ckanext-ingest 1.4.1

No project description provided

ckanext-ingest

Framework for data import from arbitrary sources.

Note: this extension has no aim to perform import of every possible data source into CKAN. Instead, it defines a structure and rules for making import more predictable, reusable and flexible.

This extension can be used if you need to:

• Create datasets/resources/etc using data from multiple files. But you want do import all files in a similar manner and don't want to spend time introducing and explaining the whole process.
• reuse ingestion logic in different projects
• share pieces of logic between different ingestion workflows

And you probably don't need it if you want to:

• import a single file using CLI once and and never do it again.

Structure

• Requirements
• Installation
• Usage
• Examples
• Advanced
• Configuration
• Interfaces
• API
  • ingest_extract_records
  • ingest_import_records

Requirements

Compatibility with core CKAN versions:

CKAN version	Compatible?
2.9	no
2.10	yes
master	yes

Installation

To install ckanext-ingest:

1. Install it via pip:

   pip install ckanext-ingest
   
   ## with basic XLSX strategy
   # pip install 'ckanext-ingest[xlsx]'
   

2. Add ingest to the ckan.plugins setting in your CKAN config file.

Usage

Data can be ingested into CKAN via ingest_import_records API action. It requires a source with the data, and it's recommended to pass an extraction strategy, to get a full control over the process.

ckanapi action ingest_import_records source@path/to/data.zip strategy="myext:extract_archive"

But before anything can be ingested you have to regiser a strategy that produces records. strategy defines how source is parsed and divided into data chunks, and record wraps single data chunk and perform actions using information from the chunk.

strategy is registered via IIngest interface. It has to be a subclass of ckanext.ingest.shared.ExtractionStrategy. The only requirement for strategy is to return iterable of records from its extract method.

record is created by strategy and it has to be a subclass of ckanext.ingest.shared.Record. Its ingest method is responsible for ingestion: depending on the record purpose, it can create/update/delete data or perform any other task that has sense.

Examples

Register custom strategy

import ckan.plugins as p

from ckanext.ingest.interfaces import IIngest

class MyPlugin(p.SingletonPlugin):
    p.implements(IIngest)

    def get_ingest_strategies(self):
        return {
          "my:custom_strategy": CustomStrategy
        }

Strategy thay reads JSON file and creates a single dataset from it.

import ckan.plugins.toolkit as tk
from ckanext.ingest.shared import ExtractionStrategy, Storage, Record, IngestionResult

class SingleJsonStrategy(ExtractionStrategy):

    def extract(self, source: Storage, options):
        # source is a readable IO stream(werkzeug.datastructures.FileStorage)
        data = json.load(source)

        # `extract` returns iterable over records. When the strategy produces
        # a single record, this record can be either yielded or returned as
        # a list with a single element
        yield SimplePackageRecord(data, {})

class SimplePackageRecord(Record):
    def ingest(self, context: ckan.types.Context) -> IngestionResult:

        dataset = tk.get_action("package_create")(context, self.data)

        # `ingest` returns a brief overview of the ingestion result
        return {
            "success": True,
            "result": dataset,
            "details": {}
        }

Strategy that reads from CSV names of organizations that must be removed from the portal

import csv
import ckan.plugins.toolkit as tk
from ckanext.ingest.shared import ExtractionStrategy, Record

class DropOrganizationsUsingCsvStrategy(ExtractionStrategy):

    def extract(self, source, options):
        # `source` is an `IO[bytes]`, so we turn in into `IO[str]`
        str_stream = StringIO(source.read().decode())
        rows = csv.DictReader(st_stream)

        for row in rows:
            # record's constructor requires two arguments:
            # the raw data and the mapping with record options.
            yield DropOrganiationRecord(row, {})

class DropOrganizationRecord(Record):
    def ingest(self, context: ckan.types.Context):
        try:
            tk.get_action("organization_delete")(context, {"id": self.data["name"]})
        except tk.ObjectNotFound:
            success = False
        else:
            success = True

        return {
            "success": success,
            "result": None,
            "details": {}
        }

Pull datasets from CKAN instance specified in JSON(like ckanext-harvest), and remove datasets that were not updated during ingestion

import json
from datetime import datetime
from ckanapi import RemoteCKAN
import ckan.plugins.toolkit as tk
from ckanext.ingest.shared import ExtractionStrategy, Record

class HarvestStrategy(ExtractionStrategy):

    def extract(self, source, options):
        details = json.load(source)
        client = RemoteCKAN(**details)

        now = datetime.utcnow()

        # produce a record that creates a package for every remote dataset
        for dataset in client.action.package_search()["results"]:
            yield SimpleDatasetRecord(row, {})

        # produce an additional record that removes stale datasets
        # (datasets that were modified before ingestion started and were
        # not updated during current ingestion)
        yield DeleteStaleDatasetsRecord({"before": now}, {})

class SimplePackageRecord(Record):
    def ingest(self, context: ckan.types.Context) -> IngestionResult:

        dataset = tk.get_action("package_create")(context, self.data)

        return {
            "success": True,
            "result": dataset,
            "details": {"remote_id": self.data["id"]}
        }


class DeleteStaleDatasetsRecord(Record):
    def ingest(self, context: ckan.types.Context) -> IngestionResult:
        before = self.data["before"].isoformat()
        result = tk.get_action("package_search")(
            context,
            {"fq": f"metadata_modified:[* TO {before}]", "fl": "id"}
        )

        deleted = []
        for dataset in result["results"]
            tk.get_action("package_delete")(context, {"id": dataset["id"]})
            deleted.append(id)

        return {
            "success": True,
            "result": deleted,
            "details": {"count": len(deleted), "before": before}
        }

Advanced

To get the most from ingestion workflows, try writing reusable strategies and records using details below

Strategy autodetection

strategy argument for actions is optional. When it missing, the plugins chooses the most appropriate strategy for the ingested source. This feature relies on can_handle and must_handle methods of the extraction strategy. Both methods receive the mimetype of the source and the source itself and return True/False.

Among all strategies that return True from can_handle, plugin selects the first strategy that returns True from must_handle as well. If there is no such strategy, the first can_handle wins.

ckanext.ingest.shared.ExtractionStrategy defines both these methods. must_handle always returns False. can_handle return True if source's mimetype is listed in mimetypes property of the handler:

class ExtractionStrategy:
    mimetypes: ClassVar[set[str]] = set()

    @classmethod
    def can_handle(cls, mime: str | None, source) -> bool:
        return mime in cls.mimetypes

    @classmethod
    def must_handle(cls, mime, source) -> bool:
        return False

If you want to register strategy that can handle JSON sources, just register strategy with an appropriate mimetypes:

class JsonStrategy(ExtractionStrategy):
    mimetypes = {"application/json"}

If there are more than one strategy that supports JSON mimetype, the first registered strategy is selected. If you want to register strategy that aalways handles JSON sources with specific name(DRINK_ME.json), disregarding the order, you can use must_handle.

Note, that must_handle is checked only when can_handle returns True, so we still using default mimetypes logic:

class DrinkMeJsonStrategy(ExtractionStrategy):
    mimetypes = {"application/json"}

    @classmethod
    def must_handle(cls, mime, source: Storage) -> bool:
        return source.filename == "DRINK_ME.json"

Record factories

ExtractionStrategy has a default implementation of extract. This default implementation calls chunks method to parse the source and get ingestable data fragments. Then, for every data chunk chunk_into_record method is called, to transform arbitrary data into a Record. Finally, extract yields whatever is produced by chunk_into_record.

Default implementation of chunks ignores the source and returns an empty list. As result, by default any source produce zero records and nothing happens.

The first thing you can do to produce a data is overriding chunks.

If you are working with CSV file, chunks can return rows from the file:

class CsvRowsStrategy(ExtractionStrategy):
    mimetypes = {"text/csv"}

    def chunks(self, source, options) -> Iterable[Any]:
        str_stream = StringIO(source.read().decode())
        rows = csv.reader(str_stream)

        yield from rows

Such strategy will produce ckanext.ingest.shared.Record for every row of the source CSV. But base Record class doesn't do much, so you need to replace it with your own Record subclass.

As mentioned before, data chunk converted into a record via chunk_into_record method. You can either override it, or use default implemmentation, which creates instances of the class stored under record_factory attribute of the strategy. Default value of this attribute is ckanext.ingest.shared.Record and if you want to use a different record implementation, do the following:

class CsvRowsStrategy(ExtractionStrategy):
    record_factory = MyCustomRecord
    ...

Strategy delegation

ExtractionStrategy.extract method is responsible for producing records. But it doesn't mean that strategy have to generate records itself. Instead, strategy can do some preparations and use another strategy in order to make records.

Let's imagine UrlStrategy that accepts file with a single line - URL of the remote portal - and pulls data from this portal. As we don't know the type of the data, we cannot tell, how records can be created from it. So, when data is fetched, we can use its mimetype to select the most suitable strategy and delegate record generation to its extract method:

import requests
import magic
from io import BytesIO
from ckanext.ingest import shared

class UrlStrategy(ExtractionStrategy):

    def extract(self, source, options) -> Iterable[Any]:
        # read URL from file-like source
        url = source.read()
        resp = requests.get(url)

        # convert response bytes into `source`
        sub_source = shared.make_storage(BytesIO(resp.content))

        # identify mimetype
        mime = magic.from_buffer(sub_source.read(1024))
        sub_source.seek(0)

        # choose the appropriate strategy
        handler = shared.get_handler_for_mimetype(mime, sub_source)

        # delegate extraction
        if handler:
            yield from handler.extract(source, options)

Strategy and Record options

ExtractionStrategy.extract and Record.ingest accept second argument options. In both cases it's a dictionary that can be used to modify the logic inside corresponding methods. Strategy options described by ckanext.ingest.shared.StrategyOptions, and record options described by ckanext.ingest.shared.RecordOptions.

Keys defined on the top-level, have sense for every strategy/record. For example, RecordOptions defines update_existing flag. If record that creates data detects existing conflicting entity, update_existing flag should be taken into account when the record is considering what to do in such case. It's only a recomendation and this flag can be ignored or you can use a different option. But using common options simplify understanding of the workflow.

For strategy there are 3 common keys:

• record_options: these options should be passed into every record produced by the strategy(RecordOptions)
• nested_strategy: if strategy delegates record creation to a different strategy, nested_strategy should be prefered over auto-detected strategy(mimetype detection)
• locator: if source is represented by some kind of collection, locator is a callable that returns specific members of collection. It can be used when parsing archives, so that strategy can extract package's metadata from one file and upload resources returned by locator into it. Or, when parsing XLSX, locator can return sheets by title to simplify processing of multiple sheets.

For any options that can be used only by a specific strategy, there is an extras option inside both StrategyOptions and RecordOptions. This dictionary can hold any data and there are no expectations to its structure.

Keys that are used often inside extras may eventually be added as recommended options to the top-level. But, as these are only recomendations, you can just ignore them and pass whatever data you need as options.

Data transformation in Record

ckanext.ingest.shared.Record class requires two parameters for initialization: raw data and options for the record. When record is created, it calls its trasform method, that copies raw data into data property. This is the best place for data mapping, before record's ingest method is called. If you want to remove all empty members from record's data, it can be done in the following way:

class DenseRecord(Record):
    def transform(self, raw: Any):
        self.data = {
            key: value
            for key, value in raw.items()
            if value is not None
        }

Record ingestion and rsults

Record usually calls one of CKAN API actions during ingestion. In order to do it properly, record needs action context, which is passed as as single argument into ingest method. But this is only the most common workflow, so if you don't use any action, just ignore the context. What is more important, is the output of the ingest. It must be a dictionary described by ckanext.ingest.shared.IngestionResult. It has three members:

• success: flag that indicates whether ingestion succeeded or failed
• result: data produced by ingestion(package, resource, organization, etc.)
• details: any other details that may be useful. For example, how many entities were modified during ingestion, which API action was used, what were the errors if ingestion failed.

These details are not required by ingestion, but they may be used for building ingestion report.

Configure record trasformation with ckanext-scheming

ckanext.ingest.record module contains PackageRecord and ResourceRecord classes that create package/resource. But their trasform method is much more interesting. It maps raw into data using field configuration from metadata schema defined by ckanext-scheming.

In order to configure mapping, add ingest_options attribute to the field defition:

- field_name: title
  label: Title
  ingest_options: {}

During transformation, every key in raw is checked agains the schema. If schema contains field with ingest_options whose field_name or label matches the key from raw, this key is copied into data and mapped to the corresponding field_name. I.e, for the field definition above, both raw versions - {"title": "hello"} and {"Title": "hello"} will turn into data with value {"title": "hello"}.

If you have completely different names in raw, use aliases(list[str]) attribute of ingest_options:

- field_name: title
  label: Title
  ingest_options:
      aliasses: [TITLE, "name of the dataset"]

In this case, {"name of the dataset": "hello"} and {"TITLE": "hello"} will turn into {"title": "hello"}.

If value requires additional processing before it can be used as a field values, specify all applied validators as convert attribute of the ingest_options:

- field_name: title
  label: Title
  ingest_options:
      convert: conver_to_lowercase json_list_or_string

convert uses the same syntax as validators attribute of the field definition. You can use any registered validator inside this field. But, unlike validators, if Invalid error raised during transformation, field is silently ignored and ingestion continues.

Any field from raw that has no corresponding field in schema(detected by field_name/label or ingest_options.aiases), is not added to the data and won't be used for package/resource creation.

Generic strategies

There are a number of strategies available out-of-the box. You probably won't use them as-is, but creating a subclass of these strategies may simplify the process and solve a couple of common problems.

ingest:scheming_csv

Defined by ckanext.ingest.strategy.csv.CsvStrategy.

ingest:recursive_zip

Defined by ckanext.ingest.strategy.zip.CsvStrategy.

ingest:xlsx

Defined by ckanext.ingest.strategy.xlsx.XlsxStrategy.

Configuration

# List of allowed ingestion strategies. If empty, all registered strategies
# are allowed
# (optional, default: )
ckanext.ingest.strategy.allowed = ingest:recursive_zip

# List of disabled ingestion strategies.
# (optional, default: )
ckanext.ingest.strategy.disabled = ingest:scheming_csv

# Base template for WebUI
# (optional, default: page.html)
ckanext.ingest.base_template = admin/index.html

# Allow moving existing resources between packages.
# (optional, default: false)
ckanext.ingest.allow_resource_transfer = true

# Rename strategies using `{"import.path.of:StrategyClass": "new_name"}` JSON
# object
# (optional, default: )
ckanext.ingest.strategy.name_mapping = {"ckanext.ingest.strategy.zip:ZipStrategy": "zip"}

Interfaces

ckanext.ingest.interfaces.IIngest interface implementations can regiser custom extraction strategies via get_ingest_strategies method::

def get_ingest_strategies() -> dict[str, type[ckanext.ingest.shared.ExtractionStrategy]]:
    """Return extraction strategies."""
    return {
        "my_plugin:xlsx_datasets": MyXlsxStrategy,
    }

API

ingest_extract_records

Extract records from the source.

This method mainly exists for debugging. It doesn't create anything, just parses the source, produces records and return record's data as a list. Because it aggregates all extracted records into a single list, it can consume a lot of memory. If you want to iterate over, consider using iter_records function that produces an iterable over records.

Args:

source: str|FileStorage - data source for records

strategy: str|None - record extraction strategy. If missing, strategy
is guessed depending on source's mimetype

options: SourceOptions - dictionary with configuration for strategy and
records. Consumed by strategies so heavily depends on the chosen
strategy.

ingest_import_records

Ingest records extracted from source.

Parse the source, convert it into Records using selected strategy, and call Record.ingest, potentially creating/updating data.

Args:

source: str|FileStorage - data source for records

strategy: str|None - record extraction strategy. If missing, strategy
is guessed depending on source's mimetype

options: SourceOptions - dictionary with configuration for strategy and
records. Consumed by strategies so heavily depends on the chosen
strategy.

defaults: dict[str, Any] - default data added to every record(if missing)

overrides: dict[str, Any] - data that unconditionally overrides record details

skip: int - number of records that are skipped without ingestion

take: int - max number of records that will be ingested