Fix qiita all tests #1107

josenavas · 2015-04-25T19:22:50Z

Build on top of #1106

Fixes all the tests in qiita_ware. Everything expected to pass now.

coveralls · 2015-04-25T19:56:41Z

Changes Unknown when pulling 658a5b5 on josenavas:fix-qiita-ware-tests into * on biocore:relax-md-req*.

…fix-qiita-ware-tests

ElDeveloper · 2015-04-28T19:07:19Z

@antgonza, quick reminder, it would be great if we can get this reviewed ASAP. Tests should be running now and this time they should all pass.

…add-qiime-map-func

antgonza · 2015-04-28T19:08:48Z

👍 if tests pass.

ElDeveloper · 2015-04-28T19:13:35Z

Same here 👍 if tests pass.

ElDeveloper · 2015-04-28T19:40:10Z

@josenavas, there's a few legitimate failures, would you mind having a look?

antgonza · 2015-04-28T19:41:18Z

Also, will it be possible to remove all QiitaDBWarning?

josenavas · 2015-04-28T19:49:38Z

Thanks guys, I know the source of the problem. What I'm going to do is merge #1109 in here, as the code in there will help me to resolve this issue. Given that the 2 PR are small, I don't think it will blow up the size of the PR :-)

ElDeveloper · 2015-04-28T19:52:53Z

Sounds like a good idea, would you mind closing 1109 then?

On (Apr-28-15|12:49), josenavas wrote:

Thanks guys, I know the source of the problem. What I'm going to do is merge #1109 in here, as the code in there will help me to resolve this issue. Given that the 2 PR are small, I don't think it will blow up the size of the PR :-)

Reply to this email directly or view it on GitHub:
#1107 (comment)

josenavas · 2015-04-28T23:21:46Z

Tests should pass now. I'm currently working on removing all the warnings.

josenavas · 2015-04-28T23:42:32Z

This should be good to go. This is the last PR os the functionality is in place. Note that the interface is still not limited, i.e. it still allows to submit to EBI although columns are missing. AFAIK, we decided that this will go in in alpha 0.2.

antgonza · 2015-04-28T23:44:35Z

qiita_db/metadata_template/prep_template.py

+
+    @property
+    def qiime_map_fp(self):
+        """The QIIME mapping file path of the prep template


This is not really clear, could you rephrase?

ElDeveloper · 2015-04-28T23:57:56Z

qiita_ware/processing_pipeline.py

-        df = df[cols]
-        out_fp = path_builder("%s_MMF.txt" % prefix)
-        output_fps.append(out_fp)
+    if 'run_prefix' in qiime_map:


I don't recall from the stack of pull requests that have been coming in, but there are tests for both of these branches? i.e. cases with run_prefix and cases without it.

Good catch, there was not. Adding right now.

Awesome, thanks!

On (Apr-28-15|17:16), josenavas wrote:

path_builder = partial(join, out_dir)

for prefix, df in pt.groupby('run_prefix'):

df = df[cols]

out_fp = path_builder("%s_MMF.txt" % prefix)

output_fps.append(out_fp)

if 'run_prefix' in qiime_map:

Good catch, there was not. Adding right now.

Reply to this email directly or view it on GitHub:
https://github.com/biocore/qiita/pull/1107/files#r29301671

josenavas · 2015-04-29T00:35:58Z

Done, I needed to modify create_qiime_mapping_file to include the reverse linker primer as a controlled column too. Should be ready for another review.

That would mean that we will need to modify the restrictions at some point to include that column to disable some processing. We should discuss this tomorrow, but I don't think it should block the release since we are not using it in the current pipeline.

ElDeveloper · 2015-04-29T00:50:57Z

It seems like there's some legitimate failures.

ElDeveloper · 2015-04-29T00:52:39Z

@biocore/qiita-admin is everyone ok with this:

Done, I needed to modify create_qiime_mapping_file to include the reverse linker primer as a controlled column too. Should be ready for another review.

That would mean that we will need to modify the restrictions at some point to include that column to disable some processing. We should discuss this tomorrow, but I don't think it should block the release since we are not using it in the current pipeline.

antgonza · 2015-04-29T00:55:05Z

I think this is a real bug as we should be doing this for all sff files that have the reverselinkerprimer ... not sure how difficult/easy is to fix

coveralls · 2015-04-29T01:41:28Z

Changes Unknown when pulling c30dd8c on josenavas:fix-qiita-ware-tests into * on biocore:relax-md-req*.

coveralls · 2015-04-29T01:42:29Z

Changes Unknown when pulling c30dd8c on josenavas:fix-qiita-ware-tests into * on biocore:relax-md-req*.

coveralls · 2015-04-29T01:51:01Z

Changes Unknown when pulling e5ae3e4 on josenavas:fix-qiita-ware-tests into * on biocore:relax-md-req*.

josenavas · 2015-04-29T02:41:49Z

@ElDeveloper that was a complete WTF error hahaha it looks I removed some characters in the code while I was trying to type in another window.

@antgonza we currently do not support this type of processing. Actually, the fact of adding the ReverseLinkerPrimer has generated new QiitaDBWarnings that are going to require me be a bit smarter in the code, as that column is not always required by QIIME.

In my opinion, you're currently biased given the discussions at today's meeting. However, I think that processing should be discussed tomorrow at the meeting, as I don't think that we have time to make it to the release... Additionally, the new issues that you recently added are related to this and they've been added to the beta milestone. I think we can solve it for the alpha 0.2, but I don't think we are going to be able to add it, let's say, in the following 2 hours...

antgonza · 2015-04-29T02:57:16Z

That fine, could you create an issue about this and assign it to the next release ?

josenavas · 2015-04-29T03:48:46Z

Done: #1121

antgonza · 2015-04-29T03:51:16Z

Thanks! However, there are still errors.

josenavas · 2015-04-29T03:52:53Z

I just pushed the fix for them!!! You're 1 minute faster...

coveralls · 2015-04-29T04:29:47Z

Changes Unknown when pulling 6c83ba4 on josenavas:fix-qiita-ware-tests into * on biocore:relax-md-req*.

ElDeveloper · 2015-04-29T05:20:28Z

Thanks @josenavas

Fix qiita all tests

josenavas added 2 commits April 25, 2015 12:04

Fixing qiita ware test util

e75c372

Fixing qiita ware tests

fa4a68b

josenavas added the testing label Apr 25, 2015

josenavas added this to the Alpha 0.1 milestone Apr 25, 2015

Merge branch 'fix-analysis-tests' into fix-qiita-ware-tests

658a5b5

Adding qiime-map property to the prep template

157b60a

josenavas mentioned this pull request Apr 27, 2015

Add qiime map func #1109

Closed

Merge branch 'relax-md-req' of https://github.com/biocore/qiita into …

a663d33

…fix-qiita-ware-tests

josenavas added the priority: high label Apr 28, 2015

Merge branch 'relax-md-req' of https://github.com/biocore/qiita into …

b19b60c

…add-qiime-map-func

Merge branch 'add-qiime-map-func' into fix-qiita-ware-tests

e7363a3

josenavas added 3 commits April 28, 2015 13:45

Fixing bug in add filepath

d464237

Fixing _get_qiime_minimal_mapping

84beb81

Fixing qiime map parsing

c30dd8c

Removing warnings from tests:

e5ae3e4

antgonza reviewed Apr 28, 2015
View reviewed changes

ElDeveloper reviewed Apr 28, 2015
View reviewed changes

josenavas added 2 commits April 28, 2015 17:21

Addressing comments

14b0c49

Adding test with reverse linker primer

0c9a47a

Fixing WTF failures

6c83ba4

ElDeveloper added a commit that referenced this pull request Apr 29, 2015

Merge pull request #1107 from josenavas/fix-qiita-ware-tests

7390538

Fix qiita all tests

ElDeveloper merged commit 7390538 into qiita-spots:relax-md-req Apr 29, 2015

Fix qiita all tests #1107

Fix qiita all tests #1107

Uh oh!

Conversation

josenavas commented Apr 25, 2015

Uh oh!

coveralls commented Apr 25, 2015

Uh oh!

ElDeveloper commented Apr 28, 2015

Uh oh!

antgonza commented Apr 28, 2015

Uh oh!

ElDeveloper commented Apr 28, 2015

Uh oh!

ElDeveloper commented Apr 28, 2015

Uh oh!

antgonza commented Apr 28, 2015

Uh oh!

josenavas commented Apr 28, 2015

Uh oh!

ElDeveloper commented Apr 28, 2015

Uh oh!

josenavas commented Apr 28, 2015

Uh oh!

josenavas commented Apr 28, 2015

Uh oh!

antgonza Apr 28, 2015

Choose a reason for hiding this comment

Uh oh!

josenavas Apr 29, 2015

Choose a reason for hiding this comment

Uh oh!

ElDeveloper Apr 28, 2015

Choose a reason for hiding this comment

Uh oh!

josenavas Apr 29, 2015

Choose a reason for hiding this comment

Uh oh!

ElDeveloper Apr 29, 2015

Choose a reason for hiding this comment

Uh oh!

josenavas commented Apr 29, 2015

Uh oh!

ElDeveloper commented Apr 29, 2015

Uh oh!

ElDeveloper commented Apr 29, 2015

Uh oh!

antgonza commented Apr 29, 2015

Uh oh!

coveralls commented Apr 29, 2015

Uh oh!

coveralls commented Apr 29, 2015

Uh oh!

coveralls commented Apr 29, 2015

Uh oh!

josenavas commented Apr 29, 2015

Uh oh!

antgonza commented Apr 29, 2015

Uh oh!

josenavas commented Apr 29, 2015

Uh oh!

antgonza commented Apr 29, 2015

Uh oh!

josenavas commented Apr 29, 2015

Uh oh!

coveralls commented Apr 29, 2015

Uh oh!

ElDeveloper commented Apr 29, 2015

Uh oh!

Uh oh!