr(str(folder.joinpath("report.html")), rendered)
else:
with open(path, "w", encoding="utf-8") as htmlout:
htmlout.write(rendered)
logger.info("Report created: {}.".format(path))