# -*- coding: utf-8 -*-
# Copyright 2017 Novo Nordisk Foundation Center for Biosustainability,
# Technical University of Denmark.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
"""Render results into pretty HTML."""
from __future__ import absolute_import
import logging
from os.path import join
from builtins import dict, str
from memote.suite.reporting.reports.report import Report
import memote.suite.reporting.plot as plt
from memote.suite.reporting.bag import ResultBagWrapper
LOGGER = logging.getLogger(__name__)
[docs]class HistoryReport(Report):
"""Render a rich report using the git repository history."""
_valid_indexes = frozenset(["time", "hash"])
def __init__(self, repository, directory, index="time", **kwargs):
"""
Initialize the git interaction and dask bag.
Parameters
----------
repository : git.Repo
An instance of the working directory git repository.
directory : str or path
Where previously collected test results can be found.
index : {'time', 'hash'}, optional
Whether to use time (the default) or commit hashes as the default
axis in plots.
"""
super(HistoryReport, self).__init__(**kwargs)
self.index_dim = index.lower()
if self.index_dim not in self._valid_indexes:
raise ValueError(
"Given index '{0}' must be one of {1}."
"".format(self.index_dim, str(self._valid_indexes)))
self.repo = repository
self.latest = self.repo.active_branch.commit
self.history = [commit.hexsha for commit in self.latest.iter_parents()]
self.history.insert(0, self.latest.hexsha)
self.directory = directory
self.files = [join(self.directory, "{}.json".format(commit))
for commit in self.history]
if len(self.files) == 0:
raise RuntimeError("There is no git branch history!")
self.bag = ResultBagWrapper(self.files)
self.bag.build_index()
self.index = {
"time": "timestamp",
"hash": "commit_hash"
}.get(index, ValueError("Unknown index type '{}'.".format(index)))
if isinstance(self.index, ValueError):
raise self.index
[docs] def render_html(self):
"""
Render a rich report for the repository.
This is currently a stub while we convert from ``jinja2`` templates
to a full Angular based report.
"""
return u""
def _collect_basic_plots(self):
"""Create plots from the basic info data frame."""
df = self.bag.get_basic_dataframe()
plots = dict()
# create genes plot
plots["genes"] = plt.scatter_line_chart(
df[[self.index, "num_genes"]], "Number of Genes")
# reactions
plots["reactions"] = plt.scatter_line_chart(
df[[self.index, "num_reactions"]],
"Number of Reactions")
# metabolites
plots["metabolites"] = plt.scatter_line_chart(
df[[self.index, "num_metabolites"]],
"Number of Metabolites")
plots["metabolites_no_formula"] = plt.scatter_line_chart(
df[[self.index, "num_metabolites_no_formula"]],
"Number of Metabolites Without Formula")
plots["metabolites_no_charge"] = plt.scatter_line_chart(
df[[self.index, "metabolites_no_charge"]],
"Number of Metabolites Without Charge")
plots["reactions_no_GPR"] = plt.scatter_line_chart(
df[[self.index, "reactions_no_GPR"]],
"Number of Reactions Without GPR Rule")
# plots["metabolic_coverage"] = plt.scatter_line_chart(
# df[[self.index, "metabolic_coverage"]],
# "Metabolic Coverage")
plots["ngam_reaction"] = plt.scatter_line_chart(
df[[self.index, "ngam_reaction"]],
"Number of Non-growth-associated Maintenance Reactions")
return plots
def _collect_consistency_plots(self):
"""Create plots from the consistency info data frame."""
df = self.bag.get_consistency_dataframe()
plots = dict()
plots["is_consistent"] = plt.boolean_chart(
df[[self.index, "is_consistent"]],
"Is Stoichiometrically Consistent")
plots["unconserved_metabolites"] = plt.scatter_line_chart(
df[[self.index, "unconserved_metabolites"]],
"Number of Unconserved Metabolites")
plots["magic_atp_production"] = plt.boolean_chart(
df[[self.index, "magic_atp_production"]],
"Has Magic ATP Production")
plots["imbalanced_reactions"] = plt.scatter_line_chart(
df[[self.index, "imbalanced_reactions"]],
"Number of Imbalanced Reactions")
plots["blocked_reactions"] = plt.scatter_line_chart(
df[[self.index, "blocked_reactions"]],
"Number of Blocked Reactions")
# TODO: Fix looped in tests.
# plots["looped_reactions"] = plt.scatter_line_chart(
# df[[self.index, "looped_reactions"]],
# "Number of Looped Reactions")
return plots
def _collect_syntax_plots(self):
"""Create plots from the syntax info data frame."""
df = self.bag.get_consistency_dataframe()
plots = dict()
# plots["reaction_compartment_suffix"] = plt.scatter_line_chart(
# df[[self.index, "reaction_compartment_suffix"]],
# "Number of Reactions with Wrong Compartment Tag")
# plots["untagged_normal_transport"] = plt.scatter_line_chart(
# df[[self.index, "untagged_normal_transport"]],
# "Number of Transport Reactions with Wrong Tag")
# plots["untagged_abc_transport"] = plt.scatter_line_chart(
# df[[self.index, "untagged_abc_transport"]],
# "Number of ABC Transport Reactions with Wrong Tag")
# plots["uppercase_metabolites"] = plt.scatter_line_chart(
# df[[self.index, "uppercase_metabolites"]],
# "Number of Uppercase Metabolite Identifiers")
plots["untagged_demand"] = plt.scatter_line_chart(
df[[self.index, "untagged_demand"]],
"Number of Wrongly Labelled Demand Reactions")
plots["false_demand"] = plt.scatter_line_chart(
df[[self.index, "false_demand"]],
"Number of Falsely Labelled Demand Reactions")
plots["untagged_sink"] = plt.scatter_line_chart(
df[[self.index, "untagged_sink"]],
"Number of Wrongly Labelled Sink Reactions")
plots["false_sink"] = plt.scatter_line_chart(
df[[self.index, "false_sink"]],
"Number of Falsely Labelled Sink Reactions")
plots["untagged_exchange"] = plt.scatter_line_chart(
df[[self.index, "untagged_exchange"]],
"Number of Wrongly Labelled Exchange Reactions")
plots["false_exchange"] = plt.scatter_line_chart(
df[[self.index, "false_exchange"]],
"Number of Falsely Labelled Exchange Reactions")
return plots
def _collect_biomass_plots(self):
"""Create plots from the biomass info data frame."""
df = self.bag.get_biomass_dataframe()
plots = dict()
# components sum
factor = "biomass_ids"
plots["biomass_sum"] = plt.scatter_line_chart(
df[[self.index, "biomass_sum", factor]],
r"$ \text{Sum of Biomass Components }"
r"[ \text{mmol} \text{g}_{\text{DW}}^{-1} \text{h}^{-1} ] $")
plots["biomass_default_flux"] = plt.scatter_line_chart(
df[[self.index, "biomass_default_flux", factor]],
r"$ \text{Biomass Flux }"
r"[ \text{mmol} \text{g}_{\text{DW}}^{-1} \text{h}^{-1} ] $")
plots["num_default_blocked_precursors"] = plt.scatter_line_chart(
df[[self.index, "num_default_blocked_precursors", factor]],
"Number of Blocked Biomass Precursors in Default Medium")
plots["num_open_blocked_precursors"] = plt.scatter_line_chart(
df[[self.index, "num_open_blocked_precursors", factor]],
"Number of Blocked Biomass Precursors in Complete Medium")
plots["gam_in_biomass"] = plt.boolean_chart(
df[[self.index, "gam_in_biomass"]],
"Biomass Contains Growth-associated Maintenance")
return plots
def _collect_annotation_plots(self):
"""Create plots from the annotation info data frame."""
pass
