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@Horneth Horneth released this May 30, 2017 · 2162 commits to develop since this release

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Migration

  • Call Caching has been improved in this version of Cromwell, specifically the time needed to determine whether or not a job can be cached
    has drastically decreased. To achieve that the database schema has been modified and a migration is required in order to preserve the pre-existing cached jobs.
    This migration is relatively fast compared to previous migrations. To get an idea of the time needed, look at the size of your CALL_CACHING_HASH_ENTRY table.
    As a benchmark, it takes 1 minute for a table with 6 million rows.
    The migration will only be executed on MySQL. Other databases will lose their previous cached jobs.
    In order to run properly on MySQL, the following flag needs to be adjusted: https://dev.mysql.com/doc/refman/5.5/en/server-system-variables.html#sysvar_group_concat_max_len
    The following query will give you a minimum to set the group_concat_max_len value to:
SELECT MAX(aggregated) as group_concat_max_len FROM
     (
           SELECT cche.CALL_CACHING_ENTRY_ID, SUM(LENGTH(CONCAT(cche.HASH_KEY, cche.HASH_VALUE))) AS aggregated
           FROM CALL_CACHING_HASH_ENTRY cche
           GROUP BY cche.CALL_CACHING_ENTRY_ID
     ) aggregation

Here is the SQL command to run to set the group_concat_max_len flag to the proper value:

SET GLOBAL group_concat_max_len = value

Where value is replaced with the value you want to set it to.

Note that the migration will fail if the flag is not set properly.

Breaking Changes

  • The response from the metadata endpoint now returns compressed HTTP responses depending on the request's headers using the following rules:
Accept-Encoding header Resulting response
Accept-Encoding: gzip compressed with Gzip
Accept-Encoding: deflate compressed with Deflate
Accept-Encoding: deflate, gzip compressed with Gzip
Accept-Encoding: identity uncompressed
no Accept-Encoding header present compressed with Gzip
  • The update to Slick 3.2 requires a database stanza to
    switch from using driver to profile.
database {
  #driver = "slick.driver.MySQLDriver$" #old
  profile = "slick.jdbc.MySQLProfile$"  #new
  db {
    driver = "com.mysql.jdbc.Driver"
    url = "jdbc:mysql://host/cromwell?rewriteBatchedStatements=true"
    user = "user"
    password = "pass"
    connectionTimeout = 5000
  }
}

Call Caching

Cromwell now supports call caching with floating Docker tags (e.g. docker: "ubuntu:latest"). Note it is still considered
a best practice to specify Docker images as hashes where possible, especially for production usages.

Within a single workflow Cromwell will attempt to resolve all floating tags to the same Docker hash, even if Cromwell is restarted
during the execution of a workflow. In call metadata the docker runtime attribute is now the same as the
value that actually appeared in the WDL:

   "runtimeAttributes": {
     "docker": "ubuntu:latest",
     "failOnStderr": "false",
     "continueOnReturnCode": "0"
   }

Previous versions of Cromwell rewrote the docker value to the hash of the Docker image.

There is a new call-level metadata value dockerImageUsed which captures the hash of the Docker image actually used to
run the call:

   "dockerImageUsed": "library/ubuntu@sha256:382452f82a8bbd34443b2c727650af46aced0f94a44463c62a9848133ecb1aa8"

Important note: There is a Cromwell-wide cache for the resolution of docker tags to docker hashes.
By default, this cache retains a tag -> hash association for 20 minutes before discarding it.
This means that if 2 workflows with a task using a docker tag (e.g. ubuntu:latest) are started within that time span, they will both be run with the same hash even if the tag latest is updated.
The purpose of this cache is to reduce the time spent by Cromwell resolving docker tags.
This cache can be adjusted or completely disabled in the configuration.

Docker

  • The Docker section of the configuration has been slightly reworked
    An option to specify how a Docker hash should be looked up has been added. Two methods are available.
    "local" will try to look for the image on the machine where cromwell is running. If it can't be found, Cromwell will try to pull the image and use the hash from the retrieved image.
    "remote" will try to look up the image hash directly on the remote repository where the image is located (Docker Hub and GCR are supported)
    Note that the "local" option will require docker to be installed on the machine running cromwell, in order for it to call the docker CLI.
  • Adds hash lookup support for public quay.io images.

WDL Feature Support

  • Added support for the new WDL basename function. Allows WDL authors to get just the file name from a File (i.e. removing the directory path)
  • Allows coercion of Map objects into Arrays of Pairs. This also allows WDL authors to directly scatter over WDL Maps.

Miscellaneous

  • Adds support for JSON file format for google service account credentials. As of Cromwell 27, PEM credentials for PAPI are deprecated and support might be removed in a future version.
google {

  application-name = "cromwell"

  auths = [
    {
      name = "service-account"
      scheme = "service_account"
      json-file = "/path/to/file.json"
    }
  ]
}

General Changes

  • The /query endpoint now supports querying by label. See the README for more information.
  • The read_X standard library functions limit accepted filesizes. These differ by type, e.g. read_bool has a smaller limit than read_string. See reference.conf for default settings.
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