Release v1.4.0.2

This release finally fully enables handling multiple Poseidon package versions with trident. It includes a significant overhaul of the selection language in forge and fetch with major changes in its implementation and, as a consequence, multiple (subtle, but strictly breaking) changes in its semantics.

Handling multiple package versions

The trident subcommands fetch, forge, genoconvert, list, rectify, survey and validate now by default consider all versions of each Poseidon package in the given base directories. Previously all of them only considered the latest versions. If this old behaviour is desired now, it can be enabled with the flag --onlyLatest for the subcommands genoconvert, list, rectify, survey and validate. fetch and forge now generally consider all package versions (if we ignore the selection language semantics) and summarize continues to consider only the latest ones.

Changes to the selection language

In the forge- and fetch-selection language it is now possible to specify which version of a Poseidon package should be forged/fetched by appending the version number after a minus: e.g. *2010_RasmussenNature-2.1.1*. This also works for the more verbose and precise syntax to describe individuals, e.g. <2010_RasmussenNature-2.1.1:Greenland_Saqqaq.SG:Inuk.SG>.

While implementing this change, we also reworked the entity selection logic. It now adheres to the following rules:

Inclusion queries

• *Pac1*: Select all individuals in the latest version of package "Pac1"
• *Pac1-1.0.1*: Select all individuals in package "Pac1" with version "1.0.1"
• Group1: Select all individuals associated with "Group1" in all latest versions of all packages
• <Ind1>: Select the individual named "Ind1", searching in all latest packages.
• <Pac1:Group1:Ind1>: Select the individual named "Ind1" associated with "Group1" in the latest version of package "Pac1"
• <Pac1-1.0.1:Group1:Ind1>: Select the individual named "Ind1" associated with "Group1" in the package "Pac1" with version "1.0.1"

Exclusion queries

• -*Pac1*: Remove all individuals in all versions of package "Pac1"
• -*Pac1-1.0.1*: Remove only individuals in package "Pac1" with version "1.0.1" (but leave other versions in)
• -Group1: Remove all individuals associated with "Group1" in all versions of all packages (not just the latest)
• -<Ind1>: Remove all individuals named "Ind1" in all versions of all packages (not just the latest).
• -<Pac1:Group1:Ind1>: Remove the individual named "Ind1" associated with "Group1", searching in all versions of package "Pac1"
• -<Pac1-1.0.1:Group1:Ind1>: Remove the individual named "Ind1" associated with "Group1", but only if they are in "Pac1" with version "1.0.1"

Missing (or mis-spelled) entities in a selection-set lead to errors now.

If the forge entity list starts with a negative entity, or if the entity list is empty, forge will still implicitly assume you want to include all individuals from only the latest packages found in the baseDirs.
Likewise, trident fetch --downloadAll considers only latest versions now.

The specific individual selection syntax (with -<Pac1-1.0.1:Group1:Ind1>) does not perform automatic duplicate resolution any more. If there is another <Ind1> somewhere within the selected entities, then this will cause an error that has to be resolved manually by adjusting the selection.

Minor additional changes

• The Web API and the list subcommand now return an extra, boolean field/column isLatest to point out if an entity (individual, group, package) is from the latest package version.
• list now also returns column headers with the --raw flag. If they are not desired, then they have to be filtered out manually on the command line (e.g. with trident list ... | tail -n+2).
• Duplicate individuals in a package collection do not anymore lead to errors. Instead, only a selection for forge (and externally also in xerxes), if resulting in multiple individuals in the selection, will lead to errors. validate will also fail by default, except --ignoreDuplicates is set.