Software Life Cycle: 1. Updating The Development Server
Contents
- 1 Overview
- 2 Document Conventions
- 3 Staging Pipeline Code
- 4 Running the Update Pipeline
- 4.1 Log Files
- 4.2 Executing the Pipeline
- 4.3 Update Steps
- 4.3.1 Mirror a new release
- 4.3.2 Unpack Acedb
- 4.3.3 Create BLAST databases
- 4.3.4 Create BLAT databases
- 4.3.5 Load genomic GFF annotations
- 4.3.6 Unpack and Load the CLUSTALW database
- 4.3.7 Compile Gene Resources
- 4.3.8 Compile Ontology Resources
- 4.3.9 Compile Orthology Resources
- 4.3.10 Compile Interaction Data
- 4.3.11 Convert GFF2 into GFF3
- 4.3.12 Create files of commonly requested datasets
- 4.3.13 Create a GBrowse-driven genetic map
- 4.3.14 Go Live
- 4.3.15 Precache content
- 4.4 Compiled file documentation and plans
Overview
This document describes the process of staging a new release of WormBase on the development server.
The automated staging pipeline consists of:
- a harness that handles logging, error trapping, and basic shared functions
- a suite of modules -- one per step -- that implement the step or make calls to helper scripts
- helper scripts in Perl or shell that assist in implementation
Control of the pipeline: You can use the pipeline in several ways:
- Launch the full pipeline via the control script, the preferred and automated method.
- Run individual steps in the context of the pipeline using control scripts in steps/, useful if the pipeline fails at a specific point.
- Directly run helper scripts outside of the logging facilities of the pipeline, useful if you need to rebuild something quickly.
Document Conventions
The current development server is
wb-dev: wb-dev.oicr.on.ca (FQDN); aka: dev.wormbase.org
When indicated, substitute WSXXX for ${RELEASE}.
System paths referred to in this document:
FTP : /usr/local/ftp/pub/wormbase WORMBASE : /usr/local/wormbase ACEDB : /usr/local/wormbase/acedb
Staging Pipeline Code
The update pipeline code is available in the website-admin module on github:
tharris> git clone git@github.com:WormBase/website-admin.git tharris> cd website-admin/update lib/ -- the shared library suite that handles updates. staging/ -- code related to staging data on the development site. production/ -- code related to the releasing data/code into production.
The contents are:
logs/ -- the logs directory for each step/update bin/ -- Perl scripts for manually launching individual steps. README.txt -- directory listing updatelog.conf -- a configuration file for the update process update.sh -- master script that fires off each step of the pipeline util/ -- various helper scripts for the update process
Running the Update Pipeline
Log Files
The Staging Pipeline creates informative logs for each step of the process. Logs are located at:
/usr/local/wormbase/logs/staging/WSXXX master.log -- Master log tracks all steps; useful for a meta-view of the pipeline. Contains INFO, WARN, ERROR, and FATAL messages. master.err -- Master error log tracks ERROR and FATAL messages encountered across all steps.
Each individual step creates its own log file capturing STDERR and STDOUT containing informative messages from the pipeline. These are useful for tracking progress and triaging problems. For example:
/usr/local/wormbase/logs/staging/WSXXX/build_blast_databases/ step.log -- step-specific log tracking everything from TRACE on up. step.err -- step-specific error log tracking ERROR and FATAL messages. Good place to check if a step breaks.
Executing the Pipeline
A single script fires off all steps of the process. You should run it inside a screen.
tharris> screen tharris> ./stage_via_pipeline.pl WSXXX (to disconnect your screen) tharris> ^a ^d (to resume your screen) tharris> screen -r
Monitor progress of the update by following the master log file:
tharris> tail -f /usr/local/wormbase/logs/staging/WSXXX/master.log
screen command reference
Update Steps
The steps that comprise the pipeline, the script to launch them, and the module that implements are listed below.
step | control script | module |
---|---|---|
Mirror a new release | steps/mirror_new_release.pl (manual) | W::U::Staging::MirrorNewRelease |
Unpack ACeDB | steps/unpack_acedb.pl (manual) | W::U::Staging::UnpackAcedb |
Create BLAST databases | steps/create_blast_databases.pl | W::U::Staging::CreateBlastDatabases |
Create BLAT databases | steps/create_blat_databases.pl | W::U::Staging::CreateBlatDatabases |
Load Genomic GFF databases | steps/load_genomic_gff_databases.pl | W::U::Staging::LoadGenomicGFFDatabases |
Unpack and Load the ClustalW database | steps/unpack_clustalw_database.pl | W::U::Staging::UnpackClustalWDatabase |
Compile Gene Summary resources | steps/compile_gene_resources.pl | W::U::Staging::CompileGeneResources |
Compile Ontology resources | steps/compile_ontology_resources.pl | W::U::Staging::CompileOntologyResources |
Compile Orthology resources | steps/compile_orthology_resources.pl | W::U::Staging::CompileOrthologyResources |
Create commonly requested datasets | steps/dump_annotations.pl | W::U::Staging::DumpAnnotations |
Go Live | steps/go_live.pl | W::U::Staging::GoLive |
Convert GFF2 To GFF3 | steps/convert_gff2togff3.pl | W::U::Staging::ConvertGFF2ToGFF3 |
Precache content | steps/precache_content.pl | W::U::Staging::PrecacheContent |
- Compile orthology resources
- Compile interaction resources
- Build and load GFF patches
- Create a GBrowse-driven genetic map
- Create a GBrowse-drive physical map
Mirror a new release
New releases are mirrored directly from the Hinxton FTP site to the primary WormBase FTP site hosted on wb-dev:/usr/local/ftp. This process is run via cron but can also be run manually.
# Mirror the next incremental release newer than what we already have: # Cron: ./steps/mirror_new_release.pl # Or mirror a specific release: ./steps/mirror_new_release.pl --release WS150 // Mirror the WS150 release to /usr/local/ftp/pub/wormbase/releases/WS150
Unpack Acedb
Unpack AceDB from the new release. Customize the new installation with skeletal files located at /usr/local/wormbase/website/classic/wspec. You will need approximately 25 GB of disk space per release.
via pipeline: ./steps/unpack_acedb.pl ${RELEASE} via helper : helpers/unpack_acedb.sh ${RELEASE} Input : Files staged at ${FTP}/releases/${RELEASE}/species Output : Unpacked AceDB files in ${ACEDB}/wormbase_${RELEASE}
When complete, you should have a new acedb directory containing:
-- database -- wgf -- wquery -- wspec
Test the database by:
> ps -ax | grep acedb ## to get acedb process number > kill -9 {AceDB proc number} ## stop current acedb process > sudo /etc/init.d/xinetd restart > saceclient localhost -port 2005
Create BLAST databases
Build nucleotide and protein BLAST databases for species with genomic sequence and conceptual translations. In addition, for C. elegans and C. briggsae, we build blast databases for ESTs and "genes" (actually clones).
Usage : ./steps/create_blast_databases.pl ${RELEASE} Input : Genomic sequence and protein FASTA files staged at: ${FTP}/releases/species/${SPECIES}.${RELEASE}.genomic.fa.gz ${FTP}/releases/species/${SPECIES}.${RELEASE}.protein.fa.gz Gene and EST sequences derived from AceDB Output : BLAST databases in ${WORMBASE}/databases/${RELEASE}/blast/${SPECIES}.
Create BLAT databases
Build BLAT databases of genomic sequence.
Usage : ./steps/create_blat_databases.pl ${RELEASE} Input : Genomic sequence FASTA files staged at ${FTP}/releases/species/${SPECIES}/${SPECIES}.${RELEASE}.genomic.fa.gz Output : BLAT .nib files in ${WORMBASE}/databases/${RELEASE}/blat/${SPECIES}
Load genomic GFF annotations
Convert GFF files into Bio::DB::GFF (GFF2) or Bio::DB::SeqFeature::Store (GFF3) databases.
Usage : ./steps/load_genomic_gff_databases.pl ${RELEASE} Input : GFF and FASTA files staged at: GFF : ${FTP}/releases/species/${SPECIES}/${SPECIES}.${RELEASE}.gff[2|3].gz DNA : ${FTP}/releases/species/${SPECIES}/${SPECIES}.${RELEASE}.genomic.fa.gz
Unpack and Load the CLUSTALW database
Usage: ./steps/unpack_clustal_database.pl {WSRELEASE} Input: ${FTP}/releases/${RELEASE}/COMPARATIVE_ANALYSIS/wormpep${RELEASE}.clw.sql.bz2 Output: a new mysql database called clustal_${RELEASE}
Compile Gene Resources
BROKEN
Create precompiled gene page files specifically to populate the Phenotype tables.
Usage : ./steps/compile_gene_resource.pl ${RELEASE} Input : AceDB data Output : Files ${WORMBASE}/databases/${RELEASE}/gene
- gene_rnai_pheno.txt (gene/gene)
- gene_xgene_pheno.txt (gene/gene)
- phenotype_id2name.txt (gene/gene)
- rnai_data.txt (gene/gene)
- variation_data.txt (gene/gene)
Compile Ontology Resources
BROKEN
TODO: This step relies on a number of external helper scripts that should ALL be folded into CompileGeneResources. They are located at
staging/helpers/gene_summary
Take the mirrored ontology files and compile them into the databases for the ontology searches.
Usage : ./steps/compile_ontology_resources.pl ${RELEASE} Input : OBO files staged at: /usr/local/ftp/pub/wormbase/releases/WSXXX/ONTOLOGY compiled data files from Compile Gene Resources step
- anatomy_association.RELEASE.wb
- anatomy_ontology.RELEASE.obo
- gene_association.RELEASE.wb
- gene_association.RELEASE.wb.cb
- gene_association.RELEASE.wb.ce
- gene_association.RELEASE.wb.cjp
- gene_association.RELEASE.wb.ppa
- gene_association.RELEASE.wb.rem
- gene_ontology.RELEASE.obo
- phenotype_association.RELEASE.wb
- phenotype_ontology.RELEASE.obo
Output : to ${WORMBASE}/database/${RELEASE}/ontology:
- id2association_counts.txt (ontology/tree_lister)
- id2name.txt (ontology/tree_lister)
- id2parents.txt (ontology/tree_lister)
- id2total_associations.txt (ontology/tree_lister)
- name2id.txt
- search_data.txt
- parent2ids.txt (ontology/tree_lister)
Compile Orthology Resources
Create precompiled orthology and disease display and search related files
This MUST be run after the ontology step above.
Usage : ./steps/compile_ortholog_data.pl ${RELEASE} <-- doesn't exist ./steps/compile_orthology_resources.pl ${RELEASE} <-- doesn't exist Input : AceDB data, omim.txt and morbidmap files from OMIM, ontology resources files
- gene_association.$RELEASE.wb.ce
Intermediate:
- all_proteins.txt
- disease_page_data.txt
- full_disease_data.txt
- gene_id2go_bp.txt
- gene_id2go_mf.txt
- gene_id2phenotype.txt
- gene_list.txt
- hs_proteins.txt
- last_processed_gene.txt
- omim2disease.txt
- omim_id2go_ids.txt
- omim_id2phenotypes.txt
- omim_id2disease_synonyms.txt
- omim_reconfigured.txt
- ortholog_other_data.txt
- ortholog_other_data_hs_only.txt
Output : Files ${WORMBASE}/databases/${RELEASE}/orthology (summary page using files in parenthesis)
- disease_search_data.txt (orthology/search)
- gene_id2omim_ids.txt (orthology/disease)
- go_id2omim_ids.txt (orthology/disease,ontology/gene)
- go_ids2descendants.txt (orthology/gene)
- hs_ensembl_id2omim.txt (orthology/gene)
- id2name.txt (orthology/disease, orthology/gene)
- name2id.txt (orthology/disease)
- omim_id2all_ortholog_data.txt (orthology/disease)
- omim_id2disease_desc.txt (orthology/disease)
- omim_id2disease_name.txt (orthology/disease,ontology/gene)
- omim_id2disease_notes.txt (orthology/disease)
- omim_id2disease.txt (orthology/gene)
- omim_id2gene_name.txt (orthology/search)
Compile Interaction Data
DEPRECATED. NO NEED TO MIGRATE THIS INTO THE NEW STAGING PIPELINE.
Create precompiled gene page files specifically to populate interaction listing pages.
Usage : ./steps/compile_interaction_data.pl ${RELEASE} Input : AceDB interaction data Output : Files ${WORMBASE}/databases/${RELEASE}/interaction
- compiled_interaction_data.txt
Convert GFF2 into GFF3
Usage: ./steps/convert_gff2_to_gff3.pl ${RELEASE}
Create files of commonly requested datasets
Usage: ./steps/dump_annotations.pl {WSRELEASE} Output: datasets in ${FTP}/releases/${RELEASE}/annotations and species/annotations
The staging harness will automatically run scripts in annotation_dumpers/*. These scripts should abide by the following conventions:
1. Be located in update/staging/annotation_dumpers 2. Be named either dump_species_* for species level data (like brief IDs) dump_resource_* for resource level data (like laboratories) 3. Follow existing examples, including available parameters. 4. Dump to STDERR and STDOUT. Notes: 1. dump_species_* will be called for each species managed by WormBase and will end up in ${FTP_ROOT}/releases/[RELEASE]/species/[G_SPECIES]/annotation/[G_SPECIES].[RELEASE].[DESCRIPTION].txt dump_resource_* will be called once and end up in ${FTP_ROOT}/datasets-wormbase/wormbase.[RELEASE].[DESCRIPTION].txt 2. The filename will be created by stripping off dump_species_ or dump_resource_. Species specific resources will be prepended with the appropriate species.
Create a GBrowse-driven genetic map
Notes...
Usage: ./steps/load_gmap_gffdb.pl ${RELEASE}
Go Live
steps/go_live.pl WSXXX
This script will
- create a series of symlinks in the FTP site (for example, to maintain the virtually organized species/ directory)
- create "current" symlinks in the FTP site for easy access.
- adjust symlinks to mysql GFF databases updated this release.
- adjust the symlink at /usr/local/wormbase/acedb/wormbase -> to point to the new wormbase_WSXXX unpacked acedb.
- Sync the staging FTP site to the production FTP site.
If you omit the WSXXX on the command line, the script will simply organize the virtual directories on the ftp site up to and including the current release. MySQL and AceDB symlinks will not be created.
Precache content
Once a release has been successfully staged and tested, we pre-cache select computationally intensive content to a CouchDB instance located on the development server.
Precaching works as follows.
1. The primary Catalyst configuration file is read.
2. For each widget set to "precache = true" in config, REST requests will be constructed against staging.wormbase.org. This will be running the NEW version of WormBase.
3A. The webapp returns HTML; the precache script stores it in the reference (production) couchdb.
OR
3B. The web app on staging.wormbase.org will automatically cache result in the reference couchdb (currently web6); the couchdb that is written to can be configured in wormbase.conf.
4. The reference couchDB will then be replicated during production release to each node, scaling horizontally.
5. During a production cycle, additional content will be stored in the reference couchdb; this is synced periodically to each node.
See CouchDB for details.
Compiled file documentation and plans
Step | File | Description | WB2 update |
---|---|---|---|
Compile Gene Resources | gene_rnai_pheno.txt |
|
TODO: update the appropriate method in Gene.pm to pull data for given gene directly from Ace |
Compile Gene Resources | gene_xgene_pheno.txt |
|
TODO: update the appropriate method in Gene.pm to pull data for given gene directly from Ace |
Compile Gene Resources | phenotype_id2name.txt |
|
TODO: function will be deprecated since individual phenotype objects will be extracted |
Compile Gene Resources | rnai_data.txt |
|
TODO: update the appropriate method in Gene.pm to pull data for given gene directly from Ace |
Compile Gene Resources | variation_data.txt |
|
TODO: update the appropriate method in Gene.pm to pull data for given gene directly from Ace |
Compile Ontology Resources | id2association_counts.txt |
| retain for browser, move into tied hash? |
Compile Ontology Resources | id2name.txt |
| retain for browser, move into tied hash? |
Compile Ontology Resources | id2parents.txt |
| retain for browser, move into tied hash? |
Compile Ontology Resources | id2total_associations.txt |
| retain for browser, move into tied hash? |
Compile Ontology Resources | search_data.txt |
| To be superceded by Xapian search |
Compile Ontology Resources | parent2ids.txt |
| retain for browser, move into tied hash? |
Compile Orthology Resources | disease_search_data.txt |
| Use data for Xapian search; work with Abby |
Compile Orthology Resources | gene_id2omim_ids.txt |
| Keep for disease object |
Compile Orthology Resources | go_id2omim_ids.txt |
|
useful for further paralog data expansion and integration |
Compile Orthology Resources | go_ids2descendants.txt |
|
useful for further paralog data expansion and integration |
Compile Orthology Resources | hs_ensembl_id2omim.txt |
|
disease UI |
Compile Orthology Resources | id2name.txt |
|
useful for further paralog data expansion and integration(?) |
Compile Orthology Resources | name2id.txt |
|
useful for further paralog data expansion and integration(?) |
Compile Orthology Resources | omim_id2all_ortholog_data.txt |
|
use to generate Xapian data; work with Abby |
Compile Orthology Resources | omim_id2disease_desc.txt |
|
use in Disease object model and UI |
Compile Orthology Resources | omim_id2disease_name.txt |
|
use in Disease object model and UI |
Compile Orthology Resources | omim_id2disease_notes.txt |
|
use in Disease object model and UI |
Compile Orthology Resources | omim_id2disease.txt |
|
use in Disease object model and UI |
Compile Orthology Resources | omim_id2gene_name.txt |
|
probably deprecate in updating Disease object model |