Branches to merge

[fbastian]

In GitLab by @vrechdelaval on Jul 3, 2018, 13:41

CURRENT BRANCHES:

• accept-other-ids (VRDL): voir Make the webapp to use the R scripts from bgee-core #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): TopAnat on strains #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 Redirect from Uniprot ID to gene page #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): Update documentation after regenerating download files #109 topanat stage selection Move stage selection to advanced options, allow to query all stages in one analysis. has been merged to topanat_issues
• issue_98 (MS): voir expressologs: find genes in another species with similar expression patterns #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: contains Beans that might be useful, but complicated to merge for now. Maybe it will be easier once the branch bgee_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 13

OLD BRANCHES:

• bgee_v14_multispecies (JW): contient le code des multi-species calls basé sur bgee_14, to keep. has been deleted and merged into review_rawdata_genestats_fixtests_oncomxnewfile_multispecies(well, a branch called multispecies has been merged, I guess it was branch bgee_v14_multispecies merged into a branch created from develop)
• 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 into review_rawdata_genestats_fixtests_oncomxnewfile
• improve-webapp: currently ongoing work; to keep. has been deleted/merged
• rank_file (JW): currently ongoing work. has been deleted/merged
• review_bgee_v14: this branch has been deleted and merged into review_rawdata_genestats_fixtests_oncomxnewfile has been deleted and merged into develop
• uniprotXref (JW): correction du fichier des xref pour UniProt. Almost done. has been deleted and merged
• review_rawdata_genestats_fixtests_oncomxnewfile: includes the former branch review_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 branch fix_tests. I guess it's ready to be merged into develop, I haven't noticed any bad effect from the merge of the ongoing work in raw_data has been deleted and merged into develop
• review_rawdata_genestats_fixtests_oncomxnewfile_multispecies: same as previous branch, + merge of branch bgee_v14_multispecies (well, merge of a branch called multispecies, I guess it was branch bgee_v14_multispecies merged into a branch created from develop) has been deleted and merged into develop
• issue108 (FB): voir species common names #108 View generation, début de React: big work, maybe someday. has been deleted, was too old and useless

[fbastian]

In GitLab by @fbastian on Jul 3, 2018, 14:34

changed the description

[fbastian]

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:
  • change capital BGEE
  • refactor code from 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

[fbastian]

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

[fbastian]

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.

[fbastian]

In GitLab by @jwollbrett on Jul 24, 2018, 15:23

Create new branch generate_rank_filesfrom develop and merge rank_file and uniprotXref into it.
This new branch contains :

• code for generation of Uniprot XRefs
• code for generation of rank files for Monarch Initiative
• refactored code from CommandGene and GenerateUniprotXRefWithExprInfo into CallService

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

[fbastian]

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

[fbastian]

In GitLab by @vrechdelaval on Aug 7, 2018, 11:03

I merged bgee_lite into develop and I deleted the branch

[fbastian]

In GitLab by @vrechdelaval on Oct 3, 2018, 15:19

The branch improve-webapp includes following modifications:

• Add GDPR banner and private policy page (issue to be closed Create a page "adopters" #141)
• Add FAQ page
• Add scroll on 'news' panel
• Add permanent link in footer
• Make visible that Bgee contains GTEx data (issue to be closed Update javascript libraries #186)
• Remove blog logo from menu
• Modify menu:
  • move 'Documentation/How to access Bgee data' to 'Download/Download overview'
  • move 'Documentation/Bgee blog' to 'About/Bgee blog'
  • move 'Documentation/Bgee sources' to 'About/Bgee sources'
  • add 'Documentation/GTEx in Bgee'
  • add 'Documentation/FAQ'
  • move 'About' to 'About/About Bgee'
  • add 'About/Bgee privacy notice'
• Fix issue Do not use p-value as a parameter of TopAnat analysis #196
• Fix issue Errors when pages are loaded (Firefox console) #187 (issue to be closed)
• Modify documentation link in download banners replacing 'i' by text
• Upgrade jQuery
• update of the download file documentation

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:

• Fix issue Problem with backslash in gene search #198
• Clarify the use of OMANodeId/OMAGroupId in the database schema
• Improvements of similarity annotation generation in bgee_pipeline
• bgee_lite generation

[fbastian]

In GitLab by @jwollbrett on Jan 23, 2019, 13:21

I merged improve-webapp into develop and I deleted the improve-webapp branch.

[fbastian]

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.

[fbastian]

In GitLab by @fbastian on Feb 20, 2019, 16:22

changed the description

[fbastian]

In GitLab by @fbastian on Mar 1, 2019, 19:21

changed the description

[fbastian]

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) 😺

[fbastian]

In GitLab by @vrechdelaval on May 21, 2019, 15:40

changed the description

[fbastian]

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).

[fbastian]

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.

[fbastian]

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)

[fbastian]

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.

[fbastian]

• 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 Uberon relation reductions in our pipeline #227 (comment) and Uberon relation reductions in our pipeline #227 (comment)). 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