Webdb workflow#57

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ryanrdoherty wants to merge 293 commits intomasterfrom webdb_workflow

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Commits on Dec 15, 2022

minor change for tM -refs #49708

Bindu Gajria
authored and
mvnural
committed
fix for geneIntronJn table; ontology source_IDs not valid, so test fix for MappingStatsGIJtmp with names

Bindu Gajria
authored and
mvnural
committed
new column CATEGORY

iodice
authored and
mvnural
committed
fix for Amoeb - #49519

Bindu Gajria
authored and
mvnural
committed
comment out clinepi and microbiome (which don't have the "newcategory"

iodice
authored and
mvnural
committed
out with category; in with displayName

iodice
authored and
mvnural
committed
embiggen DISPLAY_NAME column

iodice
authored and
mvnural
committed
move AssociatedDataset tuning table

iodice
authored and
mvnural
committed
store webapp name so we can make the link

iodice
authored and
mvnural
committed
move to right repository

iodice
authored and
mvnural
committed
fix ontology source_IDs, for geneIntronTable

Bindu Gajria
authored and
mvnural
committed
not show broken/unneeded table in downloads

Bindu Gajria
authored and
mvnural
committed
for synteny, got to use internal_abbrev in the SQL - refs #49445

Bindu Gajria
authored and
mvnural
committed
fix PFAM links - refs #49522

Bindu Gajria
authored and
mvnural
committed
fix PFAM link_2 - refs #49522

Bindu Gajria
authored and
mvnural
committed
fix term width for geneListDataset processQuery, for portal

Bindu Gajria
authored and
mvnural
committed
fix strain name, possibly on in Fungi -refs #49444

Bindu Gajria
authored and
mvnural
committed
made GenesWithApolloAnnotation internal

Paul Wilkinson
authored and
mvnural
committed
fix EST blast issue for VB - refs #49836

Bindu Gajria
authored and
mvnural
committed
Updated SQL for GenesWithApolloAnnotation to fix bug

Paul Wilkinson
authored and
mvnural
committed
TranscriptAttributes: handle overflow in listagg()

iodice
authored and
mvnural
committed
change to bld-61

Haiming Wang
authored and
mvnural
committed
redmine #49878 UX Nov 16 2022

aurreco-uga
authored and
mvnural
committed
allow synteny tracks in TrichDB -refs #49876

Bindu Gajria
authored and
mvnural
committed
allow synteny url for TrichDB -refs #49876

Bindu Gajria
authored and
mvnural
committed
add previous annotation track -refs #49850

Bindu Gajria
authored and
mvnural
committed
fix minor typo

Bindu Gajria
authored and
mvnural
committed
cleanup: remove unused and broken SnpChipRecordClass.Strains table from model

Bindu Gajria
authored and
mvnural
committed
dep upgrades and compatibility

ryanrdoherty
authored and
mvnural
committed
Fix duplicate Available for community annotation column

Paul Wilkinson
authored and
mvnural
committed
fix PreferredProducts for downloads - refs #49919

Bindu Gajria
authored and
mvnural
committed
add filterParam to FileRecords Q - refs #48101

Bindu Gajria
authored and
mvnural
committed
add filterParam to FileRecords Q - refs #48101

Bindu Gajria
authored and
mvnural
committed
remove NR alignment track for cgloCBS148.51 taxon - refs #49960

Bindu Gajria
authored and
mvnural
committed
allow Amoeba to have the NonnuclearGenomicRegio Q - fixes #49987

Bindu Gajria
authored and
mvnural
committed
removed unneeded and unused Q

Bindu Gajria
authored and
mvnural
committed
injectors for RNASeq MetaCycle datasets - refs #43007

Bindu Gajria
authored and
mvnural
committed
fix typo - refs #43007

Bindu Gajria
authored and
mvnural
committed
remove unneeded file

Bindu Gajria
authored and
mvnural
committed
fix injectors for 2 RNASeq MetaCycle datasets - refs #43007

Bindu Gajria
authored and
mvnural
committed
fix injectors for 2 RNASeq MetaCycle datasets - refs #43007

Bindu Gajria
authored and
mvnural
committed
add transposable element track for tvagGE2022

jbrestel
authored and
mvnural
committed
te genes are processed transcripts

jbrestel
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mvnural
committed
grey red/blue for te genes

jbrestel
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mvnural
committed
metacycle param was being injected multiple times

jbrestel
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mvnural
committed
fix the template file to not have all the dataset hardcoding! (was done by Lin) - refs #43007

Bindu Gajria
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mvnural
committed
fix Lin's mistake! - refs #43007

Bindu Gajria
authored and
mvnural
committed
updated the help info on the column title

Paul Wilkinson
authored and
mvnural
committed
add mobile element table

iodice
authored and
mvnural
committed
GenesByGeneModelChars take over from GenesByGeneType in dataset pages - refs #50026

Bindu Gajria
authored and
mvnural
committed
comment DbPres dependeny for tMs to finish!

Bindu Gajria
authored and
mvnural
committed
FungiDB not to be included in "metacycle_study" as Hurley_studu was postponed

Bindu Gajria
authored and
mvnural
committed
Allow use of multiple profile set in RNAseq questions

kathryncrouch
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mvnural
committed
Custom templates for Hehl dataset

kathryncrouch
authored and
mvnural
committed
Allow setting custom param queries

kathryncrouch
authored and
mvnural
committed
Add custom injector for Hehl dataset

kathryncrouch
authored and
mvnural
committed
Customisation for Hehl dataset

kathryncrouch
authored and
mvnural
committed
blast sequence parameter regex not needed

aurreco-uga
authored and
mvnural
committed
add ref to question when asked for; remove unused lines of code

jbrestel
authored and
mvnural
committed
Postgres updates continued
mvnural
committed
Postgres updates continued
mvnural
committed
postgres updates continued
mvnural
committed

Commits on Jan 20, 2023

Commits on Feb 8, 2023

Commits on Nov 27, 2023

Merge branch 'master' into webdb_workflow.
mvnural
committed

Commits on Apr 18, 2024

temp remove long read table
jbrestel
committed

Commits on Oct 30, 2024

Merge branch 'master' into webdb_workflow
mvnural
committed

Commits on Dec 3, 2024

Merge branch 'master' into webdb_workflow
mvnural
committed

Commits on Dec 5, 2024

cleanup
Bindu Gajria
committed
remove extra tag (from merge)
Bindu Gajria
committed
remove double mention of "metacycle_amplitude"
Bindu Gajria
committed

Commits on Dec 9, 2024

add jbrowse-gene mini record (#51 )
steve-fischer-200
authored

Commits on Dec 11, 2024

comment out sql lines with REGEXP_LIKE and add "CHECK AND FIX" comment to each; also comment out GenomicsInternalHyperlink and ApolloUpdate tables for now
Bindu Gajria
committed
comment out ApolloUpdateGene table for now
Bindu Gajria
committed
fix GeneProduct
Bindu Gajria
committed
fix varchar2 to varchar
Bindu Gajria
committed
fixed typo in varchar
Bindu Gajria
committed

Commits on Dec 12, 2024

Commits on Dec 15, 2024

comment sql with regexp_like for now; to FIX later
Bindu Gajria
committed

Commits on Jan 2, 2025

fix sql for TranscriptPathway
Bindu Gajria
committed
commenting out TranscriptGenomicSequence for now
Bindu Gajria
committed
fix CREATE statement for GeneMaxIntronGIJ
Bindu Gajria
committed

Commits on Jan 3, 2025

commit out :
Bindu Gajria
committed
replace varchr2 with varchar
Bindu Gajria
committed
subquery in FROM must have an alias
Bindu Gajria
committed

Commits on Jan 6, 2025

fixes for GenesByLopit, for UniDB
Bindu Gajria
committed
fix SQL for CellularLocalization; TODO: unify sql between components
Bindu Gajria
committed
commit 2 transcriptAttributes for now - till "pivot" is handled in sql
Bindu Gajria
committed
fix Toxo and Tryo LOPIT datasets attribute queries
Bindu Gajria
committed

Commits on Jan 7, 2025

make MSPeptideSummary anew - take 1
Bindu Gajria
committed
add needed columns MSPeptideSummary anew - take 2
Bindu Gajria
committed
typo in MSPeptideSummary - take 3
Bindu Gajria
committed

Commits on Jan 8, 2025

clean up for MSPeptideSummary
Bindu Gajria
committed
uncomment GenomicsInternalHyperlink
Bindu Gajria
committed
fix the SQL for MassAssay
Bindu Gajria
committed
fix GenesByMassSpec SQL
Bindu Gajria
committed
fix SQL for MassSpec gene table
Bindu Gajria
committed

Commits on Jan 9, 2025

InterPro gene table SQL fixed
Bindu Gajria
committed

Commits on Jan 13, 2025

add missing $prefix
sufenhu
committed
fix for GeneVQ.DomainAccession SQL
Bindu Gajria
committed
fix for GenesByInterproDomain query
Bindu Gajria
committed
Merge branch 'webdb_workflow' of github.com:VEuPathDB/ApiCommonModel into webdb_workflow
Bindu Gajria
committed
REMOVE InterproResults tuning table, as it is NOT needed anymore
Bindu Gajria
committed

Commits on Jan 14, 2025

Ininiated a branch for to test iedb epitopes
sybah2
committed
add version param for signalP
Bindu Gajria
committed
fix GenesWithSignalPeptide query
Bindu Gajria
committed
fix SignalP gene table
Bindu Gajria
committed
remove EST records, attr + tables
Bindu Gajria
committed
remove GenesByESTOverlap Q
Bindu Gajria
committed
Besides the two BLAST similarity Qs, delete all other EST Questions
Bindu Gajria
committed
assign PlasmoDB (and UniDB) version 70.2 for now
Bindu Gajria
committed

Commits on Jan 15, 2025

Updated the gene queries, params, question and record for the iedb epitope
sybah2
committed
Updated the geneQueries.xml withe distinct
sybah2
committed
assign PlasmoDB (and UniDB) version 70.1
Bindu Gajria
committed
uncommit TranscriptGenomicSequence
Bindu Gajria
committed
comment a transcript Attr TO FIX later
Bindu Gajria
committed

Commits on Jan 16, 2025

Updated tyhe iedb organism prams and gene queries
sybah2
committed
fix SQL for MSModifiedPeptideSummary;
Bindu Gajria
committed
comment out TranscriptGenomicSequence again; MUST FIX
Bindu Gajria
committed
fix MSTranscriptSummary SQL
Bindu Gajria
committed

Commits on Jan 17, 2025

Commits on Jan 21, 2025

fix MassAssay param SQL (handle issue of concatenation with NULL string)
Bindu Gajria
committed

Commits on Jan 22, 2025

fix definition of MSModifiedPeptideSummary
Bindu Gajria
committed
fix SQL having "HAVING [condtion]
Bindu Gajria
committed
fix PTMAssay SQL
Bindu Gajria
committed

Commits on Jan 23, 2025

Revert "remove EST records, attr + tables"
Bindu Gajria
committed
BUSCO data not loaded yet; so commenting out those attributes for now; TO BE FIXED
Bindu Gajria
committed
uncomment Organism record/attr/table files
Bindu Gajria
committed
Updated the geneQestions, geneTabbleQuries and associated params for iedb tables
sybah2
committed
Update the organismParams for the iedb epitopes
sybah2
committed
fix org query results by restricting results with project_id
Bindu Gajria
committed
fix typos
Bindu Gajria
committed
fix org params, by restricting results with project_id
Bindu Gajria
committed

Commits on Jan 24, 2025

fix PdbSimilarity defintion
Bindu Gajria
committed
remove unneeded index from PdbSimilarity
Bindu Gajria
committed

Commits on Jan 28, 2025

Updated the Oragnism param for the iedp and description of the IEDB page and the params for the search.
sybah2
committed

Commits on Jan 29, 2025

fix for MassSpecMod table
Bindu Gajria
committed
fix SQL of Profile table. In brief, study and studyLink tables have been essentially replaced by nodeSet and nodeNodeSet in the Study schema
Bindu Gajria
committed

Commits on Jan 30, 2025

fix SQL of ProfileSamples and ExpressionGraphsData table
Bindu Gajria
committed
minor fix for ProfileSamples
Bindu Gajria
committed
fix typo
Bindu Gajria
committed
fix SQL of ExpressionGraphsData table
Bindu Gajria
committed
Merge branch 'webdb_workflow' into iedb_epitopes_sy
jbrestel
authored
Merge pull request #53 from VEuPathDB/iedb_epitopes_sy
jbrestel
authored

Commits on Jan 31, 2025

Updated the organismParam.xml for the IEDB epitope
sybah2
committed

Commits on Feb 2, 2025

switching Plasmo & Uni to buildNumber 70.2 (sites to point to UniDB_shu_B)
Bindu Gajria
committed

Commits on Feb 3, 2025

cleanup, i.e remove "from dual" in dst files
Bindu Gajria
committed
Merge pull request #55 from VEuPathDB/iedb_epitopes_sy
sybah2
authored
Added new TrackConfig modules for Pbrowse tracks
Paul Wilkinson
committed
Added new track objects for protein browser
Paul Wilkinson
committed
Edited Store classes and Track Config for Pbrowse tracks
Paul Wilkinson
committed
fix typo
Bindu Gajria
committed
Merge branch 'webdb_workflow' of github.com:VEuPathDB/ApiCommonModel into webdb_workflow
Bindu Gajria
committed

Commits on Feb 4, 2025

fix the modification_site for MassSpecMod table
Bindu Gajria
committed
replace unsuppoorted REGEXP_SUBSTR with SPLIT_PART in SQL, for various Graph tables
Bindu Gajria
committed
Updated iedb geneRecord and geneTableQuries
sybah2
committed
Merge branch 'webdb_workflow' of github.com:VEuPathDB/ApiCommonModel into webdb_workflow
sybah2
committed
remove EstsBySimilarity query
Bindu Gajria
committed
Merge branch 'webdb_workflow' of github.com:VEuPathDB/ApiCommonModel into webdb_workflow
Bindu Gajria
committed
remove EstsBySimilarity question
Bindu Gajria
committed
fix import to allow for EST Blast
Bindu Gajria
committed

Commits on Feb 5, 2025

update PdbSumilarity table
Bindu Gajria
committed
fix PdbSimilarities gene table
Bindu Gajria
committed
fix PdbSimilarities query
Bindu Gajria
committed
fix SQL error in CellularLocalization (for tryp)
Bindu Gajria
committed
GenesByLopit to be FIXED for tryp, and unified
Bindu Gajria
committed
BUSCO data not loaded yet; so commenting out those attributes for Tryp + Vect too; TO BE FIXED
Bindu Gajria
committed

Commits on Feb 6, 2025

fix typo
Bindu Gajria
committed
fix the "all" organism SQL, which had a "CONNECT BY prior"
Bindu Gajria
committed
moving Tryp and VB also to postgres version
Bindu Gajria
committed

Commits on Feb 7, 2025

COMMENT out : TEMPLATE_ANCHOR metaCycleQuestion for now, and the not-injected (why?) Galinski_Mmulatta_Infected_with_Pcynomolgi_* questions
Bindu Gajria
committed
BUSCO data not loaded yet; so commenting out those attributes for UniDB
Bindu Gajria
committed
minor fix
Bindu Gajria
committed
Remove explicit tablespace declarations from DDLs for postgres.
mvnural
committed
first pass for fixing profileAttributeQueriesStrandSpecificRNASeq and profileAttributeQueries DST params
Bindu Gajria
committed
Merge branch 'webdb_workflow' of github.com:VEuPathDB/ApiCommonModel into webdb_workflow
Bindu Gajria
committed
allow injectTemplates again, BUT just for one dataset
Bindu Gajria
committed
add node_type column to Profile table
Bindu Gajria
committed

Commits on Feb 9, 2025

add node_type column to Profile table - fix sql
Bindu Gajria
committed
add node_type column to Profile table - fix sql 2
Bindu Gajria
committed
add node_type column to ProfileType and ProfileSamples tables
Bindu Gajria
committed

Commits on Feb 10, 2025

fix SQL for rnaseq FC and Percentile profile params
Bindu Gajria
committed
fix RnaSeqStats tuning table
Bindu Gajria
committed
fix RnaSeqStats tuning table; fix typos
Bindu Gajria
committed

Commits on Feb 11, 2025

fix hardFloorRnaSeq param sql
Bindu Gajria
committed
FIX for GenesByRnaSeqFoldChange - omg! looks ok.
Bindu Gajria
committed
fix rnaSeqPctProfileSetParamQuery query
Bindu Gajria
committed
Branch to update the the Iedb front end searches
sybah2
committed

Commits on Feb 12, 2025

Commits on Feb 13, 2025

fix "profile_set_names" query correctly!
Bindu Gajria
committed
space char needed
Bindu Gajria
committed

Commits on Feb 14, 2025

Commits on Feb 17, 2025

Commits on Feb 19, 2025

Commits on Feb 21, 2025

add PostgreSQL db driver for DBI module
Bindu Gajria
committed

Commits on Feb 24, 2025

commented out setDisplayMode as compact
Paul Wilkinson
committed
setViewDetailsContent to NA
Paul Wilkinson
committed
Added getters and setters for BaseUrl
Paul Wilkinson
committed
Added getters and setters for BaseUrl and fixed StoreType
Paul Wilkinson
committed
Changed hard coded relativePathToGffFile to UniDB path
Paul Wilkinson
committed

Commits on Feb 26, 2025

use build num 70 for pg sites
bindu
committed
cache not done; commenting for now
bindu
committed
cache not done; commenting for now
bindu
committed
fix path to gff dir
bindu
committed
fix sql to be pg-compatible
bindu
committed
file formatting fix
bindu
committed
fix path error
bindu
committed
comment out stuff to do with CACHE
bindu
committed
TODO - COMMENT out longRead track for now
bindu
committed
TODO - COMMENT out dnaseq and rnaseq junctions tracks for now
bindu
committed