diff --git a/CHANGELOG.md b/CHANGELOG.md
index c9ad73b2aa6bc13b276c3cb40d180f3886a4d93c..cc80b4470c4a250c0058aac0852c6f4c9a768478 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -5,6 +5,25 @@ All notable changes to this project will be documented in this file.
The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+## [0.9.0] - 2024-09-05 ##
+
+### Added ###
+
+* New converters for XML documents/trees/tags: XMLFile, XMLTag, XMLTextNode
+
+### Changed ###
+
+* Moved the optional `hdf5_converter` to the `converters`
+ submodule. When updating from 0.8 or below, this means that you have
+ to adapt the converter package path in your cfood definition from
+ `caoscrawler.hdf5_converter` to
+ `caoscrawler.converters.hdf5_converter`.
+
+### Fixed ###
+
+* Use `urllib.parse.urljoin` to generate link addresses in status
+ mails, preventing wrong addresses, e.g., due to superfluous `/`.
+
## [0.8.0] - 2024-08-23 ##
### Added ###
diff --git a/CITATION.cff b/CITATION.cff
index e219f1cb1868394a2997bf6ea93fc921d86163c4..17d5ad333414d6836868f572d4f0b742a7a2e636 100644
--- a/CITATION.cff
+++ b/CITATION.cff
@@ -17,6 +17,6 @@ authors:
given-names: Alexander
orcid: https://orcid.org/0000-0003-4124-9649
title: CaosDB - Crawler
-version: 0.8.0
+version: 0.9.0
doi: 10.3390/data9020024
-date-released: 2024-08-23
\ No newline at end of file
+date-released: 2024-09-05
\ No newline at end of file
diff --git a/README_SETUP.md b/README_SETUP.md
deleted file mode 120000
index d478016ecde09dab8820d398b15df325f4159380..0000000000000000000000000000000000000000
--- a/README_SETUP.md
+++ /dev/null
@@ -1 +0,0 @@
-src/doc/README_SETUP.md
\ No newline at end of file
diff --git a/README_SETUP.md b/README_SETUP.md
new file mode 100644
index 0000000000000000000000000000000000000000..32f0bb89a6051bc2ec4be0bae6cf06cd1a540f8b
--- /dev/null
+++ b/README_SETUP.md
@@ -0,0 +1,34 @@
+# Getting started with the CaosDB Crawler #
+
+## Installation
+see INSTALL.md
+
+## Run Unit Tests
+
+1. Install additional dependencies:
+ - h5py
+2. Run `pytest unittests`.
+
+## Documentation ##
+We use sphinx to create the documentation. Docstrings in the code should comply
+with the Googly style (see link below).
+
+Build documentation in `src/doc` with `make doc`. Note that for the
+automatic generation of the complete API documentation, it is
+necessary to first install this library with all its optional
+dependencies, i.e., `pip install .[h5-crawler,spss]`.
+
+### Requirements ###
+
+- `sphinx`
+- `sphinx-autoapi`
+- `recommonmark`
+- `sphinx-rtd-theme`
+
+### How to contribute ###
+
+- [Google Style Python Docstrings](https://sphinxcontrib-napoleon.readthedocs.io/en/latest/example_google.html)
+- [Google Style Python Docstrings 2nd reference](https://github.com/google/styleguide/blob/gh-pages/pyguide.md#38-comments-and-docstrings)
+- [References to other documentation](https://www.sphinx-doc.org/en/master/usage/extensions/intersphinx.html#role-external)
+
+
diff --git a/setup.cfg b/setup.cfg
index 1e321bba1233f3672c1848248145839bc8d4f79b..48f3974ffefcd6d09e10be029300781b00b3dc73 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -1,6 +1,6 @@
[metadata]
name = caoscrawler
-version = 0.8.0
+version = 0.9.0
author = Alexander Schlemmer
author_email = alexander.schlemmer@ds.mpg.de
description = A new crawler for caosdb
diff --git a/src/caoscrawler/__init__.py b/src/caoscrawler/__init__.py
index 41b96323b1106d8ce28caadc4a2da012f3dc22ea..ba4844e15387cd13aa15db88521b2022fa52bfd6 100644
--- a/src/caoscrawler/__init__.py
+++ b/src/caoscrawler/__init__.py
@@ -1,15 +1,5 @@
from . import converters, utils
-try:
- from .conv_impl.spss import SPSSConverter
-except ImportError as err:
- SPSSConverter: type = utils.MissingImport(
- name="SPSSConverter", hint="Try installing with the `spss` extra option.",
- err=err)
from .crawl import Crawler, SecurityMode
from .version import CfoodRequiredVersionError, get_caoscrawler_version
__version__ = get_caoscrawler_version()
-
-# Convenience members #########################################################
-# mypy: disable-error-code="attr-defined"
-converters.SPSSConverter = SPSSConverter
diff --git a/src/caoscrawler/cfood-schema.yml b/src/caoscrawler/cfood-schema.yml
index 6609d8eb05135b17f5f6d9526df255b810de112a..acc3911f21d320146d0c35abc9d781541ee151ac 100644
--- a/src/caoscrawler/cfood-schema.yml
+++ b/src/caoscrawler/cfood-schema.yml
@@ -73,6 +73,9 @@ cfood:
- H5Dataset
- H5Group
- H5Ndarray
+ - XMLFile
+ - XMLTag
+ - XMLTextNode
- PropertiesFromDictElement
description: Type of this converter node.
match:
diff --git a/src/caoscrawler/conv_impl/__init__.py b/src/caoscrawler/conv_impl/__init__.py
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/src/caoscrawler/converters/__init__.py b/src/caoscrawler/converters/__init__.py
new file mode 100644
index 0000000000000000000000000000000000000000..540a4cfca9ff19248baab2bc0fe8d10987d4bd1f
--- /dev/null
+++ b/src/caoscrawler/converters/__init__.py
@@ -0,0 +1,32 @@
+# encoding: utf-8
+#
+# This file is a part of the LinkAhead Project.
+#
+# Copyright (C) 2024 Indiscale GmbH <info@indiscale.com>
+# Copyright (C) 2024 Daniel Hornung <d.hornung@indiscale.com>
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Affero 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 Affero General Public License for more details.
+#
+# You should have received a copy of the GNU Affero General Public License
+# along with this program. If not, see <https://www.gnu.org/licenses/>.
+
+"""Submdule containing all default and optional converters."""
+
+from .. import utils
+from .converters import *
+from .xml_converter import *
+
+try:
+ from .spss import SPSSConverter
+except ImportError as err:
+ SPSSConverter: type = utils.MissingImport(
+ name="SPSSConverter", hint="Try installing with the `spss` extra option.",
+ err=err)
diff --git a/src/caoscrawler/converters.py b/src/caoscrawler/converters/converters.py
similarity index 98%
rename from src/caoscrawler/converters.py
rename to src/caoscrawler/converters/converters.py
index 0eee8965512ed39add9a9688c531c540f80d7df2..f31a0f4463ea805472044e5bd7697ed1316d1d9b 100644
--- a/src/caoscrawler/converters.py
+++ b/src/caoscrawler/converters/converters.py
@@ -41,12 +41,12 @@ import yaml
import yaml_header_tools
from jsonschema import ValidationError, validate
-from .stores import GeneralStore, RecordStore
-from .structure_elements import (BooleanElement, DictElement, Directory, File,
- FloatElement, IntegerElement, JSONFile,
- ListElement, NoneElement, StructureElement,
- TextElement)
-from .utils import has_parent
+from ..stores import GeneralStore, RecordStore
+from ..structure_elements import (BooleanElement, DictElement, Directory, File,
+ FloatElement, IntegerElement, JSONFile,
+ ListElement, NoneElement, StructureElement,
+ TextElement)
+from ..utils import has_parent
# These are special properties which are (currently) treated differently
# by the converters:
@@ -316,7 +316,10 @@ def create_records(values: GeneralStore, records: RecordStore, def_records: dict
class Converter(object, metaclass=ABCMeta):
- """Converters treat StructureElements contained in the hierarchical sturcture."""
+ """Converters treat StructureElements contained in the hierarchical sturcture.
+
+ This is the abstract super class for all Converters.
+ """
def __init__(self, definition: dict, name: str, converter_registry: dict):
"""
@@ -582,6 +585,12 @@ class Converter(object, metaclass=ABCMeta):
class DirectoryConverter(Converter):
+ """
+ Converter that matches and handles structure elements of type directory.
+
+ This is one typical starting point of a crawling procedure.
+ """
+
def create_children(self, generalStore: GeneralStore, element: StructureElement):
# TODO: See comment on types and inheritance
if not isinstance(element, Directory):
diff --git a/src/caoscrawler/hdf5_converter.py b/src/caoscrawler/converters/hdf5_converter.py
similarity index 98%
rename from src/caoscrawler/hdf5_converter.py
rename to src/caoscrawler/converters/hdf5_converter.py
index 482d59c12d2d0b8540c01bd04da718d9c514ddc4..a4d974bd53fc4b0e22d155f01a6a47295b79e984 100644
--- a/src/caoscrawler/hdf5_converter.py
+++ b/src/caoscrawler/converters/hdf5_converter.py
@@ -36,8 +36,8 @@ import linkahead as db
from .converters import (convert_basic_element, Converter, DictElementConverter,
match_name_and_value, SimpleFileConverter)
-from .stores import GeneralStore, RecordStore
-from .structure_elements import DictElement, File, FloatElement, IntegerElement, StructureElement
+from ..stores import GeneralStore, RecordStore
+from ..structure_elements import DictElement, File, FloatElement, IntegerElement, StructureElement
def convert_attributes(elt: Union[h5py.File, h5py.Group, h5py.Dataset]):
diff --git a/src/caoscrawler/conv_impl/spss.py b/src/caoscrawler/converters/spss.py
similarity index 99%
rename from src/caoscrawler/conv_impl/spss.py
rename to src/caoscrawler/converters/spss.py
index 5dfad0ff8be55e2ca3ddf0db3397dbac5fc9f2b0..b4f03aeaed6663be98487a4780bb96237e72e27e 100644
--- a/src/caoscrawler/conv_impl/spss.py
+++ b/src/caoscrawler/converters/spss.py
@@ -28,7 +28,7 @@ import pandas as pd
import pyreadstat
import yaml
-from .. import converters
+from . import converters
from ..stores import GeneralStore
from ..structure_elements import (File, StructureElement)
from typing import Optional, Any
diff --git a/src/caoscrawler/converters/xml_converter.py b/src/caoscrawler/converters/xml_converter.py
new file mode 100644
index 0000000000000000000000000000000000000000..d1d8b8871f9dad9762f35ee79e1a9106c259f4a9
--- /dev/null
+++ b/src/caoscrawler/converters/xml_converter.py
@@ -0,0 +1,215 @@
+# encoding: utf-8
+#
+# This file is a part of the LinkAhead Project.
+#
+# Copyright (C) 2024 Indiscale GmbH <info@indiscale.com>
+# Copyright (C) 2024 Alexander Schlemmer
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Affero 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 Affero General Public License for more details.
+#
+# You should have received a copy of the GNU Affero General Public License
+# along with this program. If not, see <https://www.gnu.org/licenses/>.
+
+"""Converters take structure elements and create Records and new structure elements from them."""
+
+from __future__ import annotations
+
+import lxml.etree
+import re
+
+from typing import Optional
+
+import linkahead as db
+
+from .converters import SimpleFileConverter, ConverterValidationError, Converter
+from ..stores import GeneralStore, RecordStore
+from ..structure_elements import (File, StructureElement,
+ XMLTagElement, XMLTextNode, XMLAttributeNode)
+
+
+class XMLFileConverter(SimpleFileConverter):
+
+ """Convert XML files. See
+ https://gitlab.indiscale.com/caosdb/src/caosdb-crawler/-/issues/145
+ for the current suggestion for the specification.
+
+ """
+
+ def create_children(self, generalStore: GeneralStore, element: StructureElement):
+ # TODO: See comment on types and inheritance
+ if not isinstance(element, File):
+ raise ValueError("create_children was called with wrong type of StructureElement")
+ with open(element.path, 'r') as xml_file:
+ xml = lxml.etree.parse(xml_file)
+ if "validate" in self.definition and self.definition["validate"]:
+ try:
+ raise NotImplementedError("XML validation not implemented yet.")
+ except ConverterValidationError as err:
+ raise ConverterValidationError(
+ "Error during the validation of the XML file:\n"
+ f"{element.path}\n" + err.message)
+
+ return [XMLTagElement(xml.getroot())]
+
+
+class XMLTagConverter(Converter):
+ def create_children(self, generalStore: GeneralStore, element: StructureElement):
+ """Children that are generated by this function are the
+ result of the xpath query given in the yaml property
+ ``xpath``. Its default (when not given) is ``child::*``, so the
+ direct children of the current xml node. The xpath expression
+ must be designed in a way that it returns xml tags (and no
+ attributes or texts). That means, that the axis ``attribute::``
+ and the function ``text()`` must not be used.
+
+ The following yaml properties can be used to generate other
+ types of nodes (text nodes and attribute nodes) as subtree
+ structure elements:
+
+ ::
+
+ # _*_ marks the default:
+ attribs_as_children: true # true / _false_
+ text_as_children: true # true / _false_
+ tags_as_children: true # _true_ / false
+
+ The default is to generate the tags matched by the xpath expression only.
+
+ - When text_as_children is set to true, text nodes will be generated that contain the text
+ contained in the matched tags.
+ - When attribs_as_children is set to true, attribute nodes will be generated from the attributes
+ of the matched tags.
+
+ Notes
+ -----
+ The default is to take the namespace map from the current node and use it in xpath queries.
+ Because default namespaces cannot be handled by xpath, it is possible to remap the default namespace
+ using the key ``default_namespace``.
+ The key ``nsmap`` can be used to define additional nsmap entries.
+
+ """
+ if not isinstance(element, XMLTagElement):
+ raise TypeError("Element must be an instance of XMLTagElement.")
+
+ # Get the namespace map from the element:
+ nsmap = element.tag.nsmap
+ # The default name of the default namespace is "default".
+ # You can overwrite it using the attribute "default_namespace" in the converter definition:
+ default_namespace = self.definition.get("default_namespace", "default")
+ if None in nsmap:
+ nsmap[default_namespace] = nsmap[None]
+ del nsmap[None]
+
+ # Set additional nsmap entries from the converter definition:
+ if "nsmap" in self.definition:
+ for key, value in self.definition["nsmap"].items():
+ nsmap[key] = value
+
+ xpath = self.definition.get("xpath", "child::*")
+ children = element.tag.xpath(xpath, namespaces=nsmap)
+ el_lst = []
+ for el in children:
+ if isinstance(el, str):
+ raise RuntimeError(
+ "Only standard xml nodes are supported as results of xpath queries.")
+ elif isinstance(el, lxml.etree._Element):
+ if self.definition.get("tags_as_children", True):
+ el_lst.append(XMLTagElement(el))
+ if self.definition.get("attribs_as_children", False):
+ for attrib in el.attrib:
+ el_lst.append(XMLAttributeNode(el, attrib))
+ if self.definition.get("text_as_children", False):
+ el_lst.append(XMLTextNode(el))
+ else:
+ raise RuntimeError("Unsupported child type.")
+ return el_lst
+
+ def typecheck(self, element: StructureElement):
+ """
+ Check whether the current structure element can be converted using
+ this converter.
+ """
+ return isinstance(element, XMLTagElement)
+
+ def match(self, element: StructureElement) -> Optional[dict]:
+ # See https://gitlab.indiscale.com/caosdb/src/caosdb-crawler/-/issues/145
+ # for a suggestion for the design of the matching algorithm.
+ if not isinstance(element, XMLTagElement):
+ raise TypeError("Element must be an instance of XMLTagElement.")
+
+ # Store the result of all individual regexp variable results:
+ vardict = {}
+
+ if "match_tag" in self.definition:
+ m_tag = re.match(self.definition["match_tag"], element.tag.tag)
+ if m_tag is None:
+ return None
+ vardict.update(m_tag.groupdict())
+
+ if "match_text" in self.definition:
+ tagtext = element.tag.text
+ if element.tag.text is None:
+ tagtext = ""
+ m_text = re.match(self.definition["match_text"], tagtext, re.DOTALL)
+ if m_text is None:
+ return None
+ vardict.update(m_text.groupdict())
+
+ if "match_attrib" in self.definition:
+ for attrib_def_key, attrib_def_value in self.definition["match_attrib"].items():
+ match_counter = 0
+ matched_m_attrib = None
+ matched_m_attrib_value = None
+ for attr_key, attr_value in element.tag.attrib.items():
+ m_attrib = re.match(attrib_def_key, attr_key)
+ if m_attrib is not None:
+ match_counter += 1
+ matched_m_attrib = m_attrib
+ m_attrib_value = re.match(attrib_def_value, attr_value)
+ if m_attrib_value is None:
+ return None
+ matched_m_attrib_value = m_attrib_value
+ # TODO: How to deal with multiple matches?
+ # There are multiple options:
+ # - Allow multiple attribute-key matches: Leads to possible overwrites of variables
+ # - Require unique attribute-key and attribute-value matches: Very complex
+ # - Only allow one single attribute-key to match and run attribute-value match separately.
+ # Currently the latter option is implemented.
+ if match_counter == 0:
+ return None
+ elif match_counter > 1:
+ raise RuntimeError("Multiple attributes match the same match_attrib entry.")
+ vardict.update(matched_m_attrib.groupdict())
+ vardict.update(matched_m_attrib_value.groupdict())
+
+ return vardict
+
+
+class XMLTextNodeConverter(Converter):
+ def create_children(self, generalStore: GeneralStore, element: StructureElement):
+ raise NotImplementedError()
+
+ def typecheck(self, element: StructureElement):
+ """
+ Check whether the current structure element can be converted using
+ this converter.
+ """
+ return isinstance(element, XMLTextNode)
+
+ def match(self, element: StructureElement) -> Optional[dict]:
+ # See https://gitlab.indiscale.com/caosdb/src/caosdb-crawler/-/issues/145
+ # for a suggestion for the design of the matching algorithm.
+ if not isinstance(element, XMLTextNode):
+ raise TypeError("Element must be an instance of XMLTextNode.")
+
+ raise NotImplementedError()
+
+ return None
diff --git a/src/caoscrawler/crawl.py b/src/caoscrawler/crawl.py
index 0f23acfdfde2a863a66f25901a85748b538f5d04..c761d730842647a1ec401966c4221811dda1cd9c 100644
--- a/src/caoscrawler/crawl.py
+++ b/src/caoscrawler/crawl.py
@@ -39,6 +39,7 @@ import sys
import traceback
import uuid
import warnings
+
from argparse import RawTextHelpFormatter
from copy import deepcopy
from datetime import datetime
@@ -72,6 +73,7 @@ from .scanner import (create_converter_registry, initialize_converters,
from .stores import GeneralStore
from .structure_elements import StructureElement
from .sync_graph import SyncGraph
+from .utils import get_shared_resource_link
logger = logging.getLogger(__name__)
@@ -750,16 +752,17 @@ one with the entities that need to be updated and the other with entities to be
# Sending an Email with a link to a form to authorize updates is
if get_config_setting("send_crawler_notifications"):
filename = OldCrawler.save_form([el[3] for el in pending_changes], path, run_id)
- text = """Dear Curator,
+ link_address = get_shared_resource_link(db.configuration.get_config()[
+ "Connection"]["url"], filename)
+ changes = "\n".join([el[3] for el in pending_changes])
+ text = f"""Dear Curator,
there where changes that need your authorization. Please check the following
carefully and if the changes are ok, click on the following link:
- {url}/Shared/{filename}
+ {link_address}
{changes}
- """.format(url=db.configuration.get_config()["Connection"]["url"],
- filename=filename,
- changes="\n".join([el[3] for el in pending_changes]))
+ """
try:
fro = get_config_setting("sendmail_from_address")
to = get_config_setting("sendmail_to_address")
@@ -899,7 +902,7 @@ the CaosDB Crawler successfully crawled the data and
if get_config_setting("create_crawler_status_records"):
text += ("You can checkout the CrawlerRun Record for more information:\n"
f"{domain}/Entity/?P=0L10&query=find%20crawlerrun%20with%20run_id=%27{run_id}%27\n\n")
- text += (f"You can download the logfile here:\n{domain}/Shared/" + logfile)
+ text += (f"You can download the logfile here:\n{get_shared_resource_link(domain, logfile)}")
send_mail(
from_addr=get_config_setting("sendmail_from_address"),
to=get_config_setting("sendmail_to_address"),
@@ -1059,7 +1062,7 @@ def crawler_main(crawled_directory_path: str,
userlog_public, htmluserlog_public, debuglog_public = configure_server_side_logging()
# TODO make this optional
_create_status_record(
- get_config_setting("public_host_url") + "/Shared/" + htmluserlog_public,
+ get_shared_resource_link(get_config_setting("public_host_url"), htmluserlog_public),
crawler.run_id)
else: # setup stdout logging for other cases
root_logger = logging.getLogger()
@@ -1128,7 +1131,7 @@ def crawler_main(crawled_directory_path: str,
# pylint: disable=E0601
domain = get_config_setting("public_host_url")
logger.error("Unexpected Error: Please tell your administrator about this and provide "
- f"the following path.\n{domain}/Shared/" + debuglog_public)
+ f"the following path.\n{get_shared_resource_link(domain, debuglog_public)}")
_update_status_record(crawler.run_id, 0, 0, status="FAILED")
return 1
diff --git a/src/caoscrawler/default_converters.yml b/src/caoscrawler/default_converters.yml
index 82e2f635f621b2e21e43b728fd9ed6865454f828..a78c1579fc05c2ede424c076e7590d25550ea2f3 100644
--- a/src/caoscrawler/default_converters.yml
+++ b/src/caoscrawler/default_converters.yml
@@ -94,3 +94,20 @@ SPSSFile:
XLSXTableConverter:
converter: XLSXTableConverter
package: caoscrawler.converters
+
+
+# -------------------------
+# XML
+# -------------------------
+
+XMLFile:
+ converter: XMLFileConverter
+ package: caoscrawler.converters
+
+XMLTag:
+ converter: XMLTagConverter
+ package: caoscrawler.converters
+
+XMLTextNode:
+ converter: XMLTextNodeConverter
+ package: caoscrawler.converters
diff --git a/src/caoscrawler/structure_elements.py b/src/caoscrawler/structure_elements.py
index 0efba91c185446e0bfbecbbb53f68aaa8a8e15d1..67cd1056b382c92485deada2058526a03b6d8535 100644
--- a/src/caoscrawler/structure_elements.py
+++ b/src/caoscrawler/structure_elements.py
@@ -24,6 +24,7 @@
#
import warnings
+import lxml.etree
class StructureElement(object):
@@ -167,3 +168,53 @@ class DictDictElement(DictElement):
def __init__(self, *args, **kwargs):
warnings.warn(DeprecationWarning("This class is depricated. Please use DictElement."))
super().__init__(*args, **kwargs)
+
+
+class XMLTagElement(StructureElement):
+ """
+ Stores elements of an XML tree.
+ """
+
+ def __init__(self, element: lxml.etree.Element):
+ super().__init__(element.getroottree().getelementpath(element))
+ self.tag = element
+
+
+class XMLTextNode(StructureElement):
+ """
+ Stores text nodes of XML trees.
+ """
+
+ def __init__(self, element: lxml.etree.Element):
+ """
+ Initializes this XML text node.
+
+ Please note that, although syntactically similar, it is semantically
+ different from TextElement:
+ - TextElements have a meaningful name, e.g. a key in a key-value pair. This name can
+ be matched using the match_name entry.
+ - XMLTextNodes just have a text and the name is just for identifying the structure element.
+ They can only be matched using the match entry in the XMLTextNodeConverter.
+ """
+ super().__init__(element.getroottree().getelementpath(element) + "/text()")
+ self.tag = element
+ self.value = element.text
+
+
+class XMLAttributeNode(StructureElement):
+ """
+ Stores text nodes of XML trees.
+ """
+
+ def __init__(self, element: lxml.etree.Element,
+ key: str):
+ """
+ Initializes this XML attribute node.
+
+ element: The xml tree element containing the attribute.
+ key: The key which identifies the attribute in the list of attributes.
+ """
+ super().__init__(element.getroottree().getelementpath(element) + "@" + key)
+ self.value = element.attrib[key]
+ self.key = key
+ self.tag = element
diff --git a/src/caoscrawler/utils.py b/src/caoscrawler/utils.py
index 096fde9b573f4ff60995498144cad3589ce7dbb2..d9a5af839068a2582859aad1b51fbc8b9713d5d1 100644
--- a/src/caoscrawler/utils.py
+++ b/src/caoscrawler/utils.py
@@ -26,7 +26,10 @@
# Some utility functions, e.g. for extending pylib.
import sys
+
+from posixpath import join as posixjoin
from typing import Optional
+from urllib.parse import urljoin
import linkahead as db
@@ -69,3 +72,18 @@ def MissingImport(name: str, hint: str = "", err: Optional[Exception] = None) ->
_DummyClass.__name__ = name
return _DummyClass
+
+
+def get_shared_resource_link(host_url, filename):
+ """Return a link adress which is basically {host_url}/Shared/{filename}.
+
+ Use urllib.parse.join and os.path.join to prevent missing or extra ``/`` and the like.
+
+ """
+
+ if not host_url.endswith('/'):
+ # Fill with trailing '/' s. that urljoin doesn't remove the context root.
+ host_url += '/'
+ # Use posixjoin to always have '/' in links, even when running on
+ # Windows systems.
+ return urljoin(host_url, posixjoin("Shared/", filename))
diff --git a/src/doc/README_SETUP.md b/src/doc/README_SETUP.md
deleted file mode 100644
index 32f0bb89a6051bc2ec4be0bae6cf06cd1a540f8b..0000000000000000000000000000000000000000
--- a/src/doc/README_SETUP.md
+++ /dev/null
@@ -1,34 +0,0 @@
-# Getting started with the CaosDB Crawler #
-
-## Installation
-see INSTALL.md
-
-## Run Unit Tests
-
-1. Install additional dependencies:
- - h5py
-2. Run `pytest unittests`.
-
-## Documentation ##
-We use sphinx to create the documentation. Docstrings in the code should comply
-with the Googly style (see link below).
-
-Build documentation in `src/doc` with `make doc`. Note that for the
-automatic generation of the complete API documentation, it is
-necessary to first install this library with all its optional
-dependencies, i.e., `pip install .[h5-crawler,spss]`.
-
-### Requirements ###
-
-- `sphinx`
-- `sphinx-autoapi`
-- `recommonmark`
-- `sphinx-rtd-theme`
-
-### How to contribute ###
-
-- [Google Style Python Docstrings](https://sphinxcontrib-napoleon.readthedocs.io/en/latest/example_google.html)
-- [Google Style Python Docstrings 2nd reference](https://github.com/google/styleguide/blob/gh-pages/pyguide.md#38-comments-and-docstrings)
-- [References to other documentation](https://www.sphinx-doc.org/en/master/usage/extensions/intersphinx.html#role-external)
-
-
diff --git a/src/doc/cfood.rst b/src/doc/cfood.rst
index 07431af0a9fb26e569be5d47f79d6a4f120df269..51c392780b44b73964921506ad3764b95e14d5ed 100644
--- a/src/doc/cfood.rst
+++ b/src/doc/cfood.rst
@@ -183,7 +183,7 @@ in a vairable with the same name (as it is the case for other Records).
Transform Functions
-------------------
You can use transform functions to alter variable values that the crawler consumes (e.g. a string
-that was matched with a reg exp). See :doc:`Converter Documentation<converters>`.
+that was matched with a reg exp). See :doc:`Converter Documentation<converters/index>`.
You can define your own transform functions by adding the the same way you add custom converters:
diff --git a/src/doc/concepts.rst b/src/doc/concepts.rst
index 770731857112b93205f0e80d623fa9183c4aa885..b3aa02a151a4d03c1531094ea01a5246cb02ba73 100644
--- a/src/doc/concepts.rst
+++ b/src/doc/concepts.rst
@@ -20,7 +20,7 @@ example a tree of Python *file objects* (StructureElements) could correspond to
Relevant sources in:
-- ``src/structure_elements.py``
+- :py:mod:`caoscrawler.structure_elements`
.. _ConceptConverters:
@@ -34,11 +34,11 @@ existing StructureElements, Converters create a tree of StructureElements.
.. image:: img/converter.png
:height: 170
-See the chapter :std:doc:`Converters<converters>` for details.
+See the chapter :std:doc:`Converters<converters/index>` for details.
Relevant sources in:
-- ``src/converters.py``
+- :py:mod:`caoscrawler.converters`
Identifiables
@@ -70,8 +70,8 @@ In the current implementation an identifiable can only use one RecordType even t
Relevant sources in
-- ``src/identifiable_adapters.py``
-- ``src/identifiable.py``
+- :py:mod:`caoscrawler.identifiable_adapters`
+- :py:mod:`caoscrawler.identifiable`
Registered Identifiables
++++++++++++++++++++++++
@@ -110,7 +110,7 @@ The crawler can be considered the main program doing the synchronization in basi
Relevant sources in:
-- ``src/crawl.py``
+- :py:mod:`caoscrawler.crawl`
diff --git a/src/doc/conf.py b/src/doc/conf.py
index 586f622150300f16e7ed669a19a09e43dbd46061..fe244e8fa4bc4a2c17fc41c79c14f5a993c22bb9 100644
--- a/src/doc/conf.py
+++ b/src/doc/conf.py
@@ -33,10 +33,10 @@ copyright = '2024, IndiScale'
author = 'Alexander Schlemmer'
# The short X.Y version
-version = '0.8.0'
+version = '0.9.0'
# The full version, including alpha/beta/rc tags
# release = '0.5.2-rc2'
-release = '0.8.0'
+release = '0.9.0'
# -- General configuration ---------------------------------------------------
diff --git a/src/doc/converters.rst b/src/doc/converters.rst
deleted file mode 100644
index f59e6d3dff0a1f75dc4e0e5bcbbee0b4ceb7e81d..0000000000000000000000000000000000000000
--- a/src/doc/converters.rst
+++ /dev/null
@@ -1,822 +0,0 @@
-Converters
-))))))))))
-
-Converters treat a StructureElement and during this process create a number of new
-StructureElements: the children of the initially treated StructureElement. Thus by treatment of
-existing StructureElements, Converters create a tree of StructureElements.
-
-.. image:: img/converter.png
- :height: 170
-
-Each StructureElement in the tree has a set of properties, organized as
-key-value pairs.
-Some of those properties are specified by the type of StructureElement. For example,
-a file could have the file name as property: ``'filename': myfile.dat``.
-Converters may define additional functions that create further values. For
-example, a regular expression could be used to get a date from a file name.
-
-CFood definition
-++++++++++++++++
-
-Converter application to data is specified via a tree-like yml file (called ``cfood.yml``, by
-convention). The yml file specifies which Converters shall be used on which StructureElements, and
-how to treat the generated *child* StructureElements.
-
-The yaml definition may look like this:
-
-.. todo::
-
- This is outdated, see ``cfood-schema.yml`` for the current specification of a ``cfood.yml``.
-
-.. code-block:: yaml
-
- <NodeName>:
- type: <ConverterName>
- match: ".*"
- records:
- Experiment1:
- parents:
- - Experiment
- - Blablabla
- date: $DATUM
- (...)
- Experiment2:
- parents:
- - Experiment
- subtree:
- (...)
-
-The **<NodeName>** is a description of what the current block represents (e.g.
-``experiment-folder``) and is used as an identifier.
-
-**<type>** selects the converter that is going to be matched against the current structure
-element. If the structure element matches (this is a combination of a typecheck and a detailed
-match, see the :py:class:`~caoscrawler.converters.Converter` source documentation for details), the
-converter will:
-
-- generate records (with :py:meth:`~caoscrawler.converters.Converter.create_records`)
-- possibly process a subtree (with :py:meth:`caoscrawler.converters.Converter.create_children`)
-
-**match** *TODO*
-
-**records** is a dict of definitions that define the semantic structure
-(see details below).
-
-**subtree** makes the yaml recursive: It contains a list of new Converter
-definitions, which work on the StructureElements that are returned by the
-current Converter.
-
-Transform Functions
-+++++++++++++++++++
-Often the situation arises, that you cannot use a value as it is found. Maybe a value should be
-increased by an offset or a string should be split into a list of pieces. In order to allow such
-simple conversions, transform functions can be named in the converter definition that are then
-applied to the respective variables when the converter is executed.
-
-.. code-block:: yaml
-
- <NodeName>:
- type: <ConverterName>
- match: ".*"
- transform:
- <TransformNodeName>:
- in: $<in_var_name>
- out: $<out_var_name>
- functions:
- - <func_name>: # name of the function to be applied
- <func_arg1>: <func_arg1_value> # key value pairs that are passed as parameters
- <func_arg2>: <func_arg2_value>
- # ...
-
-An example that splits the variable ``a`` and puts the generated list in ``b`` is the following:
-
-.. code-block:: yaml
-
- Experiment:
- type: Dict
- match: ".*"
- transform:
- param_split:
- in: $a
- out: $b
- functions:
- - split: # split is a function that is defined by default
- marker: "|" # its only parameter is the marker that is used to split the string
- records:
- Report:
- tags: $b
-
-This splits the string in '$a' and stores the resulting list in '$b'. This is here used to add a
-list valued property to the Report Record.
-
-
-There are a number of transform functions that are defined by default (see
-``src/caoscrawler/default_transformers.yml``). You can define custom transform functions by adding
-them to the cfood definition (see :doc:`CFood Documentation<cfood>`).
-
-
-Standard Converters
-+++++++++++++++++++
-
-These are the standard converters that exist in a default installation. For writing and applying
-*custom converters*, see :ref:`below <Custom Converters>`.
-
-Directory Converter
-===================
-The Directory Converter creates StructureElements for each File and Directory
-inside the current Directory. You can match a regular expression against the
-directory name using the 'match' key.
-
-Simple File Converter
-=====================
-The Simple File Converter does not create any children and is usually used if
-a file shall be used as it is and be inserted and referenced by other entities.
-
-Markdown File Converter
-=======================
-Reads a YAML header from Markdown files (if such a header exists) and creates
-children elements according to the structure of the header.
-
-DictElement Converter
-=====================
-
-DictElement → StructureElement
-
-Creates a child StructureElement for each key in the dictionary.
-
-Typical Subtree converters
---------------------------
-The following StructureElement types are typically created by the DictElement converter:
-
-- BooleanElement
-- FloatElement
-- TextElement
-- IntegerElement
-- ListElement
-- DictElement
-
-Note that you may use ``TextElement`` for anything that exists in a text format that can be
-interpreted by the server, such as date and datetime strings in ISO-8601 format.
-
-Scalar Value Converters
-=======================
-`BooleanElementConverter`, `FloatElementConverter`, `TextElementConverter`, and
-`IntegerElementConverter` behave very similarly.
-
-These converters expect `match_name` and `match_value` in their definition
-which allow to match the key and the value, respectively.
-
-Note that there are defaults for accepting other types. For example,
-FloatElementConverter also accepts IntegerElements. The default
-behavior can be adjusted with the fields `accept_text`, `accept_int`,
-`accept_float`, and `accept_bool`.
-
-The following denotes what kind of StructureElements are accepted by default
-(they are defined in `src/caoscrawler/converters.py`):
-
-- BooleanElementConverter: bool, int
-- FloatElementConverter: int, float
-- TextElementConverter: text, bool, int, float
-- IntegerElementConverter: int
-- ListElementConverter: list
-- DictElementConverter: dict
-
-YAMLFileConverter
-=================
-
-A specialized Dict Converter for yaml files: Yaml files are opened and the contents are
-converted into dictionaries that can be further converted using the typical subtree converters
-of dict converter.
-
-**WARNING**: Currently unfinished implementation.
-
-JSONFileConverter
-=================
-
-
-
-
-TableConverter
-==============
-
-Table → DictElement
-
-A generic converter (abstract) for files containing tables.
-Currently, there are two specialized implementations for XLSX files and CSV files.
-
-All table converters generate a subtree of dicts, which in turn can be converted with DictElementConverters:
-For each row in the table the TableConverter generates a DictElement (structure element). The key of the
-element is the row number. The value of the element is a dict containing the mapping of
-column names to values of the respective cell.
-
-Example:
-
-.. code-block:: yaml
-
- subtree:
- TABLE: # Any name for the table as a whole
- type: CSVTableConverter
- match: ^test_table.csv$
- records:
- (...) # Records edited for the whole table file
- subtree:
- ROW: # Any name for a data row in the table
- type: DictElement
- match_name: .*
- match_value: .*
- records:
- (...) # Records edited for each row
- subtree:
- COLUMN: # Any name for a specific type of column in the table
- type: FloatElement
- match_name: measurement # Name of the column in the table file
- match_value: (?P<column_value).*)
- records:
- (...) # Records edited for each cell
-
-
-XLSXTableConverter
-==================
-
-XLSX File → DictElement
-
-CSVTableConverter
-=================
-
-CSV File → DictElement
-
-PropertiesFromDictConverter
-===========================
-
-The :py:class:`~caoscrawler.converters.PropertiesFromDictConverter` is
-a specialization of the
-:py:class:`~caoscrawler.converters.DictElementConverter` and offers
-all its functionality. It is meant to operate on dictionaries (e.g.,
-from reading in a json or a table file), the keys of which correspond
-closely to properties in a LinkAhead datamodel. This is especially
-handy in cases where properties may be added to the data model and
-data sources that are not yet known when writing the cfood definition.
-
-The converter definition of the
-:py:class:`~caoscrawler.converters.PropertiesFromDictConverter` has an
-additional required entry ``record_from_dict`` which specifies the
-Record to which the properties extracted from the dict are attached
-to. This Record is identified by its ``variable_name`` by which it can
-be referred to further down the subtree. You can also use the name of
-a Record that was specified earlier in the CFood definition in order
-to extend it by the properties extracted from a dict. Let's have a
-look at a simple example. A CFood definition
-
-.. code-block:: yaml
-
- PropertiesFromDictElement:
- type: PropertiesFromDictElement
- match: ".*"
- record_from_dict:
- variable_name: MyRec
- parents:
- - MyType1
- - MyType2
-
-applied to a dictionary
-
-.. code-block:: json
-
- {
- "name": "New name",
- "a": 5,
- "b": ["a", "b", "c"],
- "author": {
- "full_name": "Silvia Scientist"
- }
- }
-
-will create a Record ``New name`` with parents ``MyType1`` and
-``MyType2``. It has a scalar property ``a`` with value 5, a list
-property ``b`` with values "a", "b" and "c", and an ``author``
-property which references an ``author`` with a ``full_name`` property
-with value "Silvia Scientist":
-
-.. image:: img/properties-from-dict-records-author.png
- :height: 210
-
-Note how the different dictionary keys are handled differently
-depending on their types: scalar and list values are understood
-automatically, and a dictionary-valued entry like ``author`` is
-translated into a reference to an ``author`` Record automatically.
-
-You can further specify how references are treated with an optional
-``references key`` in ``record_from_dict``. Let's assume that in the
-above example, we have an ``author`` **Property** with datatype
-``Person`` in our data model. We could add this information by
-extending the above example definition by
-
-
-.. code-block:: yaml
-
- PropertiesFromDictElement:
- type: PropertiesFromDictElement
- match: ".*"
- record_from_dict:
- variable_name: MyRec
- parents:
- - MyType1
- - MyType2
- references:
- author:
- parents:
- - Person
-
-so that now, a ``Person`` record with a ``full_name`` property with
-value "Silvia Scientist" is created as the value of the ``author``
-property:
-
-.. image:: img/properties-from-dict-records-person.png
- :height: 200
-
-For the time being, only the parents of the referenced record can be
-set via this option. More complicated treatments can be implemented
-via the ``referenced_record_callback`` (see below).
-
-Properties can be blacklisted with the ``properties_blacklist``
-keyword, i.e., all keys listed under ``properties_blacklist`` will be
-excluded from automated treatment. Since the
-:py:class:`~caoscrawler.converters.PropertiesFromDictConverter` has
-all the functionality of the
-:py:class:`~caoscrawler.converters.DictElementConverter`, individual
-properties can still be used in a subtree. Together with
-``properties_blacklist`` this can be used to add custom treatment to
-specific properties by blacklisting them in ``record_from_dict`` and
-then treating them in the subtree the same as you would do it in the
-standard
-:py:class:`~caoscrawler.converters.DictElementConverter`. Note that
-the blacklisted keys are excluded on **all** levels of the dictionary,
-i.e., also when they occur in a referenced entity.
-
-For further customization, the
-:py:class:`~caoscrawler.converters.PropertiesFromDictConverter` can be
-used as a basis for :ref:`custom converters<Custom Converters>` which
-can make use of its ``referenced_record_callback`` argument. The
-``referenced_record_callback`` can be a callable object which takes
-exactly a Record as an argument and needs to return that Record after
-doing whatever custom treatment is needed. Additionally, it is given
-the ``RecordStore`` and the ``ValueStore`` in order to be able to
-access the records and values that have already been defined from
-within ``referenced_record_callback``. Such a function might look the
-following:
-
-.. code-block:: python
-
- def my_callback(rec: db.Record, records: RecordStore, values: GeneralStore):
- # do something with rec, possibly using other records or values from the stores...
- rec.description = "This was updated in a callback"
- return rec
-
-It is applied to all Records that are created from the dictionary and
-it can be used to, e.g., transform values of some properties, or add
-special treatment to all Records of a specific
-type. ``referenced_record_callback`` is applied **after** the
-properties from the dictionary have been applied as explained above.
-
-
-Further converters
-++++++++++++++++++
-
-More converters, together with cfood definitions and examples can be found in
-the `LinkAhead Crawler Extensions Subgroup
-<https://gitlab.com/linkahead/crawler-extensions>`_ on gitlab. In the following,
-we list converters that are shipped with the crawler library itself but are not
-part of the set of standard converters and may require this library to be
-installed with additional optional dependencies.
-
-HDF5 Converters
-===============
-
-For treating `HDF5 Files
-<https://docs.hdfgroup.org/hdf5/develop/_s_p_e_c.html>`_, there are in total
-four individual converters corresponding to the internal structure of HDF5
-files: the :ref:`H5FileConverter` which opens the file itself and creates
-further structure elements from HDF5 groups, datasets, and included
-multi-dimensional arrays that are in turn treated by the
-:ref:`H5GroupConverter`, the :ref:`H5DatasetConverter`, and the
-:ref:`H5NdarrayConverter`, respectively. You need to install the LinkAhead
-crawler with its optional ``h5-crawler`` dependency for using these converters.
-
-The basic idea when crawling HDF5 files is to treat them very similar to
-:ref:`dictionaries <DictElement Converter>` in which the attributes on root,
-group, or dataset level are essentially treated like ``BooleanElement``,
-``TextElement``, ``FloatElement``, and ``IntegerElement`` in a dictionary: They
-are appended as children and can be accessed via the ``subtree``. The file
-itself and the groups within may contain further groups and datasets, which can
-have their own attributes, subgroups, and datasets, very much like
-``DictElements`` within a dictionary. The main difference to any other
-dictionary type is the presence of multi-dimensional arrays within HDF5
-datasets. Since LinkAhead doesn't have any datatype corresponding to these, and
-since it isn't desirable to store these arrays directly within LinkAhead for
-reasons of performance and of searchability, we wrap them within a specific
-Record as explained :ref:`below <H5NdarrayConverter>`, together with more
-metadata and their internal path within the HDF5 file. Users can thus query for
-datasets and their arrays according to their metadata within LinkAhead and then
-use the internal path information to access the dataset within the file
-directly. The type of this record and the property for storing the internal path
-need to be reflected in the datamodel. Using the default names, you would need a
-datamodel like
-
-.. code-block:: yaml
-
- H5Ndarray:
- obligatory_properties:
- internal_hdf5-path:
- datatype: TEXT
-
-although the names of both property and record type can be configured within the
-cfood definition.
-
-A simple example of a cfood definition for HDF5 files can be found in the `unit
-tests
-<https://gitlab.com/linkahead/linkahead-crawler/-/blob/main/unittests/h5_cfood.yml?ref_type=heads>`_
-and shows how the individual converters are used in order to crawl a `simple
-example file
-<https://gitlab.com/linkahead/linkahead-crawler/-/blob/main/unittests/hdf5_dummy_file.hdf5?ref_type=heads>`_
-containing groups, subgroups, and datasets, together with their respective
-attributes.
-
-H5FileConverter
----------------
-
-This is an extension of the
-:py:class:`~caoscrawler.converters.SimpleFileConverter` class. It opens the HDF5
-file and creates children for any contained group or dataset. Additionally, the
-root-level attributes of the HDF5 file are accessible as children.
-
-H5GroupConverter
-----------------
-
-This is an extension of the
-:py:class:`~caoscrawler.converters.DictElementConverter` class. Children are
-created for all subgroups and datasets in this HDF5 group. Additionally, the
-group-level attributes are accessible as children.
-
-H5DatasetConverter
-------------------
-
-This is an extension of the
-:py:class:`~caoscrawler.converters.DictElementConverter` class. Most
-importantly, it stores the array data in HDF5 dataset into
-:py:class:`~caoscrawler.hdf5_converter.H5NdarrayElement` which is added to its
-children, as well as the dataset attributes.
-
-H5NdarrayConverter
-------------------
-
-This converter creates a wrapper record for the contained dataset. The name of
-this record needs to be specified in the cfood definition of this converter via
-the ``recordname`` option. The RecordType of this record can be configured with
-the ``array_recordtype_name`` option and defaults to ``H5Ndarray``. Via the
-given ``recordname``, this record can be used within the cfood. Most
-importantly, this record stores the internal path of this array within the HDF5
-file in a text property, the name of which can be configured with the
-``internal_path_property_name`` option which defaults to ``internal_hdf5_path``.
-
-Custom Converters
-+++++++++++++++++
-
-As mentioned before it is possible to create custom converters.
-These custom converters can be used to integrate arbitrary data extraction and ETL capabilities
-into the LinkAhead crawler and make these extensions available to any yaml specification.
-
-Tell the crawler about a custom converter
-=========================================
-
-To use a custom crawler, it must be defined in the ``Converters`` section of the CFood yaml file.
-The basic syntax for adding a custom converter to a definition file is:
-
-.. code-block:: yaml
-
- Converters:
- <NameOfTheConverterInYamlFile>:
- package: <python>.<module>.<name>
- converter: <PythonClassName>
-
-The Converters section can be either put into the first or the second document of the cfood yaml file.
-It can be also part of a single-document yaml cfood file. Please refer to :doc:`the cfood documentation<cfood>` for more details.
-
-Details:
-
-- **<NameOfTheConverterInYamlFile>**: This is the name of the converter as it is going to be used in the present yaml file.
-- **<python>.<module>.<name>**: The name of the module where the converter class resides.
-- **<PythonClassName>**: Within this specified module there must be a class inheriting from base class :py:class:`caoscrawler.converters.Converter`.
-
-Implementing a custom converter
-===============================
-
-Converters inherit from the :py:class:`~caoscrawler.converters.Converter` class.
-
-The following methods are abstract and need to be overwritten by your custom converter to make it work:
-
-:py:meth:`~caoscrawler.converters.Converter.create_children`:
- Return a list of child StructureElement objects.
-
-- :py:meth:`~caoscrawler.converters.Converter.match`
-- :py:meth:`~caoscrawler.converters.Converter.typecheck`
-
-
-Example
-=======
-
-In the following, we will explain the process of adding a custom converter to a yaml file using
-a SourceResolver that is able to attach a source element to another entity.
-
-**Note**: This example might become a standard crawler soon, as part of the scifolder specification. See https://doi.org/10.3390/data5020043 for details. In this documentation example we will, therefore, add it to a package called "scifolder".
-
-First we will create our package and module structure, which might be:
-
-.. code-block::
-
- scifolder_package/
- README.md
- setup.cfg
- setup.py
- Makefile
- tox.ini
- src/
- scifolder/
- __init__.py
- converters/
- __init__.py
- sources.py # <- the actual file containing
- # the converter class
- doc/
- unittests/
-
-Now we need to create a class called "SourceResolver" in the file "sources.py". In this - more advanced - example, we will not inherit our converter directly from :py:class:`~caoscrawler.converters.Converter`, but use :py:class:`~caoscrawler.converters.TextElementConverter`. The latter already implements :py:meth:`~caoscrawler.converters.Converter.match` and :py:meth:`~caoscrawler.converters.Converter.typecheck`, so only an implementation for :py:meth:`~caoscrawler.converters.Converter.create_children` has to be provided by us.
-Furthermore we will customize the method :py:meth:`~caoscrawler.converters.Converter.create_records` that allows us to specify a more complex record generation procedure than provided in the standard implementation. One specific limitation of the standard implementation is, that only a fixed
-number of records can be generated by the yaml definition. So for any applications - like here - that require an arbitrary number of records to be created, a customized implementation of :py:meth:`~caoscrawler.converters.Converter.create_records` is recommended.
-In this context it is recommended to make use of the function :func:`caoscrawler.converters.create_records` that implements creation of record objects from python dictionaries of the same structure
-that would be given using a yaml definition (see next section below).
-
-.. code-block:: python
-
- import re
- from caoscrawler.stores import GeneralStore, RecordStore
- from caoscrawler.converters import TextElementConverter, create_records
- from caoscrawler.structure_elements import StructureElement, TextElement
-
-
- class SourceResolver(TextElementConverter):
- """
- This resolver uses a source list element (e.g. from the markdown readme file)
- to link sources correctly.
- """
-
- def __init__(self, definition: dict, name: str,
- converter_registry: dict):
- """
- Initialize a new directory converter.
- """
- super().__init__(definition, name, converter_registry)
-
- def create_children(self, generalStore: GeneralStore,
- element: StructureElement):
-
- # The source resolver does not create children:
-
- return []
-
- def create_records(self, values: GeneralStore,
- records: RecordStore,
- element: StructureElement,
- file_path_prefix):
- if not isinstance(element, TextElement):
- raise RuntimeError()
-
- # This function must return a list containing tuples, each one for a modified
- # property: (name_of_entity, name_of_property)
- keys_modified = []
-
- # This is the name of the entity where the source is going to be attached:
- attach_to_scientific_activity = self.definition["scientific_activity"]
- rec = records[attach_to_scientific_activity]
-
- # The "source" is a path to a source project, so it should have the form:
- # /<Category>/<project>/<scientific_activity>/
- # obtain these information from the structure element:
- val = element.value
- regexp = (r'/(?P<category>(SimulationData)|(ExperimentalData)|(DataAnalysis))'
- '/(?P<project_date>.*?)_(?P<project_identifier>.*)'
- '/(?P<date>[0-9]{4,4}-[0-9]{2,2}-[0-9]{2,2})(_(?P<identifier>.*))?/')
-
- res = re.match(regexp, val)
- if res is None:
- raise RuntimeError("Source cannot be parsed correctly.")
-
- # Mapping of categories on the file system to corresponding record types in CaosDB:
- cat_map = {
- "SimulationData": "Simulation",
- "ExperimentalData": "Experiment",
- "DataAnalysis": "DataAnalysis"}
- linkrt = cat_map[res.group("category")]
-
- keys_modified.extend(create_records(values, records, {
- "Project": {
- "date": res.group("project_date"),
- "identifier": res.group("project_identifier"),
- },
- linkrt: {
- "date": res.group("date"),
- "identifier": res.group("identifier"),
- "project": "$Project"
- },
- attach_to_scientific_activity: {
- "sources": "+$" + linkrt
- }}, file_path_prefix))
-
- # Process the records section of the yaml definition:
- keys_modified.extend(
- super().create_records(values, records, element, file_path_prefix))
-
- # The create_records function must return the modified keys to make it compatible
- # to the crawler functions:
- return keys_modified
-
-
-If the recommended (python) package structure is used, the package containing the converter
-definition can just be installed using `pip install .` or `pip install -e .` from the
-`scifolder_package` directory.
-
-The following yaml block will register the converter in a yaml file:
-
-.. code-block:: yaml
-
- Converters:
- SourceResolver:
- package: scifolder.converters.sources
- converter: SourceResolver
-
-
-Using the `create_records` API function
-=======================================
-
-The function :func:`caoscrawler.converters.create_records` was already mentioned above and it is
-the recommended way to create new records from custom converters. Let's have a look at the
-function signature:
-
-.. code-block:: python
-
- def create_records(values: GeneralStore, # <- pass the current variables store here
- records: RecordStore, # <- pass the current store of CaosDB records here
- def_records: dict): # <- This is the actual definition of new records!
-
-
-`def_records` is the actual definition of new records according to the yaml cfood specification
-(work in progress, in the docs). Essentially you can do everything here, that you could do
-in the yaml document as well, but using python source code.
-
-Let's have a look at a few examples:
-
-.. code-block:: yaml
-
- DirConverter:
- type: Directory
- match: (?P<dir_name>.*)
- records:
- Experiment:
- identifier: $dir_name
-
-This block will just create a new record with parent `Experiment` and one property
-`identifier` with a value derived from the matching regular expression.
-
-Let's formulate that using `create_records`:
-
-.. code-block:: python
-
- dir_name = "directory name"
-
- record_def = {
- "Experiment": {
- "identifier": dir_name
- }
- }
-
- keys_modified = create_records(values, records,
- record_def)
-
-The `dir_name` is set explicitely here, everything else is identical to the yaml statements.
-
-
-The role of `keys_modified`
-===========================
-
-You probably have noticed already, that :func:`caoscrawler.converters.create_records` returns
-`keys_modified` which is a list of tuples. Each element of `keys_modified` has two elements:
-
-- Element 0 is the name of the record that is modified (as used in the record store `records`).
-- Element 1 is the name of the property that is modified.
-
-It is important, that the correct list of modified keys is returned by
-:py:meth:`~caoscrawler.converters.Converter.create_records` to make the crawler process work.
-
-So, a sketch of a typical implementation within a custom converter could look like this:
-
-
-.. code-block:: python
-
- def create_records(self, values: GeneralStore,
- records: RecordStore,
- element: StructureElement,
- file_path_prefix: str):
-
- # Modify some records:
- record_def = {
- # ...
- }
-
- keys_modified = create_records(values, records,
- record_def)
-
- # You can of course do it multiple times:
- keys_modified.extend(create_records(values, records,
- record_def))
-
- # You can also process the records section of the yaml definition:
- keys_modified.extend(
- super().create_records(values, records, element, file_path_prefix))
- # This essentially allows users of your converter to customize the creation of records
- # by providing a custom "records" section additionally to the modifications provided
- # in this implementation of the Converter.
-
- # Important: Return the list of modified keys!
- return keys_modified
-
-
-More complex example
-====================
-
-Let's have a look at a more complex examples, defining multiple records:
-
-.. code-block:: yaml
-
- DirConverter:
- type: Directory
- match: (?P<dir_name>.*)
- records:
- Project:
- identifier: project_name
- Experiment:
- identifier: $dir_name
- Project: $Project
- ProjectGroup:
- projects: +$Project
-
-
-This block will create two new Records:
-
-- A project with a constant identifier
-- An experiment with an identifier, derived from a regular expression and a reference to the new project.
-
-Furthermore a Record `ProjectGroup` will be edited (its initial definition is not given in the
-yaml block): The project that was just created will be added as a list element to the property
-`projects`.
-
-Let's formulate that using `create_records` (again, `dir_name` is constant here):
-
-.. code-block:: python
-
- dir_name = "directory name"
-
- record_def = {
- "Project": {
- "identifier": "project_name",
- }
- "Experiment": {
- "identifier": dir_name,
- "Project": "$Project",
- }
- "ProjectGroup": {
- "projects": "+$Project",
- }
-
- }
-
- keys_modified = create_records(values, records,
- record_def)
-
-Debugging
-=========
-
-You can add the key `debug_match` to the definition of a Converter in order to create debugging
-output for the match step. The following snippet illustrates this:
-
-.. code-block:: yaml
-
- DirConverter:
- type: Directory
- match: (?P<dir_name>.*)
- debug_match: True
- records:
- Project:
- identifier: project_name
-
-
-Whenever this Converter tries to match a StructureElement, it logs what was tried to macht against
-what and what the result was.
diff --git a/src/doc/converters/cfood_definition.rst b/src/doc/converters/cfood_definition.rst
new file mode 100644
index 0000000000000000000000000000000000000000..ea2f14b23bec04e659aa3166f089c7d274f74811
--- /dev/null
+++ b/src/doc/converters/cfood_definition.rst
@@ -0,0 +1,53 @@
+CFood definition
+++++++++++++++++
+
+Converter application to data is specified via a tree-like yml file (called ``cfood.yml``, by
+convention). The yml file specifies which Converters shall be used on which StructureElements, and
+how to treat the generated *child* StructureElements.
+
+The yaml definition may look like this:
+
+.. todo::
+
+ This is outdated, see ``cfood-schema.yml`` for the current specification of a ``cfood.yml``.
+
+.. code-block:: yaml
+
+ <NodeName>:
+ type: <ConverterName>
+ match: ".*"
+ records:
+ Experiment1:
+ parents:
+ - Experiment
+ - Blablabla
+ date: $DATUM
+ (...)
+ Experiment2:
+ parents:
+ - Experiment
+ subtree:
+ (...)
+
+The **<NodeName>** is a description of what the current block represents (e.g.
+``experiment-folder``) and is used as an identifier.
+
+**<type>** selects the converter that is going to be matched against
+the current structure element. If the structure element matches (this
+is a combination of a typecheck and a detailed match, see the
+:py:class:`~caoscrawler.converters.converters.Converter` source
+documentation for details), the converter will:
+
+- generate records (with
+ :py:meth:`~caoscrawler.converters.converters.Converter.create_records`)
+- possibly process a subtree (with
+ :py:meth:`~caoscrawler.converters.converters.Converter.create_children`)
+
+**match** *TODO*
+
+**records** is a dict of definitions that define the semantic structure
+(see details below).
+
+**subtree** makes the yaml recursive: It contains a list of new Converter
+definitions, which work on the StructureElements that are returned by the
+current Converter.
diff --git a/src/doc/converters/custom_converters.rst b/src/doc/converters/custom_converters.rst
new file mode 100644
index 0000000000000000000000000000000000000000..2738d66c483148fdecb9b189edac45e5b9a55a8b
--- /dev/null
+++ b/src/doc/converters/custom_converters.rst
@@ -0,0 +1,344 @@
+Custom Converters
++++++++++++++++++
+
+As mentioned before it is possible to create custom converters.
+These custom converters can be used to integrate arbitrary data extraction and ETL capabilities
+into the LinkAhead crawler and make these extensions available to any yaml specification.
+
+Tell the crawler about a custom converter
+=========================================
+
+To use a custom crawler, it must be defined in the ``Converters`` section of the CFood yaml file.
+The basic syntax for adding a custom converter to a definition file is:
+
+.. code-block:: yaml
+
+ Converters:
+ <NameOfTheConverterInYamlFile>:
+ package: <python>.<module>.<name>
+ converter: <PythonClassName>
+
+The Converters section can be either put into the first or the second
+document of the cfood yaml file. It can be also part of a
+single-document yaml cfood file. Please refer to :doc:`the cfood
+documentation<../cfood>` for more details.
+
+Details:
+
+- **<NameOfTheConverterInYamlFile>**: This is the name of the converter as it is going to be used in the present yaml file.
+- **<python>.<module>.<name>**: The name of the module where the converter class resides.
+- **<PythonClassName>**: Within this specified module there must be a class inheriting from base class :py:class:`caoscrawler.converters.converters.Converter`.
+
+Implementing a custom converter
+===============================
+
+Converters inherit from the :py:class:`~caoscrawler.converters.converters.Converter` class.
+
+The following methods are abstract and need to be overwritten by your custom converter to make it work:
+
+:py:meth:`~caoscrawler.converters.converters.Converter.create_children`:
+ Return a list of child StructureElement objects.
+
+- :py:meth:`~caoscrawler.converters.converters.Converter.match`
+- :py:meth:`~caoscrawler.converters.converters.Converter.typecheck`
+
+
+Example
+=======
+
+In the following, we will explain the process of adding a custom converter to a yaml file using
+a SourceResolver that is able to attach a source element to another entity.
+
+**Note**: This example might become a standard crawler soon, as part of the scifolder specification. See https://doi.org/10.3390/data5020043 for details. In this documentation example we will, therefore, add it to a package called "scifolder".
+
+First we will create our package and module structure, which might be:
+
+.. code-block::
+
+ scifolder_package/
+ README.md
+ setup.cfg
+ setup.py
+ Makefile
+ tox.ini
+ src/
+ scifolder/
+ __init__.py
+ converters/
+ __init__.py
+ sources.py # <- the actual file containing
+ # the converter class
+ doc/
+ unittests/
+
+Now we need to create a class called "SourceResolver" in the file "sources.py". In this - more advanced - example, we will not inherit our converter directly from :py:class:`~caoscrawler.converters.converters.Converter`, but use :py:class:`~caoscrawler.converters.converters.TextElementConverter`. The latter already implements :py:meth:`~caoscrawler.converters.converters.Converter.match` and :py:meth:`~caoscrawler.converters.converters.Converter.typecheck`, so only an implementation for :py:meth:`~caoscrawler.converters.converters.Converter.create_children` has to be provided by us.
+Furthermore we will customize the method :py:meth:`~caoscrawler.converters.converters.Converter.create_records` that allows us to specify a more complex record generation procedure than provided in the standard implementation. One specific limitation of the standard implementation is, that only a fixed
+number of records can be generated by the yaml definition. So for any applications - like here - that require an arbitrary number of records to be created, a customized implementation of :py:meth:`~caoscrawler.converters.converters.Converter.create_records` is recommended.
+In this context it is recommended to make use of the function :func:`caoscrawler.converters.converters.create_records` that implements creation of record objects from python dictionaries of the same structure
+that would be given using a yaml definition (see next section below).
+
+.. code-block:: python
+
+ import re
+ from caoscrawler.stores import GeneralStore, RecordStore
+ from caoscrawler.converters import TextElementConverter, create_records
+ from caoscrawler.structure_elements import StructureElement, TextElement
+
+
+ class SourceResolver(TextElementConverter):
+ """
+ This resolver uses a source list element (e.g. from the markdown readme file)
+ to link sources correctly.
+ """
+
+ def __init__(self, definition: dict, name: str,
+ converter_registry: dict):
+ """
+ Initialize a new directory converter.
+ """
+ super().__init__(definition, name, converter_registry)
+
+ def create_children(self, generalStore: GeneralStore,
+ element: StructureElement):
+
+ # The source resolver does not create children:
+
+ return []
+
+ def create_records(self, values: GeneralStore,
+ records: RecordStore,
+ element: StructureElement,
+ file_path_prefix):
+ if not isinstance(element, TextElement):
+ raise RuntimeError()
+
+ # This function must return a list containing tuples, each one for a modified
+ # property: (name_of_entity, name_of_property)
+ keys_modified = []
+
+ # This is the name of the entity where the source is going to be attached:
+ attach_to_scientific_activity = self.definition["scientific_activity"]
+ rec = records[attach_to_scientific_activity]
+
+ # The "source" is a path to a source project, so it should have the form:
+ # /<Category>/<project>/<scientific_activity>/
+ # obtain these information from the structure element:
+ val = element.value
+ regexp = (r'/(?P<category>(SimulationData)|(ExperimentalData)|(DataAnalysis))'
+ '/(?P<project_date>.*?)_(?P<project_identifier>.*)'
+ '/(?P<date>[0-9]{4,4}-[0-9]{2,2}-[0-9]{2,2})(_(?P<identifier>.*))?/')
+
+ res = re.match(regexp, val)
+ if res is None:
+ raise RuntimeError("Source cannot be parsed correctly.")
+
+ # Mapping of categories on the file system to corresponding record types in CaosDB:
+ cat_map = {
+ "SimulationData": "Simulation",
+ "ExperimentalData": "Experiment",
+ "DataAnalysis": "DataAnalysis"}
+ linkrt = cat_map[res.group("category")]
+
+ keys_modified.extend(create_records(values, records, {
+ "Project": {
+ "date": res.group("project_date"),
+ "identifier": res.group("project_identifier"),
+ },
+ linkrt: {
+ "date": res.group("date"),
+ "identifier": res.group("identifier"),
+ "project": "$Project"
+ },
+ attach_to_scientific_activity: {
+ "sources": "+$" + linkrt
+ }}, file_path_prefix))
+
+ # Process the records section of the yaml definition:
+ keys_modified.extend(
+ super().create_records(values, records, element, file_path_prefix))
+
+ # The create_records function must return the modified keys to make it compatible
+ # to the crawler functions:
+ return keys_modified
+
+
+If the recommended (python) package structure is used, the package containing the converter
+definition can just be installed using `pip install .` or `pip install -e .` from the
+`scifolder_package` directory.
+
+The following yaml block will register the converter in a yaml file:
+
+.. code-block:: yaml
+
+ Converters:
+ SourceResolver:
+ package: scifolder.converters.sources
+ converter: SourceResolver
+
+
+Using the `create_records` API function
+=======================================
+
+The function :func:`caoscrawler.converters.converters.create_records` was already mentioned above and it is
+the recommended way to create new records from custom converters. Let's have a look at the
+function signature:
+
+.. code-block:: python
+
+ def create_records(values: GeneralStore, # <- pass the current variables store here
+ records: RecordStore, # <- pass the current store of CaosDB records here
+ def_records: dict): # <- This is the actual definition of new records!
+
+
+`def_records` is the actual definition of new records according to the yaml cfood specification
+(work in progress, in the docs). Essentially you can do everything here, that you could do
+in the yaml document as well, but using python source code.
+
+Let's have a look at a few examples:
+
+.. code-block:: yaml
+
+ DirConverter:
+ type: Directory
+ match: (?P<dir_name>.*)
+ records:
+ Experiment:
+ identifier: $dir_name
+
+This block will just create a new record with parent `Experiment` and one property
+`identifier` with a value derived from the matching regular expression.
+
+Let's formulate that using `create_records`:
+
+.. code-block:: python
+
+ dir_name = "directory name"
+
+ record_def = {
+ "Experiment": {
+ "identifier": dir_name
+ }
+ }
+
+ keys_modified = create_records(values, records,
+ record_def)
+
+The `dir_name` is set explicitely here, everything else is identical to the yaml statements.
+
+
+The role of `keys_modified`
+===========================
+
+You probably have noticed already, that :func:`caoscrawler.converters.converters.create_records` returns
+`keys_modified` which is a list of tuples. Each element of `keys_modified` has two elements:
+
+- Element 0 is the name of the record that is modified (as used in the record store `records`).
+- Element 1 is the name of the property that is modified.
+
+It is important, that the correct list of modified keys is returned by
+:py:meth:`~caoscrawler.converters.converters.Converter.create_records` to make the crawler process work.
+
+So, a sketch of a typical implementation within a custom converter could look like this:
+
+
+.. code-block:: python
+
+ def create_records(self, values: GeneralStore,
+ records: RecordStore,
+ element: StructureElement,
+ file_path_prefix: str):
+
+ # Modify some records:
+ record_def = {
+ # ...
+ }
+
+ keys_modified = create_records(values, records,
+ record_def)
+
+ # You can of course do it multiple times:
+ keys_modified.extend(create_records(values, records,
+ record_def))
+
+ # You can also process the records section of the yaml definition:
+ keys_modified.extend(
+ super().create_records(values, records, element, file_path_prefix))
+ # This essentially allows users of your converter to customize the creation of records
+ # by providing a custom "records" section additionally to the modifications provided
+ # in this implementation of the Converter.
+
+ # Important: Return the list of modified keys!
+ return keys_modified
+
+
+More complex example
+====================
+
+Let's have a look at a more complex examples, defining multiple records:
+
+.. code-block:: yaml
+
+ DirConverter:
+ type: Directory
+ match: (?P<dir_name>.*)
+ records:
+ Project:
+ identifier: project_name
+ Experiment:
+ identifier: $dir_name
+ Project: $Project
+ ProjectGroup:
+ projects: +$Project
+
+
+This block will create two new Records:
+
+- A project with a constant identifier
+- An experiment with an identifier, derived from a regular expression and a reference to the new project.
+
+Furthermore a Record `ProjectGroup` will be edited (its initial definition is not given in the
+yaml block): The project that was just created will be added as a list element to the property
+`projects`.
+
+Let's formulate that using `create_records` (again, `dir_name` is constant here):
+
+.. code-block:: python
+
+ dir_name = "directory name"
+
+ record_def = {
+ "Project": {
+ "identifier": "project_name",
+ }
+ "Experiment": {
+ "identifier": dir_name,
+ "Project": "$Project",
+ }
+ "ProjectGroup": {
+ "projects": "+$Project",
+ }
+
+ }
+
+ keys_modified = create_records(values, records,
+ record_def)
+
+Debugging
+=========
+
+You can add the key `debug_match` to the definition of a Converter in order to create debugging
+output for the match step. The following snippet illustrates this:
+
+.. code-block:: yaml
+
+ DirConverter:
+ type: Directory
+ match: (?P<dir_name>.*)
+ debug_match: True
+ records:
+ Project:
+ identifier: project_name
+
+
+Whenever this Converter tries to match a StructureElement, it logs what was tried to macht against
+what and what the result was.
diff --git a/src/doc/converters/further_converters.rst b/src/doc/converters/further_converters.rst
new file mode 100644
index 0000000000000000000000000000000000000000..a334c8778f440e108fd141b0fc53ec06765deb8c
--- /dev/null
+++ b/src/doc/converters/further_converters.rst
@@ -0,0 +1,100 @@
+Further converters
+++++++++++++++++++
+
+More converters, together with cfood definitions and examples can be found in
+the `LinkAhead Crawler Extensions Subgroup
+<https://gitlab.com/linkahead/crawler-extensions>`_ on gitlab. In the following,
+we list converters that are shipped with the crawler library itself but are not
+part of the set of standard converters and may require this library to be
+installed with additional optional dependencies.
+
+HDF5 Converters
+===============
+
+For treating `HDF5 Files
+<https://docs.hdfgroup.org/hdf5/develop/_s_p_e_c.html>`_, there are in total
+four individual converters corresponding to the internal structure of HDF5
+files: the :ref:`H5FileConverter` which opens the file itself and creates
+further structure elements from HDF5 groups, datasets, and included
+multi-dimensional arrays that are in turn treated by the
+:ref:`H5GroupConverter`, the :ref:`H5DatasetConverter`, and the
+:ref:`H5NdarrayConverter`, respectively. You need to install the LinkAhead
+crawler with its optional ``h5-crawler`` dependency for using these converters.
+
+The basic idea when crawling HDF5 files is to treat them very similar to
+:ref:`dictionaries <DictElement Converter>` in which the attributes on root,
+group, or dataset level are essentially treated like ``BooleanElement``,
+``TextElement``, ``FloatElement``, and ``IntegerElement`` in a dictionary: They
+are appended as children and can be accessed via the ``subtree``. The file
+itself and the groups within may contain further groups and datasets, which can
+have their own attributes, subgroups, and datasets, very much like
+``DictElements`` within a dictionary. The main difference to any other
+dictionary type is the presence of multi-dimensional arrays within HDF5
+datasets. Since LinkAhead doesn't have any datatype corresponding to these, and
+since it isn't desirable to store these arrays directly within LinkAhead for
+reasons of performance and of searchability, we wrap them within a specific
+Record as explained :ref:`below <H5NdarrayConverter>`, together with more
+metadata and their internal path within the HDF5 file. Users can thus query for
+datasets and their arrays according to their metadata within LinkAhead and then
+use the internal path information to access the dataset within the file
+directly. The type of this record and the property for storing the internal path
+need to be reflected in the datamodel. Using the default names, you would need a
+datamodel like
+
+.. code-block:: yaml
+
+ H5Ndarray:
+ obligatory_properties:
+ internal_hdf5-path:
+ datatype: TEXT
+
+although the names of both property and record type can be configured within the
+cfood definition.
+
+A simple example of a cfood definition for HDF5 files can be found in the `unit
+tests
+<https://gitlab.com/linkahead/linkahead-crawler/-/blob/main/unittests/h5_cfood.yml?ref_type=heads>`_
+and shows how the individual converters are used in order to crawl a `simple
+example file
+<https://gitlab.com/linkahead/linkahead-crawler/-/blob/main/unittests/hdf5_dummy_file.hdf5?ref_type=heads>`_
+containing groups, subgroups, and datasets, together with their respective
+attributes.
+
+H5FileConverter
+---------------
+
+This is an extension of the
+:py:class:`~caoscrawler.converters.converters.SimpleFileConverter`
+class. It opens the HDF5 file and creates children for any contained
+group or dataset. Additionally, the root-level attributes of the HDF5
+file are accessible as children.
+
+H5GroupConverter
+----------------
+
+This is an extension of the
+:py:class:`~caoscrawler.converters.converters.DictElementConverter`
+class. Children are created for all subgroups and datasets in this
+HDF5 group. Additionally, the group-level attributes are accessible as
+children.
+
+H5DatasetConverter
+------------------
+
+This is an extension of the
+:py:class:`~caoscrawler.converters.converters.DictElementConverter`
+class. Most importantly, it stores the array data in HDF5 dataset into
+:py:class:`~caoscrawler.converters.hdf5_converter.H5NdarrayElement`
+which is added to its children, as well as the dataset attributes.
+
+H5NdarrayConverter
+------------------
+
+This converter creates a wrapper record for the contained dataset. The name of
+this record needs to be specified in the cfood definition of this converter via
+the ``recordname`` option. The RecordType of this record can be configured with
+the ``array_recordtype_name`` option and defaults to ``H5Ndarray``. Via the
+given ``recordname``, this record can be used within the cfood. Most
+importantly, this record stores the internal path of this array within the HDF5
+file in a text property, the name of which can be configured with the
+``internal_path_property_name`` option which defaults to ``internal_hdf5_path``.
diff --git a/src/doc/converters/index.rst b/src/doc/converters/index.rst
new file mode 100644
index 0000000000000000000000000000000000000000..38fc11335a2640f645e9b4e093690d1ffa7cd07f
--- /dev/null
+++ b/src/doc/converters/index.rst
@@ -0,0 +1,29 @@
+Converters
+))))))))))
+
+Converters treat a StructureElement and during this process create a number of new
+StructureElements: the children of the initially treated StructureElement. Thus by treatment of
+existing StructureElements, Converters create a tree of StructureElements.
+
+.. image:: ../img/converter.png
+ :height: 170
+ :alt: Converters are Python classes that tell the crawler how to
+ interprete StructureElements.
+
+Each StructureElement in the tree has a set of properties, organized as
+key-value pairs.
+Some of those properties are specified by the type of StructureElement. For example,
+a file could have the file name as property: ``'filename': myfile.dat``.
+Converters may define additional functions that create further values. For
+example, a regular expression could be used to get a date from a file name.
+
+.. toctree::
+ :maxdepth: 1
+ :caption: Contents:
+
+ CFood definition<cfood_definition>
+ Standard converters<standard_converters>
+ Further converters<further_converters>
+ Custom converters<custom_converters>
+ Transform functions<transform_functions>
+
diff --git a/src/doc/converters/standard_converters.rst b/src/doc/converters/standard_converters.rst
new file mode 100644
index 0000000000000000000000000000000000000000..586b84b48be78f1307298a11ad61a2448c3c3cd7
--- /dev/null
+++ b/src/doc/converters/standard_converters.rst
@@ -0,0 +1,333 @@
+Standard Converters
++++++++++++++++++++
+
+These are the standard converters that exist in a default installation. For writing and applying
+*custom converters*, see :ref:`below <Custom Converters>`.
+
+Directory Converter
+===================
+The Directory Converter creates StructureElements for each File and Directory
+inside the current Directory. You can match a regular expression against the
+directory name using the 'match' key.
+
+Simple File Converter
+=====================
+The Simple File Converter does not create any children and is usually used if
+a file shall be used as it is and be inserted and referenced by other entities.
+
+Markdown File Converter
+=======================
+Reads a YAML header from Markdown files (if such a header exists) and creates
+children elements according to the structure of the header.
+
+DictElement Converter
+=====================
+
+DictElement → StructureElement
+
+Creates a child StructureElement for each key in the dictionary.
+
+Typical Subtree converters
+--------------------------
+The following StructureElement types are typically created by the DictElement converter:
+
+- BooleanElement
+- FloatElement
+- TextElement
+- IntegerElement
+- ListElement
+- DictElement
+
+Note that you may use ``TextElement`` for anything that exists in a text format that can be
+interpreted by the server, such as date and datetime strings in ISO-8601 format.
+
+Scalar Value Converters
+=======================
+`BooleanElementConverter`, `FloatElementConverter`, `TextElementConverter`, and
+`IntegerElementConverter` behave very similarly.
+
+These converters expect `match_name` and `match_value` in their definition
+which allow to match the key and the value, respectively.
+
+Note that there are defaults for accepting other types. For example,
+FloatElementConverter also accepts IntegerElements. The default
+behavior can be adjusted with the fields `accept_text`, `accept_int`,
+`accept_float`, and `accept_bool`.
+
+The following denotes what kind of StructureElements are accepted by default
+(they are defined in `src/caoscrawler/converters.py`):
+
+- BooleanElementConverter: bool, int
+- FloatElementConverter: int, float
+- TextElementConverter: text, bool, int, float
+- IntegerElementConverter: int
+- ListElementConverter: list
+- DictElementConverter: dict
+
+YAMLFileConverter
+=================
+
+A specialized Dict Converter for yaml files: Yaml files are opened and the contents are
+converted into dictionaries that can be further converted using the typical subtree converters
+of dict converter.
+
+**WARNING**: Currently unfinished implementation.
+
+JSONFileConverter
+=================
+
+
+
+
+TableConverter
+==============
+
+Table → DictElement
+
+A generic converter (abstract) for files containing tables.
+Currently, there are two specialized implementations for XLSX files and CSV files.
+
+All table converters generate a subtree of dicts, which in turn can be converted with DictElementConverters:
+For each row in the table the TableConverter generates a DictElement (structure element). The key of the
+element is the row number. The value of the element is a dict containing the mapping of
+column names to values of the respective cell.
+
+Example:
+
+.. code-block:: yaml
+
+ subtree:
+ TABLE: # Any name for the table as a whole
+ type: CSVTableConverter
+ match: ^test_table.csv$
+ records:
+ (...) # Records edited for the whole table file
+ subtree:
+ ROW: # Any name for a data row in the table
+ type: DictElement
+ match_name: .*
+ match_value: .*
+ records:
+ (...) # Records edited for each row
+ subtree:
+ COLUMN: # Any name for a specific type of column in the table
+ type: FloatElement
+ match_name: measurement # Name of the column in the table file
+ match_value: (?P<column_value).*)
+ records:
+ (...) # Records edited for each cell
+
+
+XLSXTableConverter
+==================
+
+XLSX File → DictElement
+
+CSVTableConverter
+=================
+
+CSV File → DictElement
+
+PropertiesFromDictConverter
+===========================
+
+The :py:class:`~caoscrawler.converters.converters.PropertiesFromDictConverter` is
+a specialization of the
+:py:class:`~caoscrawler.converters.converters.DictElementConverter` and offers
+all its functionality. It is meant to operate on dictionaries (e.g.,
+from reading in a json or a table file), the keys of which correspond
+closely to properties in a LinkAhead datamodel. This is especially
+handy in cases where properties may be added to the data model and
+data sources that are not yet known when writing the cfood definition.
+
+The converter definition of the
+:py:class:`~caoscrawler.converters.converters.PropertiesFromDictConverter` has an
+additional required entry ``record_from_dict`` which specifies the
+Record to which the properties extracted from the dict are attached
+to. This Record is identified by its ``variable_name`` by which it can
+be referred to further down the subtree. You can also use the name of
+a Record that was specified earlier in the CFood definition in order
+to extend it by the properties extracted from a dict. Let's have a
+look at a simple example. A CFood definition
+
+.. code-block:: yaml
+
+ PropertiesFromDictElement:
+ type: PropertiesFromDictElement
+ match: ".*"
+ record_from_dict:
+ variable_name: MyRec
+ parents:
+ - MyType1
+ - MyType2
+
+applied to a dictionary
+
+.. code-block:: json
+
+ {
+ "name": "New name",
+ "a": 5,
+ "b": ["a", "b", "c"],
+ "author": {
+ "full_name": "Silvia Scientist"
+ }
+ }
+
+will create a Record ``New name`` with parents ``MyType1`` and
+``MyType2``. It has a scalar property ``a`` with value 5, a list
+property ``b`` with values "a", "b" and "c", and an ``author``
+property which references an ``author`` with a ``full_name`` property
+with value "Silvia Scientist":
+
+.. image:: ../img/properties-from-dict-records-author.png
+ :height: 210
+ :alt: A Record "New Name" and an author Record with full_name
+ "Silvia Scientist" are generated and filled automatically.
+
+Note how the different dictionary keys are handled differently
+depending on their types: scalar and list values are understood
+automatically, and a dictionary-valued entry like ``author`` is
+translated into a reference to an ``author`` Record automatically.
+
+You can further specify how references are treated with an optional
+``references key`` in ``record_from_dict``. Let's assume that in the
+above example, we have an ``author`` **Property** with datatype
+``Person`` in our data model. We could add this information by
+extending the above example definition by
+
+
+.. code-block:: yaml
+
+ PropertiesFromDictElement:
+ type: PropertiesFromDictElement
+ match: ".*"
+ record_from_dict:
+ variable_name: MyRec
+ parents:
+ - MyType1
+ - MyType2
+ references:
+ author:
+ parents:
+ - Person
+
+so that now, a ``Person`` record with a ``full_name`` property with
+value "Silvia Scientist" is created as the value of the ``author``
+property:
+
+.. image:: ../img/properties-from-dict-records-person.png
+ :height: 200
+ :alt: A new Person Record is created which is referenced as an
+ author.
+
+For the time being, only the parents of the referenced record can be
+set via this option. More complicated treatments can be implemented
+via the ``referenced_record_callback`` (see below).
+
+Properties can be blacklisted with the ``properties_blacklist``
+keyword, i.e., all keys listed under ``properties_blacklist`` will be
+excluded from automated treatment. Since the
+:py:class:`~caoscrawler.converters.converters.PropertiesFromDictConverter` has
+all the functionality of the
+:py:class:`~caoscrawler.converters.converters.DictElementConverter`, individual
+properties can still be used in a subtree. Together with
+``properties_blacklist`` this can be used to add custom treatment to
+specific properties by blacklisting them in ``record_from_dict`` and
+then treating them in the subtree the same as you would do it in the
+standard
+:py:class:`~caoscrawler.converters.converters.DictElementConverter`. Note that
+the blacklisted keys are excluded on **all** levels of the dictionary,
+i.e., also when they occur in a referenced entity.
+
+For further customization, the
+:py:class:`~caoscrawler.converters.converters.PropertiesFromDictConverter`
+can be used as a basis for :ref:`custom converters<Custom Converters>`
+which can make use of its ``referenced_record_callback`` argument. The
+``referenced_record_callback`` can be a callable object which takes
+exactly a Record as an argument and needs to return that Record after
+doing whatever custom treatment is needed. Additionally, it is given
+the ``RecordStore`` and the ``ValueStore`` in order to be able to
+access the records and values that have already been defined from
+within ``referenced_record_callback``. Such a function might look the
+following:
+
+.. code-block:: python
+
+ def my_callback(rec: db.Record, records: RecordStore, values: GeneralStore):
+ # do something with rec, possibly using other records or values from the stores...
+ rec.description = "This was updated in a callback"
+ return rec
+
+It is applied to all Records that are created from the dictionary and
+it can be used to, e.g., transform values of some properties, or add
+special treatment to all Records of a specific
+type. ``referenced_record_callback`` is applied **after** the
+properties from the dictionary have been applied as explained above.
+
+XML Converters
+==============
+
+There are the following converters for XML content:
+
+
+XMLFileConverter
+----------------
+
+This is a converter that loads an XML file and creates an XMLElement containing the
+root element of the XML tree. It can be matched in the subtree using the XMLTagConverter.
+
+XMLTagConverter
+---------------
+
+The XMLTagConverter is a generic converter for XMLElements with the following main features:
+
+- It allows to match a combination of tag name, attribute names and text contents using the keys:
+
+ - ``match_tag``: regexp, default empty string
+ - ``match_attrib``: dictionary of key-regexps and value-regexp
+ pairs. Each key matches an attribute name and the corresponding
+ value matches its attribute value.
+ - ``match_text``: regexp, default empty string
+- It allows to traverse the tree using XPath (using Python lxml's xpath functions):
+
+ - The key ``xpath`` is used to set the xpath expression and has a
+ default of ``child::*``. Its default would generate just the list of
+ sub nodes of the current node. The result of the xpath expression
+ is used to generate structure elements as children. It furthermore
+ uses the keys ``tags_as_children``, ``attribs_as_children`` and
+ ``text_as_children`` to decide which information from the found
+ nodes will be used as children:
+ - ``tags_as_children``: (default ``true``) For each xml tag element
+ found by the xpath expression, generate one XMLTag structure
+ element. Its name is the full path to the tag using the function
+ ``getelementpath`` from ``lxml``.
+ - ``attribs_as_children``: (default ``false``) For each xml tag element
+ found by the xpath expression, generate one XMLAttributeNode
+ structure element for each of its attributes. The name of the
+ respective attribute node has the form: ``<full path of the tag> @
+ <name of the attribute>`` **Please note:** Currently, there is no
+ converter implemented that can match XMLAttributeNodes.
+ - ``text_as_children``: (default ``false``) For each xml tag element
+ found by the xpath expression, generate one XMLTextNode structure
+ element containing the text content of the tag element. Note that
+ in case of multiple text elements, only the first one is
+ added. The name of the respective attribute node has the form:
+ ``<full path of the tag> /text()`` to the tag using the function
+ ``getelementpath`` from ``lxml``. **Please note:** Currently, there is
+ no converter implemented that can match XMLAttributeNodes.
+
+Namespaces
+**********
+
+The default is to take the namespace map from the current node and use
+it in xpath queries. Because default namespaces cannot be handled by
+xpath, it is possible to remap the default namespace using the key
+``default_namespace``. The key ``nsmap`` can be used to define
+additional nsmap entries.
+
+XMLTextNodeConverter
+--------------------
+
+In the future, this converter can be used to match XMLTextNodes that
+are generated by the XMLTagConverter.
diff --git a/src/doc/converters/transform_functions.rst b/src/doc/converters/transform_functions.rst
new file mode 100644
index 0000000000000000000000000000000000000000..22df35c8521ea0d70b2ebf7b7c8bc7c52e176bd3
--- /dev/null
+++ b/src/doc/converters/transform_functions.rst
@@ -0,0 +1,47 @@
+Transform Functions
++++++++++++++++++++
+Often the situation arises, that you cannot use a value as it is found. Maybe a value should be
+increased by an offset or a string should be split into a list of pieces. In order to allow such
+simple conversions, transform functions can be named in the converter definition that are then
+applied to the respective variables when the converter is executed.
+
+.. code-block:: yaml
+
+ <NodeName>:
+ type: <ConverterName>
+ match: ".*"
+ transform:
+ <TransformNodeName>:
+ in: $<in_var_name>
+ out: $<out_var_name>
+ functions:
+ - <func_name>: # name of the function to be applied
+ <func_arg1>: <func_arg1_value> # key value pairs that are passed as parameters
+ <func_arg2>: <func_arg2_value>
+ # ...
+
+An example that splits the variable ``a`` and puts the generated list in ``b`` is the following:
+
+.. code-block:: yaml
+
+ Experiment:
+ type: Dict
+ match: ".*"
+ transform:
+ param_split:
+ in: $a
+ out: $b
+ functions:
+ - split: # split is a function that is defined by default
+ marker: "|" # its only parameter is the marker that is used to split the string
+ records:
+ Report:
+ tags: $b
+
+This splits the string in '$a' and stores the resulting list in '$b'. This is here used to add a
+list valued property to the Report Record.
+
+
+There are a number of transform functions that are defined by default (see
+``src/caoscrawler/default_transformers.yml``). You can define custom transform functions by adding
+them to the cfood definition (see :doc:`CFood Documentation<../cfood>`).
diff --git a/src/doc/how-to-upgrade.md b/src/doc/how-to-upgrade.md
index 30d23f8f3a4ad88f6b3f4fca18013e26fbcb1dc1..8af805ea30cc85cdde88d789ee3538b2bbaef7e3 100644
--- a/src/doc/how-to-upgrade.md
+++ b/src/doc/how-to-upgrade.md
@@ -1,5 +1,45 @@
# How to upgrade
+
+## 0.8.x to 0.9.0
+
+If you were using the optional HDF5 converter classes, you need to
+adapt the package path in your cfood definition from the **old**
+
+```yaml
+Converters:
+ H5Dataset:
+ converter: H5DatasetConverter
+ package: caoscrawler.hdf5_converter
+ H5File:
+ converter: H5FileConverter
+ package: caoscrawler.hdf5_converter
+ H5Group:
+ converter: H5GroupConverter
+ package: caoscrawler.hdf5_converter
+ H5Ndarray:
+ converter: H5NdarrayConverter
+ package: caoscrawler.hdf5_converter
+```
+
+to the **new** paths:
+
+```yaml
+Converters:
+ H5Dataset:
+ converter: H5DatasetConverter
+ package: caoscrawler.converters.hdf5_converter
+ H5File:
+ converter: H5FileConverter
+ package: caoscrawler.converters.hdf5_converter
+ H5Group:
+ converter: H5GroupConverter
+ package: caoscrawler.converters.hdf5_converter
+ H5Ndarray:
+ converter: H5NdarrayConverter
+ package: caoscrawler.converters.hdf5_converter
+```
+
## 0.6.x to 0.7.0
If you added Parents to Records at multiple places in the CFood, you must now
do this at a single location because this key now overwrites previously set
diff --git a/src/doc/index.rst b/src/doc/index.rst
index 8a02ec62e50308a28899e71b4664f626dfa0c27b..a72389b1f4b94430b2c5ff2bfee9757193327ed7 100644
--- a/src/doc/index.rst
+++ b/src/doc/index.rst
@@ -10,7 +10,7 @@ CaosDB-Crawler Documentation
Getting started<getting_started/index>
Tutorials<tutorials/index>
Concepts<concepts>
- Converters<converters>
+ Converters<converters/index>
CFoods (Crawler Definitions)<cfood>
Macros<macros>
How to upgrade<how-to-upgrade>
diff --git a/unittests/example_cfood.yml b/unittests/example_cfood.yml
index 798e540fa25e49bf610ea21653db41a0bddc4d5f..59cb601395f73bd26ed81bd6ea9c51f670798d36 100644
--- a/unittests/example_cfood.yml
+++ b/unittests/example_cfood.yml
@@ -1,6 +1,6 @@
---
metadata:
- crawler-version: 0.7.2
+ crawler-version: 0.9.0
---
Definitions:
type: Definitions
diff --git a/unittests/h5_cfood.yml b/unittests/h5_cfood.yml
index 4b95a0a31bc43a902eb63dc3aa09b805fc28c2aa..dc789a85aabcbdc32388fd91460d42d477630f37 100644
--- a/unittests/h5_cfood.yml
+++ b/unittests/h5_cfood.yml
@@ -1,20 +1,20 @@
---
metadata:
- crawler-version: 0.7.2
+ crawler-version: 0.9.0
---
Converters:
H5Dataset:
converter: H5DatasetConverter
- package: caoscrawler.hdf5_converter
+ package: caoscrawler.converters.hdf5_converter
H5File:
converter: H5FileConverter
- package: caoscrawler.hdf5_converter
+ package: caoscrawler.converters.hdf5_converter
H5Group:
converter: H5GroupConverter
- package: caoscrawler.hdf5_converter
+ package: caoscrawler.converters.hdf5_converter
H5Ndarray:
converter: H5NdarrayConverter
- package: caoscrawler.hdf5_converter
+ package: caoscrawler.converters.hdf5_converter
# Top-level, we have just the HDF5 file.
ParentDirectory:
type: Directory
diff --git a/unittests/scifolder_cfood.yml b/unittests/scifolder_cfood.yml
index ca5fa589b5903e0c0d8ef3dcb2528ea79e0f8cee..f32c24e772b86ab8adf530d20ec208722b74deac 100644
--- a/unittests/scifolder_cfood.yml
+++ b/unittests/scifolder_cfood.yml
@@ -4,7 +4,7 @@
---
metadata:
- crawler-version: 0.7.2
+ crawler-version: 0.9.0
---
Definitions:
type: Definitions
diff --git a/unittests/test_converters.py b/unittests/test_converters.py
index e12302514d16f077882e41d6ff5995953f2228f8..0522c4e6fd31239b9b3ae1f803ef5799ad2c5423 100644
--- a/unittests/test_converters.py
+++ b/unittests/test_converters.py
@@ -46,8 +46,8 @@ from caoscrawler.converters import (Converter, ConverterValidationError,
ListElementConverter, MarkdownFileConverter,
PropertiesFromDictConverter,
YAMLFileConverter,
- _AbstractScalarValueElementConverter,
handle_value, replace_variables)
+from caoscrawler.converters.converters import _AbstractScalarValueElementConverter
from caoscrawler.crawl import Crawler
from caoscrawler.scanner import (_load_definition_from_yaml_dict,
create_converter_registry,
@@ -507,7 +507,7 @@ MyElement:
two_doc_yaml = """
---
metadata:
- crawler-version: 0.7.2
+ crawler-version: 0.9.0
Converters:
MyNewType:
converter: MyNewTypeConverter
@@ -643,9 +643,10 @@ def test_load_converters():
# converter classes can be loaded from their respective packages.
# Please adapt, if defaults change!
- assert len(converter_registry) == 25
+ assert len(converter_registry) == 28
# All of them are contained in caoscrawler.converters
+ # except for the xml converters:
for conv_key, conv in converter_registry.items():
assert conv["package"] == "caoscrawler.converters"
# ... and their names all end in "Converter"
diff --git a/unittests/test_h5_converter.py b/unittests/test_h5_converter.py
index 7f244e2cbdccb0d4eee6a62f59e9cea5684295a6..95060451badb0523cf91c70e5be345e35ec3964d 100644
--- a/unittests/test_h5_converter.py
+++ b/unittests/test_h5_converter.py
@@ -26,9 +26,9 @@ from pytest import fixture, importorskip
import linkahead as db
from caoscrawler.debug_tree import DebugTree
-from caoscrawler.hdf5_converter import (convert_basic_element_with_nd_array,
- convert_h5_element, H5GroupElement,
- H5DatasetElement, H5NdarrayElement)
+from caoscrawler.converters.hdf5_converter import (convert_basic_element_with_nd_array,
+ convert_h5_element, H5GroupElement,
+ H5DatasetElement, H5NdarrayElement)
from caoscrawler.scanner import scan_directory
from caoscrawler.structure_elements import (FloatElement, ListElement,
TextElement)
diff --git a/unittests/test_macros.py b/unittests/test_macros.py
index 020098676407f1f70932559b1a995af9f9644fe9..cfa405e5041fb4324b7de98ffcb942cf4b040715 100644
--- a/unittests/test_macros.py
+++ b/unittests/test_macros.py
@@ -142,7 +142,7 @@ def test_multi_macros_toplevel(register_macros, macro_store_reset):
dat_loader = list(yaml.safe_load_all("""
---
metadata:
- crawler-version: 0.7.2
+ crawler-version: 0.9.0
macros:
- !defmacro
name: test_one
@@ -171,7 +171,7 @@ def test_load_definition(register_macros, macro_store_reset):
txt = """
---
metadata:
- crawler-version: 0.7.2
+ crawler-version: 0.9.0
---
extroot:
type: Directory
@@ -188,7 +188,7 @@ extroot:
cfood = _temp_file_load("""
---
metadata:
- crawler-version: 0.7.2
+ crawler-version: 0.9.0
macros:
- !defmacro
name: test_one
@@ -272,7 +272,7 @@ def test_macros_in_macros(register_macros, macro_store_reset):
cfood = _temp_file_load("""
---
metadata:
- crawler-version: 0.7.2
+ crawler-version: 0.9.0
macros:
- !defmacro
name: one_macro
@@ -319,7 +319,7 @@ def test_silent_overwrite(register_macros, macro_store_reset):
cfood = _temp_file_load("""
---
metadata:
- crawler-version: 0.7.2
+ crawler-version: 0.9.0
macros:
- !defmacro
name: one_macro
@@ -350,7 +350,7 @@ def test_circular_macro_definition(register_macros, macro_store_reset):
cfood = _temp_file_load("""
---
metadata:
- crawler-version: 0.7.2
+ crawler-version: 0.9.0
macros:
- !defmacro
name: test_one
@@ -401,7 +401,7 @@ def test_use_macro_twice():
cfood = _temp_file_load("""
---
metadata:
- crawler-version: 0.7.2
+ crawler-version: 0.9.0
macros:
- !defmacro
name: test_twice
@@ -436,7 +436,7 @@ def test_documentation_example_2():
cfood = _temp_file_load("""
---
metadata:
- crawler-version: 0.7.2
+ crawler-version: 0.9.0
macros:
- !defmacro
name: MarkdownFile
@@ -474,7 +474,7 @@ def test_documentation_example_1():
cfood = _temp_file_load("""
---
metadata:
- crawler-version: 0.7.2
+ crawler-version: 0.9.0
macros:
- !defmacro
name: SimulationDatasetFile
@@ -523,7 +523,7 @@ def test_def_replacements():
cfood = _temp_file_load("""
---
metadata:
- crawler-version: 0.7.2
+ crawler-version: 0.9.0
macros:
- !defmacro
name: test_def_replacements
diff --git a/unittests/test_parent_cfood.yml b/unittests/test_parent_cfood.yml
index cd63e81b270117841128a34765a9635a036c52ec..21b49a2db8ac44f806c77718b2fa49fbc7488828 100644
--- a/unittests/test_parent_cfood.yml
+++ b/unittests/test_parent_cfood.yml
@@ -1,6 +1,6 @@
---
metadata:
- crawler-version: 0.7.2
+ crawler-version: 0.9.0
---
Definitions:
type: Definitions
diff --git a/unittests/test_utilities.py b/unittests/test_utilities.py
index dfb79c8b6b10909952174cf24c3aa9198f3b7743..15e84a609149ac602ee80b7357f7622566563792 100644
--- a/unittests/test_utilities.py
+++ b/unittests/test_utilities.py
@@ -22,7 +22,7 @@
import pytest
from caoscrawler.crawl import split_restricted_path
-from caoscrawler.utils import MissingImport
+from caoscrawler.utils import get_shared_resource_link, MissingImport
def test_split_restricted_path():
@@ -66,3 +66,17 @@ def test_dummy_class():
assert "(Not Important)" in msg
orig_msg = str(err_info.value.__cause__)
assert orig_msg == "Old error"
+
+
+def test_shared_resource_link():
+
+ assert get_shared_resource_link(
+ "https://example.com/", "file.txt") == "https://example.com/Shared/file.txt"
+ assert get_shared_resource_link(
+ "https://example.com", "file.txt") == "https://example.com/Shared/file.txt"
+ assert get_shared_resource_link(
+ "https://example.com", "path/to/file.txt") == "https://example.com/Shared/path/to/file.txt"
+ assert get_shared_resource_link(
+ "https://example.com/context-root", "path/to/file.txt") == "https://example.com/context-root/Shared/path/to/file.txt"
+ assert get_shared_resource_link(
+ "https://example.com/context-root/", "path/to/file.txt") == "https://example.com/context-root/Shared/path/to/file.txt"
diff --git a/unittests/test_xml_converter.py b/unittests/test_xml_converter.py
new file mode 100644
index 0000000000000000000000000000000000000000..fb4c7746fa2d0b6c3d4ec95fc1de3139493a703f
--- /dev/null
+++ b/unittests/test_xml_converter.py
@@ -0,0 +1,296 @@
+#!/usr/bin/env python3
+# encoding: utf-8
+#
+# This file is a part of the LinkAhead Project.
+#
+# Copyright (C) 2024 Indiscale GmbH <info@indiscale.com>
+# Copyright (C) 2024 Alexander Schlemmer <a.schlemmer@indiscale.com>
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Affero 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 Affero General Public License for more details.
+#
+# You should have received a copy of the GNU Affero General Public License
+# along with this program. If not, see <https://www.gnu.org/licenses/>.
+#
+
+"""
+test the XML converters
+"""
+import importlib
+import json
+import pytest
+import sys
+import yaml
+
+from lxml.etree import fromstring
+from pathlib import Path
+
+from caoscrawler.converters import XMLTagConverter
+from caoscrawler.scanner import load_definition
+from caoscrawler.stores import GeneralStore
+from caoscrawler.structure_elements import XMLTagElement
+
+
+UNITTESTDIR = Path(__file__).parent
+
+
+@pytest.fixture
+def converter_registry():
+ converter_registry: dict[str, dict[str, str]] = {
+ "XMLTag": {
+ "converter": "XMLTagConverter",
+ "package": "caoscrawler.converters"},
+
+ "XMLTextNode": {
+ "converter": "XMLTextNodeConverter",
+ "package": "caoscrawler.converters"},
+ }
+
+ for key, value in converter_registry.items():
+ module = importlib.import_module(value["package"])
+ value["class"] = getattr(module, value["converter"])
+ return converter_registry
+
+
+@pytest.fixture
+def basic_xmltag_converter(converter_registry):
+ return XMLTagConverter(yaml.safe_load("""
+type: XMLTag
+match_tag: a
+match_attrib: # default is the empty dictionary
+ "(?P<ref>(href|url))": "test(?P<number>[0-9])" # either the "href" or the "url" attribute must be set
+ alt: (.+) # this attribute must be present and contain at least one character
+match_text: \\s*(?P<node_text>.+)\\s*
+
+subtree:
+ img:
+ type: XMLTag
+ match_name: img
+ match_attrib:
+ src: test2
+"""), "TestXMLTagConverter", converter_registry)
+
+
+@pytest.fixture
+def basic_xpath_xmltag_converter(converter_registry):
+ return XMLTagConverter(yaml.safe_load("""
+type: XMLTag
+match_tag: a
+match_attrib: # default is the empty dictionary
+ "(?P<ref>(href|url))": "test(?P<number>[0-9])" # either the "href" or the "url" attribute must be set
+ alt: (.+) # this attribute must be present and contain at least one character
+match_text: \\s*(?P<node_text>.+)\\s*
+xpath: child::*/*
+
+subtree:
+ img:
+ type: XMLTag
+ match_name: img
+ match_attrib:
+ src: test2
+ testnode:
+ type: XMLTag
+ match_name: testnode
+"""), "TestXMLTagConverter", converter_registry)
+
+
+def test_simple_xml(basic_xmltag_converter):
+ """
+ Test for basic xml conversion functionality.
+ """
+ xml_text = """
+ <a href="test1" alt="no link">
+ test <img src="test2"/>
+ </a>
+ """
+
+ xml = fromstring(xml_text)
+ tag = XMLTagElement(xml)
+ assert tag.name == "."
+
+ m = basic_xmltag_converter.match(tag)
+
+ assert m is not None
+ assert m["ref"] == "href"
+ assert m["number"] == "1"
+ assert m["node_text"] == "test "
+
+
+def test_not_matching(basic_xmltag_converter):
+ m = basic_xmltag_converter.match(XMLTagElement(fromstring("""
+ <a href="test1">
+ test <img src="test2"/>
+ </a>
+ """)))
+
+ assert m is None # alt-attribute was missing
+
+ m = basic_xmltag_converter.match(XMLTagElement(fromstring("""
+ <a href="test" alt="no link">
+ test <img src="test2"/>
+ </a>
+ """)))
+
+ assert m is None # href attribute did not match
+
+ m = basic_xmltag_converter.match(XMLTagElement(fromstring("""
+ <a href="test1" url="http" alt="no link">
+ test <img src="test2"/>
+ </a>
+ """)))
+
+ assert m is None # href and url must not be present simultaneously
+
+ m = basic_xmltag_converter.match(XMLTagElement(fromstring("""
+ <a href="test1" alt="no link"><img src="test2"/></a>
+ """)))
+
+ assert m is None # text node is empty
+
+ m = basic_xmltag_converter.match(XMLTagElement(fromstring("""
+ <a href="test1" alt="no link"/>
+ """)))
+
+ assert m is None # text node is empty
+
+ # TODO: adapt converter -> empty (==None) text node is equivalent to empty string text node
+ # TODO: adapt tests
+ # TODO: how to match " ajskdlfjaldsf ajsdklfjadkl " without the whitespaces in regexp correctly?
+
+
+def test_nested_simple_xml(basic_xmltag_converter, basic_xpath_xmltag_converter):
+ """
+ Test for xml conversion including children.
+ """
+ xml_text = """
+ <a href="test1" alt="no link">
+ test <img src="test2"/>
+ </a>
+ """
+
+ tag = XMLTagElement(fromstring(xml_text))
+ m = basic_xmltag_converter.match(tag)
+ assert m is not None
+
+ general_store = GeneralStore()
+ children = basic_xmltag_converter.create_children(general_store, tag)
+
+ assert len(children) == 1
+ assert isinstance(children[0], XMLTagElement)
+ assert children[0].name == "img"
+
+ xml_text = """
+ <a href="test1" alt="no link">
+ test <img src="test2">
+ <testnode/> </img>
+ </a>
+ """
+
+ tag = XMLTagElement(fromstring(xml_text))
+ m = basic_xpath_xmltag_converter.match(tag)
+ assert m is not None
+
+ general_store = GeneralStore()
+ children = basic_xpath_xmltag_converter.create_children(general_store, tag)
+
+ assert len(children) == 1
+ assert isinstance(children[0], XMLTagElement)
+ assert children[0].name == "img/testnode"
+
+
+def test_namespace_xml(converter_registry):
+ """
+ Test for xml conversion including children.
+ Nodes have namespaces.
+ """
+
+ xml_text = """
+ <root xmlns="default-namespace" xmlns:test="alternative-namespace">
+ <node1 active="true">
+ Bla
+ </node1>
+ <node1 active="true" size="45">
+ text
+ <node2 xmlns="sub-namespace">
+ <node3>
+ ok
+ </node3>
+ </node2>
+ <test:node2>
+ sep
+ </test:node2>
+ </node1>
+ </root>
+"""
+
+ # Test unsupported xpath (containing text()):
+ converter = XMLTagConverter(yaml.safe_load("""
+type: XMLTag
+match_tag: "{default-namespace}root"
+xpath: "default:node1/text()"
+default_namespace: default
+"""), "TestXMLTagConverter", converter_registry)
+
+ tag = XMLTagElement(fromstring(xml_text))
+ m = converter.match(tag)
+ assert m is not None
+
+ with pytest.raises(RuntimeError, match="Only standard xml nodes.*"):
+ converter.create_children(GeneralStore(), tag)
+
+ # Test complex xml using namespaces and text nodes:
+ converter = XMLTagConverter(yaml.safe_load("""
+type: XMLTag
+match_tag: "{default-namespace}root"
+xpath: "default:node1"
+default_namespace: default
+attribs_as_children: false
+text_as_children: true
+tags_as_children: false
+"""), "TestXMLTagConverter", converter_registry)
+ children = converter.create_children(GeneralStore(), tag)
+ assert len(children) == 2
+ assert children[0].name == "{default-namespace}node1[1]/text()"
+ assert children[0].value.strip() == "Bla"
+ assert children[1].name == "{default-namespace}node1[2]/text()"
+ assert children[1].value.strip() == "text"
+
+ # Check child generation of attributes:
+ converter = XMLTagConverter(yaml.safe_load("""
+type: XMLTag
+match_tag: "{default-namespace}root"
+xpath: "default:node1"
+default_namespace: default
+attribs_as_children: true
+text_as_children: false
+tags_as_children: false
+"""), "TestXMLTagConverter", converter_registry)
+ children = converter.create_children(GeneralStore(), tag)
+
+ assert len(children) == 3
+ assert children[0].name == "{default-namespace}node1[1]@active"
+ assert children[0].value.strip() == "true"
+ assert children[1].name == "{default-namespace}node1[2]@active"
+ assert children[1].value.strip() == "true"
+ assert children[2].name == "{default-namespace}node1[2]@size"
+ assert children[2].value.strip() == "45"
+
+ # Test setting nsmap entries:
+ converter = XMLTagConverter(yaml.safe_load("""
+type: XMLTag
+match_tag: "{default-namespace}root"
+xpath: "//s:node2"
+default_namespace: default
+nsmap:
+ s: sub-namespace
+"""), "TestXMLTagConverter", converter_registry)
+ children = converter.create_children(GeneralStore(), tag)
+ assert len(children) == 1
+ assert children[0].name == "{default-namespace}node1[2]/{sub-namespace}node2"