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The Ingest Stacks

Introduction

This section covers the service stacks that are used for curation and for crawling.

  • w3act - where curators define what should be crawled, and describe what has been crawled.
  • fc - the Frequent Crawler, which crawls sites as instructed in w3act.
  • dc - the Domain Crawler, which us used to crawl all UK sites, once per year.

The crawl_log_db service is not in use, but contains a useful example of how a Solr service and it's associated schema can be set up using the Solr API rather than maintaining XML configuration files.

  • TBA move-to-S3?

The Ingest services work together in quite complicated ways, so this page attempts to describe some of the core workflows. This should help determine what's happened if anything goes wrong.

How the Frequent Crawl works

  • Web Archivists define the crawl targets in the W3ACT tool. This covers seed URLs, crawl schedules, and some additional options like scope, size/cap and whether to ignore robots.txt.
  • An Apache Airflow task (see the manage/airflow folder) exports this data in standard Crawl Feed JSONL format files (one for NPLD crawls, another for By-Permission crawls).
  • Another Airflow task reads these feeds every hour, and if a crawl is due to launch that hour, sends a URL launch message to the relevant Kafka topic (fc.tocrawl.npld or fc.tocrawl.bypm).
    • Crucially, this task takes the crawl spec and maps the details onto the relevant Heritrix sheets.
  • Each of the NPLD and BYPM crawls uses a separate Heritrix3 instance and crawl job. Those are running continuously, listening to the corresponding fc.tocrawl.XXX topic for instructions.
  • When each Heritrix receives the message, it clears any quotas and sets the relevant Heritrix configuration for the seed target URL host using the Heritrix 'sheets' configuration system. It then passed the requested URL through the crawler scope decide rules, and if it is accepted, enqueues the URL for crawling in the Heritrix frontier.
  • The Heritrix 'ToeThreads' pick up the enqueued URLs from the frontier, and will attempt to download them, extract any onward URLs, and pass those through the scope rules and to the frontier.
  • If configured to do so, every URL the crawler discovered and passes the scope rules is logged in a dedicated Kafka topic (fc.inscope.npld or fc.bypm.inscope). This can potentially be useful for debugging, or in extreme cases, reconstructing the crawl frontier. In practice, it is generally not used and can usually be ignored.
  • For every URL that Heritrix attempts to download, the result is logged to the crawl.log file and the the shared fc.crawled Kafka topic.
  • For every URL Heritrix downloads successfully, the timestamp and digest/hash are stored in the 'Recently Crawled Database', which is based on an instance of OutbackCDX. This is used to decide whether the time has come to revisit a given URL, and to de-duplicated successfully-downloaded HTTP responses.
  • If requested, either because it is a seed or because the URL is explicitly marked for web rendering, URLs can be passed to the 'WebRender' service rather than downloaded directly by Heritrix.
    • The WebRender service is an internal HTTP API that accepts a request to render a URL, spins up a browser to render that page, takes screenshots, and then extracts any onward URLs and passes them back to Heritrix when the HTTP API call completes.
    • This renderer uses a WARC-writing proxy to write the NPLD/BYPM results to separate WARC files, and has additional models to record these events in the Kafka fc.crawled topic and in the OutbackCDX instance used to record what the crawl has seen and when it has seen it.
  • Every request and reponse is written to a WARC file. In the case of Heritrix3, this is immediately followed by a metadata record that records what URLs were extracted from that response etc.
  • Before writing each response into a WARC file, Heritrix streams the content into the ClamAV service for malware detection. If anything is detected, the item is stored in separate 'viral' WARC files.
  • The crawl.log file is rotated daily as part of the crawl checkpointing cycle. These crawl logs are considered impotant provenance and are transferred to HDFS along with the WARCs.
  • The filesystem layout on HDFS means we need to put the WARCs from the web rendering process in with the corresponding Heritrix job output folders. There is an Airflow task that attempts to tidy up the WARCs and logs so they can be uploaded in the right place.

The Kafka fc.crawled topic is not intended to be kept long term, but can be used to integrate with other systems to provide some insight into what's going on. In the past, we have used an ELK service to consume events and build a database that can be queried from the Grafana instance that is embedded as part of the W3ACT stack. We also used a custom activity analysis script as part of the access stack, so the API can report on recent crawler activity. This was how the 'crawl blobs' visualisation worked, as documented at https://blogs.bl.uk/webarchive/2019/10/-ukwa-website-crawl-one-hour-in-one-minute.html and deployed at https://ukwa-vis.glitch.me/.

Note that it is possible to use the crawl-time OutbackCDX collection from PyWB, and that a 'crawler' collection endpoint is configured as part of QA Wayback that works precisely this way. This does mean you can see immediately what has been crawled, but due to a bug with how de-duplication events are stored by the warcprox OutbackCDX plugin this doesn't always work properly at present.

How the Domain Crawl works

The domain crawler is very similar to the frequent crawler, but scaled up and bit, and a bit simpler:

  • No launch cycle. A large seed list is assembled and then directly fed into the Kafa launch topic and scope configuration files.
  • No web pages are rendered in browsers (because it's computationally very expensive), so those parts are not needed.

How the Document Harvester works

The Frequent Crawler also provides the basis of the Document Harvester system. This is mostly a crawl post-processing workflow, which proceeds as follows:

  1. Curators mark Targets as being Watched in W3ACT.
  2. The w3act_export workflow running on Airflow exports the data from W3ACT into files that contain this information.
  3. The usual move-to-hdfs scripts move WARCs and logs onto the Hadoop store.
  4. The TrackDB file tracking database gets updated so recent WARCs and crawl logs are known to the system. (See the update_trackdb_* tasks on http://airflow.api.wa.bl.uk/).
  5. The usual web archiving workflow indexes WARCs into the CDX service so items become available.
  6. The Document Harvester ddhapt_log_analyse workflow runs Hadoop jobs that take the W3ACT export data and use it to find potential documents in the crawl log.
    1. This currently means PDF files on Watched Targets.
    2. For each, a record is pushed to a dedicate PostgreSQL Document Database (a part of the W3ACT stack), with a status of NEW.
  7. The Document Harvester ddhapt_process_docs workflow gets the most recent NEW documents from the Document Database and attempts to enrich the metadata and post them to W3ACT.
    1. Currently, the metadata enrichment process talks to the live web rather than the web archive.
    2. In general, PDFs are associated with the website they are found from (the landing page), linked to the Target.
    3. For GOV.UK, we rely on the PDFs having a rel=up HTTP header that unambigiously links a PDF to it's landing page.
    4. The enriched metadata is then used to push a request to W3ACT. This metadata includes an access URL that points to the UKWA website on the public web (see here for details).
    5. W3ACT checks the file in question can be accessed via Wayback and calculates the checksum of the payload, or throws an error if it's not ready yet.
    6. If the submission works, the record is updated in the Document Database so it's no longer NEW.
    7. If it fails, it will be re-run in the future, so once it's available in Wayback it should turn up in W3ACT.
  8. Curators review the Documents found for the Targets they own, and update the metadata as needed.
  9. Curators then submit the Documents, which creats a XML SIP file that is passed to a DLS ingest process.
  10. The DLS ingest process passes the metadata to MER and to Aleph.
  11. The MER version is not used further.
  12. The Aleph version then becomes the master metadata record, and is passed to Primo and LDLs via the Metadata Aggregator.
  13. Links in e.g. Primo point to the access URLs included with the records, meaning users can find and access the documents.

Known Failure Modes

The Document Harvester has been fairly reliable in recent years, but some known failure modes may help resolve issues.

  • Under certain circumstances, Heritrix has been known to stop rotating crawl logs properly. If this happens, crawl log files may stop appearing or get lost. Fixing this may require creating an empty crawl.log file in the right place so a checkpoint can rotate the files correctly, or in the worst cases, a full crawler restart. If this happens, crawl logs will stop arriving on HDFS.
  • If there is a problem with the file tracking database getting updated to slowly, then the Document Harvester Airflow workflows may run but see nothing to process. This can be determined by checking the logs via Airflow, and checking that the expected number of crawl log files for that day were found. Clearing the job so Airflow re-runs it will resolve any gaps.
  • If there is a problem with W3ACT (either directly, or with how it talks to the curators Wayback instance), then jobs may fail to upload processed Documents to W3ACT. This can be spotted by checking the logs via Airflow, but note that any Documents that have not yet been CDX indexed are expected to be logged as errors at this point, so it can be difficult to tell things apart. It may be necessary to inspect the W3ACT container logs to determine if there's a problem with W3ACT itself.

Debugging Approach

Problems will generally be raised by Jennie Grimshaw, who is usually able and happy to supply some example Document URLs that should have been spotted. This is very useful in that it provides some test URLs to run checks with, e.g.

  • Check the URLs actually work and use curl -v to see if the Link: rel=up header is present (for GOV.UK) which helps find the landing page URL.
  • Check the crawl-time CDX index (currently at http://crawler06.bl.uk:8081/fc) to check if the URLs have been crawler at all.
  • Check the access time CDX index (currently at http://cdx.api.wa.bl.uk/data-heritrix) to check if the items have been indexed correctly.
  • Check the Curator Wayback service (https://www.webarchive.org.uk/act/wayback/archive/) to see if the URLs are accessible.
  • Query the PostgreSQL Document Database to see if the URL was found by the crawl log processor and what the status of it is.

Overall, the strategy is to work out where the problem has occurred in the chain of events outlined in the first section, and then modify and/or re-run the workflows as needed.

Operations

This section covers some common operations when interacting with the Ingest services. In particular, the operations for the Frequent Crawler (FC) and the Domain Crawler (DC) are very similar, so these are documented here.

Crawler Service Operations

Both the FC and the DC use the same software and same set of service stacks, just with different configuration via various environment variables.

Both services have:

  • A Kafka stack, as Kafka used to launch crawls and capture a copy of the crawl log. This should always be started first, as Heritrix doesn't not always cope when Kafka is not up and running. Note that the service being ready can take a lot longer than the Docker service takes to start up, depending on how large the topic logs are.
  • A Kafka UI stack. This is optional, but useful for checking Kafka is actually ready for use, and for inspecting the contents of the Kafka topics.
  • A Worker stack, which contains one or two Heritrix instances, and supporting services like ClamAV.
  • A Wayback stack, which is optional, and can be used to look at what has been crawled (as long as the WARCs are still held locally).

Deploying Kafka

Each deployment should have a script for starting Kafka, e.g. fc/prod/deploy-fc-kafka.sh. This will require configuration for different servers, e.g. where is the fast disk where the files can be stored.

Assuming the deployment works, even after the Docker Service is running, it's necessary to wait for Kafka to be ready. In a new setup this should be quick, but for a setup with a lot of existing data it might take a while for Kafka to check all the parition files of all the topcs. e.g. if you run:

docker service logs --tail 100 -f fc_kafka_kafka

You might see a lot of:

...Loading producer state from snapshot files...

Before it settles down and says it's listening for connections. This can also be checked by starting the associated Kafka UI stack, which should provide a UI on port 9000 that lets you inspect the topics, once Kafka is available. It may sometimes be necessary to force the UI to restart so it properly re-checks:

docker service update --force fc_kafka_ui_kafka_ui

Configuring Kafka

If this is a new Kafka setup, then the relevant topics will need to be created, see e.g. fc/prod/kafka-create-topics.sh.

The Frequent Crawl has separate topics for launching NPLD or By-Permission crawls, and a shared topic for logging what has been crawled. The Domain Crawler only support NPLD crawls.

One additional factor is configuration for how long Kafka keeps messages. We want to configure Kafka to forget messages after an appropriate time, not necessarily use the default seven days. An example of doing this for the domain crawl 'in scope URL' log is available here.

e.g. the fc.crawled topic should retain messages for 30 days. e.g. these commands run from inside the Kafka Docker container (docker exec -it ...):

bash-4.4#  /opt/kafka/bin/kafka-topics.sh --alter --zookeeper zookeeper:2181 --topic fc.crawled --config retention.ms=2592000000
Updated config for topic "fc.crawled".
bash-4.4#  /opt/kafka/bin/kafka-topics.sh --describe --zookeeper zookeeper:2181 --topic fc.crawled
Topic:fc.crawled        PartitionCount:16       ReplicationFactor:1     Configs:retention.ms=2592000000,compression.type=snappy

The default of seven days is likely fine for the 'fc.tocrawl.*` logs.

Deploying the crawlers

Similarly to Kafka, use the supplied scripts (or varient of them) to launch the crawler services. This includes things like a set of ClamAV scanners, any web-page rendering services, and an embedded Prometheus for federated monitoring.

A few differnet things need to be set up when running a crawler:

  • Check scope surts and exclusions. These are on shared files with the host, and may need updating based on data from W3ACT/curators. FC manages scope and seeds via Kafka, but exclusions are manual. DC needs explicit scope and exclusion configuration.
  • Update the Geo-IP DB for DC: ukwa#123

Note that setting up seeds, scope and exclusions for the domain crawl is particularly involved, and is documented at TBA IS ON GITLAB

Comparing the crawlers

The Domain Crawler is very similar to the Frequent Crawler. Some notable differences are:

  • DC runs more ToeThreads so more can be downloaded at once.
  • DC sets je.cleaner.threads to 16 (from the default of 1) so the otherwise huge crawl state files can get cleaned up as the crawl goes. (Note large numbers of cleaner threads went very badly, causing memory exhaustion)
  • The DC uses a Bloom filter to track which URLs have already been crawled, rather than a disk database, as that uses much more disk space.
  • The DC uses MAX_RETRIES=3 rather than the high value of 10 used for FC.
  • The DC uses a GeoIP DB (GeoLite2-City.mmdb) to look for UK URLs on non-UK domains. This is built into the Heritrix crawled Docker image, and there is an outstanding issue about keeping this up to date:ukwa#123

Moving the results

Need details on:

  • FC uses Gluster and move-to-hdfs scripts
  • DC uses Airflow to run rclone to send data directly to Hadoop

Shutting down the Docker Services

Before doing this, a recent crawl checkpoint should have been taken (see below), which means it should not make much difference how exactly the service is halted. To attempt to keep things as clean as possible, first terminate and then teardown the job(s) via the Heritrix UI.

Then remove the crawl stack:

docker stack rm fc_crawl

Note that the crawler containers are configured to wait a few minutes before being forced to shut down, in case they are writing a checkpoint. If the services fail to shut down, it may be necessary to restart Docker itself. This means all the services get restarted with the current deployment configuration.

service docker restart

Even this can be quite slow sometimes, so be patient. There can be a lot of old logs knocking about, so it can help to prune the system:

docker system prune -f

Crawl Operations

The current crawl engine relies on Heritrix3 state management to keep track of crawl state, and this was not designed to cope under un-supervised system restarts. i.e. rather than being stateless, or delegating state management to something that ensures the live state is preserved immediately, we need to manage ensuring the runtime state is recorded on disk. This is why crawler operations are more complex than other areas.

Starting Crawls

As stated above, before going any further, we need to ensure that Kafka has completed starting up and is ready for producers and consumers to connect.

  • Build.
  • Select Checkpoint. If expected checkpoints are not present, this means something went wrong while writing them. This should be reported to try to determine and address the root cause, but there's not much to be done other than select the most recent valid checkpoint.
  • Launch.

Stopping Crawls

If possible, we wish to preserve the current state of the crawl, so we try to cleanly shut down while making a checkpoint to restart from.

Note that for our frequent crawls, we run two Heritrix services, one for NPLD content and one for by-permission crawling. When performing a full stop of the frequent crawls, both services need to be dealt with cleanly. When running on crawler06, this means:

Pause the crawl job(s)

For all Heritrixes in the Docker Stack: log into the Heritrix3 control UI, and pause any job(s) on the crawler that are in the RUNNING state. This can take a while (say up to two hours) as each worker thread tries to finish it's work neatly. Sometimes pausing never completes because of some bug, in which case we proceed anyway and accept some inaccuracies in the crawl state. If it works, all RUNNING jobs will now be in the state PAUSED.

Checkpoint the job(s)

Via the UI, request a checkpoint. If there's not been one for a while, this can be quite slow (tens of minutes). If it works, a banner should flash up with the checkpoint ID, which should be noted so the crawl can be resumed from the right checkpoint. If the checkpointing fails, the logs will need to be checked for errors, as unless a new checkpoint is succefully completed, it will likely not be valid.

As an example, under some circumstances the log rotation does not work correctly. This means non-timestamped log files may be missing, which means when the next checkpoint runs, there are errors like:

$ docker logs --tail 100 fc_crawl_npld-heritrix-worker.1.h21137sr8l31niwsx3m3o7jri
....
SEVERE: org.archive.crawler.framework.CheckpointService checkpointFailed  Checkpoint failed [Wed May 19 12:47:13 GMT 2021]
java.io.IOException: Unable to move /heritrix/output/frequent-npld/20210424211346/logs/runtime-errors.log to /heritrix/output/frequent-npld/20210424211346/logs/runtime-erro
rs.log.cp00025-20210519124709

These errors can be avoided by adding empty files in the right place, e.g.

touch /mnt/gluster/fc/heritrix/output/frequent-npld/20210424211346/logs/runtime-errors.log

But immediately re-attempting to checkpoint a paused crawl will usually fail with:

Checkpoint not made -- perhaps no progress since last? (see logs)

This is because the system will not attempt a new checkpoint if the crawl state has not changed. Therefore, to force a new checkpoint, it is necessary to briefly un-pause the crawl so some progress is made, then re-pause and re-checkpoint.

Shutdown

At this point, all activity should have stopped, so it should not make much difference how exactly the service is halted. To attempt to keep things as clean as possible, first terminate and then teardown the job(s) via the Heritrix UI.

You can now shut down the services...

Handling Crawler Complaints

Occasionally, we need to stop a crawler from crawling a site. Usually this is due an email complaining about the crawler finding 404s on a site that otherwise doesn't get crawled much. Although it's rare we're really doing anything wrong in terms of the legal framework, we usually err on the side of caution and block the crawler from crawling their site. The complaints often don't make this easy, as they often redact most of the host name, leaving us to rely on the timestamp and path of the URL to work out the hostname so we can use that to block the crawler from visiting.

There's usually three steps to this, working in concert with the Web Archivist role(s) who usually coordinate the response to the complaint.

  1. Check what's been going on. Use the crawl-time CDX index, or the Kafka UI, or just grep the relevant crawl.log to verify what's going on an work out the host name in question.
  2. Update the relevant crawlers' exclusion file to add the URL or SURT to the block list (which the crawler will then automatically read).
  3. Check no further activity has been logged.

One important variation is that we sometimes get automated complaints through AWS or JANET rather than via web hosts contacting UKWA. In this case, we often do not have any way to contact the actual webmaster, so we just have to block the crawl and report back to the network supplier.

In the case of the frequent crawls, this should be done by Nicola updating W3ACT records as NEVER CRAWL, and then the relevant excluded-surts file being updated based on that. See the FC setup documentation at https://github.com/ukwa/aws-fc-setup/tree/main#configuring-the-crawls ... However, that automated update was not completed, and should really be a new Airflow task!

It's more of a priority for the domain crawl, in which case the equivalent excluded-surts file is updated manually. This file uses a syntax called 'Surt Prefix Scope, as defined in http://crawler.archive.org/articles/user_manual/config.html#scopes - this means a specific host/URL-prefix can be blocked by just adding it to that file, or a SURT can be used, prefixed with a +. If you check the Heritrix job/container logs, you should see that Heritrix quickly notices the exclusion file is updated and loads in the changes. It will also grumble if it can't parse the lines.

Checking the crawls

nohup python -m crawldb.parquet.cli import /mnt/data/fc/heritrix/output/frequent-npld/20231124123728/logs/crawl.log.cp00029-20231213123735 /mnt/data/fc/crawl-db/npld-log-cp00026.parquet &

Then tailing nohup.out to check on progress...

Deal with dead seeds? Count Tweet data load?