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 = open(self.raw_caption).read() + 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)
def __init__(self, path, job, caption=None):
self.caption = ""
if caption is not None:
try:
from jinja2 import Template
except ImportError as e:
raise WorkflowError(
"Pyhton package jinja2 must be installed to create reports."
)
snakemake = Snakemake(job.input, job.output, job.params,
job.wildcards, job.threads, job.resources,
job.log, job.dag.workflow.config,
job.rule.name)
try:
caption = Template(
open(caption).read()).render(snakemake=snakemake)
self.caption = publish_parts(caption,
writer_name="html")["body"]
except Exception as e:
raise WorkflowError(
"Error loading caption file of output "
"marked for report.", e)
self.data, self.mime = data_uri(path)
self.id = uuid.uuid4()
self.path = path
def mock_snakemake(rulename, **wildcards):
"""
This function is expected to be executed from the 'scripts'-directory of '
the snakemake project. It returns a snakemake.script.Snakemake object,
based on the Snakefile.
If a rule has wildcards, you have to specify them in **wildcards.
Parameters
----------
rulename: str
name of the rule for which the snakemake object should be generated
**wildcards:
keyword arguments fixing the wildcards. Only necessary if wildcards are
needed.
"""
import snakemake as sm
import os
from pypsa.descriptors import Dict
from snakemake.script import Snakemake
script_dir = Path(__file__).parent.resolve()
assert Path.cwd().resolve() == script_dir, \
f'mock_snakemake has to be run from the repository scripts directory {script_dir}'
os.chdir(script_dir.parent)
for p in sm.SNAKEFILE_CHOICES:
if os.path.exists(p):
snakefile = p
break
workflow = sm.Workflow(snakefile)
workflow.include(snakefile)
workflow.global_resources = {}
rule = workflow.get_rule(rulename)
dag = sm.dag.DAG(workflow, rules=[rule])
wc = Dict(wildcards)
job = sm.jobs.Job(rule, dag, wc)
def make_accessable(*ios):
for io in ios:
for i in range(len(io)):
io[i] = os.path.abspath(io[i])
make_accessable(job.input, job.output, job.log)
snakemake = Snakemake(job.input, job.output, job.params, job.wildcards,
job.threads, job.resources, job.log,
job.dag.workflow.config, job.rule.name, None,)
# create log and output dir if not existent
for path in list(snakemake.log) + list(snakemake.output):
Path(path).parent.mkdir(parents=True, exist_ok=True)
os.chdir(script_dir)
return snakemake
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.rule.module_globals["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,
)
else:
self.caption = ""