improving redbiom help and fixing bugs #2306

antgonza · 2017-09-20T23:18:06Z

@wasade, @josenavas, @tanaes. Now the help looks like this:

[DO NOT MERGE] August 24th Release

…into printable-to-utf8

replace printable for try/except utf-8

* Adding branch description * Adding spaces * Adding timeline

upgrading software

…client-to-qiita

r_client to qiita

rm moi and ipython

…-create_raw_data

* add is_from_analysis to artifact_handlers * fix test_post_metadata * fix error

@ElDeveloper

* fix qiita-spots#1293 * flake8 * fix errors * addressing @ElDeveloper comments

rm sudo

fix awaiting_approval list bug

@antgonza

* Fix qiita-spots#2276 * Factoring out generate nginx directory file list * Factoring out the nginx file list writing * Factoring out generating the file list of an artifact * Factoring out the header setting * Addressing @antgonza's comment * Addressing @wasade's comments

codecov-io · 2017-09-21T01:48:16Z

Codecov Report

Merging #2306 into release-candidate will increase coverage by <.01%.
The diff coverage is 100%.

@@                 Coverage Diff                  @@
##           release-candidate   #2306      +/-   ##
====================================================
+ Coverage              93.79%   93.8%   +<.01%     
====================================================
  Files                    163     163              
  Lines                  18579   18579              
====================================================
+ Hits                   17427   17428       +1     
+ Misses                  1152    1151       -1

Impacted Files	Coverage Δ
qiita_pet/test/test_qiita_redbiom.py	`98.5% <ø> (ø)`	⬆️
qiita_pet/handlers/qiita_redbiom.py	`96.1% <100%> (+1.29%)`	⬆️

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josenavas · 2017-09-21T01:56:30Z

@antgonza which is the base branch that you are creating your working branch? You should probably create it from the "release-candidate" branch, and you will not have the issue with all the commits showing up here.

antgonza · 2017-09-21T02:16:14Z

that's what I did and if you see there are only 3 files changing ...

wasade · 2017-09-21T04:12:29Z

qiita_pet/handlers/qiita_redbiom.py

+        except:
+            message = (
+                'Not a valid search: "%s", are you sure this is a '
+                'valid query value?' % query)


They probably won't be sure. What about: "The query ("%s") did not work and may be malformed. Please check the search help for more information on the queries."

wasade · 2017-09-21T04:14:22Z

qiita_pet/templates/redbiom.html

+        <br/>
+        <ul>
+          <li>
+            Find all samples in which the GreenGenes feature 4479944 is found: "4479944"


GreenGenes -> Greengenes

wasade · 2017-09-21T04:15:51Z

qiita_pet/templates/redbiom.html

+        </ul>
+      </li>
+      <li><b>Taxon</b>:<br/>
+        The search will be only on closed reference and based on the taxonomies available. Note that you need to use the GreenGenes nomenclature.


Same here

"...nomenclature of a rank prefix and taxon (e.g., o__Clostridiales for order level Clostridiales)."

I would also remind folks that there are dual underscores between rank and name.

so maybe:

The search will be only on closed reference and based on the taxonomies available. Only exact matches are returned. Note that currently only the Greengenes taxonomy is searchable, and that it requires nomenclature of a rank prefix, two underscores, and then the name (e.g., o__Clostridiales for order level Clostridiales).

tanaes · 2017-09-21T04:27:21Z

qiita_pet/templates/redbiom.html

+          </li>
+        </ul>
+      </li>
+      <li>


So just to be clear, it's not possible to combine metadata searches with sequence searches? Like, I can find all ACGTTTGCCAGCAAAGACT in samples where ph < 7?

that's correct, could you add a new issues about this in https://github.com/biocore/redbiom/issues ? Thanks!

It's possible with redbiom. Remember the command line interface is intended for piping, so this specific functionality may not be exposed to the CLI but is not be a problem with the API. The high level approach is:

fetch the set of samples containing feature X

fetch the set of samples corresponding to metadata criteria Y

assess the set intersection of X and Y

right, this might be possible by adding a GUI where you can "connect" searches but not sure it it will be easier to do this via redbiom directly ...

antgonza

realized that I never submitted these comments.

antgonza · 2017-09-21T11:48:48Z

qiita_pet/handlers/qiita_redbiom.py

+        except:
+            message = (
+                'Not a valid search: "%s", are you sure this is a '
+                'valid query value?' % query)


antgonza · 2017-09-21T11:49:06Z

qiita_pet/templates/redbiom.html

+          </li>
+        </ul>
+      </li>
+      <li>


that's correct, could you add a new issues about this in https://github.com/biocore/redbiom/issues ? Thanks!

antgonza · 2017-09-21T11:49:38Z

qiita_pet/templates/redbiom.html

+        <br/>
+        <ul>
+          <li>
+            Find all samples in which the GreenGenes feature 4479944 is found: "4479944"


antgonza · 2017-09-21T11:49:59Z

qiita_pet/templates/redbiom.html

+        </ul>
+      </li>
+      <li><b>Taxon</b>:<br/>
+        The search will be only on closed reference and based on the taxonomies available. Note that you need to use the GreenGenes nomenclature.


antgonza · 2017-09-21T14:23:55Z

thanks @josenavas, @tanaes or @wasade able to merge?

josenavas and others added 30 commits August 23, 2017 07:05

Merge pull request qiita-spots#2249 from biocore/release-candidate

6080742

[DO NOT MERGE] August 24th Release

replace printable for try/except utf-8

52e98a5

add sleeps for tests

e367b54

moving wait_for_prep_information_job

5f7177e

just leaving the changes on this pr

01da18f

Fixing tests

2ae9511

Reverting changes

2026d0c

dist: precise

f098fcf

Merge branch 'printable-to-utf8' of https://github.com/antgonza/qiita …

97a8397

…into printable-to-utf8

addressing @josenavas comments

e195e07

Merge pull request qiita-spots#2255 from antgonza/printable-to-utf8

ef4f566

replace printable for try/except utf-8

fix-2212

7d5da5c

Adding branch description to Contributing (qiita-spots#2256)

21f0287

* Adding branch description * Adding spaces * Adding timeline

Merge branch 'dev' of https://github.com/biocore/qiita into dev

2e102b4

upgrading software

de5c89f

mv r_client to qiita

6248208

from redis import Redis

eb19870

Merge pull request qiita-spots#2261 from antgonza/upgrading-software

120e9ac

upgrading software

Merge branch 'remove-moi' of https://github.com/biocore/qiita into r_…

58e2dab

…client-to-qiita

Merge pull request qiita-spots#2262 from antgonza/r_client-to-qiita

8b4ce80

r_client to qiita

rm moi and ipython

fa7cf3d

Move qiita_db/private.py -> qiita_ware/private_plugin.py

a47c13b

_system_call as system_call

c8c1b59

flake8

c46c05f

rm create_raw_data

f7e9b1e

Transferring VAMPS submission to internal job

c16b177

rm other unnecessary files

4de94cd

addressing @josenavas comment

f50dc35

Merge pull request qiita-spots#2263 from antgonza/rm-moi-ipython

d4f8d8c

rm moi and ipython

Merge branch 'remove-moi' of https://github.com/biocore/qiita into rm…

925a3a5

…-create_raw_data

antgonza and others added 18 commits September 18, 2017 14:00

add is_from_analysis to artifact_handlers (qiita-spots#2293)

15b849f

* add is_from_analysis to artifact_handlers * fix test_post_metadata * fix error

WIP: rm sudo from travis

81bd7b3

adding sed for config file

191199c

fix sed

53579aa

rm &

d12ed87

cat redis.conf

ea5d647

using local redis.conf

4c40d83

# protected-mode yes

fad8935

# supervised no

91bdbbc

redis-server --port 7777 &

e0d83bc

Fix 1293 (qiita-spots#2291)

1b7e38c

* fix qiita-spots#1293 * flake8 * fix errors * addressing @ElDeveloper comments

rm redis.conf

6adf8b1

fix awaiting_approval list bug

20226ed

Merge pull request qiita-spots#2295 from antgonza/rm-sudo

d5ecf8a

rm sudo

Merge pull request qiita-spots#2296 from antgonza/awaiting_approval-list

33054b2

fix awaiting_approval list bug

merging with dev

7749e00

fix qiita-spots#2304

e9e84db

wasade reviewed Sep 21, 2017

View reviewed changes

tanaes reviewed Sep 21, 2017

View reviewed changes

address @tanaes and @wasade comments

6eccdff

antgonza mentioned this pull request Sep 21, 2017

Delete study with tags #2309

Merged

antgonza commented Sep 21, 2017

View reviewed changes

josenavas approved these changes Sep 21, 2017

View reviewed changes

wasade merged commit 4a30c79 into qiita-spots:release-candidate Sep 21, 2017

antgonza mentioned this pull request Sep 21, 2017

Redbiom search issues in Qiita-rc #2304

Closed

improving redbiom help and fixing bugs #2306

improving redbiom help and fixing bugs #2306

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antgonza commented Sep 20, 2017

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antgonza commented Sep 21, 2017

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codecov-io commented Sep 21, 2017 •

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