Last modified 6 months ago Last modified on 03/08/11 10:12:21

  1. Post-processing
    1. Sequence Features
      1. create-chromosome-locations-and-lengths
      2. transfer-sequences
      3. create-references
      4. create-intron-features
    2. Overlapping and Flanking Features
      1. create-intergenic-region-features
      2. create-overlap-relations-flymine
      3. create-bioseg-location-index
      4. create-overlap-view
      5. create-gene-flanking-features
    3. Data
      1. do-sources
    4. Webapp
      1. create-search-index
      2. create-attribute-indexes
      3. summarise-objectstore
      4. create-autocomplete-index

Post-processing

These are steps that run after the data loading is completed. They are used to set calculate/set fields that are difficult to do when data loading or that require multiple sources to be loaded.

Sequence Features

create-chromosome-locations-and-lengths

For genome features this will set the chromosome, chromosomeLocation and length fields which are added to make querying more convenient. Some parts of the webapp specific to genome features expect chromosomeLocation to be filled in.

Should I use it? - Yes, if you have loaded genome annotation.

transfer-sequences

Where a Chromosome has a sequence this will find genome features located on it that don't have sequence set this will calculate and set the sequence for those features. This will no longer be needed when InterMine works correctly with clobs.

Should I use it? - Yes, if you have loaded genome annotation without sequence set for all features.

create-references

Create shortcut references/collections to make querying more obvious. We are trying to eliminate the need to use this.

Should I use it? - Yes, for the moment if you are using standard InterMine sources.

create-intron-features

If you have loaded genome annotation that include exons but does not specify introns this will create Intron objects and name them appropriately.

Should I use it? - If genome annotation you have loaded does not include introns.

Overlapping and Flanking Features

create-intergenic-region-features

Looks at gene locations on chromosomes and calculates new IntergenicRegion features to represent the intergenic regions. These are useful in combination with overlaps for working out, e.g. binding sites that overlap the upstream intergenic region of a gene. Each Gene gets a reference to its upstream and downstream intergenic regions.

Should I use it? - Yes, if you have loaded genome annotation and think IntergenicRegions sound useful.

create-overlap-relations-flymine

Search through genome features and find any that overlap one another - e.g. to find P-element insertions overlapping exons or binding sites overlapping upstream intergenic regions. Creates OverlapRelation objects between those features that overlap. The configuration of which classes to exclude in calculations specified in postprocess/resources/overlap.config.

Should I run it? - Yes, if you have genome annotation and would like to query overlaps.

create-bioseg-location-index

Create a bioseg GIST index on the location table to help with overlap queries.

Should I run it? - Yes, if you have genome annotation and would like to query overlaps and have bioseg installed.

create-overlap-view

Replace the sequencefeatureoverlappingfeatures table with a view that uses the bioseg type to calculate the overlaps.

Should I run it? - Yes, if you have genome annotation and would like to query overlaps and have bioseg installed.

create-gene-flanking-features

Create features to represent flanking regions of configurable distance either side of gene features. These will be used in overlap queries.

Should I run it? - Yes, if you have genome annotation and would like to query flanking regions.

Data

do-sources

This searches through all sources included in project.xml and runs post-processing steps if any exist. Looks for the property postprocessor.class in the project.properties of each source, the class specified should be a subclass of org.intermine.postprocess.PostProcessor.

Should I use it? - Yes, if you are using standard InterMine sources, they may have post-processing steps.

Webapp

create-search-index

Creates the lucene search index used by the webapp.

Should I run it? Yes, if you are releasing a webapp.

create-attribute-indexes

Create indexes on all attributes to help speed up queries.

Should I use it? - Always. It should be run last of all post-processing steps.

summarise-objectstore

Counts of the number of objects of each class and for class fields that have a small number of value, a list of those values. See ObjectStoreSummaryProperties for more information.

Should I use it? - Always.

create-autocomplete-index

Creates the indexes for the fields set to be autocompleted in the ObjectStoreSummaryProperties file.

Should I use it? - Yes, if you have a webapp.

See: RunningABuild