gnu: arriba: Use SEARCH-INPUT-FILE and -DIRECTORY. - guix

diff options

author	Ricardo Wurmus <rekado@elephly.net>	2023-05-12 22:40:18 +0200
committer	Ricardo Wurmus <rekado@elephly.net>	2023-05-12 22:40:18 +0200
commit	662e2e82b1b32b98077ffbf35cf2a6985a2c75e3 (patch)
tree	30b03a7de5a6f6cac6444d7d67898827892a8e54 /gnu/ci.scm
parent	001d9b1c64dd7274044f4168272146883f34201b (diff)
download	guix-662e2e82b1b32b98077ffbf35cf2a6985a2c75e3.tar.gz guix-662e2e82b1b32b98077ffbf35cf2a6985a2c75e3.zip

gnu: arriba: Use SEARCH-INPUT-FILE and -DIRECTORY.

* gnu/packages/bioinformatics.scm (arriba)[arguments]: Use SEARCH-INPUT-DIRECTORY and SEARCH-INPUT-FILE; use G-expression; drop trailing #T from build phases.

Diffstat (limited to 'gnu/ci.scm')

0 files changed, 0 insertions, 0 deletions

>89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311

# SPDX-License-Identifier: GPL-3.0-or-later

# Data structure for querying URL patterns.
#
# This file is part of Hydrilla&Haketilo.
#
# Copyright (C) 2021, 2022 Wojtek Kosior
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program.  If not, see <https://www.gnu.org/licenses/>.
#
#
# I, Wojtek Kosior, thereby promise not to sue for violation of this
# file's license. Although I request that you do not make use of this
# code in a proprietary program, I am not going to enforce this in
# court.

"""
This module defines data structures for querying data using URL patterns.
"""

import typing as t
import dataclasses as dc

from immutables import Map

from .url_patterns import ParsedPattern, ParsedUrl, parse_url#, catchall_pattern
from .translations import smart_gettext as _


WrapperStoredType = t.TypeVar('WrapperStoredType', bound=t.Hashable)

@dc.dataclass(frozen=True, unsafe_hash=True, order=True)
class StoredTreeItem(t.Generic[WrapperStoredType]):
    """
    In the Pattern Tree, each item is stored together with the pattern used to
    register it.
    """
    item:    WrapperStoredType
    pattern: ParsedPattern


NodeStoredType = t.TypeVar('NodeStoredType')

@dc.dataclass(frozen=True)
class PatternTreeNode(t.Generic[NodeStoredType]):
    """...."""
    SelfType = t.TypeVar('SelfType', bound='PatternTreeNode[NodeStoredType]')

    ChildrenType = Map[str, SelfType]

    children:      'ChildrenType'             = Map()
    literal_match: t.Optional[NodeStoredType] = None

    def is_empty(self) -> bool:
        """...."""
        return len(self.children) == 0 and self.literal_match is None

    def update_literal_match(
            self:           'SelfType',
            new_match_item: t.Optional[NodeStoredType]
    ) -> 'SelfType':
        """...."""
        return dc.replace(self, literal_match=new_match_item)

    def get_child(self: 'SelfType', child_key: str) -> t.Optional['SelfType']:
        """...."""
        return self.children.get(child_key)

    def remove_child(self: 'SelfType', child_key: str) -> 'SelfType':
        """...."""
        try:
            children = self.children.delete(child_key)
        except:
            children = self.children

        return dc.replace(self, children=children)

    def set_child(self: 'SelfType', child_key: str, child: 'SelfType') \
        -> 'SelfType':
        """...."""
        return dc.replace(self, children=self.children.set(child_key, child))


BranchStoredType = t.TypeVar('BranchStoredType')

BranchItemUpdater = t.Callable[
    [t.Optional[BranchStoredType]],
    t.Optional[BranchStoredType]
]

@dc.dataclass(frozen=True)
class PatternTreeBranch(t.Generic[BranchStoredType]):
    """...."""
    SelfType = t.TypeVar(
        'SelfType',
        bound = 'PatternTreeBranch[BranchStoredType]'
    )

    root_node: PatternTreeNode[BranchStoredType] = PatternTreeNode()

    def is_empty(self) -> bool:
        """...."""
        return self.root_node.is_empty()

    def update(
            self:         'SelfType',
            segments:     t.Iterable[str],
            item_updater: BranchItemUpdater
    ) -> 'SelfType':
        """
        .......
        """
        node = self.root_node
        nodes_segments = []

        for segment in segments:
            next_node = node.get_child(segment)

            nodes_segments.append((node, segment))

            node = PatternTreeNode() if next_node is None else next_node

        node = node.update_literal_match(item_updater(node.literal_match))

        while nodes_segments:
            prev_node, segment = nodes_segments.pop()

            if node.is_empty():
                node = prev_node.remove_child(segment)
            else:
                node = prev_node.set_child(segment, node)

        return dc.replace(self, root_node=node)

    def search(self, segments: t.Sequence[str]) -> t.Iterable[BranchStoredType]:
        """
        Yields all matches of this segments sequence against the tree. Results
        are produced in order from greatest to lowest pattern specificity.
        """
        nodes = [self.root_node]

        for segment in segments:
            next_node = nodes[-1].get_child(segment)
            if next_node is None:
                break

            nodes.append(next_node)

        nsegments = len(segments)
        cond_literal = lambda: len(nodes) == nsegments
        cond_wildcard = [
            lambda: len(nodes) + 1 == nsegments and segments[-1] != '*',
            lambda: len(nodes) + 1 <  nsegments,
            lambda: len(nodes) + 1 != nsegments or  segments[-1] != '***'
        ]

        while nodes:
            node = nodes.pop()

            wildcard_matches = [node.get_child(wc) for wc in ('*', '**', '***')]

            for match_node, condition in [
                    (node, cond_literal),
                    *zip(wildcard_matches, cond_wildcard)
            ]:
                if match_node is not None:
                    if match_node.literal_match is not None:
                        if condition():
                            yield match_node.literal_match


FilterStoredType  = t.TypeVar('FilterStoredType', bound=t.Hashable)
FilterWrappedType = StoredTreeItem[FilterStoredType]

def filter_by_trailing_slash(
        items: t.Iterable[FilterWrappedType],
        with_slash: bool
) -> t.FrozenSet[FilterWrappedType]:
    """...."""
    return frozenset(wrapped for wrapped in items
                     if with_slash == wrapped.pattern.has_trailing_slash)

TreeStoredType = t.TypeVar('TreeStoredType', bound=t.Hashable)

StoredSet      = t.FrozenSet[StoredTreeItem[TreeStoredType]]
PathBranch     = PatternTreeBranch[StoredSet]
DomainBranch   = PatternTreeBranch[PathBranch]
TreeRoot       = Map[t.Tuple[str, t.Optional[int]], DomainBranch]

@dc.dataclass(frozen=True)
class PatternTree(t.Generic[TreeStoredType]):
    """
    "Pattern Tree" is how we refer to the data structure used for querying
    Haketilo patterns. Those look like 'https://*.example.com/ab/***'. The goal
    is to make it possible to quickly retrieve all known patterns that match
    a given URL.
    """
    SelfType = t.TypeVar('SelfType', bound='PatternTree[TreeStoredType]')

    _by_scheme_and_port: TreeRoot = Map()

    def _register(
            self:           'SelfType',
            parsed_pattern: ParsedPattern,
            item:           TreeStoredType,
            register:       bool = True
    ) -> 'SelfType':
        """
        Make an item wrapped in StoredTreeItem object queryable through the
        Pattern Tree by the given parsed URL pattern.
        """
        wrapped_item = StoredTreeItem(item, parsed_pattern)

        def item_updater(item_set: t.Optional[StoredSet]) \
            -> t.Optional[StoredSet]:
            """...."""
            if item_set is None:
                item_set = frozenset()

            if register:
                item_set = item_set.union((wrapped_item,))
            else:
                item_set = item_set.difference((wrapped_item,))

            return None if len(item_set) == 0 else item_set

        def path_branch_updater(path_branch: t.Optional[PathBranch]) \
            -> t.Optional[PathBranch]:
            """...."""
            if path_branch is None:
                path_branch = PatternTreeBranch()

            path_branch = path_branch.update(
                parsed_pattern.path_segments,
                item_updater
            )

            return None if path_branch.is_empty() else path_branch

        key         = (parsed_pattern.scheme, parsed_pattern.port)
        domain_tree = self._by_scheme_and_port.get(key, PatternTreeBranch())

        new_domain_tree = domain_tree.update(
            parsed_pattern.domain_labels,
            path_branch_updater
        )

        if new_domain_tree.is_empty():
            try:
                new_root = self._by_scheme_and_port.delete(key)
            except KeyError:
                new_root = self._by_scheme_and_port
        else:
            new_root = self._by_scheme_and_port.set(key, new_domain_tree)

        return dc.replace(self, _by_scheme_and_port=new_root)

    def register(
            self:           'SelfType',
            parsed_pattern: ParsedPattern,
            item:           TreeStoredType
    ) -> 'SelfType':
        """
        Make item queryable through the Pattern Tree by the given URL pattern.
        """
        return self._register(parsed_pattern, item)

    def deregister(
            self:           'SelfType',
            parsed_pattern: ParsedPattern,
            item:           TreeStoredType
    ) -> 'SelfType':
        """
        Make item no longer queryable through the Pattern Tree by the given URL
        pattern.
        """
        return self._register(parsed_pattern, item, register=False)

    def search(self, url: t.Union[ParsedUrl, str]) -> t.Iterable[StoredSet]:
        """
        ....
        """
        parsed_url = parse_url(url) if isinstance(url, str) else url

        key = (parsed_url.scheme, parsed_url.port)
        domain_tree = self._by_scheme_and_port.get(key)
        if domain_tree is None:
            return

        if parsed_url.has_trailing_slash:
            slash_options = [True, False]
        else:
            slash_options = [False]

        for path_tree in domain_tree.search(parsed_url.domain_labels):
            for item_set in path_tree.search(parsed_url.path_segments):
                for with_slash in slash_options:
                    items = filter_by_trailing_slash(item_set, with_slash)
                    if len(items) > 0:
                        yield items


context:
space:
mode: