Open fbastian opened 4 years ago
In GitLab by @fbastian on Jul 3, 2018, 14:34
changed the description
In GitLab by @fbastian on Jul 3, 2018, 14:38
@vrechdelaval: to check before merge. @jwollbrett will make the merges into develop
accept-other-ids
gene-list-msg
issue_109
topanat_3
@jwollbrett: to check before merge. Either @vrechdelaval or @fbastian makes the merges.
rank_file
uniprotXref
:
BGEE
CommandGene
into CallService
To be merged by @vrechdelaval into develop
:
bgee_lite
(JW): sub-database of bgee for biosoda
hotfix_rankComparator
: @jwollbrett adds a test and merges into develop
In GitLab by @vrechdelaval on Jul 10, 2018, 16:35
I did the code review on bgee_lite
. @jwollbrett has some modifications to do before I can merge it into develop
In GitLab by @fbastian on Jul 23, 2018, 14:43
Merge the branch raw_data
into develop
before merging the branch review_bgee_v14
: raw_data
has been created from develop
, and review_bgee_v14
has been merged into it, so that some conflicts were already resolved. It will be easier for merging the following modifications made into review_bgee_v14
.
In GitLab by @jwollbrett on Jul 24, 2018, 15:23
Create new branch generate_rank_files
from develop and merge rank_file
and uniprotXref
into it.
This new branch contains :
Branches rank_file
and uniprotXref
have been deleted.
@vrechdelaval can do the code review for branch generate_rank_files
.
I did all modifications asked by @vrechdelaval for the branch bgee_lite
. @vrechdelaval should be able to merge it in develop
In GitLab by @vrechdelaval on Jul 30, 2018, 15:23
gene-list-msg
, issue_109
and topanat_3
has been updated for Bgee 14 and merged into topanat_issues
(created from develop
). Same work is in progress for accept-other-ids
In GitLab by @vrechdelaval on Aug 7, 2018, 11:03
I merged bgee_lite
into develop
and I deleted the branch
In GitLab by @vrechdelaval on Oct 3, 2018, 15:19
The branch improve-webapp
includes following modifications:
The code review will be done by @jwollbrett. He will merge improve-webapp
into develop
.
@fbastian will merge develop
into master
.
Other modifications in develop
that will be merged into master
with this merge:
OMANodeId
/OMAGroupId
in the database schemaIn GitLab by @jwollbrett on Jan 23, 2019, 13:21
I merged improve-webapp
into develop
and I deleted the improve-webapp
branch.
In GitLab by @fbastian on Feb 13, 2019, 17:57
I merged develop
into master
, see https://gitlab.isb-sib.ch/Bgee/bgee_apps/issues/191#note_8455 for changes included. Issue #207 was opened following the merge.
In GitLab by @fbastian on Feb 20, 2019, 16:22
changed the description
In GitLab by @fbastian on Mar 1, 2019, 19:21
changed the description
In GitLab by @jwollbrett on May 6, 2019, 17:35
I merged sphinx-dev
into develop
.
It will be possible to close 4 issues when develop is merged to master (#81, #158, #181, #183) :smiley_cat:
In GitLab by @vrechdelaval on May 21, 2019, 15:40
changed the description
In GitLab by @vrechdelaval on Jul 10, 2019, 11:09
@jwollbrett @fbastian It seems that I finished with schema.org (https://gitlab.isb-sib.ch/Bgee/bgee_apps/issues/203). The branch is bioschemas-final
. It includes the species pages (#216).
In GitLab by @vrechdelaval on Jul 15, 2019, 16:32
@jwollbrett @fbastian I did the export of expression comparison table (#215) in branch expr-comp-export
. But I merged it with bioschemas-final
into species-schema-export
to be able to deploy both on devbgee.
In GitLab by @vrechdelaval on Jul 16, 2019, 14:01
When Bioschemas markups will be in prod, we should add Bgee DataDatalog into Bioschemas (see https://gitlab.isb-sib.ch/Bgee/bgee_apps/issues/217)
In GitLab by @jwollbrett on Oct 9, 2019, 12:27
In order to deploy a new version of the webapp I created a new branch called species-schema-export_expr_scrore
based on develop. I merged 2 branches in it :
species-schema-export
containing export of expression comparison and bioschemas.expr_score
containing a new expression score metric normalized across species with values between 0 and 100.I solved a bug in the sorting approach of expression comparison tables, updated some schemas markup in order to fit recommandations (using https://search.google.com/structured-data/testing-tool/ ), and updated the news section
The new version of the webapp has been tested on devbioinfo and then deployed on prod.
Finally I merged this branch with develop and removed all branches not used anymore.
anat_entity_page: JW checks to keep it or not
issue_178: JW checks
issue_98: JW checks. Update: in progress, source of the inconsistencies between topGO and our code identified (see https://github.com/BgeeDB/bgee_apps/issues/227#issuecomment-676198708 and https://github.com/BgeeDB/bgee_apps/issues/227#issuecomment-676274311). Need to wait for correction of relations in database with Bgee 14.2.
master_using_global_ranks, master_using_global_ranks_display_all_calls: FB; global/self ranks: in static attribute; organ minimum or average on gene page: for now it's hardcoded in CommandGene, can stay like that, or code preparation for average; all/observed calls as an attribute of the display method
correct_uberon: FB reviews/merges it
hotfix_webapp: ongoing work to be released. Update: done, merged into develop, then deleted.
bgee_v14_OMAHierarchicalGroup: JW and FB will discuss it
topanat_issues: finish the gene list message, problem that the popover is not displayed. FB: merge into a new branch from develop, and see if it works. Update: merged using bgee_v14_topanat_issues, everything works now except the gene list message. It's because the Angular code injected need to be compiled to work (see https://www.timsommer.be/using-compile-to-compile-html-strings-in-angular/). I don't do it now since the branch accept-other-ids makes lots of change to gene list message. Update2: merged bgee_v14_accept-other-ids into bgee_v14_topanat_issues, this indeed fixes the problem of gene list message. Update3: branch merged into develop then deleted
~~accept-other-ids: FB: merge into a new branch from develop, and see if it works => then try to adapt accept-other-ids and topanat_issues => accept-other-ids is not accepting gene names. Update: merged using bgee_v14_accept-other-ids, then merged into bgee_v14_topanat_issues, then merged into develop and deleted.~~
multi-sp-expr-2: what do we do?
bastien and bastien_master to delete after his master
In GitLab by @vrechdelaval on Jul 3, 2018, 13:41
CURRENT BRANCHES:
accept-other-ids
(VRDL): voir #92 Other IDs than Ensembl. Je n’ai jamais fini de tester cette fonctionnalité, elle est basée sur Bgee 13, elle ne doit pas être mergée. To keep.anat_entity_page
(JW): #151 First step to an anatomical entity page Implémentation non finie basée sur Bgee 13, elle ne doit pas être mergée. To keep.bgee_v14_OMAHierarchicalGroup
(JW). Currently ongoing work. To keep.gene-list-msg
(VRDL): voir #119 Various display improvements « number of genes found in the found species and a tooltip with details »; Implémentation non finie selon l’issue, elle ne doit pas être mergée.issue_109
(VRDL): #109 topanat stage selection Move stage selection to advanced options, allow to query all stages in one analysis. has been merged to topanat_issuesissue_98
(MS): voir #98 Make TopAnat super-fast when used with no decorrelation, basé sur Bgee 13: some work to base it on bgee 14, maybe not the highest priority.multi-sp-expr-2
(VRDL): début de l’implémentation de la génération des fichiers multi-species : implémentation des beans avec supercsv, basée sur Bgee 13: containsBean
s that might be useful, but complicated to merge for now. Maybe it will be easier once the branchbgee_v14_multispecies
is completed? We keep it for now.test_topanat_conditions_graph
(FB): basées sur Bgee 13. Seul commit 96de0b4 : « quick and dirty implementation of TopAnat on graph of Conditions. Not to be used in prod! ». Just a test of feasibility. To keep.topanat_3
(FB): corrections de topanat-web/issue#130 Trigger reload of the page when clicking on a "recent job" et topanat-web/issues#126 Adapt table rows to number of results basées sur Bgee 13OLD BRANCHES:
bgee_v14_multispecies
(JW): contient le code des multi-species calls basé sur bgee_14, to keep. has been deleted and merged intoreview_rawdata_genestats_fixtests_oncomxnewfile_multispecies
(well, a branch calledmultispecies
has been merged, I guess it was branchbgee_v14_multispecies
merged into a branch created fromdevelop
)fix_tests
(all). Currently ongoing work. To keep. Fred: bgee-dao-api, bgee-dao-sql; Julien: bgee-core; Valentine: bgee-webapp; has been deleted and merged intoreview_rawdata_genestats_fixtests_oncomxnewfile
improve-webapp
: currently ongoing work; to keep. has been deleted/mergedrank_file
(JW): currently ongoing work. has been deleted/mergedreview_bgee_v14
: this branch has been deleted and merged intoreview_rawdata_genestats_fixtests_oncomxnewfile
has been deleted and merged intodevelop
uniprotXref
(JW): correction du fichier des xref pour UniProt. Almost done. has been deleted and mergedreview_rawdata_genestats_fixtests_oncomxnewfile
: includes the former branchreview_bgee_v14
, plus beginning of work on raw data, generation of statistics on genes (originally for OncoMX), generation of a new download file for OncoMX, and the branchfix_tests
. I guess it's ready to be merged intodevelop
, I haven't noticed any bad effect from the merge of the ongoing work inraw_data
has been deleted and merged intodevelop
review_rawdata_genestats_fixtests_oncomxnewfile_multispecies
: same as previous branch, + merge of branchbgee_v14_multispecies
(well, merge of a branch calledmultispecies
, I guess it was branchbgee_v14_multispecies
merged into a branch created fromdevelop
) has been deleted and merged intodevelop
issue108
(FB): voir #108 View generation, début de React: big work, maybe someday. has been deleted, was too old and useless