report.py

import json
import os
from collections import defaultdict, Counter
from datetime import date, datetime
from itertools import chain, repeat, groupby
from operator import itemgetter

import requests
from lxml import etree
from lxml.builder import ElementMaker
from lxml.etree import Comment
from more_itertools import pairwise

import csv
from html import escape
from pathlib import Path
from typing import Iterable, List, Dict, Mapping, Tuple, Sequence, Union, Generator, Any, Optional

import networkx as nx

from .config import config
from .bibliography import BiblSource
from .graph import MacrogenesisInfo, EARLIEST, LATEST, DAY, Node, MultiEdge
from .graphutils import pathlink, collapse_timeline, expand_edges, in_path
from .uris import Reference, Witness, Inscription, UnknownRef, AmbiguousRef
from .visualize import write_dot, simplify_graph

logger = config.getLogger(__name__)

RELATION_LABELS = {'not_before': 'nicht vor',
                   'not_after': 'nicht nach',
                   'from_': 'von',
                   'to': 'bis',
                   'when': 'am',
                   'temp-syn': 'ca. gleichzeitig',
                   'temp-pre': 'zeitlich vor',
                   None: '???'
                   }


class HtmlTable:
    """
    Helper class to create a simple HTML table from some kind of data.
    """

    def __init__(self, **table_attrs):
        """
        Creates a new table.

        Args:
            **table_attrs: attributes for the `<table>` elements. For the attribute names, leading and trailing `_` are
             stripped and remaining `_` are transformed to hyphens, so ``HtmlTable(class_='example', data_order='<')``
             will generate ``<table class="example" data-order="&lt;"/>``
        """
        self.titles = []
        self.attrs = []
        self.header_attrs = []
        self.formatters = []
        self.table_attrs = table_attrs
        self.rows = []
        self.row_attrs = []

    def column(self, title='', format_spec=None, attrs={}, **header_attrs):
        """
        Adds a column to this table.

        Args:
            title: The column header as a string (possibly containing an HTML fragment)
            format_spec: How to format each column value. This can be either a format string (see :meth:`str.format`),
                    a format spec (see :func:`format`), a one-argument function or other callable or None (which will
                    result in ``format(value)``)
            **attrs: Attributes to be supplied to each `<td>`

        Returns: self
        """
        self.titles.append(title)

        if format_spec is None:
            formatter = format
        elif callable(format_spec):
            formatter = format_spec
        elif isinstance(format_spec, str) and '{' in format_spec:
            formatter = format_spec.format
        else:
            formatter = lambda data: format(data, format_spec)

        self.formatters.append(formatter)
        self.attrs.append(attrs)
        self.header_attrs.append(header_attrs)
        return self

    def row(self, row, **row_attrs):
        """
        Adds a row to this table's stored data. This data will be used by the zero-argument version of :meth:`format_table`

        The rows are exposed as a list via the property `rows`

        Args:
            row: A tuple (or, in fact, any iterable) of values, prefereably as many as there are rows.
            **row_attrs: HTML Attributes for the row. See the note for `__init__`

        Returns:
            self
        """
        if len(row) > len(self.formatters):
            raise IndexError('{} values in row, but only {} formatters: {}', len(row), len(self.formatters), row)
        self.rows.append(row)
        self.row_attrs.append(row_attrs)
        return self

    @staticmethod
    def _build_attrs(attrdict: Dict):
        """Converts a dictionary of attributes to a string that may be pasted into an HTML start tag."""
        return ''.join(
                ' {}="{!s}"'.format(attr.strip('_').replace('_', '-'), escape(value)) for attr, value in attrdict.items())

    def _format_column(self, index, data) -> str:
        """
        Returns the HTML for the given cell.

        This looks up the configured formatter for the column and calls it to
        rendr the data, and it will also configure the cell attributes.

        Args:
            index: index of the column
            data:  data to display

        Returns:
            String containing HTML `<td>` element
        """
        try:
            attributes = self._build_attrs(self.attrs[index])
            content = self.formatters[index](data)
            return f'<td{attributes}>{content}</td>'
        except Exception as e:
            raise ValueError('Error formatting column %s' % self.titles[index]) from e

    def _format_row(self, row: Iterable, **rowattrs) -> str:
        """
        Returns the HTML for a column with the given row.
        Args:
            row: the row to format
            **rowattrs: attributes for the row

        Returns: a string containing an HTML `<tr>` element

        """
        attributes = self._build_attrs(rowattrs)
        try:
            return f'<tr{attributes}>' + ''.join(
                    self._format_column(index, column) for index, column in enumerate(row)) + '</tr>'
        except:
            logger.exception('Error formatting row %s', row)
            return f'<tr class="pure-alert pure-error"><td>Error formatting row {row}</td></tr>'

    def _format_rows(self, rows: Iterable[Iterable]) -> Generator[str, None, None]:
        """Formats the given rows."""
        for row in rows:
            yield self._format_row(row)

    def _format_header(self):
        """
        Formats the table header.
        """
        column_headers = ''.join(['<th{1}>{0}</th>'.format(title, self._build_attrs(attrs))
                                  for title, attrs in zip(self.titles, self.header_attrs)])
        return '<table class="pure-table"{1}><thead>{0}</thead><tbody>'.format(column_headers, self._build_attrs(self.table_attrs))

    def _format_footer(self):
        return '</tbody></table>'

    def format_table(self, rows=None, row_attrs=None):
        """
        Actually formats the table.

        In the zero-argument form, this uses the rows added previously using the `row` method. Otherwise, the given
        data is used.

        Args:
            rows: If given, the rows to format. This is a list of n-tuples, for n columns.
            row_attrs: If given, this should be a list that contains a mapping with the attributes for each row.

        Returns:
            string containing HTML code for the table
        """
        if rows is None:
            rows = self.rows
            row_attrs = self.row_attrs
        if row_attrs is None:
            row_attrs = repeat({})
        return self._format_header() + ''.join(
                (self._format_row(row, **attrs) for row, attrs in zip(rows, row_attrs))) + self._format_footer()


def write_html(filename: Path, content: str, head: str = None, breadcrumbs: List[Dict[str,str]] = [],
               graph_id: str = None,
               graph_options: Dict[str,object] = dict(controlIconsEnabled=True)) -> None:
    """
    Writes a html page.
    Args:
        filename: out file path
        content: formatted contents for the main part
        head: heading, will become the last of the breadcrumbs
        breadcrumbs: list of dictionaries with keys _caption_ and _link_, first (macrogenesis) and last (head) omitted
        graph_id: if present, initialize javascript for graph with the given id
        graph_options: if present, options for the svg viewer js
    """
    if head is not None:
        breadcrumbs = breadcrumbs + [dict(caption=head)]
    breadcrumbs = [dict(caption='Makrogenese-Lab', link='/macrogenesis')] + breadcrumbs
    prefix = """<?php include "../includes/header.php"?>
     <section>"""
    require = "requirejs(['faust_common', 'svg-pan-zoom'], function(Faust, svgPanZoom)"
    if graph_id is not None:
        init = f"""
        graph = document.getElementById('{graph_id}');
        bbox = graph.getBoundingClientRect();
        if (bbox.height > (window.innerHeight - bbox.top)) {{
            graph.height = window.innerHeight - bbox.top;
            graph.width = '100%';
        }}
        svgPanZoom('#{graph_id}', {json.dumps(graph_options)})
        """
    else:
        init = ''
    suffix = f"""</section>
    <script type="text/javascript">
        requirejs(['faust_common', 'svg-pan-zoom', 'sortable', 'jquery', 'jquery.table'],
        function(Faust, svgPanZoom, Sortable, $, $table) {{
            document.getElementById('breadcrumbs').appendChild(Faust.createBreadcrumbs({json.dumps(breadcrumbs)}));
            {init}
            Sortable.init();
            $("table[data-sortable]").fixedtableheader();
        }});
    </script>
    <?php include "../includes/footer.php"?>"""
    with open(filename, 'wt', encoding='utf-8') as f:
        f.write(prefix)
        f.write(content)
        f.write(suffix)


def report_components(graphs: MacrogenesisInfo):
    target = config.path.report_dir
    logger.info('Writing component overview to %s', target)
    target.mkdir(parents=True, exist_ok=True)
    report = f"""<h3>{len(graphs.conflicts)} stark zusammenhängende Komponenten</h3>
    <p>Stark zusammenhängende Komponenten sind Teilgraphen, in denen jeder Knoten von
    jedem anderen erreichbar ist. Hier ist keine Ordnung möglich, ohne dass Kanten entfernt
    werden.</p>
    """
    sccs = [component for component in nx.strongly_connected_components(graphs.base) if len(component) > 1]
    scc_subgraphs = [nx.subgraph(graphs.base, scc) for scc in sccs]
    scc_table = _report_subgraphs(scc_subgraphs, target, 'scc-{0:02d}')
    report += scc_table.format_table()

    wccs = [nx.subgraph(graphs.working, component) for component in nx.weakly_connected_components(graphs.working)]
    report += f"""<h3>{len(wccs)} schwach zusammenhängende Komponenten</h3>
    <p>Zwischen unterschiedlichen schwach zusammenhängenden Komponenten gibt es keine Verbindungen.</p>"""

    wcc_table = _report_subgraphs(wccs, target, 'wcc-{0:02d}')
    report += wcc_table.format_table()
    write_html(target / 'components.php', report, head="Komponenten")


def _report_subgraphs(removed_edges, out, pattern, breadcrumbs=[], head_pattern='%d'):
    table = HtmlTable().column('Nummer', format_spec='<a href="' + pattern + '">{0}</a>') \
        .column('Dokumente') \
        .column('Relationen') \
        .column('Entfernte Relationen') \
        .column('Quellen', format_spec=lambda s: ", ".join(map(str, s))) \
        .column('Entfernte Quellen', format_spec=lambda s: ", ".join(map(str, s)))
    for index, subgraph in enumerate(removed_edges, start=1):
        refs = len([node for node in subgraph.nodes if isinstance(node, Reference)])
        all_edges = list(subgraph.edges(keys=True, data=True))
        removed_edges = [(u, v, k, attr) for (u, v, k, attr) in all_edges if 'delete' in attr and attr['delete']]
        relations = [(u, v, k, attr) for (u, v, k, attr) in all_edges if 'delete' not in attr or not attr['delete']]
        sources = {attr['source'].citation for u, v, k, attr in relations if 'source' in attr}
        conflict_sources = {attr['source'].citation for u, v, k, attr in removed_edges}
        table.row((index, refs, len(relations), len(removed_edges), sources, conflict_sources))
        write_dot(subgraph, out / (pattern + "-graph.dot").format(index))
        write_html(out / (pattern + '.php').format(index),
                   f"""<object id="refgraph" class="refgraph" type="image/svg+xml"
                          data="{pattern.format(index)}-graph.svg"></object>\n""",
                   graph_id='refgraph', breadcrumbs=breadcrumbs, head=head_pattern.format(index))
    return table


def write_bibliography_stats(graph: nx.MultiDiGraph):
    bibls = defaultdict(Counter)
    for u, v, attr in graph.edges(data=True):
        if 'source' in attr:
            bibls[attr['source'].uri][attr['kind']] += 1
    kinds = sorted({str(kind) for bibl in bibls.values() for kind in bibl.keys()})
    totals = Counter({ref: sum(types.values()) for ref, types in bibls.items()})
    with open('sources.tsv', 'wt', encoding='utf-8') as out:
        writer = csv.writer(out, delimiter='\t')
        writer.writerow(['Reference', 'Weight', 'Total'] + kinds)
        for bibl, total in totals.most_common():
            writer.writerow([bibl, BiblSource(bibl).weight, total] + [bibls[bibl][kind] for kind in kinds])

def _fmt_node(node: Union[Reference, object]):
    """Formats a node by creating a link of possible"""
    if isinstance(node, Reference):
        return f'<a href="{node.filename.stem}">{node}</a>'
    else:
        return format(node)


def _edition_link(ref: Reference):
    """Creates a link or links into the edition for the node."""
    if isinstance(ref, Witness):
        return f'<a href="/document?sigil={ref.sigil_t}">{ref}</a>'
    elif isinstance(ref, Inscription):
        return f'Inskription {ref.inscription} von {_edition_link(ref.witness)}'
    elif isinstance(ref, UnknownRef):
        return ''
    elif isinstance(ref, AmbiguousRef):
        return ", ".join(_edition_link(wit) for wit in ref.witnesses)
    else:
        return format(ref)


class RefTable(HtmlTable):
    """
    Builds a table of references.
    """

    def __init__(self, base: nx.MultiDiGraph, **table_attrs):
        super().__init__(data_sortable="true", **table_attrs)
        (self.column('Nr.', data_sortable="numericplus")
             .column('Knoten davor', data_sortable="numericplus")
             .column('Objekt', data_sortable="sigil", format_spec=_fmt_node)
             .column('Typ / Edition', data_sortable="sigil", format_spec=_edition_link)
             .column('nicht vor', data_sortable="alpha", format_spec=lambda d: format(d) if d != EARLIEST else "")
             .column('nicht nach', data_sortable="alpha", format_spec=lambda d: format(d) if d != LATEST else "")
             .column('erster Vers', data_sortable="numericplus")
             .column('Aussagen', data_sortable="numericplus")
             .column('<a href="conflicts">Konflikte</a>', data_sortable="numericplus"))
        self.base = base


    def reference(self, ref: Reference, index: Optional[int] = None, write_subpage: bool = False):
        """
        Adds the given reference to the table.

        Args:
            ref: the object for which the row will be created
            index: if present, the index to display for the node.
            write_subpage: if true, create a subpage with all assertions for the referende
        """
        if ref in self.base:
            if index is None:
                index = self.base.node[ref]['index']
            assertions = list(chain(self.base.in_edges(ref, data=True), self.base.out_edges(ref, data=True)))
            conflicts = [assertion for assertion in assertions if 'delete' in assertion[2] and assertion[2]['delete']]
            self.row((f'<a href="refs#idx{index}">{index}</a>', ref.rank, ref, ref, ref.earliest, ref.latest,
                          getattr(ref, 'min_verse', ''), len(assertions), len(conflicts)),
                         id=f'idx{index}', class_=type(ref).__name__)
            if write_subpage:
                self._last_ref_subpage(DAY, ref)
        else:
            self.row((index, 0, format(ref), ref, '', '', getattr(ref, 'min_verse', ''), ''),
                         class_='pure-fade-40', title='Keine Macrogenesedaten', id=f'idx{index}')

    def _last_ref_subpage(self, DAY, ref):
        """Writes a subpage for ref, but only if it’s the last witness we just wrote"""
        target = config.path.report_dir
        basename = target / ref.filename
        relevant_nodes = {ref} | set(self.base.predecessors(ref)) | set(self.base.successors(ref))
        if ref.earliest != EARLIEST:
            relevant_nodes |= set(nx.shortest_path(self.base, ref.earliest - DAY, ref))
        if ref.latest != LATEST:
            relevant_nodes |= set(nx.shortest_path(self.base, ref, ref.latest + DAY))
        ref_subgraph = self.base.subgraph(relevant_nodes)
        write_dot(ref_subgraph, basename.with_name(basename.stem + '-graph.dot'), highlight=ref)
        report = f"<!-- {repr(ref)} -->\n"
        report += self.format_table(self.rows[-1:])
        report += f"""<object id="refgraph" class="refgraph" type="image/svg+xml" data="{basename.with_name(basename.stem+'-graph.svg').name}"></object>\n"""
        kinds = {'not_before': 'nicht vor',
                 'not_after': 'nicht nach',
                 'from_': 'von',
                 'to': 'bis',
                 'when': 'am',
                 'temp-syn': 'ca. gleichzeitig',
                 'temp-pre': 'entstanden nach',
                 'orphan': '(Verweis)',
                 'inscription': 'Inskription von',
                 None: '???'
                 }
        assertionTable = (HtmlTable(data_sortable='true')
                          .column('berücksichtigt?', data_sortable_type='alpha')
                          .column('Aussage', data_sortable_type='alpha')
                          .column('Bezug', data_sortable_type='sigil', format_spec=_fmt_node)
                          .column('Quelle', data_sortable_type='bibliography', format_spec=_fmt_source)
                          .column('Kommentare', format_spec=_fmt_comments)
                          .column('XML', format_spec=_fmt_xml))
        for (u, v, attr) in self.base.in_edges(ref, data=True):
            delete_ = 'delete' in attr and attr['delete']
            assertionTable.row((
                f'<a href="{pathlink(u, v)}">nein</a>' if attr.get('delete', False) else \
                    'ignoriert' if attr.get('ignore', False) else 'ja',
                                kinds[attr['kind']],
                                u + DAY if isinstance(u, date) else u,
                                attr,
                                attr.get('comments', []),
                                attr.get('xml', [])),
                               class_='delete' if delete_ else str(attr['kind']))
        kinds['temp-pre'] = 'entstanden vor'
        for (u, v, attr) in self.base.out_edges(ref, data=True):
            delete_ = 'delete' in attr and attr['delete']
            assertionTable.row((f'<a href="{pathlink(u, v).stem}">nein</a>' if delete_ else 'ja',
                                kinds[attr['kind']],
                                v - DAY if isinstance(v, date) else v,
                                attr,
                                attr.get('comments', []),
                                attr.get('xml', [])),
                               class_='delete' if delete_ else str(attr['kind']))
        write_html(basename.with_suffix('.php'), report + assertionTable.format_table(),
                   breadcrumbs=[dict(caption='Referenzen', link='refs')],
                   head=str(ref), graph_id='refgraph')


class AssertionTable(HtmlTable):

    def __init__(self, **table_attrs):
        super().__init__(data_sortable='true', **table_attrs)
        (self.column('berücksichtigt?', data_sortable_type="alpha")
             .column('Subjekt',  _fmt_node, data_sortable_type="sigil")
             .column('Relation',  RELATION_LABELS.get, data_sortable_type="alpha")
             .column('Objekt', _fmt_node, data_sortable_type="sigil")
             .column('Quelle', _fmt_source, data_sortable_type="bibliography")
             .column('Kommentare', _fmt_comments, data_sortable_type="alpha")
             .column('XML', _fmt_xml, data_sortable_type="alpha"))

    def edge(self, u: Reference, v: Reference, attr: Dict[str,object]):
        classes = [attr['kind']] if 'kind' in attr and attr['kind'] is not None else ['unknown-kind']
        if attr.get('ignore', False): classes.append('ignore')
        if attr.get('delete', False): classes.append('delete')
        self.row((
            f'<a href="{pathlink(u, v)}">nein</a>' if attr.get('delete', False) else \
                'ignoriert' if attr.get('ignore', False) else 'ja',
            u,
            attr['kind'],
            v,
            attr,
            attr.get('comments', []),
            attr.get('xml', '')),
        class_=' '.join(classes))

def _fmt_source(attrs):
    source: BiblSource = attrs['source']
    result = f'<a href="{source.filename}">{source.citation}</a>'
    if 'sources' in attrs:
        result += ' ' + '; '.join(s.detail for s in attrs['sources'])
    elif source.detail:
        result += ' ' + source.detail
    return result


def _source_link(file: Path, line: Optional[Union[int, str]] = None, text: Optional[Union[int, str]] = None) -> str:
    file = file.relative_to('macrogenesis')
    if text is None:
        text = file
        if line is not None:
            text += ': ' + str(line)
    href = os.path.join(config.xmlroot, os.fspath(file))
    if line is not None:
        href += '#L' + str(line)
    return f'<a href="{href}">{text}</a>'


def _fmt_xml(xml: Union[Tuple[Path, int], Sequence[Tuple[str, int]]]):
    if not xml:
        return ""

    if isinstance(xml[0], Path):
        return _source_link(xml[0], xml[1], f"{xml[0].relative_to('macrogenesis')}: {xml[1]}")
    else:
        result = []
        for file, lines in groupby(xml, itemgetter(0)):
            result.append(_source_link(file) + ': ' + ", ".join(_source_link(file, line, line) for (_, line) in lines))
        return "; ".join(result)


def _fmt_comments(comments):
    if not comments:
        return ""
    return " / ".join(str(comment) for comment in comments if comment)


def report_downloads(graphs: MacrogenesisInfo):
    target = config.path.report_dir
    target.mkdir(exist_ok=True, parents=True)

    simplified = simplify_graph(graphs.base)
    nx.write_gexf(simplified, str(target / 'base.gexf'))
    nx.write_edgelist(simplified, str(target / 'base.edges'))
    graphs.save(target / "macrogen-info.zip")

    write_html(target / 'downloads.php', """
    <section>
    <p>Downloadable files for the base graph in various formats:</p>
    <ol>
        <li><a href='base.gexf'>GEXF</a></li>
        <li><a href='base.edges'>Edge List</a></li>
        <li><a href='macrogen-info.zip'>MacrogenesisInfo for the faust-macrogen library</a></li>
    <ol>
    </section>
    <h4>Nodes</h4>
    <p>The <strong>nodes</strong> are either URIs or dates in ISO 8601 format. URIs of the form
       <code>faust://document/<var>scheme</var>/<var>sigil</var></code> denote a witness (document)
       that has the identifier <var>sigil</var> in the respective identifier scheme. 
       <code>faust://inscription/<var>scheme</var>/<var>sigil</var>/<var>id</var></code> denote an 
       inscription (single “writing event”) on the respective document.</p>
        <p>If some URI has a <var>scheme</var> ≠ <code>faustedition</code>, then it was not possible to map it to
       a document in the edition. You may still try the sigil with the search. Otherwise, the document can be
       displayed at <code>http://faustedition.net/document?sigil=<var>sigil</var></code>.
       </p>
    <p>Dates are always of the form YYYY-MM-DD.</p>
    
    <h4>Edges</h4>
    <p>The edges have attributes that describe them further:</p>
    <table class="pure-table">
      <tr>
        <th>Attribute</th><th>Value(s)</th><th>Meaning (<var>u</var> → <var>v</var>)</th>
      </tr>
      <tr>
        <td rowspan="3">kind</td>
        <td>
            <code>not_before</code>, <code>not_after</code>, <code>from_</code>, <code>to_</code>, <code>when</code>,
            <code>timeline</code>
        </td>
        <td>These all essentially mean <var>u</var> happened before <var>v</var></td>
      </tr>
      <tr>
        <td><code>timeline</code></td>
        <td><var>v</var> is the next date after date node <var>u</var></td>
      </tr>
      <tr>
        <td><code>temp-syn</code></td>
        <td><var>u</var> and <var>v</var> happened about at the same time
      </tr>
      <tr>
        <td>ignore</td>
        <td>boolean</td>
        <td>if present and true, this edge is to be ignored for philological reasons</td>
      </tr>
      <tr>
         <td>delete</td>
         <td>boolean</td>
         <td>if present and true, this edge has been removed by the minimum feedback edge set heuristics</td>
      </tr>
      <tr>
          <td>weight</td>
          <td>positive integer</td>
          <td>trust in edge, generated mainly from sources</td>
      </tr>
      <tr>
        <td>source</td>
        <td>URI</td>
        <td>URI identifying the source for this assertion</td>
      </tr>
      <tr>
         <td>xml</td>
         <td></td>
         <td>file name and line of the <a href="https://github.com/faustedition/faust-xml/tree/master/xml/macrogenesis">XML file</a>
          with this assertion</td>
      </tr>
    </table>
    
    <h4>MacrogenesisInfo</h4>
    <p>The <a href='macrogen-info.zip'>macrogen-info.zip</a> file contains the data required to recreate the graph info
    in the <a href='https://github.com/faustedition/faust-macrogen'>faust-macrogen</a> library. To do so, run:</p>
    <pre lang='python'>
    from macrogen import MacrogenesisInfo
    graphs = MacrogenesisInfo('macrogen-info.zip')
    </pre>
    <p>Note this is barely tested yet.</p>
    """, "Downloads")


def report_refs(graphs: MacrogenesisInfo):
    # Fake dates for when we don’t have any earliest/latest info

    target = config.path.report_dir
    target.mkdir(exist_ok=True, parents=True)

    nx.write_yaml(simplify_graph(graphs.base), str(target / 'base.yaml'))
    nx.write_yaml(simplify_graph(graphs.working), str(target / 'working.yaml'))
    nx.write_yaml(simplify_graph(graphs.dag), str(target / 'dag.yaml'))

    nx.write_gpickle(graphs.dag, str(target / 'dag.gpickle'))
    nx.write_gpickle(graphs.working, str(target / 'working.gpickle'))
    nx.write_gpickle(graphs.base, str(target / 'base.gpickle'))

    refs = graphs.order_refs()
    overview = RefTable(graphs.base)

    for index, ref in enumerate(refs, start=1):
        overview.reference(ref, index, write_subpage=True)

    write_html(target / 'refs.php', overview.format_table(), head="Referenzen")

    # write_dot(simplify_graph(graphs.base), str(target / 'base.dot'), record=False)
    # write_dot(simplify_graph(graphs.working), str(target / 'working.dot'), record=False)
    # write_dot(simplify_graph(graphs.dag), str(target / 'dag.dot'), record=False)

def _invert_mapping(mapping: Mapping) -> Dict:
    result = defaultdict(set)
    for key, value in mapping.items():
        result[value].add(key)
    return result


def report_missing(graphs: MacrogenesisInfo):
    target = config.path.report_dir
    refs = {node for node in graphs.base.nodes if isinstance(node, Reference)}
    all_wits = {wit for wit in Witness.database.values() if isinstance(wit, Witness)}
    used_wits = {wit for wit in refs if isinstance(wit, Witness)}
    unknown_refs = {wit for wit in refs if isinstance(wit, UnknownRef)}
    missing_wits = all_wits - used_wits
    inscr = {inscr: inscr.witness for inscr in refs if isinstance(inscr, Inscription)}
    wits_with_inscr = _invert_mapping(inscr)
    report = f"""
    <h2>Fehlende Zeugen</h2>
    <p>Für {len(missing_wits)} von insgesamt {len(used_wits)} Zeugen <a href="#missing">liegen keine Makrogenesedaten
       vor</a>. Bei {len(missing_wits & wits_with_inscr.keys())} davon sind zumindest Informationen über
       Inskriptionen hinterlegt. Umgekehrt gibt es <a href="#unknown">zu {len(unknown_refs)} Referenzen in der
       Makrogenese</a> keine Entsprechung in der Edition.</p>
    <h3 id="missing">Zeugen ohne Makrogenesedaten</h3>
    """
    missing_table = (HtmlTable()
                     .column('Zeuge ohne Daten', format_spec=_edition_link)
                     .column('Inskriptionen', format_spec=lambda refs: ", ".join(map(_fmt_node, refs))))
    report += missing_table.format_table(
            (ref, wits_with_inscr[ref]) for ref in sorted(missing_wits, key=lambda r: r.sort_tuple()))
    report += '\n<h3 id="unknown">Unbekannte Referenzen</h3>'
    unknown_table = (HtmlTable()
                     .column('Referenz')
                     .column('URI'))
    report += unknown_table.format_table((ref, ref.uri) for ref in sorted(unknown_refs))
    write_html(target / 'missing.php', report, head="Fehlendes")
    for ref in missing_wits:
        missing_path = target / ref.filename.with_suffix('.php')
        logger.info('Writing missing page for %s to %s', ref, missing_path)
        write_html(missing_path,
                   f"""
                   <p class="pure-alert pure-alert-warning"><strong>Für {ref} liegen noch keine Makrogenesedaten vor.</strong>
                   Ggf. fehlt auch nur die Zuordnung zur richtigen Sigle – siehe in der <a href="refs">Liste der Referenzen</a>.</p>
                   """,
                   head=format(ref))


def _format_collapsed_path(path: List[Node]):
    collapsed = []
    for i in range(len(path)):
        if 0 < i < len(path)-1 and isinstance(path[i], date) and isinstance(path[i-1], date) and isinstance(path[i+1], date):
            continue
        collapsed.append(path[i])
    return " → ".join(map(_fmt_node, collapsed))


def _report_conflict(graphs: MacrogenesisInfo, u, v):
    target = config.path.report_dir
    reportfile = pathlink(u, v)
    cyclefile = reportfile.with_name(reportfile.stem + '-cycles.php')
    graphfile = reportfile.with_name(reportfile.stem + '-graph.dot')
    cyclegraphfile = reportfile.with_name(graphfile.stem + '-graph.dot')
    relevant_nodes = {u} | set(graphs.base.predecessors(u)) | set(graphs.base.successors(u)) \
                     | {v} | set(graphs.base.predecessors(v)) | set(graphs.base.successors(v))
    counter_path = []
    try:
        counter_path = nx.shortest_path(graphs.dag, v, u, weight='iweight')
        involved_cycles = {cycle for cycle in graphs.simple_cycles if in_path((u, v), cycle, True)}
        relevant_nodes = set(counter_path)

        #counter_desc = " → ".join(map(_fmt_node, counter_path))
        counter_desc = _format_collapsed_path(counter_path)
        counter_html = f'<p><strong>Pfad in Gegenrichtung:</strong> {counter_desc}</p>'
    except nx.NetworkXNoPath:
        counter_html = f'<p>kein Pfad in Gegenrichtung ({_fmt_node(v)} … {_fmt_node(u)}) im Sortiergraphen</p>'
    except nx.NodeNotFound:
        logger.exception('Node not found!? %s or %s', u, v)
        counter_html = ''
    counter_graph: nx.MultiDiGraph = nx.subgraph(graphs.base, relevant_nodes)
    for _, _, trigger_node in counter_graph.edges(data='trigger_node'):
        if trigger_node:
            relevant_nodes.add(trigger_node)
            logger.info('Adding trigger node %s to %s', trigger_node, reportfile.stem)
    counter_graph: nx.MultiDiGraph = nx.subgraph(graphs.base, relevant_nodes).copy()

    if involved_cycles:
        counter_html += f"<p>Teil von mindestens <a href='{cyclefile.stem}'>{len(involved_cycles)} einfachen Zyklen</a></p>"

    # Highlight conflicting edges, counter path and the two nodes of the conflicting edge(s)
    for v1, v2 in [(u, v)] + list(pairwise(nx.shortest_path(counter_graph, v, u, weight='iweight'))):
        for k, attr in counter_graph.get_edge_data(v1, v2).items():
            attr['highlight'] = True
    counter_graph.node[u]['highlight'] = True
    counter_graph.node[v]['highlight'] = True

    counter_graph = collapse_timeline(counter_graph)
    cycle_graph = counter_graph.copy()

    for cycle in involved_cycles:
        cycle_graph.add_edges_from(expand_edges(graphs.base, pairwise(cycle)))

    write_dot(counter_graph, str(target / graphfile))
    write_dot(cycle_graph, str(target / cyclegraphfile))

    table = AssertionTable()
    for k, attr in graphs.base.get_edge_data(u, v).items():
        table.edge(u, v, attr)

    write_html(target / reportfile,
               f"""
               {table.format_table()}
               {counter_html}
               <object id="refgraph" type="image/svg+xml" data="{graphfile.with_suffix('.svg')}"></object>
               """,
               graph_id='refgraph',
               head=f'Entfernte Kante {u} → {v}', breadcrumbs=[dict(caption="Entfernte Kanten", link='conflicts')])
    write_html(target / cyclefile,
               f"""
               {table.format_table()}
               {counter_html}
               <object id="refgraph" type="image/svg+xml" data="{cyclegraphfile.with_suffix('.svg')}"></object>
               """,
               graph_id='refgraph',
               head=f'Entfernte Kante {u} → {v}', breadcrumbs=[dict(caption="Entfernte Kanten", link='conflicts')])

    return reportfile


def report_conflicts(graphs: MacrogenesisInfo):
    target = config.path.report_dir
    table = AssertionTable()
    removed_edges = [(u, v, k, attr) for (u, v, k, attr) in graphs.base.edges(keys=True, data=True) if
                     'delete' in attr and attr['delete']]
    for index, (u, v, k, attr) in enumerate(sorted(removed_edges, key=lambda t: getattr(t[0], 'index', 0)), start=1):
        reportfile = _report_conflict(graphs, u, v)
        table.edge(u, v, attr)
    write_html(target / 'conflicts.php', table.format_table(), head=f'{len(removed_edges)} entfernte Kanten')


def report_sources(graphs: MacrogenesisInfo):
    target = config.path.report_dir
    by_source = defaultdict(list)
    for u, v, k, attr in graphs.base.edges(keys=True, data=True):
        if 'source' in attr:
            by_source[attr['source'].uri].append((u, v, k, attr))

    def _fmt_source(uri):
        source = BiblSource(uri)
        return f'<a href="{source.filename}">{source}</a>'

    sources_table = (HtmlTable(data_sortable='true')
                     .column('Quelle', format_spec=_fmt_source, data_sortable_type='bibliography')
                     .column('Aussagen', data_sortable_type='numericplus')
                     .column('entfernt', data_sortable_type='numericplus')
                     .column('Nutzungsanteil', format_spec='{:.1f} %', data_sortable_type='numericplus')
                     .column('Gewicht', data_sortable_type='numericplus')
                     .column('Zeugen', data_sortable_type='numericplus'))
    with (target / "sources_data.csv").open('wt', encoding='utf-8') as sources_csv_file:
        csv_writer = csv.writer(sources_csv_file)
        csv_writer.writerow(('Source', 'Label', 'Weight', 'Assertions', 'Conflicts', 'Ignored', 'Usage',  'Witnesses'))
        for uri, edges in sorted(by_source.items()):
            source = BiblSource(uri)
            filename = target / (source.filename + '.php')
            graphfile = filename.with_name(filename.stem + '-graph.dot')
            logger.info('%d assertions from %s', len(edges), source.citation)
            # subgraph = graphs.base.edge_subgraph([(u,v,k) for u,v,k,attr in edges])
            subgraph = graphs.base.subgraph({u for u, v, k, attr in edges} | {v for u, v, k, attr in edges})
            all_edges = {edge[:3] for edge in edges}
            ignored = {edge[:3] for edge in edges if edge[3].get('ignore', False)}
            conflicts = {edge[:3] for edge in edges if edge[3].get('delete', False)} - ignored
            used = all_edges - conflicts - ignored
            ratio = len(used) / len(conflicts | used) if conflicts | used else 0

            write_dot(subgraph, graphfile)
            witness_count = len([node for node in subgraph.nodes if isinstance(node, Reference)])
            sources_table.row((uri,
                               len(edges),
                               len(conflicts),
                               ratio*100,
                               source.weight,
                               witness_count))
            csv_writer.writerow((uri, source.citation, source.weight, len(edges), len(conflicts), len(ignored), ratio, witness_count))
            current_table = AssertionTable()
            for u, v, k, attr in edges:
                current_table.edge(u, v, attr)
            write_html(target / (source.filename + '.php'),
                       f"""<p><a href="/bibliography#{source.filename}">{source.citation} in der Bibliographie</a></p>
                       <object id="refgraph" type="image/svg+xml" data="{graphfile.with_suffix('.svg').name}"></object>
                           {current_table.format_table()}""",
                       graph_id='refgraph',
                       breadcrumbs=[dict(caption='Quellen', link='sources')],
                       head=source.citation)

    write_html(target / 'sources.php', sources_table.format_table(), head='Quellen')


def report_index(graphs):
    target = config.path.report_dir

    pages = [('refs', 'Zeugen', 'Alle referenzierten Dokumente in der erschlossenen Reihenfolge'),
             ('scenes', 'nach Szene', 'Die relevanten Zeugen für jede Szene'),
             ('conflicts', 'entfernte Aussagen', 'Aussagen, die algorithmisch als Konflikt identifiziert und entfernt wurden'),
             ('components', 'Komponenten', 'stark und schwach zusammenhängende Komponenten des Ausgangsgraphen'),
             ('missing', 'Fehlendes', 'Zeugen, zu denen keine Aussagen zur Makrogenese vorliegen, und unbekannte Zeugen'),
             ('sources', 'Quellen', 'Aussagen nach Quelle aufgeschlüsselt'),
             ('dag', 'sortierrelevanter Gesamtgraph', 'Graph aller für die Sortierung berücksichtigter Aussagen (einzoomen!)'),
             ('tred', 'transitive Reduktion', '<a href="https://de.wikipedia.org/w/index.php?title=Transitive_Reduktion">Transitive Reduktion</a> des Gesamtgraphen'),
             ('help', 'Legende', 'Legende zu den Graphen'),
             ('downloads', 'Downloads', 'Graphen zum Download')]
    links = "\n".join(('<tr><td><a href="{}" class="pure-button pure-button-tile">{}</td><td>{}</td></tr>'.format(*page) for page in pages))
    report = f"""
      <p>
        Dieser Bereich der Edition enthält experimentelle Informationen zur Makrogenese, er wurde zuletzt
        am {datetime.now()} generiert.
      </p>
      <section class="center pure-g-r">

        <article class="pure-u-1">
            <table class="pure-table">
                {links}
            </table>
        </article>

      </section>
    """


    write_html(target / "index.php", report)
    logger.info('Writing DAG ...')
    write_dot(graphs.dag, target / 'dag-graph.dot')
    write_html(target / 'dag.php', '<object type="image/svg+xml" data="dag-graph.svg" id="refgraph"/>',
               graph_id='refgraph', head='Effektiver Gesamtgraph (ohne Konflikte)',
               graph_options=dict(controlIconsEnabled=True, maxZoom=200))

    logger.info('Creating transitive reduction ...')
    tred_base = nx.MultiDiGraph(nx.transitive_reduction(graphs.dag))
    tred = nx.edge_subgraph(graphs.dag, tred_base.edges)
    write_dot(tred, target / 'tred-graph.dot')
    write_html(target / 'tred.php', '<object type="image/svg+xml" data="tred-graph.svg" id="refgraph"/>',
               graph_id='refgraph', head='Transitive Reduktion',
               graph_options=dict(controlIconsEnabled=True, maxZoom=200))

def report_help():
    target = config.path.report_dir
    def demo_graph(u, v, extend=None, **edge_attr) -> nx.MultiDiGraph:
        G = nx.MultiDiGraph() if extend is None else extend.copy()
        G.add_edge(u, v, **edge_attr)
        return G

    w1 = Witness({'uri': 'faust://help/wit1', 'sigil': 'Zeuge 1', 'sigil_t': 'Zeuge_1'})
    w2 = Witness({'uri': 'faust://help/wit2', 'sigil': 'Zeuge 2', 'sigil_t': 'Zeuge_2'})
    d1 = date(1799, 1, 17)
    d2 = date(1799, 2, 5)
    d3 = date(1799, 1, 28)

    g1 = demo_graph(w1, w2, kind='temp-pre', label='Quelle 1')
    g1a = g1.copy()
    g1a.add_edge(w2, w1, kind='temp-pre', delete=True, label='Quelle 2')
    g1a.add_edge(w2, w1, kind='temp-pre', ignore=True, label='Quelle 3')
    g2 = demo_graph(w1, w2, kind='temp-syn', label='Quelle 2')
    g3 = demo_graph(d1 - DAY, w1, kind='not_before', source='Quelle 1')
    g3.add_edge(w1, d2 + DAY, kind='not_after', source='Quelle 1')
    g4 = demo_graph(d1 - DAY, w1, kind='from_', source='Quelle 2')
    g4.add_edge(w1, d2 + DAY, kind='to_', source='Quelle 2')
    g5 = demo_graph(d3 - DAY, w2, kind='when', source='Quelle 2')
    g5.add_edge(w2, d3 + DAY, kind='when', source='Quelle 2')

    i1 = Witness.get('faust://inscription/faustedition/2_IV_H.19/i_uebrige')
    i1w = i1.witness
    g_orphan = demo_graph(i1, i1w, kind='orphan', source='faust://orphan/adoption')

    help_graphs = dict(pre=g1, conflict=g1a, syn=g2, dating=g3, interval=g4, when=g5, orphan=g_orphan)
    for name, graph in help_graphs.items():
        write_dot(graph, str(target / f'help-{name}.dot'))

    report = f"""
    <p>Die Graphen repräsentieren Aussagen aus der Literatur zu zeitlichen Verhältnissen von Zeugen.</p>
    <p>Die <strong>Zeugen</strong> sind durch Ovale mit der Sigle oder Inskriptionsbezeichnung repräsentiert.
       Zeugen, die nicht in der Edition sind, steht <code>siglentyp: </code> voran. Die Zeugenbezeichnungen
       sind klickbar und führen zur Makrogeneseseite des entsprechenden Zeugen. Verwenden Sie den Link in der
       Spalte <em>Edition</em> der oberen Tabelle, um zur Darstellung des Zeugen in der Dokumentenansicht zu
       gelangen.</p>
    <p><strong>Pfeile</strong> bedeuten immer <em>zeitlich vor</em>. Im Vergleich zu termini a quo bzw. ad quem
    sind die Datumsangaben deshalb um einen Tag versetzt.</p>
    <p><a href="/intro_macrogenesis">Lesen Sie eine ausführlichere Einführung zum Makrogenese-Lab.</a></p>
    <table class="pure-table">
        <thead><th>Graph</th><th>Bedeutung</th></thead>
        <tbody>
        <tr><td><img src="help-pre.svg" /></td>
            <td>Laut Quelle 1 entstand {w1} vor {w2}</td></tr>
        <tr><td><img src="help-conflict.svg" /></td>
            <td>Laut Quelle 1 entstand {w1} vor {w2},
                laut Quelle 2 und Quelle 3 entstand {w2} vor {w1}.<br/>
                Die Aussage von Quelle 2 wird bei der heuristischen Konfliktbeseitugung aus dem Graphen entfernt.<br/>
                Die Aussage von Quelle 3 bereits vor der heuristischen Konfliktbeseitigung aus dem Graphen entfernt (Quelle allgemein unglaubwürdig oder konkrete Aussage unbegründet).</td></tr>
        <tr><td><img src="help-syn.svg"/></td>
            <td>Laut Quelle 2 entstand {w1} etwa gleichzeitig mit {w2}.</td></tr>
        <tr><td><img src="help-dating.svg"/></td>
            <td>Laut Quelle 1 entstand {w1} nicht vor {d1} und nicht nach {d2}.
                Der gepunktete Pfeil repräsentiert den Zeitstrahl, er führt immer zum nächsten im Graph repräsentierten Datum.
            </td></tr>
        <tr><td><img src="help-interval.svg"/></td>
            <td>Laut Quelle 2 wurde vom {d1} bis zum {d2} an {w1} gearbeitet.</td></tr>
        <tr><td><img src="help-when.svg"/></td>
            <td>Laut Quelle 2 entstand {w2} am {d3}.</td></tr>
        <tr><td><img src="help-orphan.svg"/></td>
            <td>{i1w} wird in den Makrogenesedaten nur indirekt über {i1} referenziert
                und über eine künstliche Kante angebunden.</td></tr>
        </tbody>
    </table>
    """

    write_html(target / 'help.php', report, 'Legende')

def _yearlabel(ref: Reference):
    earliest_year = ref.earliest.year
    latest_year = ref.latest.year
    if earliest_year == latest_year:
        return str(earliest_year)
    else:
        sep = " … "
        result = ""
        if ref.earliest != EARLIEST:
            result += str(earliest_year)
        result += sep
        if ref.latest != LATEST:
            result += str(latest_year)
        return result if result != sep else ""


class ByScene:
    def __init__(self, graphs: MacrogenesisInfo):
        scene_xml: etree._ElementTree = etree.parse('scenes.xml')
        self.scenes = scene_xml.xpath('//f:scene[@first-verse]', namespaces=config.namespaces)
        bargraph_info = requests.get('http://dev.digital-humanities.de/ci/job/faust-gen-fast/lastSuccessfulBuild/artifact/target/www/data/genetic_bar_graph.json').json()
        self.intervals = {Witness.get('faust://document/faustedition/' + doc['sigil_t']): doc['intervals'] for doc in bargraph_info}
        self.ordering = list(enumerate(graphs.order_refs()))
        self.graphs = graphs

    def report(self):
        target = config.path.report_dir
        sceneTable = (HtmlTable()
                      .column('#')
                      .column('Szene')
                      .column('Verse', format_spec=lambda t: '{} – {}'.format(*t))
                      .column('Zeugen'))
        for scene in self.scenes:
            witnessTable = RefTable(self.graphs.base)
            title = scene.xpath('f:title/text()', namespaces=config.namespaces)[0]
            start, end = int(scene.get('first-verse')), int(scene.get('last-verse'))
            scene_wits = [(index, wit) for index, wit in self.ordering if self.relevant(wit, start, end)]
            for index, witness in scene_wits:
                witnessTable.reference(witness, index)
            scene_wits = {wit for _, wit in scene_wits}
            scene_nodes = scene_wits | {node   for wit in scene_wits if wit in self.graphs.base
                                        for node in chain(self.graphs.base.predecessors(wit),
                                                          self.graphs.base.successors(wit))
                                        if isinstance(node, date)}
            scene_subgraph = self.graphs.base.subgraph(scene_nodes)
            basename = 'scene_' + scene.get('n').replace('.', '-')
            subgraph_page = Path(basename + '-subgraph.php')
            graph_name = Path(basename + '-graph.dot')
            sceneTable.row((scene.get('n'), f'<a href="{basename}">{title}</a>', (start, end), len(scene_wits)))
            write_dot(scene_subgraph, target / graph_name)
            write_html(target / subgraph_page,
                       f"""<object id="refgraph" type="image/svg+xml" data="{graph_name.with_suffix('.svg')}"></object>""",
                       graph_id='refgraph',
                       head="Szenengraph", breadcrumbs=[dict(caption='nach Szene', link='scenes'),
                                                        dict(caption=title, link=basename)])
            write_html(target / (basename + '.php'),
                       f"""
                       <p><a href="{subgraph_page.stem}">Szenengraph</a> ·
                       <a href="/genesis_bargraph?rangeStart={start}&amp;rangeEnd={end}">Balkendiagramm</a></p>
                       {witnessTable.format_table()}""",
                       head=title, breadcrumbs=[dict(caption='nach Szene', link='scenes')])
        write_html(target / "scenes.php", sceneTable.format_table(), head='nach Szene')

    def relevant(self, witness: Reference, first_verse: int, last_verse: int) -> bool:
        try:
            for interval in self.intervals[witness]:
                if first_verse <= interval['start'] <= last_verse or \
                        first_verse <= interval['end'] <= last_verse or \
                        interval['start'] <= first_verse <= interval['end']  or \
                        interval['start'] <= last_verse <= interval['end']:
                    return True
        except KeyError:
            return False
        return False

def report_scenes(graphs):
    ByScene(graphs).report()

def write_order_xml(graphs):
    target: Path = config.path.report_dir
    logger.debug('Writing reports to %s', target.absolute())
    F = ElementMaker(namespace='http://www.faustedition.net/ns', nsmap=config.namespaces)
    root = F.order(
            Comment('This file has been generated from the macrogenesis data. Do not edit.'),
            *[F.item(format(witness),
                     index=format(index),
                     uri=witness.uri,
                     sigil_t=witness.sigil_t,
                     earliest=witness.earliest.isoformat() if witness.earliest != EARLIEST else '',
                     latest=witness.latest.isoformat() if witness.latest != LATEST else '',
                     yearlabel=_yearlabel(witness))
              for index, witness in enumerate(graphs.order_refs(), start=1)
              if isinstance(witness, Witness)],
            generated=datetime.now().isoformat())
    target.mkdir(parents=True, exist_ok=True)
    root.getroottree().write(str(target / 'order.xml'), pretty_print=True)

    stats = graphs.year_stats()
    data = dict(max=max(stats.values()), counts=stats)
    with (target / 'witness-stats.json').open('wt', encoding='utf-8') as out:
        json.dump(data, out)