Update Barcode Scanner #632

teravest · 2014-02-20T17:50:06Z

Addresses issue #626

This updates the barcode scanner to be able to edit the fields in the barcode table.

I also created a controlled vocabulary for the sequencing_status column.

I also rewrote a giant req.write in barcode_utils.psp so that it was in html instead of a string.

This add the ability to change biomass_remaining, sequencing_status and obsolete from the barcode scanner

ElDeveloper · 2014-02-21T00:21:40Z

Make a header for american gut vs the name of the project.
For biomass remaining change checkbox to drop down.
In the edit existing kit in the american gut utilities remove the project drop down.
Make project group table that determines where the project belongs to.
Add a column to project
Add a column to project_barcode

teravest · 2014-02-21T22:34:34Z

Ok all these changes should be made with the info we have right now.

ElDeveloper · 2014-02-21T22:35:24Z

👍

teravest · 2014-02-21T23:22:49Z

This is on webdev now :)

adamrp · 2014-02-21T23:29:59Z

Thanks!

On Fri, Feb 21, 2014 at 4:22 PM, teravest [email protected] wrote:

This is on webdev now :)

Reply to this email directly or view it on GitHubhttps://github.com//pull/632#issuecomment-35784374
.

adamrp · 2014-02-21T23:31:36Z

Minor aesthetic comment: can you change the <td> status rectangle (the thing that's green, red, purple, etc.) to have colspan=2 and align=center?

adamrp · 2014-02-21T23:41:22Z

metadata checker gets triggered regardless of project and/or project_group, so that should be conditional for AG at this point

adamrp · 2014-02-21T23:53:00Z

The default value for "Sequencing Status" in the database is NULL, so I think there needs to be an "unknown" (or "N/A" or something to that effect) option in that dropdown

adamrp · 2014-02-22T00:00:48Z

Many of the fields have a "Current: " next to them (I assume so that you can tell if you're changing something before you hit submit?), but others don't.

adamrp · 2014-02-22T00:01:40Z

Barcode 000007185 is office succession, but the checkbox or emailing says "Send kit owner an email" I might be mistaken, but I don't think that study has kits

adamrp · 2014-02-22T00:02:41Z

Not sure, but I think only projects in the AG project group currently work (do not have access to SQL developer atm)

teravest · 2014-02-24T15:10:23Z

I forgot the code to look up the barcode itself currently uses a stored procedure that looks in an american gut table. So this will only work with American Gut right now. I am going separate that into two stored procedures and only call the american gut one if it is an american gut barcode :)

teravest · 2014-02-24T22:52:33Z

Updates are deployed on Webdev
Here is a list of barcodes to test with. One from each project
000000001
000006136
000005074
000007185
000005038
000007869
000010307
000011423
000006020

teravest · 2014-03-03T17:03:44Z

Updated webdev again this morning.

adamrp · 2014-03-05T21:35:43Z

database/procedures/get_project_group.sql

+open group_name_ for
+select g.group_name from project_groups g inner join project p on g.group_id = p.group_id 
+where p.project = project_name;
+  null;


what's the null for? Doesn't appear to be in other SPs

uhg, I always forget to remove those. Its from the create new procedure thing on sql developer. I want to wait till tomorrow to do this so we don't lose it.

adamrp · 2014-03-05T22:00:00Z

www/wwwadmin/barcode_util.psp

+                                            form['obsolete_status'])
+            data_access.setBarcodeProjType(form['project'], prev_barcode)
+            req.write("General Barcode Information Updated<br>")
+        except:


Can you except a particular type of Exception here?

Do you guys know what type of exceptions the database throws?

Not offhand, might have to check cx_Oracle docs

ElDeveloper · 2014-03-06T20:30:07Z

@teravest not sure if this has to be part of this pull request, but I looked for barcode 000004595 and sent an e-mail, the e-mail came in as:

   In order to help you in adding these details, the side of the sample tube 000004595 reads:
      sample date: [Field('sample_date', ''), Field('sample_date', '')] 
      sample time: [Field('sample_time', ''), Field('sample_time', '')]

I'm looking at the code now.

ElDeveloper · 2014-03-06T20:31:14Z

python_code/data_access/qiime_data_access.py

+        con = self.getMetadataDatabaseConnection()
+        result = con.cursor()
+        con.cursor().callproc('get_sequencing_statuses', [result])
+        seq_statuses = [row[0] for row in result]


Can this fail with an IndexError and should this be caught?

I don't think so. Even if no rows are returned seq_statuses will end up as an empty list. And unless the procedure returns a row with zero fields (I don't think this is possible), row[0] will always exist. This might be the kind of place you'd use an assert, I guess, because these tests would be for things that should not be possible

Gotcha, thanks for the explanation.

ElDeveloper · 2014-03-06T21:29:16Z

ElDeveloper · 2014-03-06T21:29:24Z

Great stuff @teravest

I will deploy this to webdev after we deploy the mapmarker to live

…issue626barcodeseparate

adamrp · 2014-03-26T17:06:58Z

@teravest, is this ready to be merged?

teravest · 2014-03-26T17:07:58Z

no, I have some things to change and its gonna need another review and more
testing :(

On Wed, Mar 26, 2014 at 11:07 AM, adamrp [email protected] wrote:

@teravest https://github.com/teravest, is this ready to be merged?

Reply to this email directly or view it on GitHubhttps://github.com//pull/632#issuecomment-38710888
.

ElDeveloper · 2014-03-26T17:17:02Z

Fair enough, thanks @teravest

teravest added 8 commits February 14, 2014 15:37

separatating barcode edits

2bd9cd8

fixed indent

7d4f3fa

updates to barcode_util

a32ffb2

working version before refactoring barcode_utils

b6f3b05

partial refactor of barcode scanner

8e7716f

Update barcode scanner to edit barcode fields

8341715

This add the ability to change biomass_remaining, sequencing_status and obsolete from the barcode scanner

clean up qiime_data_access.py

97363ae

adding barcode status

d7a3683

teravest added 2 commits February 21, 2014 11:14

updated biomass and made headers for general vs project

f3316e2

added project group and display by project group

285d769

fixed separation of barcode vs project info

0152739

remove try except in favor of if statment

539f896

adamrp reviewed Mar 5, 2014
View reviewed changes

ElDeveloper reviewed Mar 6, 2014
View reviewed changes

teravest added 4 commits March 6, 2014 15:41

in the middle of addressing comments

4bb433e

changes based on review comments.

2f85224

I will deploy this to webdev after we deploy the mapmarker to live

Merge branch 'master' of https://github.com/qiime/qiime_web_app into …

58f2fa6

…issue626barcodeseparate

cleanup bugs and edit barcode

5d3d31d

fixed form name conflict

c3472f3

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Update Barcode Scanner #632

Update Barcode Scanner #632

teravest commented Feb 20, 2014

ElDeveloper commented Feb 21, 2014

teravest commented Feb 21, 2014

ElDeveloper commented Feb 21, 2014

teravest commented Feb 21, 2014

adamrp commented Feb 21, 2014

adamrp commented Feb 21, 2014

adamrp commented Feb 21, 2014

adamrp commented Feb 21, 2014

adamrp commented Feb 22, 2014

adamrp commented Feb 22, 2014

adamrp commented Feb 22, 2014

teravest commented Feb 24, 2014

teravest commented Feb 24, 2014

teravest commented Mar 3, 2014

adamrp Mar 5, 2014

teravest Mar 6, 2014

adamrp Mar 5, 2014

ElDeveloper Mar 6, 2014

teravest Mar 6, 2014

adamrp Mar 6, 2014

ElDeveloper commented Mar 6, 2014

ElDeveloper Mar 6, 2014

adamrp Mar 6, 2014

ElDeveloper Mar 6, 2014

ElDeveloper commented Mar 6, 2014

ElDeveloper commented Mar 6, 2014

adamrp commented Mar 26, 2014

teravest commented Mar 26, 2014

ElDeveloper commented Mar 26, 2014

Update Barcode Scanner #632

Are you sure you want to change the base?

Update Barcode Scanner #632

Conversation

teravest commented Feb 20, 2014

ElDeveloper commented Feb 21, 2014

teravest commented Feb 21, 2014

ElDeveloper commented Feb 21, 2014

teravest commented Feb 21, 2014

adamrp commented Feb 21, 2014

adamrp commented Feb 21, 2014

adamrp commented Feb 21, 2014

adamrp commented Feb 21, 2014

adamrp commented Feb 22, 2014

adamrp commented Feb 22, 2014

adamrp commented Feb 22, 2014

teravest commented Feb 24, 2014

teravest commented Feb 24, 2014

teravest commented Mar 3, 2014

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

ElDeveloper commented Mar 6, 2014

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

ElDeveloper commented Mar 6, 2014

ElDeveloper commented Mar 6, 2014

adamrp commented Mar 26, 2014

teravest commented Mar 26, 2014

ElDeveloper commented Mar 26, 2014