Source code for

__author__ = "Johannes Köster"
__copyright__ = "Copyright 2021, Johannes Köster"
__email__ = ""
__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 import (
from snakemake.exceptions import WorkflowError
from snakemake.script import Snakemake
from snakemake import __version__
from snakemake.common import num_if_possible, lazy_property
from snakemake import logging

[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): """ handles most of the """ result = 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)
[docs]class EmbeddedFigure(Figure, EmbeddedMixin): pass
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" "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.""" mime, encoding = mime_from_file(file) if encoding is None: encoding = defaultenc with open(file, "rb") as f: return data_uri(, 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 "",, ) 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]class Category: def __init__(self, name, wildcards, job): if name is None: name = "Other" self.is_other = True else: self.is_other = False try: name = apply_wildcards(name, wildcards) except AttributeError as e: raise WorkflowError("Failed to resolve wildcards.", e, rule=job.rule) = name h = hashlib.sha256() h.update(name.encode()) = h.hexdigest() def __eq__(self, other): return def __hash__(self): return def __lt__(self, other): if == "other": return False return
[docs]class RuleRecord: def __init__(self, job, job_rec): import yaml = 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 = 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):"Loading script code for rule {}".format( _, source, language, _ = script.get_source( self._rule.script, self._rule.workflow.sourcecache, self._rule.basedir ) sources = [source.decode()] elif self._rule.wrapper is not None and not contains_wildcard( self._rule.wrapper ):"Loading wrapper code for rule {}".format( _, 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.decode()] 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( source, lexer, HtmlFormatter(linenos=True, cssclass="source", wrapcode=True), ) for source in sources ] 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 self._rule.output @property def input(self): return self._rule.input def __eq__(self, other): return ( == 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, ): self.name_overwrite = name_overwrite self.mode_embedded = mode_embedded self.path = path = os.path.basename(path) self.size = os.path.getsize(self.path)"Adding {} ({:.2g} MB).".format(, self.size / 1e6)) self.raw_caption = caption self.mime, _ = mime_from_file(self.path) self.workflow = workflow h = hashlib.sha256() h.update(path.encode()) = 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() self.png_uri = self._png_uri() @lazy_property def png_content(self): assert self.is_img convert = shutil.which("magick") if convert is not None: try: # 2048 aims at a reasonable balance between what displays # can show in a png-preview image and what renders quick # into a small enough png max_width = "2048" max_height = "2048" # '>' means only larger images scaled down to within max-dimensions max_spec = max_width + "x" + max_height + ">" png = sp.check_output( ["magick", "convert", "-resize", max_spec, self.path, "png:-"], stderr=sp.PIPE, ) return png except sp.CalledProcessError as e: logger.warning( "Failed to convert image to png with " "imagemagick convert: {}".format(e.stderr) ) else: logger.warning( "Command convert not in $PATH. Install " "imagemagick in order to have embedded " "images and pdfs in the report." ) def _png_uri(self): if self.is_img: png = self.png_content if self.mode_embedded: if png is not None: uri = data_uri( png, os.path.basename(self.path) + ".png", mime="image/png" ) return uri else: if png is not None: return os.path.join("data/thumbnails", def _data_uri(self): if self.mode_embedded: return data_uri_from_file(self.path) else: return os.path.join("data/raw",, 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,, None, ) try: caption = ( + rst_links ) caption = env.from_string(caption).render( snakemake=snakemake, categories=categories, files=files ) self.caption = json.dumps( publish_parts(caption, writer_name="html")["body"] ) except Exception as e: raise WorkflowError( "Error loading caption file of output marked for report.", 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 rulegraph_d3_spec(dag): try: import networkx as nx from networkx.drawing.nx_agraph import graphviz_layout from networkx.readwrite import json_graph except ImportError as e: raise WorkflowError( "Python packages networkx and pygraphviz must be " "installed to create reports.", e, ) g = nx.DiGraph() g.add_nodes_from(sorted( for job in for job in target = for dep in dag.dependencies[job]: source = g.add_edge(source, target) pos = graphviz_layout(g, "dot", args="-Grankdir=BT") xmax = max(x for x, y in pos.values()) + 100 # add offset to account for labels ymax = max(y for x, y in pos.values()) def encode_node(node): x, y = pos[node] return {"rule": node, "fx": x, "fy": y} nodes = list(map(encode_node, g.nodes)) idx = {node: i for i, node in enumerate(g.nodes)} links = [{"target": idx[u], "source": idx[v], "value": 1} for u, v in g.edges] return {"nodes": nodes, "links": links}, xmax, ymax
[docs]def get_resource_as_string(url): r = requests.get(url) if r.status_code == return r.text raise WorkflowError( "Failed to download resource needed for " "report: {}".format(url) )
[docs]def auto_report(dag, path, stylesheet=None): try: from jinja2 import Template, Environment, PackageLoader 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 = except (Exception, BaseException) as e: raise WorkflowError("Unable to read custom report stylesheet.", e)"Creating report...") env = Environment( loader=PackageLoader("snakemake", "report"), 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 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 ) 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, ) ) 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" ) 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: print(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: # 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) # rulegraph rulegraph, xmax, ymax = rulegraph_d3_spec(dag) # configfiles configfiles = [ConfigfileRecord(f) for f in dag.workflow.configfiles] seen = set() files = [ seen.add( or res for cat in results.values() for subcat in cat.values() for res in subcat if not in seen ] rst_links = textwrap.dedent( """ .. _Workflow: javascript:show_panel('workflow') .. _Statistics: javascript:show_panel('statistics') {% for cat, catresults in categories|dictsort %} .. _{{ }}: javascript:show_panel("{{ }}") {% endfor %} {% for res in files %} .. _{{ }}: javascript:show_panel("{{ }}") {% 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 as f: class Snakemake: config = dag.workflow.config text = + rst_links text = publish_parts( env.from_string(text).render( snakemake=Snakemake, categories=results, files=files ), writer_name="html", )["body"] # record time now = "{} {}".format(, 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." ) template = env.get_template("report.html.jinja2")"Downloading resources and rendering HTML.") rendered = template.render( results=results, results_size=results_size, configfiles=configfiles, text=text, rulegraph_nodes=rulegraph["nodes"], rulegraph_links=rulegraph["links"], rulegraph_width=xmax + 20, rulegraph_height=ymax + 20, runtimes=runtimes, timeline=timeline, rules=[rec for recs in rules.values() for rec in recs], version=__version__, now=now, pygments_css=HtmlFormatter(style="trac").get_style_defs(".source"), custom_stylesheet=custom_stylesheet, mode_embedded=mode_embedded, ) # TODO look into supporting .WARC format, also see ( 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 thumbnail if result.is_img and result.png_content: zipout.writestr( str(folder.joinpath(result.png_uri)), result.png_content ) # 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)"Report created: {}.".format(path))