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BgeeDB / bgee_apps

Source code of the Java Bgee applications
https://www.bgee.org/
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Release Bgee 14.0 #174

Open fbastian opened 4 years ago

fbastian commented 4 years ago

In GitLab by @fbastian on Jan 22, 2018, 16:23

We need to prepare Bgee for release 14.0 (or .1?). Things that come to my mind:

fbastian commented 4 years ago

In GitLab by @vrechdelaval on Jan 22, 2018, 16:39

We should check that issue #155 (Fixes for topanat v13 and v14)

fbastian commented 4 years ago

In GitLab by @smoretti on Jan 23, 2018, 13:55

Add a way to have the current year for the copyright instead of hard-coded it.

Currently hard-coded "2018" in src/main/java/org/bgee/view/html/HtmlParentDisplay.java

Use int year = Calendar.getInstance().get(Calendar.YEAR); instead of hard-coded year

fbastian commented 4 years ago

In GitLab by @smoretti on Jan 23, 2018, 14:39

Also #170 & #166

fbastian commented 4 years ago

In GitLab by @smoretti on Jan 24, 2018, 17:03

Check also #173

fbastian commented 4 years ago

In GitLab by @vrechdelaval on Jan 30, 2018, 16:47

mentioned in commit 6aff9175509af66f2916f5e4a90bc32616b4e7db

fbastian commented 4 years ago

In GitLab by @vrechdelaval on Jan 30, 2018, 16:47

put somewhere some "archive" links?

"Archive" links are already present on the home page (bottom right)

removal of all "beta" stuff

If I'm not mistaken, there are only 2 "beta": image and version (both in hero). Commit 2383bb2 fixes management of version in webapp using bgee.properties file and commit 6aff9175 updates image and version number

fbastian commented 4 years ago

In GitLab by @fbastian on Feb 5, 2018, 18:51

Note to self TODO:

fbastian commented 4 years ago

In GitLab by @smoretti on Feb 6, 2018, 13:06

copy the request parameters of Bgee 13 to Bgee 14 folder

Has to be done with rsync as we did during last production server switch.

fbastian commented 4 years ago

In GitLab by @fbastian on Feb 6, 2018, 13:08

Ha yes, but also I simply need to copy them in the bgee 14 folder on bioinfo.

fbastian commented 4 years ago

In GitLab by @fbastian on Feb 7, 2018, 14:22

TODO: generate download file archives in .gz rather than .zip

fbastian commented 4 years ago

In GitLab by @fbastian on Feb 7, 2018, 14:23

TODO: change minify version number both for bgee 13 and 14.

fbastian commented 4 years ago

In GitLab by @fbastian on Feb 13, 2018, 01:13

Remaining TODOs:

fbastian commented 4 years ago

In GitLab by @vrechdelaval on Feb 13, 2018, 11:28

fbastian commented 4 years ago

In GitLab by @vrechdelaval on Feb 13, 2018, 12:00

Edit: fixed by 34b36e1

fbastian commented 4 years ago

In GitLab by @fbastian on Feb 13, 2018, 12:25

The example 3 not working: it's because the parameter data_qual can now takes the values bronze/silver/gold, and not anymore low/high. I copied the requestParameters files from bgee 13 to bgee 14 for maximum compatibility (so that people can still find the analyses they made in the past).

Either I remove all requestParameters file containing the parameter data_qual, or I try to replace in these files data_qual=high with data_qual=gold. Any good unix command to do it, anybody? :p

fbastian commented 4 years ago

In GitLab by @vrechdelaval on Feb 13, 2018, 12:56

replace in these files data_qual=high with data_qual=gold

To replace all occurrences in all files in the current directory sed 's/data_qual=high/data_qual=gold/g' * should work.
You can edit files in-place, saving backups with the specified extension using option -i <extension> (e.g. sed -i .bck 's/data_qual=high/data_qual=gold/g' *)

fbastian commented 4 years ago

In GitLab by @jwollbrett on Feb 13, 2018, 13:04

if you want to replace recursively this command should work find ./ -type f -name "*.file_extension" -exec sed -i 's/data_qual=high/data_qual=gold/g' {} \;

fbastian commented 4 years ago

In GitLab by @fbastian on Feb 13, 2018, 13:07

Actually I realize that changing this value would normally change the hash used to name the file storing the parameters. So we have an incompatibility of requestParameters between bgee 13 and 14, and I should not simply search/replace them.

I think the solution is to not copy the requestParameters files containing data_qual=high.

=> users who used a high data quality won't be able to retrieve parameters of an analysis in Bgee 14 by using a link generated on Bgee 13. I think it's the cleanest solution, but inconvenient for users. What do you think? Ping @marcrr

fbastian commented 4 years ago

In GitLab by @jwollbrett on Feb 13, 2018, 13:19

I tried to run a topAnat analysis with a pvalue threshold equals to 0.5. The result table still contains pvalue <= 1 https://rbgee.unil.ch/?page=top_anat#/result/f16a1045d236cd2d56939852332019e5b98f3f74/

fbastian commented 4 years ago

In GitLab by @fbastian on Feb 13, 2018, 13:26

I tried to run a topAnat analysis with a pvalue threshold equals to 0.5. The result table still contains pvalue <= 1 https://rbgee.unil.ch/?page=top_anat#/result/f16a1045d236cd2d56939852332019e5b98f3f74/

Ha yeah, funny, the threshold is taken into account to count the results, but not to actually filter them. I guess the problem is also present in the R package. See #178

fbastian commented 4 years ago

In GitLab by @marcrr on Feb 13, 2018, 14:33

users who used a high data quality won't be able to retrieve parameters of an analysis in Bgee 14 by using a link generated on Bgee 13. I think it's the cleanest solution, but inconvenient for users. What do you think?

Do we have a choice? ;)

Could we propose a link to TopAnat in Bgee13 or a generation of a new computation with high replaced by gold?

Also: how many / what %% of conserved analyses are with data quality high?

fbastian commented 4 years ago

In GitLab by @fbastian on Feb 13, 2018, 15:09

Actually I think of a solution for backward compatibility of this parameter.

fbastian commented 4 years ago

In GitLab by @jwollbrett on Feb 13, 2018, 16:59

fbastian commented 4 years ago

In GitLab by @fbastian on Feb 14, 2018, 01:07

Ha yes, you're right @jwollbrett. I don't think I will change that before the release.

Otherwise:

example 3 doesn't work

Fixed. I managed to make the data_qual parameter backward compatible.

In TopAnat result, we can have BGEE:0 (root)

Not fixed. Yep it's not an actual Uberon term, just a fake single root that we add to the ontology for TopAnat to work. We could filter it out. It appears only if FDR threshold is set to 1.

At the bottom, if the source is Bgee, the link is not https. Should we need to fix dataSource table?

Fixed (almost). I changed the value in the SQL file in bgee_pipeline. But I'm too lazy to update it in the database and to regenerate a dump.

in menu Download -> BgeeDB R package links to ...

Fixed.

should we replace mrr group page

No, we own the bioinfo @ unil :D

I let this issue open until remaining points of https://gitlab.isb-sib.ch/Bgee/bgee_apps/issues/172#note_7159 are addressed.

fbastian commented 4 years ago

In GitLab by @jwollbrett on Jul 24, 2018, 16:14

Some points of https://gitlab.isb-sib.ch/Bgee/bgee_apps/issues/172#note_7159 have been adressed :