EBIvariation/eva-common-pyutils issues and pull requests

#59 - EVA-3622 - Add option to return only the text of a Biosample query

Pull Request - State: closed - Opened by tcezard about 2 months ago

#58 - EVA-3604 - contig alias get methods

Pull Request - State: closed - Opened by tcezard 2 months ago

#57 - EVA-3624: Add biosamples communicators

Pull Request - State: closed - Opened by apriltuesday 3 months ago

#56 - Change properties file generating to new accessioning/clustering

Pull Request - State: closed - Opened by tcezard 5 months ago

#55 - Additional requests to NCBI with API key

Pull Request - State: closed - Opened by tcezard 6 months ago

#54 - Limit failure during requests to NCBI API

Pull Request - State: closed - Opened by tcezard 6 months ago

#53 - EVA-3403 Check port forwarding is running

Pull Request - State: closed - Opened by tcezard 6 months ago

#52 - Change to mongo 6 and update the executable name

Pull Request - State: closed - Opened by tcezard 6 months ago

#51 - EVA-3438 - Allow command to output a variable log level

Pull Request - State: closed - Opened by tcezard 7 months ago

#50 - EVA-3335 - Resolve patch assemblies to proper assembly code

Pull Request - State: closed - Opened by sundarvenkata-EBI 11 months ago

#49 - EVA-3414 add Writable config script

Pull Request - State: closed - Opened by nitin-ebi 12 months ago

#48 - EVA-3322 - refactor

Pull Request - State: closed - Opened by tcezard about 1 year ago

#47 - EVA-3322 - Proposal for refactor of pyutils

Pull Request - State: closed - Opened by tcezard about 1 year ago - 1 comment

#46 - EVA-3378 read scientific name from evapro db

Pull Request - State: closed - Opened by nitin-ebi about 1 year ago - 1 comment

#45 - EVA-3386: Check Ensembl rapid release for supported assemblies

Pull Request - State: closed - Opened by apriltuesday about 1 year ago

#44 - EVA-3362 scientific name fixes

Pull Request - State: closed - Opened by nitin-ebi about 1 year ago

#43 - Use scientific name when no common name is available

Pull Request - State: closed - Opened by tcezard about 1 year ago

#42 - EVA-3298 - Update release properties generation

Pull Request - State: closed - Opened by apriltuesday over 1 year ago

#41 - Prevent log duplication when importing modules

Pull Request - State: closed - Opened by tcezard over 1 year ago

#40 - EVA-2637 mongo username and password should be retained in property file when they are null/empty

Pull Request - State: closed - Opened by nitin-ebi over 1 year ago

#39 - EVA-3253 - Support multiple mongos hosts in properties generation

Pull Request - State: closed - Opened by sundarvenkata-EBI over 1 year ago

#38 - EVA-3243: adding missing job tracker db details for accession import job

Pull Request - State: closed - Opened by nitin-ebi over 1 year ago

#37 - EVA-3208 - Add methods in assembly and metadata utils

Pull Request - State: closed - Opened by sundarvenkata-EBI over 1 year ago

#36 - EVA-3147: added properties for variant load and accession import jobs

Pull Request - State: closed - Opened by nitin-ebi over 1 year ago - 1 comment

#35 - EVA-3172 Spring properties refactor

Pull Request - State: closed - Opened by tcezard over 1 year ago

#34 - EVA-3096 - Get accession db from settings in properties generator

Pull Request - State: closed - Opened by apriltuesday almost 2 years ago

#33 - Add script to archive folder

Pull Request - State: closed - Opened by tcezard almost 2 years ago - 1 comment

#32 - EVA-3050 - Library methods to support assembly ingestion processing

Pull Request - State: closed - Opened by apriltuesday almost 2 years ago

#31 - set sensible defaults on mongo clients

Pull Request - State: closed - Opened by apriltuesday almost 2 years ago

#30 - EVA-3012: Refactor functions to add assembly and taxonomy to pyutils

Pull Request - State: closed - Opened by tcezard about 2 years ago

#29 - Allow nextflow pipeline to be joined without dependencies

Pull Request - State: closed - Opened by tcezard about 2 years ago

#28 - Fix test

Pull Request - State: closed - Opened by tcezard over 2 years ago

#27 - Adding function to config_utils for retrieving the creds for contig_alias db

Pull Request - State: closed - Opened by itsroops over 2 years ago - 2 comments

#26 - EV-2766 - Add new function to retrieve the taxonomy info from NCBI

Pull Request - State: closed - Opened by tcezard over 2 years ago

#25 - Add function to get count service credentials from maven profile

Pull Request - State: closed - Opened by andresfsilva over 2 years ago

#24 - Adding file handler function

Pull Request - State: closed - Opened by itsroops over 2 years ago

#23 - Fix query and retrieval

Pull Request - State: closed - Opened by tcezard almost 3 years ago

#22 - EVA-2308 - Variant warehouse db name

Pull Request - State: closed - Opened by tcezard about 3 years ago

#21 - EVA-2517 - Extract normalisation function for scientific names

Pull Request - State: closed - Opened by tcezard about 3 years ago

#20 - EVA-2448 - Refactor database credential access

Pull Request - State: closed - Opened by apriltuesday about 3 years ago

#19 - EVA-2469 - Make assembly report download more reliable

Pull Request - State: closed - Opened by sundarvenkata-EBI over 3 years ago - 1 comment

#18 - EVA-2429 - script for incremental migration - adding import, export, get_pg_uri f functions

Pull Request - State: closed - Opened by nitin-ebi over 3 years ago

#17 - EVA-2364 download single sequence

Pull Request - State: closed - Opened by tcezard over 3 years ago

#16 - EVA-2389 - Support generating and running non-linear Nextflow pipelines

Pull Request - State: closed - Opened by sundarvenkata-EBI over 3 years ago

#15 - EVA-2369 - Added Data Archive Method

Pull Request - State: closed - Opened by nitin-ebi over 3 years ago - 1 comment

#14 - EVA-2338 - Add object models for Mongo instance and Nextflow pipeline

Pull Request - State: closed - Opened by sundarvenkata-EBI over 3 years ago

#13 - EVA-2252 Get database name

Pull Request - State: closed - Opened by andresfsilva over 3 years ago

#12 - EVA-2115 - Add a configuration reader

Pull Request - State: closed - Opened by tcezard almost 4 years ago

#11 - EVA-2210 - Added function to get normalized scientific name from Ensembl

Pull Request - State: closed - Opened by sundarvenkata-EBI almost 4 years ago

#10 - Refined search for genome folder

Pull Request - State: closed - Opened by tcezard almost 4 years ago

#9 - EVA-1729 - Fix the port forwarding order - local comes first

Pull Request - State: closed - Opened by sundarvenkata-EBI about 4 years ago

#8 - EVA-2132 - genome downloader

Pull Request - State: closed - Opened by tcezard about 4 years ago - 1 comment

#7 - EVA-2150 - Changes to support the ticket

Pull Request - State: closed - Opened by sundarvenkata-EBI about 4 years ago - 1 comment

#6 - EVA-2115 Add methods to read properties from a settings xml and download the eva settings

Pull Request - State: closed - Opened by andresfsilva about 4 years ago

#5 - EVA-2150 - Changes to support the ticket

Pull Request - State: closed - Opened by sundarvenkata-EBI about 4 years ago

#4 - EVA-2086 - Updates made to support validation scripts

Pull Request - State: closed - Opened by sundarvenkata-EBI about 4 years ago

#3 - EVA-1729 - Refactored common functions in the release automation scripts into utilities

Pull Request - State: closed - Opened by sundarvenkata-EBI about 4 years ago

#2 - Revert "EVA-1729 - Refactored common functions in the release automation scripts into utiliities"

Pull Request - State: closed - Opened by sundarvenkata-EBI about 4 years ago

#1 - EVA-1729 - Refactored common functions in the release automation scripts into utiliities

Pull Request - State: closed - Opened by sundarvenkata-EBI about 4 years ago

GitHub / EBIvariation/eva-common-pyutils issues and pull requests