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generate biom and metadata release #2066

Merged
merged 7 commits into from Feb 3, 2017
Merged

generate biom and metadata release #2066

merged 7 commits into from Feb 3, 2017

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antgonza
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I don't think we have an issue for this. Anyway, this adds the functionality to qiita-cron-job of generating a tgz and txt with all the biom/metadata files in the db that are under a given status. The output files will be stored in the working directory under the release folder and with a name containing the study status and the portal, like: QIITA-private-013117-031445.tgz, QIITA-private-013117-031445.txt.

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Coverage Status

Coverage decreased (-0.003%) to 91.542% when pulling 228bc70 on antgonza:generate_biom_and_metadata_release into 4e380e0 on biocore:master.

@antgonza
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This is ready for review; everything worked fine in the qiita-test, took ~25min to run. @wasade the resulting files for your testing are in qiita-test@/projects/qiita_test_data/testlocal/working_dir/releases

-rw-r--r--+  1 qiita_t qiita 1.7G Jan 31 02:49 QIITA-public-013117-022747.tgz
-rw-r--r--+  1 qiita_t qiita 175K Jan 31 02:49 QIITA-public-013117-022747.txt

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wasade commented Jan 31, 2017 via email

@antgonza
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If I understand your questions correctly, yes, that's where you should deploy: qiita-test.

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wasade commented Jan 31, 2017 via email

@antgonza
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@jdereus

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wasade commented Jan 31, 2017 via email

josenavas
josenavas suggested changes Feb 2, 2017
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This does what we need at this moment. However is making assumptions and adds hardcoded values that depend on the plugins.

In my opinion this feels a bit hackish and we should think better how to do this, specially if we are going to add the shotgun pipeline soon. I think it is better to take a step back and think better how do we want to name the human_cmd and/or skip tables (why to skip tables? they're part of the public dataset).

qiita_db/test/test_util.py Outdated
'processed_data/1_study_1001_closed_reference_otu_table.biom',
'templates/1_19700101-000000.txt',
'templates/1_prep_1_19700101-000000.txt',
('processed_data/1_study_1001_closed_reference_otu_table_'
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minor, but you don't need the ( ) in here.

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k

qiita_db/util.py Outdated

Parameters
----------
study_status : str
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Should then this be optional with default to public?

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k

qiita_db/util.py Outdated
continue

# [0] latest is first, [1] only getting the filepath
sample_fp = a.study.sample_template.get_filepaths()[0][1]
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This call and the next if statement can be outside of the inner loop, since the sample template is defined per study. (i.e. move after for s in studies)

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k

qiita_db/util.py Outdated
for p in a.parents:
pp = p.processing_parameters
pp_cmd_name = pp.command.name
if pp_cmd_name == 'Trimming':
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I guess this works, but this is hardcoding something to a plugin value... The whole point of plugins was to avoid this kind of things on the Qiita code...

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Agree but this is a functionality we need and we can always improve as we move forward ...

qiita_db/util.py Outdated
human_cmd = ', '.join(human_cmd)

for _, fp, fp_type in a.filepaths:
if fp_type != 'biom' or 'only-16s' in fp:
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Same with the only-16s...

qiita_db/util.py Outdated
sample_fp = sample_fp[bdir_len:]
cmd_name = a.processing_parameters.command.name

# this loop is necessary as in theory an artifact can be
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If this is generating the BIOM tables from the processing pipeline, we cannot generate an artifact from multiple prep info files, and it is not just a temporal limitation, is part of the design. So do we really need this?

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no but no reason to not leave it ... right?

antgonza
antgonza commented Feb 2, 2017
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I agree that this is not perfect but as you pointed out: it does what we need right now. We can always improve as we move forward with other plugins. Now, the 2 special cases are due to deblur/trimming, which is not ideal but should be fine for other "regular" pipelines. In other words, I think is worth finishing this and improve as we see things moving forward, which is easier than predicting the future.

qiita_db/test/test_util.py Outdated
'processed_data/1_study_1001_closed_reference_otu_table.biom',
'templates/1_19700101-000000.txt',
'templates/1_prep_1_19700101-000000.txt',
('processed_data/1_study_1001_closed_reference_otu_table_'
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k

qiita_db/util.py Outdated

Parameters
----------
study_status : str
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k

qiita_db/util.py Outdated
continue

# [0] latest is first, [1] only getting the filepath
sample_fp = a.study.sample_template.get_filepaths()[0][1]
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k

qiita_db/util.py Outdated
sample_fp = sample_fp[bdir_len:]
cmd_name = a.processing_parameters.command.name

# this loop is necessary as in theory an artifact can be
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no but no reason to not leave it ... right?

qiita_db/util.py Outdated
for p in a.parents:
pp = p.processing_parameters
pp_cmd_name = pp.command.name
if pp_cmd_name == 'Trimming':
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Agree but this is a functionality we need and we can always improve as we move forward ...

@coveralls
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Coverage Status

Coverage decreased (-0.01%) to 91.532% when pulling 5733d24 on antgonza:generate_biom_and_metadata_release into 4e380e0 on biocore:master.

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Coverage Status

Coverage decreased (-0.01%) to 91.532% when pulling d36ae77 on antgonza:generate_biom_and_metadata_release into 4e380e0 on biocore:master.

josenavas
josenavas suggested changes Feb 3, 2017
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Just one comment that I missed during my first pass!

qiita_db/util.py Outdated
if sample_fp.startswith(bdir):
sample_fp = sample_fp[bdir_len:]

for a in s.artifacts():
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Sorry - I missed this one!

for a in s.artifacts(artifact_type='BIOM')

and remove the next if statement. This should speed up a bit this function.

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Coverage Status

Coverage decreased (-0.01%) to 91.532% when pulling 2def09f on antgonza:generate_biom_and_metadata_release into 4e380e0 on biocore:master.

ElDeveloper
ElDeveloper approved these changes Feb 3, 2017
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qiita_db/util.py Outdated
----------
study_status : str, optional
The study status to search for. Note that this should always be set
to 'public' but having this expose helps with testing
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expose -> exposed.

Is it useful to describe what are the other possible values of this argument?

qiita_db/util.py
sample_fp = sample_fp[bdir_len:]

for a in s.artifacts(artifact_type='BIOM'):
if a.processing_parameters is None:
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What would be a biom table without processing parameters? A table that failed or is currently processing?

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A table that was uploaded directly to qiita ...

qiita_db/util.py Outdated
with open(txt_name, 'w') as txt, topen(tgz_name, "w|gz") as tgz:
# writing header for txt
txt.write("biom_fp\tsample_fp\tprep_fp\tqiita_artifact_id\tcommand\n")
for biom_fp, sample_fp, prep_fp, prep_id, human_cmd in data:
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veeeeeeeeery minor but prep_id here is really an artifact_id, the variable assignment is correct though 🙄

qiita_db/test/test_util.py
def test_generate_biom_and_metadata_release(self):
tgz, txt = qdb.util.generate_biom_and_metadata_release('private')
self.files_to_remove.extend([tgz, txt])

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The file objects are not being closed, would you mind closing them?

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Coverage Status

Coverage decreased (-0.02%) to 91.526% when pulling 5c65d1a on antgonza:generate_biom_and_metadata_release into 4e380e0 on biocore:master.

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Coverage Status

Coverage decreased (-0.008%) to 91.537% when pulling 5c65d1a on antgonza:generate_biom_and_metadata_release into 4e380e0 on biocore:master.

@ElDeveloper ElDeveloper merged commit 6360675 into qiita-spots:master Feb 3, 2017
antgonza pushed a commit that referenced this pull request Feb 6, 2017
@josenavas @antgonza
Analysis refactor master (#2070)
3fdb802 
* fix #1505

* improving some GUI stuff

* improving some GUI stuff - missing lines

* addressing all comments

* ready for review

* New DB structure

* Adding python patch

* Adding a biom so we can actually execute the patch

* Fixing the patch to correctly transfer the information from the old structure to the new one

* Fixing patch

* Fixing patch and a few other bits to make the patch run successfully

* These files are no longer needed

* Removing unused code

* Droping analysis status table

* Linking the analysis with all the artifacts

* Fixing typo

* Fixing HTML and dbschema files

* Adding analyisis jobs

* Extending the artifact to work with the analysis

* Allowing multiomics datatype

* Adding private_job_submitter and modifying proc job handler to use it

* Adding logging column to the analysis

* Adding datatype to the analysis-processing job table

* Adding REST endpoint to access the analysis metadata

* Adding private jobs to plugin

* Fixing typo

* Fixing the processing jobs complete

* Removing the old job code

* Oops removed the wrong file

* Removing QiitaStatusObject because it is not used

* fixing metautil

* Fixing porntal, setup and sql tests

* Fixing user and util

* Fixing qiita_db

* fix #1987

* Updating to master

* Addressing @antgonza's comments

* initial commit

* requested changes

* fix filter job list

* Fixing server cert (#2051)

* fix get_studies

* flake8

* fix #503

* fix #2010

* fix #1913

* fix errors

* addressing @josenavas comment

* flake8

* fix #1010

* fix #1066 (#2058)

* addressing @josenavas comments

* fix #1961

* fix #1837

* Automatic jobs & new stats (#2057)

* fix #814, fix #1636

* fixing error in test-env

* fixing stats.html call

* adding img

* addressing @josenavas comments

* rm for loops

* addresssing @ElDeveloper comments

* generalizing this functionality

* fix #1816

* Taking into account non-phylogenetic metrics in beta diversity

* fix #1959

* Addressing @antgonza's comments

* addressing @josenavas comments

* addressing @josenavas comments

* fixing error

* fixed?

* addressing @josenavas comments

* Actually fixing merge conflicts

* addressing @wasade comments

* fix flake8

* generate biom and metadata release (#2066)

* initial commit

* adding portal

* addressing @josenavas comments

* pid -> qiita_artifact_id

* addressing @josenavas comments

* addressing @ElDeveloper comments

* rm 50.sql

* database changes to fix 969

* adding delete

* addressing @josenavas comments

* addressing @ElDeveloper comments

* duh!
antgonza pushed a commit that referenced this pull request Feb 8, 2017
@josenavas @antgonza
Sync-ing with master (again) (#2073)
1377640 
* fix #1505

* improving some GUI stuff

* improving some GUI stuff - missing lines

* addressing all comments

* ready for review

* fix #1987

* initial commit

* requested changes

* fix filter job list

* Fixing server cert (#2051)

* fix get_studies

* flake8

* fix #503

* fix #2010

* fix #1913

* fix errors

* addressing @josenavas comment

* flake8

* fix #1010

* fix #1066 (#2058)

* addressing @josenavas comments

* fix #1961

* fix #1837

* Automatic jobs & new stats (#2057)

* fix #814, fix #1636

* fixing error in test-env

* fixing stats.html call

* adding img

* addressing @josenavas comments

* rm for loops

* addresssing @ElDeveloper comments

* generalizing this functionality

* fix #1816

* fix #1959

* addressing @josenavas comments

* addressing @josenavas comments

* fixing error

* fixed?

* addressing @josenavas comments

* addressing @wasade comments

* fix flake8

* generate biom and metadata release (#2066)

* initial commit

* adding portal

* addressing @josenavas comments

* pid -> qiita_artifact_id

* addressing @josenavas comments

* addressing @ElDeveloper comments

* rm 50.sql

* database changes to fix 969

* adding delete

* addressing @josenavas comments

* addressing @ElDeveloper comments

* duh!

* fix generate_biom_and_metadata_release (#2072)

* fix generate_biom_and_metadata_release

* addressing @ElDeveloper comment
antgonza pushed a commit that referenced this pull request Feb 9, 2017
@josenavas @antgonza
Fix qiita ware (#2074)
ee170a0 
* fix #1505

* improving some GUI stuff

* improving some GUI stuff - missing lines

* addressing all comments

* ready for review

* fix #1987

* initial commit

* requested changes

* fix filter job list

* Fixing server cert (#2051)

* fix get_studies

* flake8

* fix #503

* fix #2010

* fix #1913

* fix errors

* addressing @josenavas comment

* flake8

* fix #1010

* fix #1066 (#2058)

* addressing @josenavas comments

* fix #1961

* fix #1837

* Automatic jobs & new stats (#2057)

* fix #814, fix #1636

* fixing error in test-env

* fixing stats.html call

* adding img

* addressing @josenavas comments

* rm for loops

* addresssing @ElDeveloper comments

* generalizing this functionality

* fix #1816

* fix #1959

* addressing @josenavas comments

* addressing @josenavas comments

* fixing error

* fixed?

* addressing @josenavas comments

* addressing @wasade comments

* fix flake8

* generate biom and metadata release (#2066)

* initial commit

* adding portal

* addressing @josenavas comments

* pid -> qiita_artifact_id

* addressing @josenavas comments

* addressing @ElDeveloper comments

* rm 50.sql

* database changes to fix 969

* adding delete

* addressing @josenavas comments

* addressing @ElDeveloper comments

* duh!

* fix generate_biom_and_metadata_release (#2072)

* fix generate_biom_and_metadata_release

* addressing @ElDeveloper comment

* Removing qiita ware code that will not be used anymore
antgonza pushed a commit that referenced this pull request Feb 10, 2017
@josenavas @antgonza
Analysis refactor GUI part1 (#2076)
a083e23 
* fix #1505

* improving some GUI stuff

* improving some GUI stuff - missing lines

* addressing all comments

* ready for review

* fix #1987

* initial commit

* requested changes

* fix filter job list

* Fixing server cert (#2051)

* fix get_studies

* flake8

* fix #503

* fix #2010

* fix #1913

* fix errors

* addressing @josenavas comment

* flake8

* fix #1010

* fix #1066 (#2058)

* addressing @josenavas comments

* fix #1961

* fix #1837

* Automatic jobs & new stats (#2057)

* fix #814, fix #1636

* fixing error in test-env

* fixing stats.html call

* adding img

* addressing @josenavas comments

* rm for loops

* addresssing @ElDeveloper comments

* generalizing this functionality

* fix #1816

* fix #1959

* addressing @josenavas comments

* addressing @josenavas comments

* fixing error

* fixed?

* addressing @josenavas comments

* addressing @wasade comments

* fix flake8

* generate biom and metadata release (#2066)

* initial commit

* adding portal

* addressing @josenavas comments

* pid -> qiita_artifact_id

* addressing @josenavas comments

* addressing @ElDeveloper comments

* rm 50.sql

* database changes to fix 969

* adding delete

* addressing @josenavas comments

* addressing @ElDeveloper comments

* duh!

* fix generate_biom_and_metadata_release (#2072)

* fix generate_biom_and_metadata_release

* addressing @ElDeveloper comment

* Removing qiita ware code that will not be used anymore

* Organizing the handlers and new analysis description page

* Addressing @antgonza's comments
antgonza pushed a commit that referenced this pull request Feb 15, 2017
@josenavas @antgonza
Analysis refactor GUI part2 (#2077)
22156ed 
* fix #1505

* improving some GUI stuff

* improving some GUI stuff - missing lines

* addressing all comments

* ready for review

* fix #1987

* initial commit

* requested changes

* fix filter job list

* Fixing server cert (#2051)

* fix get_studies

* flake8

* fix #503

* fix #2010

* fix #1913

* fix errors

* addressing @josenavas comment

* flake8

* fix #1010

* fix #1066 (#2058)

* addressing @josenavas comments

* fix #1961

* fix #1837

* Automatic jobs & new stats (#2057)

* fix #814, fix #1636

* fixing error in test-env

* fixing stats.html call

* adding img

* addressing @josenavas comments

* rm for loops

* addresssing @ElDeveloper comments

* generalizing this functionality

* fix #1816

* fix #1959

* addressing @josenavas comments

* addressing @josenavas comments

* fixing error

* fixed?

* addressing @josenavas comments

* addressing @wasade comments

* fix flake8

* generate biom and metadata release (#2066)

* initial commit

* adding portal

* addressing @josenavas comments

* pid -> qiita_artifact_id

* addressing @josenavas comments

* addressing @ElDeveloper comments

* rm 50.sql

* database changes to fix 969

* adding delete

* addressing @josenavas comments

* addressing @ElDeveloper comments

* duh!

* fix generate_biom_and_metadata_release (#2072)

* fix generate_biom_and_metadata_release

* addressing @ElDeveloper comment

* Removing qiita ware code that will not be used anymore

* Organizing the handlers and new analysis description page

* Connecting the analysis creation and making interface responsive

* Addressing @antgonza's comments

* Removing unused code
antgonza pushed a commit that referenced this pull request Apr 24, 2017
@josenavas @antgonza
Analysis refactor gui part3 (#2078)
015dd41 
* fix #1505

* improving some GUI stuff

* improving some GUI stuff - missing lines

* addressing all comments

* ready for review

* fix #1987

* initial commit

* requested changes

* fix filter job list

* Fixing server cert (#2051)

* fix get_studies

* flake8

* fix #503

* fix #2010

* fix #1913

* fix errors

* addressing @josenavas comment

* flake8

* fix #1010

* fix #1066 (#2058)

* addressing @josenavas comments

* fix #1961

* fix #1837

* Automatic jobs & new stats (#2057)

* fix #814, fix #1636

* fixing error in test-env

* fixing stats.html call

* adding img

* addressing @josenavas comments

* rm for loops

* addresssing @ElDeveloper comments

* generalizing this functionality

* fix #1816

* fix #1959

* addressing @josenavas comments

* addressing @josenavas comments

* fixing error

* fixed?

* addressing @josenavas comments

* addressing @wasade comments

* fix flake8

* generate biom and metadata release (#2066)

* initial commit

* adding portal

* addressing @josenavas comments

* pid -> qiita_artifact_id

* addressing @josenavas comments

* addressing @ElDeveloper comments

* rm 50.sql

* database changes to fix 969

* adding delete

* addressing @josenavas comments

* addressing @ElDeveloper comments

* duh!

* fix generate_biom_and_metadata_release (#2072)

* fix generate_biom_and_metadata_release

* addressing @ElDeveloper comment

* Removing qiita ware code that will not be used anymore

* Organizing the handlers and new analysis description page

* Connecting the analysis creation and making interface responsive

* Addressing @antgonza's comments

* Initial artifact GUI refactor

* Removing unused code

* Adding can_edit call to the analysis

* Fixing artifact rest API since not all artifacts have study

* Adding can_be_publicized call to analysis

* Adding QiitaHTTPError to handle errors gracefully

* Adding safe_execution contextmanager

* Fixing typo

* Adding qiita test checker

* Adapting some artifact handlers

* Fixing typo

* Addressing @antgonza's comments

* Addressing @antgonza's comments
antgonza pushed a commit that referenced this pull request Apr 24, 2017
@josenavas @antgonza
Analysis refactor gui part4 (#2079)
937b13f 
* fix #1505

* improving some GUI stuff

* improving some GUI stuff - missing lines

* addressing all comments

* ready for review

* fix #1987

* initial commit

* requested changes

* fix filter job list

* Fixing server cert (#2051)

* fix get_studies

* flake8

* fix #503

* fix #2010

* fix #1913

* fix errors

* addressing @josenavas comment

* flake8

* fix #1010

* fix #1066 (#2058)

* addressing @josenavas comments

* fix #1961

* fix #1837

* Automatic jobs & new stats (#2057)

* fix #814, fix #1636

* fixing error in test-env

* fixing stats.html call

* adding img

* addressing @josenavas comments

* rm for loops

* addresssing @ElDeveloper comments

* generalizing this functionality

* fix #1816

* fix #1959

* addressing @josenavas comments

* addressing @josenavas comments

* fixing error

* fixed?

* addressing @josenavas comments

* addressing @wasade comments

* fix flake8

* generate biom and metadata release (#2066)

* initial commit

* adding portal

* addressing @josenavas comments

* pid -> qiita_artifact_id

* addressing @josenavas comments

* addressing @ElDeveloper comments

* rm 50.sql

* database changes to fix 969

* adding delete

* addressing @josenavas comments

* addressing @ElDeveloper comments

* duh!

* fix generate_biom_and_metadata_release (#2072)

* fix generate_biom_and_metadata_release

* addressing @ElDeveloper comment

* Removing qiita ware code that will not be used anymore

* Organizing the handlers and new analysis description page

* Connecting the analysis creation and making interface responsive

* Addressing @antgonza's comments

* Initial artifact GUI refactor

* Removing unused code

* Adding can_edit call to the analysis

* Fixing artifact rest API since not all artifacts have study

* Adding can_be_publicized call to analysis

* Adding QiitaHTTPError to handle errors gracefully

* Adding safe_execution contextmanager

* Fixing typo

* Adding qiita test checker

* Adapting some artifact handlers

* Abstracting the graph reloading and adding some documentation

* Fixing typo

* Fixing changing artifact visibility

* Fixing delete

* Fixing artifact deletion
antgonza pushed a commit that referenced this pull request Apr 25, 2017
@josenavas @antgonza
Analysis refactor gui part5 (#2115)
f21d896 
* fix #1505

* improving some GUI stuff

* improving some GUI stuff - missing lines

* addressing all comments

* ready for review

* fix #1987

* initial commit

* requested changes

* fix filter job list

* Fixing server cert (#2051)

* fix get_studies

* flake8

* fix #503

* fix #2010

* fix #1913

* fix errors

* addressing @josenavas comment

* flake8

* fix #1010

* fix #1066 (#2058)

* addressing @josenavas comments

* fix #1961

* fix #1837

* Automatic jobs & new stats (#2057)

* fix #814, fix #1636

* fixing error in test-env

* fixing stats.html call

* adding img

* addressing @josenavas comments

* rm for loops

* addresssing @ElDeveloper comments

* generalizing this functionality

* fix #1816

* fix #1959

* addressing @josenavas comments

* addressing @josenavas comments

* fixing error

* fixed?

* addressing @josenavas comments

* addressing @wasade comments

* fix flake8

* generate biom and metadata release (#2066)

* initial commit

* adding portal

* addressing @josenavas comments

* pid -> qiita_artifact_id

* addressing @josenavas comments

* addressing @ElDeveloper comments

* rm 50.sql

* database changes to fix 969

* adding delete

* addressing @josenavas comments

* addressing @ElDeveloper comments

* duh!

* fix generate_biom_and_metadata_release (#2072)

* fix generate_biom_and_metadata_release

* addressing @ElDeveloper comment

* Removing qiita ware code that will not be used anymore

* Organizing the handlers and new analysis description page

* Connecting the analysis creation and making interface responsive

* Addressing @antgonza's comments

* Initial artifact GUI refactor

* Removing unused code

* Adding can_edit call to the analysis

* Fixing artifact rest API since not all artifacts have study

* Adding can_be_publicized call to analysis

* Adding QiitaHTTPError to handle errors gracefully

* Adding safe_execution contextmanager

* Fixing typo

* Adding qiita test checker

* Adapting some artifact handlers

* Abstracting the graph reloading and adding some documentation

* Fixing typo

* Fixing changing artifact visibility

* Fixing delete

* Fixing artifact deletion

* Adding default parameters to the commands

* Fixing processing page

* Fixing variable name

* Changing bdiv metrics to single choice

* Fixing patch

* Various small fixes to be able to run tests on the plugins

* Addressing @antgonza's comments
antgonza pushed a commit that referenced this pull request Apr 25, 2017
@josenavas @antgonza
Analysis refactor gui part6 (#2116)
7cf4559 
* fix #1505

* improving some GUI stuff

* improving some GUI stuff - missing lines

* addressing all comments

* ready for review

* fix #1987

* initial commit

* requested changes

* fix filter job list

* Fixing server cert (#2051)

* fix get_studies

* flake8

* fix #503

* fix #2010

* fix #1913

* fix errors

* addressing @josenavas comment

* flake8

* fix #1010

* fix #1066 (#2058)

* addressing @josenavas comments

* fix #1961

* fix #1837

* Automatic jobs & new stats (#2057)

* fix #814, fix #1636

* fixing error in test-env

* fixing stats.html call

* adding img

* addressing @josenavas comments

* rm for loops

* addresssing @ElDeveloper comments

* generalizing this functionality

* fix #1816

* fix #1959

* addressing @josenavas comments

* addressing @josenavas comments

* fixing error

* fixed?

* addressing @josenavas comments

* addressing @wasade comments

* fix flake8

* generate biom and metadata release (#2066)

* initial commit

* adding portal

* addressing @josenavas comments

* pid -> qiita_artifact_id

* addressing @josenavas comments

* addressing @ElDeveloper comments

* rm 50.sql

* database changes to fix 969

* adding delete

* addressing @josenavas comments

* addressing @ElDeveloper comments

* duh!

* fix generate_biom_and_metadata_release (#2072)

* fix generate_biom_and_metadata_release

* addressing @ElDeveloper comment

* Removing qiita ware code that will not be used anymore

* Organizing the handlers and new analysis description page

* fixing timestamp

* rm formats

* st -> pt

* Connecting the analysis creation and making interface responsive

* Addressing @antgonza's comments

* Initial artifact GUI refactor

* Removing unused code

* moving to ISO 8601 - wow :'(

* fix errors

* addressing @wasade comments

* Adding can_edit call to the analysis

* Fixing artifact rest API since not all artifacts have study

* Adding can_be_publicized call to analysis

* Adding QiitaHTTPError to handle errors gracefully

* Adding safe_execution contextmanager

* Fixing typo

* Adding qiita test checker

* Adapting some artifact handlers

* Abstracting the graph reloading and adding some documentation

* Fixing typo

* Fixing changing artifact visibility

* Fixing delete

* Fixing artifact deletion

* Adding default parameters to the commands

* Fixing processing page

* Fixing variable name

* fixing private/public studies

* Changing bdiv metrics to single choice

* sanbox-to-sandbox

* flake8

* Fixing patch

* fixing other issues

* adding share documentation

* psycopg2 <= 2.7

* psycopg2 < 2.7

* Various small fixes to be able to run tests on the plugins

* Solving merge conflicts
antgonza pushed a commit that referenced this pull request May 17, 2017
@josenavas @antgonza
Analysis refactor gui part7 (#2117)
39a03e3 
* fix #1505

* improving some GUI stuff

* improving some GUI stuff - missing lines

* addressing all comments

* ready for review

* fix #1987

* initial commit

* requested changes

* fix filter job list

* Fixing server cert (#2051)

* fix get_studies

* flake8

* fix #503

* fix #2010

* fix #1913

* fix errors

* addressing @josenavas comment

* flake8

* fix #1010

* fix #1066 (#2058)

* addressing @josenavas comments

* fix #1961

* fix #1837

* Automatic jobs & new stats (#2057)

* fix #814, fix #1636

* fixing error in test-env

* fixing stats.html call

* adding img

* addressing @josenavas comments

* rm for loops

* addresssing @ElDeveloper comments

* generalizing this functionality

* fix #1816

* fix #1959

* addressing @josenavas comments

* addressing @josenavas comments

* fixing error

* fixed?

* addressing @josenavas comments

* addressing @wasade comments

* fix flake8

* generate biom and metadata release (#2066)

* initial commit

* adding portal

* addressing @josenavas comments

* pid -> qiita_artifact_id

* addressing @josenavas comments

* addressing @ElDeveloper comments

* rm 50.sql

* database changes to fix 969

* adding delete

* addressing @josenavas comments

* addressing @ElDeveloper comments

* duh!

* fix generate_biom_and_metadata_release (#2072)

* fix generate_biom_and_metadata_release

* addressing @ElDeveloper comment

* Removing qiita ware code that will not be used anymore

* Organizing the handlers and new analysis description page

* fixing timestamp

* rm formats

* st -> pt

* Connecting the analysis creation and making interface responsive

* Addressing @antgonza's comments

* Initial artifact GUI refactor

* Removing unused code

* moving to ISO 8601 - wow :'(

* fix errors

* addressing @wasade comments

* Adding can_edit call to the analysis

* Fixing artifact rest API since not all artifacts have study

* Adding can_be_publicized call to analysis

* Adding QiitaHTTPError to handle errors gracefully

* Adding safe_execution contextmanager

* Fixing typo

* Adding qiita test checker

* Adapting some artifact handlers

* Abstracting the graph reloading and adding some documentation

* Fixing typo

* Fixing changing artifact visibility

* Fixing delete

* Fixing artifact deletion

* Adding default parameters to the commands

* Fixing processing page

* Fixing variable name

* fixing private/public studies

* Changing bdiv metrics to single choice

* sanbox-to-sandbox

* flake8

* Fixing patch

* fixing other issues

* adding share documentation

* psycopg2 <= 2.7

* psycopg2 < 2.7

* Various small fixes to be able to run tests on the plugins

* Adding private module

* Fixing processing job completion

* Fixing patch 52

* Fixing call

* Fixing complete

* small fixes

* Adding processing handlers

* Fixing url and bug on processing job workflow

* Adding the private script runner

* Adding is_analysis column to the command

* Adding retrieval of commands excluding analysis commands

* Addressing bug on retrieving information from redis

* Enabling the command register endpoint to provide if the command is analysis only

* Addressing @antgonza's comments

* Addressing @wasade's comments
antgonza pushed a commit that referenced this pull request Jun 1, 2017
@josenavas @antgonza
Analysis refactor allow users change dflt params (#2136)
3051113 
* fix #1505

* improving some GUI stuff

* improving some GUI stuff - missing lines

* addressing all comments

* ready for review

* fix #1987

* initial commit

* requested changes

* fix filter job list

* Fixing server cert (#2051)

* fix get_studies

* flake8

* fix #503

* fix #2010

* fix #1913

* fix errors

* addressing @josenavas comment

* flake8

* fix #1010

* fix #1066 (#2058)

* addressing @josenavas comments

* fix #1961

* fix #1837

* Automatic jobs & new stats (#2057)

* fix #814, fix #1636

* fixing error in test-env

* fixing stats.html call

* adding img

* addressing @josenavas comments

* rm for loops

* addresssing @ElDeveloper comments

* generalizing this functionality

* fix #1816

* fix #1959

* addressing @josenavas comments

* addressing @josenavas comments

* fixing error

* fixed?

* addressing @josenavas comments

* addressing @wasade comments

* fix flake8

* generate biom and metadata release (#2066)

* initial commit

* adding portal

* addressing @josenavas comments

* pid -> qiita_artifact_id

* addressing @josenavas comments

* addressing @ElDeveloper comments

* rm 50.sql

* database changes to fix 969

* adding delete

* addressing @josenavas comments

* addressing @ElDeveloper comments

* duh!

* fix generate_biom_and_metadata_release (#2072)

* fix generate_biom_and_metadata_release

* addressing @ElDeveloper comment

* Removing qiita ware code that will not be used anymore

* Organizing the handlers and new analysis description page

* fixing timestamp

* rm formats

* st -> pt

* Connecting the analysis creation and making interface responsive

* Addressing @antgonza's comments

* Initial artifact GUI refactor

* Removing unused code

* moving to ISO 8601 - wow :'(

* fix errors

* addressing @wasade comments

* Adding can_edit call to the analysis

* Fixing artifact rest API since not all artifacts have study

* Adding can_be_publicized call to analysis

* Adding QiitaHTTPError to handle errors gracefully

* Adding safe_execution contextmanager

* Fixing typo

* Adding qiita test checker

* Adapting some artifact handlers

* Abstracting the graph reloading and adding some documentation

* Fixing typo

* Fixing changing artifact visibility

* Fixing delete

* Fixing artifact deletion

* Adding default parameters to the commands

* Fixing processing page

* Fixing variable name

* fixing private/public studies

* Changing bdiv metrics to single choice

* sanbox-to-sandbox

* flake8

* Fixing patch

* fixing other issues

* adding share documentation

* psycopg2 <= 2.7

* psycopg2 < 2.7

* Various small fixes to be able to run tests on the plugins

* Adding private module

* Fixing processing job completion

* Fixing patch 52

* Fixing call

* Fixing complete

* small fixes

* Adding processing handlers

* Fixing url and bug on processing job workflow

* Adding the private script runner

* Adding is_analysis column to the command

* Adding retrieval of commands excluding analysis commands

* Addressing bug on retrieving information from redis

* Enabling the command register endpoint to provide if the command is analysis only

* Addressing @antgonza's comments

* Addressing @wasade's comments

* Supporting multiple choice

* Adding documentation

* Modifying handler to pass allow_change_optionals

* returning optional parameters

* Addressing bug found by @antgonza

* Enabling changing the default parameters

* Adding correct class

* Allowing user to change default parameters

* Fixing bug with commands listing

* Addressing @wasade's comments
antgonza pushed a commit that referenced this pull request Jun 1, 2017
@josenavas @antgonza
Arbitrary summary HTML (#2138)
2a1129a 
* fix #1505

* improving some GUI stuff

* improving some GUI stuff - missing lines

* addressing all comments

* ready for review

* fix #1987

* initial commit

* requested changes

* fix filter job list

* Fixing server cert (#2051)

* fix get_studies

* flake8

* fix #503

* fix #2010

* fix #1913

* fix errors

* addressing @josenavas comment

* flake8

* fix #1010

* fix #1066 (#2058)

* addressing @josenavas comments

* fix #1961

* fix #1837

* Automatic jobs & new stats (#2057)

* fix #814, fix #1636

* fixing error in test-env

* fixing stats.html call

* adding img

* addressing @josenavas comments

* rm for loops

* addresssing @ElDeveloper comments

* generalizing this functionality

* fix #1816

* fix #1959

* addressing @josenavas comments

* addressing @josenavas comments

* fixing error

* fixed?

* addressing @josenavas comments

* addressing @wasade comments

* fix flake8

* generate biom and metadata release (#2066)

* initial commit

* adding portal

* addressing @josenavas comments

* pid -> qiita_artifact_id

* addressing @josenavas comments

* addressing @ElDeveloper comments

* rm 50.sql

* database changes to fix 969

* adding delete

* addressing @josenavas comments

* addressing @ElDeveloper comments

* duh!

* fix generate_biom_and_metadata_release (#2072)

* fix generate_biom_and_metadata_release

* addressing @ElDeveloper comment

* Removing qiita ware code that will not be used anymore

* Organizing the handlers and new analysis description page

* fixing timestamp

* rm formats

* st -> pt

* Connecting the analysis creation and making interface responsive

* Addressing @antgonza's comments

* Initial artifact GUI refactor

* Removing unused code

* moving to ISO 8601 - wow :'(

* fix errors

* addressing @wasade comments

* Adding can_edit call to the analysis

* Fixing artifact rest API since not all artifacts have study

* Adding can_be_publicized call to analysis

* Adding QiitaHTTPError to handle errors gracefully

* Adding safe_execution contextmanager

* Fixing typo

* Adding qiita test checker

* Adapting some artifact handlers

* Abstracting the graph reloading and adding some documentation

* Fixing typo

* Fixing changing artifact visibility

* Fixing delete

* Fixing artifact deletion

* Adding default parameters to the commands

* Fixing processing page

* Fixing variable name

* fixing private/public studies

* Changing bdiv metrics to single choice

* sanbox-to-sandbox

* flake8

* Fixing patch

* fixing other issues

* adding share documentation

* psycopg2 <= 2.7

* psycopg2 < 2.7

* Various small fixes to be able to run tests on the plugins

* Adding private module

* Fixing processing job completion

* Fixing patch 52

* Fixing call

* Fixing complete

* small fixes

* Adding processing handlers

* Fixing url and bug on processing job workflow

* Adding the private script runner

* Adding is_analysis column to the command

* Adding retrieval of commands excluding analysis commands

* Addressing bug on retrieving information from redis

* Enabling the command register endpoint to provide if the command is analysis only

* Addressing @antgonza's comments

* Addressing @wasade's comments

* Supporting multiple choice

* Adding documentation

* Modifying handler to pass allow_change_optionals

* returning optional parameters

* Addressing bug found by @antgonza

* Enabling changing the default parameters

* Adding correct class

* Allowing user to change default parameters

* Fixing bug with commands listing

* Enabling arbitrary htmls in the summary

* Addressing @wasade's comments

* Addressing @antgonza's comment
antgonza pushed a commit that referenced this pull request Jun 1, 2017
@josenavas @antgonza
Analysis refactor sync with master - DEPENDS ON #2138 (#2139)
f5cff17 
* fix #1505

* improving some GUI stuff

* improving some GUI stuff - missing lines

* addressing all comments

* ready for review

* fix #1987

* initial commit

* requested changes

* fix filter job list

* Fixing server cert (#2051)

* fix get_studies

* flake8

* fix #503

* fix #2010

* fix #1913

* fix errors

* addressing @josenavas comment

* flake8

* fix #1010

* fix #1066 (#2058)

* addressing @josenavas comments

* fix #1961

* fix #1837

* Automatic jobs & new stats (#2057)

* fix #814, fix #1636

* fixing error in test-env

* fixing stats.html call

* adding img

* addressing @josenavas comments

* rm for loops

* addresssing @ElDeveloper comments

* generalizing this functionality

* fix #1805

* adding button

* fix errors

* fix #1816

* fixing failures tests

* fix #1959

* addressing @josenavas comments

* addressing @josenavas comments

* fixing error

* fixed?

* addressing @josenavas comments

* addressing @wasade comments

* fix flake8

* generate biom and metadata release (#2066)

* initial commit

* adding portal

* addressing @josenavas comments

* pid -> qiita_artifact_id

* addressing @josenavas comments

* addressing @ElDeveloper comments

* rm 50.sql

* database changes to fix 969

* adding delete

* addressing @josenavas comments

* addressing @ElDeveloper comments

* duh!

* fix generate_biom_and_metadata_release (#2072)

* fix generate_biom_and_metadata_release

* addressing @ElDeveloper comment

* Removing qiita ware code that will not be used anymore

* Organizing the handlers and new analysis description page

* fixing timestamp

* rm formats

* st -> pt

* Connecting the analysis creation and making interface responsive

* Addressing @antgonza's comments

* Initial artifact GUI refactor

* Removing unused code

* moving to ISO 8601 - wow :'(

* fix errors

* addressing @wasade comments

* Adding can_edit call to the analysis

* Fixing artifact rest API since not all artifacts have study

* Adding can_be_publicized call to analysis

* Adding QiitaHTTPError to handle errors gracefully

* Adding safe_execution contextmanager

* Fixing typo

* Adding qiita test checker

* Adapting some artifact handlers

* Abstracting the graph reloading and adding some documentation

* Fixing typo

* Fixing changing artifact visibility

* Fixing delete

* Fixing artifact deletion

* Adding default parameters to the commands

* Fixing processing page

* Fixing variable name

* fixing private/public studies

* Changing bdiv metrics to single choice

* sanbox-to-sandbox

* flake8

* Fixing patch

* fixing other issues

* adding share documentation

* psycopg2 <= 2.7

* psycopg2 < 2.7

* Various small fixes to be able to run tests on the plugins

* Adding private module

* Fixing processing job completion

* Fixing patch 52

* Fixing call

* Fixing complete

* small fixes

* init commit

* fixing errors

* fixing errors due to update

* Making the download work

* Fixing tests

* working status

* adding tags, the right way!

* fix error

* Addressing @antgonza's comments

* Adding missing test

* Ignoring tgz - thanks @antgonza

* addressing @josenavas comments

* list study tags

* fix error

* adding tags to public

* adding docs

* addressing @wasade comment

* addressing @josenavas and @wasade comments

* addressing @wasade request

* fix #2091

* option 2: @ElDeveloper and @josenavas

* A minimal REST API for Qiita (#2094)

* TST: Add initial test cases for study handler

* ENH: Add initial study rest api

* API: test if a study exists

* ENH: oauth2 forced

* Get back basic study deets

* TST: test for samples collection

* API: rest get sample IDs from a study

* ENH: samples/info handler

* broken routes

* API: request sample metadata

* ENH/API: Add methods to check for a study person

* ENH/API: Add POST methods for study person

* TST: Add tests for from_name_and_affiliation

* TST: study creation

* BUG: Add headers to tests

* ENH: create study

* Adjust GET on study description

* API: Add endpoints for preparation creation

* TST: 200 :D

* TST: Correctly verify study instantiation

* TST: prep artifact creation

* ENH/API: associate artifacts with a preparation

* TST: test study statys

* ENH: study status

* Removed trailing whitespace

* STY: PEP8

* MAINT: refactor, centralize setup boilerplate

* REFACTOR: Remove repeated code

* DOC: Remove unnecessary comments

* REFACTOR: Missing removal of pattern

* STY: Fix PEP8 errors

* BUG: Incorrectly changed error code

* BUG/TST: Fix typo in tests

* Addressing an @antgonza comment

* Another @antgonza comment

* RVW: Address review comments

* ENH: Cleanup webserver and name-spaces

* ENH: Improve error messages

* ENH: Add more descriptive error message

* TST: Exercise different argument types

* DOC: Add documentation for REST API

* ENH: Remove extra comma

* ENH/DOC: update/add samples to sample information via rest (#2097)

* Changing how artifact visibility works (#2098)

* changing how artifact visibility works

* fixing code

* fix errors

* fixing edit check access

* fix

* fix #2086

* flak8

* addressing @ElDeveloper comments + fixes

* adding the final changes

* fix failures

* get_qiita_version -> generate_biom_and_metadata_release

* download raw data

* adding missing empty files

* Adding endpoint to retrieve list of person (#2103)

* Adding missing endpoint

* Addressing @ElDeveloper comment

* fix #2086 (#2102)

* fix #2086

* flak8

* addressing @ElDeveloper comments + fixes

* adding the final changes

* fix failures

* get_qiita_version -> generate_biom_and_metadata_release

* addressing @wasade comments and fix errors

* fix error?

* rm vfabu + addressing @wasade and @josenavas comments + fix errors

* just being dumb!

* Deblur quality mention (#2107)

* Revised rst values used for section headers (#2108)

* Adding processing handlers

* Fixing latlongs (#2120)

* public studies are being shown in the user own studies

* fix #2069 - adding tests

* flake8

* Fixing url and bug on processing job workflow

* Adding the private script runner

* Adding is_analysis column to the command

* Adding retrieval of commands excluding analysis commands

* Addressing bug on retrieving information from redis

* Enabling the command register endpoint to provide if the command is analysis only

* Improving study list speed (#2123)

* init commit

* reading if ...

* fixing tests

* rethinking listint

* split SQL

* reseting sql

* ignoring prep_total_samples

* finishing changes

* adding comment: @ElDeveloper

* adding message: @josenavas

* addressing @ElDeveloper, @josenavas @jdereus comments

* fixing download buttons show (#2127)

* fixing download buttons show

* addressing @ElDeveloper comment

* connecting tutorials to CMI

* adding link in main page

* fixing prep getting-started

* mv complex designs

* fix idents

* Addressing @antgonza's comments

* Addressing @wasade's comments

* Supporting multiple choice

* Adding documentation

* limiting number of jobs retrieved

* Modifying handler to pass allow_change_optionals

* returning optional parameters

* Addressing bug found by @antgonza

* Enabling changing the default parameters

* Adding correct class

* Allowing user to change default parameters

* Fixing bug with commands listing

* Enabling arbitrary htmls in the summary

* Prepping for merge hell

* Addressing @wasade's comments

* Addressing @antgonza's comment
antgonza pushed a commit that referenced this pull request Jun 1, 2017
@josenavas @antgonza
Analysis refactor sync w master 2 (#2141)
e7d31f2 
* fix #1505

* improving some GUI stuff

* improving some GUI stuff - missing lines

* addressing all comments

* ready for review

* fix #1987

* initial commit

* requested changes

* fix filter job list

* Fixing server cert (#2051)

* fix get_studies

* flake8

* fix #503

* fix #2010

* fix #1913

* fix errors

* addressing @josenavas comment

* flake8

* fix #1010

* fix #1066 (#2058)

* addressing @josenavas comments

* fix #1961

* fix #1837

* Automatic jobs & new stats (#2057)

* fix #814, fix #1636

* fixing error in test-env

* fixing stats.html call

* adding img

* addressing @josenavas comments

* rm for loops

* addresssing @ElDeveloper comments

* generalizing this functionality

* fix #1805

* adding button

* fix errors

* fix #1816

* fixing failures tests

* fix #1959

* addressing @josenavas comments

* addressing @josenavas comments

* fixing error

* fixed?

* addressing @josenavas comments

* addressing @wasade comments

* fix flake8

* generate biom and metadata release (#2066)

* initial commit

* adding portal

* addressing @josenavas comments

* pid -> qiita_artifact_id

* addressing @josenavas comments

* addressing @ElDeveloper comments

* rm 50.sql

* database changes to fix 969

* adding delete

* addressing @josenavas comments

* addressing @ElDeveloper comments

* duh!

* fix generate_biom_and_metadata_release (#2072)

* fix generate_biom_and_metadata_release

* addressing @ElDeveloper comment

* fixing timestamp

* rm formats

* st -> pt

* moving to ISO 8601 - wow :'(

* fix errors

* addressing @wasade comments

* fixing private/public studies

* sanbox-to-sandbox

* flake8

* fixing other issues

* adding share documentation

* psycopg2 <= 2.7

* psycopg2 < 2.7

* init commit

* fixing errors

* fixing errors due to update

* Making the download work

* Fixing tests

* working status

* adding tags, the right way!

* fix error

* Addressing @antgonza's comments

* Adding missing test

* Ignoring tgz - thanks @antgonza

* addressing @josenavas comments

* list study tags

* fix error

* adding tags to public

* adding docs

* addressing @wasade comment

* addressing @josenavas and @wasade comments

* addressing @wasade request

* fix #2091

* option 2: @ElDeveloper and @josenavas

* A minimal REST API for Qiita (#2094)

* TST: Add initial test cases for study handler

* ENH: Add initial study rest api

* API: test if a study exists

* ENH: oauth2 forced

* Get back basic study deets

* TST: test for samples collection

* API: rest get sample IDs from a study

* ENH: samples/info handler

* broken routes

* API: request sample metadata

* ENH/API: Add methods to check for a study person

* ENH/API: Add POST methods for study person

* TST: Add tests for from_name_and_affiliation

* TST: study creation

* BUG: Add headers to tests

* ENH: create study

* Adjust GET on study description

* API: Add endpoints for preparation creation

* TST: 200 :D

* TST: Correctly verify study instantiation

* TST: prep artifact creation

* ENH/API: associate artifacts with a preparation

* TST: test study statys

* ENH: study status

* Removed trailing whitespace

* STY: PEP8

* MAINT: refactor, centralize setup boilerplate

* REFACTOR: Remove repeated code

* DOC: Remove unnecessary comments

* REFACTOR: Missing removal of pattern

* STY: Fix PEP8 errors

* BUG: Incorrectly changed error code

* BUG/TST: Fix typo in tests

* Addressing an @antgonza comment

* Another @antgonza comment

* RVW: Address review comments

* ENH: Cleanup webserver and name-spaces

* ENH: Improve error messages

* ENH: Add more descriptive error message

* TST: Exercise different argument types

* DOC: Add documentation for REST API

* ENH: Remove extra comma

* ENH/DOC: update/add samples to sample information via rest (#2097)

* Changing how artifact visibility works (#2098)

* changing how artifact visibility works

* fixing code

* fix errors

* fixing edit check access

* fix

* fix #2086

* flak8

* addressing @ElDeveloper comments + fixes

* adding the final changes

* fix failures

* get_qiita_version -> generate_biom_and_metadata_release

* download raw data

* adding missing empty files

* Adding endpoint to retrieve list of person (#2103)

* Adding missing endpoint

* Addressing @ElDeveloper comment

* fix #2086 (#2102)

* fix #2086

* flak8

* addressing @ElDeveloper comments + fixes

* adding the final changes

* fix failures

* get_qiita_version -> generate_biom_and_metadata_release

* addressing @wasade comments and fix errors

* fix error?

* rm vfabu + addressing @wasade and @josenavas comments + fix errors

* just being dumb!

* Deblur quality mention (#2107)

* Revised rst values used for section headers (#2108)

* Fixing latlongs (#2120)

* public studies are being shown in the user own studies

* fix #2069 - adding tests

* flake8

* Improving study list speed (#2123)

* init commit

* reading if ...

* fixing tests

* rethinking listint

* split SQL

* reseting sql

* ignoring prep_total_samples

* finishing changes

* adding comment: @ElDeveloper

* adding message: @josenavas

* addressing @ElDeveloper, @josenavas @jdereus comments

* fixing download buttons show (#2127)

* fixing download buttons show

* addressing @ElDeveloper comment

* connecting tutorials to CMI

* adding link in main page

* fixing prep getting-started

* mv complex designs

* fix idents

* limiting number of jobs retrieved
antgonza pushed a commit that referenced this pull request Jul 21, 2017
@josenavas @antgonza
Analysis refactor db (#2040) (#2067)
8ad7064 
* Analysis refactor db (#2040)

* New DB structure

* Adding python patch

* Adding a biom so we can actually execute the patch

* Fixing the patch to correctly transfer the information from the old structure to the new one

* Fixing patch

* Fixing patch and a few other bits to make the patch run successfully

* These files are no longer needed

* Droping analysis status table

* Linking the analysis with all the artifacts

* Fixing typo

* Fixing HTML and dbschema files

* Adding analyisis jobs

* Adding logging column to the analysis

* Addressing @antgonza's comments

* Taking into account non-phylogenetic metrics in beta diversity

* Analysis refactor fix analysis (#2044)

* New DB structure

* Adding python patch

* Adding a biom so we can actually execute the patch

* Fixing the patch to correctly transfer the information from the old structure to the new one

* Fixing patch

* Fixing patch and a few other bits to make the patch run successfully

* These files are no longer needed

* Removing unused code

* Droping analysis status table

* Linking the analysis with all the artifacts

* Fixing typo

* Fixing HTML and dbschema files

* Adding analyisis jobs

* Extending the artifact to work with the analysis

* Allowing multiomics datatype

* Adding private_job_submitter and modifying proc job handler to use it

* Adding logging column to the analysis

* Adding datatype to the analysis-processing job table

* Adding REST endpoint to access the analysis metadata

* Adding private jobs to plugin

* Fixing typo

* Fixing the processing jobs complete

* Addressing @antgonza's comments

* Taking into account non-phylogenetic metrics in beta diversity

* Addressing @antgonza's comments

* Addressing @ElDeveloper's comments

* Remove old job code (#2045)

* New DB structure

* Adding python patch

* Adding a biom so we can actually execute the patch

* Fixing the patch to correctly transfer the information from the old structure to the new one

* Fixing patch

* Fixing patch and a few other bits to make the patch run successfully

* These files are no longer needed

* Removing unused code

* Droping analysis status table

* Linking the analysis with all the artifacts

* Fixing typo

* Fixing HTML and dbschema files

* Adding analyisis jobs

* Extending the artifact to work with the analysis

* Allowing multiomics datatype

* Adding private_job_submitter and modifying proc job handler to use it

* Adding logging column to the analysis

* Adding datatype to the analysis-processing job table

* Adding REST endpoint to access the analysis metadata

* Adding private jobs to plugin

* Fixing typo

* Fixing the processing jobs complete

* Removing the old job code

* Oops removed the wrong file

* Addressing @antgonza's comments

* Taking into account non-phylogenetic metrics in beta diversity

* Addressing @antgonza's comments

* Fixes Qiita db (#2046)

* New DB structure

* Adding python patch

* Adding a biom so we can actually execute the patch

* Fixing the patch to correctly transfer the information from the old structure to the new one

* Fixing patch

* Fixing patch and a few other bits to make the patch run successfully

* These files are no longer needed

* Removing unused code

* Droping analysis status table

* Linking the analysis with all the artifacts

* Fixing typo

* Fixing HTML and dbschema files

* Adding analyisis jobs

* Extending the artifact to work with the analysis

* Allowing multiomics datatype

* Adding private_job_submitter and modifying proc job handler to use it

* Adding logging column to the analysis

* Adding datatype to the analysis-processing job table

* Adding REST endpoint to access the analysis metadata

* Adding private jobs to plugin

* Fixing typo

* Fixing the processing jobs complete

* Removing the old job code

* Oops removed the wrong file

* Removing QiitaStatusObject because it is not used

* fixing metautil

* Fixing porntal, setup and sql tests

* Fixing user and util

* Fixing qiita_db

* Addressing @antgonza's comments

* Taking into account non-phylogenetic metrics in beta diversity

* Addressing @antgonza's comments

* Analysis refactor master (#2070)

* fix #1505

* improving some GUI stuff

* improving some GUI stuff - missing lines

* addressing all comments

* ready for review

* New DB structure

* Adding python patch

* Adding a biom so we can actually execute the patch

* Fixing the patch to correctly transfer the information from the old structure to the new one

* Fixing patch

* Fixing patch and a few other bits to make the patch run successfully

* These files are no longer needed

* Removing unused code

* Droping analysis status table

* Linking the analysis with all the artifacts

* Fixing typo

* Fixing HTML and dbschema files

* Adding analyisis jobs

* Extending the artifact to work with the analysis

* Allowing multiomics datatype

* Adding private_job_submitter and modifying proc job handler to use it

* Adding logging column to the analysis

* Adding datatype to the analysis-processing job table

* Adding REST endpoint to access the analysis metadata

* Adding private jobs to plugin

* Fixing typo

* Fixing the processing jobs complete

* Removing the old job code

* Oops removed the wrong file

* Removing QiitaStatusObject because it is not used

* fixing metautil

* Fixing porntal, setup and sql tests

* Fixing user and util

* Fixing qiita_db

* fix #1987

* Updating to master

* Addressing @antgonza's comments

* initial commit

* requested changes

* fix filter job list

* Fixing server cert (#2051)

* fix get_studies

* flake8

* fix #503

* fix #2010

* fix #1913

* fix errors

* addressing @josenavas comment

* flake8

* fix #1010

* fix #1066 (#2058)

* addressing @josenavas comments

* fix #1961

* fix #1837

* Automatic jobs & new stats (#2057)

* fix #814, fix #1636

* fixing error in test-env

* fixing stats.html call

* adding img

* addressing @josenavas comments

* rm for loops

* addresssing @ElDeveloper comments

* generalizing this functionality

* fix #1816

* Taking into account non-phylogenetic metrics in beta diversity

* fix #1959

* Addressing @antgonza's comments

* addressing @josenavas comments

* addressing @josenavas comments

* fixing error

* fixed?

* addressing @josenavas comments

* Actually fixing merge conflicts

* addressing @wasade comments

* fix flake8

* generate biom and metadata release (#2066)

* initial commit

* adding portal

* addressing @josenavas comments

* pid -> qiita_artifact_id

* addressing @josenavas comments

* addressing @ElDeveloper comments

* rm 50.sql

* database changes to fix 969

* adding delete

* addressing @josenavas comments

* addressing @ElDeveloper comments

* duh!

* Sync-ing with master (again) (#2073)

* fix #1505

* improving some GUI stuff

* improving some GUI stuff - missing lines

* addressing all comments

* ready for review

* fix #1987

* initial commit

* requested changes

* fix filter job list

* Fixing server cert (#2051)

* fix get_studies

* flake8

* fix #503

* fix #2010

* fix #1913

* fix errors

* addressing @josenavas comment

* flake8

* fix #1010

* fix #1066 (#2058)

* addressing @josenavas comments

* fix #1961

* fix #1837

* Automatic jobs & new stats (#2057)

* fix #814, fix #1636

* fixing error in test-env

* fixing stats.html call

* adding img

* addressing @josenavas comments

* rm for loops

* addresssing @ElDeveloper comments

* generalizing this functionality

* fix #1816

* fix #1959

* addressing @josenavas comments

* addressing @josenavas comments

* fixing error

* fixed?

* addressing @josenavas comments

* addressing @wasade comments

* fix flake8

* generate biom and metadata release (#2066)

* initial commit

* adding portal

* addressing @josenavas comments

* pid -> qiita_artifact_id

* addressing @josenavas comments

* addressing @ElDeveloper comments

* rm 50.sql

* database changes to fix 969

* adding delete

* addressing @josenavas comments

* addressing @ElDeveloper comments

* duh!

* fix generate_biom_and_metadata_release (#2072)

* fix generate_biom_and_metadata_release

* addressing @ElDeveloper comment

* Removing qiita ware code that will not be used anymore

* Fix qiita ware (#2074)

* fix #1505

* improving some GUI stuff

* improving some GUI stuff - missing lines

* addressing all comments

* ready for review

* fix #1987

* initial commit

* requested changes

* fix filter job list

* Fixing server cert (#2051)

* fix get_studies

* flake8

* fix #503

* fix #2010

* fix #1913

* fix errors

* addressing @josenavas comment

* flake8

* fix #1010

* fix #1066 (#2058)

* addressing @josenavas comments

* fix #1961

* fix #1837

* Automatic jobs & new stats (#2057)

* fix #814, fix #1636

* fixing error in test-env

* fixing stats.html call

* adding img

* addressing @josenavas comments

* rm for loops

* addresssing @ElDeveloper comments

* generalizing this functionality

* fix #1816

* fix #1959

* addressing @josenavas comments

* addressing @josenavas comments

* fixing error

* fixed?

* addressing @josenavas comments

* addressing @wasade comments

* fix flake8

* generate biom and metadata release (#2066)

* initial commit

* adding portal

* addressing @josenavas comments

* pid -> qiita_artifact_id

* addressing @josenavas comments

* addressing @ElDeveloper comments

* rm 50.sql

* database changes to fix 969

* adding delete

* addressing @josenavas comments

* addressing @ElDeveloper comments

* duh!

* fix generate_biom_and_metadata_release (#2072)

* fix generate_biom_and_metadata_release

* addressing @ElDeveloper comment

* Removing qiita ware code that will not be used anymore

* Organizing the handlers and new analysis description page

* Connecting the analysis creation and making interface responsive

* Addressing @antgonza's comments

* Initial artifact GUI refactor

* Removing unused code

* Analysis refactor GUI part1 (#2076)

* fix #1505

* improving some GUI stuff

* improving some GUI stuff - missing lines

* addressing all comments

* ready for review

* fix #1987

* initial commit

* requested changes

* fix filter job list

* Fixing server cert (#2051)

* fix get_studies

* flake8

* fix #503

* fix #2010

* fix #1913

* fix errors

* addressing @josenavas comment

* flake8

* fix #1010

* fix #1066 (#2058)

* addressing @josenavas comments

* fix #1961

* fix #1837

* Automatic jobs & new stats (#2057)

* fix #814, fix #1636

* fixing error in test-env

* fixing stats.html call

* adding img

* addressing @josenavas comments

* rm for loops

* addresssing @ElDeveloper comments

* generalizing this functionality

* fix #1816

* fix #1959

* addressing @josenavas comments

* addressing @josenavas comments

* fixing error

* fixed?

* addressing @josenavas comments

* addressing @wasade comments

* fix flake8

* generate biom and metadata release (#2066)

* initial commit

* adding portal

* addressing @josenavas comments

* pid -> qiita_artifact_id

* addressing @josenavas comments

* addressing @ElDeveloper comments

* rm 50.sql

* database changes to fix 969

* adding delete

* addressing @josenavas comments

* addressing @ElDeveloper comments

* duh!

* fix generate_biom_and_metadata_release (#2072)

* fix generate_biom_and_metadata_release

* addressing @ElDeveloper comment

* Removing qiita ware code that will not be used anymore

* Organizing the handlers and new analysis description page

* Addressing @antgonza's comments

* Adding can_edit call to the analysis

* Fixing artifact rest API since not all artifacts have study

* Adding can_be_publicized call to analysis

* Adding QiitaHTTPError to handle errors gracefully

* Adding safe_execution contextmanager

* Fixing typo

* Adding qiita test checker

* Adapting some artifact handlers

* Abstracting the graph reloading and adding some documentation

* Fixing typo

* Fixing changing artifact visibility

* Fixing delete

* Fixing artifact deletion

* Adding default parameters to the commands

* Fixing processing page

* Fixing variable name

* Analysis refactor GUI part2 (#2077)

* fix #1505

* improving some GUI stuff

* improving some GUI stuff - missing lines

* addressing all comments

* ready for review

* fix #1987

* initial commit

* requested changes

* fix filter job list

* Fixing server cert (#2051)

* fix get_studies

* flake8

* fix #503

* fix #2010

* fix #1913

* fix errors

* addressing @josenavas comment

* flake8

* fix #1010

* fix #1066 (#2058)

* addressing @josenavas comments

* fix #1961

* fix #1837

* Automatic jobs & new stats (#2057)

* fix #814, fix #1636

* fixing error in test-env

* fixing stats.html call

* adding img

* addressing @josenavas comments

* rm for loops

* addresssing @ElDeveloper comments

* generalizing this functionality

* fix #1816

* fix #1959

* addressing @josenavas comments

* addressing @josenavas comments

* fixing error

* fixed?

* addressing @josenavas comments

* addressing @wasade comments

* fix flake8

* generate biom and metadata release (#2066)

* initial commit

* adding portal

* addressing @josenavas comments

* pid -> qiita_artifact_id

* addressing @josenavas comments

* addressing @ElDeveloper comments

* rm 50.sql

* database changes to fix 969

* adding delete

* addressing @josenavas comments

* addressing @ElDeveloper comments

* duh!

* fix generate_biom_and_metadata_release (#2072)

* fix generate_biom_and_metadata_release

* addressing @ElDeveloper comment

* Removing qiita ware code that will not be used anymore

* Organizing the handlers and new analysis description page

* Connecting the analysis creation and making interface responsive

* Addressing @antgonza's comments

* Removing unused code

* Changing bdiv metrics to single choice

* Fixing patch

* Various small fixes to be able to run tests on the plugins

* Adding private module

* Fixing processing job completion

* Fixing patch 52

* Fixing call

* Fixing complete

* small fixes

* Analysis refactor gui part3 (#2078)

* fix #1505

* improving some GUI stuff

* improving some GUI stuff - missing lines

* addressing all comments

* ready for review

* fix #1987

* initial commit

* requested changes

* fix filter job list

* Fixing server cert (#2051)

* fix get_studies

* flake8

* fix #503

* fix #2010

* fix #1913

* fix errors

* addressing @josenavas comment

* flake8

* fix #1010

* fix #1066 (#2058)

* addressing @josenavas comments

* fix #1961

* fix #1837

* Automatic jobs & new stats (#2057)

* fix #814, fix #1636

* fixing error in test-env

* fixing stats.html call

* adding img

* addressing @josenavas comments

* rm for loops

* addresssing @ElDeveloper comments

* generalizing this functionality

* fix #1816

* fix #1959

* addressing @josenavas comments

* addressing @josenavas comments

* fixing error

* fixed?

* addressing @josenavas comments

* addressing @wasade comments

* fix flake8

* generate biom and metadata release (#2066)

* initial commit

* adding portal

* addressing @josenavas comments

* pid -> qiita_artifact_id

* addressing @josenavas comments

* addressing @ElDeveloper comments

* rm 50.sql

* database changes to fix 969

* adding delete

* addressing @josenavas comments

* addressing @ElDeveloper comments

* duh!

* fix generate_biom_and_metadata_release (#2072)

* fix generate_biom_and_metadata_release

* addressing @ElDeveloper comment

* Removing qiita ware code that will not be used anymore

* Organizing the handlers and new analysis description page

* Connecting the analysis creation and making interface responsive

* Addressing @antgonza's comments

* Initial artifact GUI refactor

* Removing unused code

* Adding can_edit call to the analysis

* Fixing artifact rest API since not all artifacts have study

* Adding can_be_publicized call to analysis

* Adding QiitaHTTPError to handle errors gracefully

* Adding safe_execution contextmanager

* Fixing typo

* Adding qiita test checker

* Adapting some artifact handlers

* Fixing typo

* Addressing @antgonza's comments

* Addressing @antgonza's comments

* Analysis refactor gui part4 (#2079)

* fix #1505

* improving some GUI stuff

* improving some GUI stuff - missing lines

* addressing all comments

* ready for review

* fix #1987

* initial commit

* requested changes

* fix filter job list

* Fixing server cert (#2051)

* fix get_studies

* flake8

* fix #503

* fix #2010

* fix #1913

* fix errors

* addressing @josenavas comment

* flake8

* fix #1010

* fix #1066 (#2058)

* addressing @josenavas comments

* fix #1961

* fix #1837

* Automatic jobs & new stats (#2057)

* fix #814, fix #1636

* fixing error in test-env

* fixing stats.html call

* adding img

* addressing @josenavas comments

* rm for loops

* addresssing @ElDeveloper comments

* generalizing this functionality

* fix #1816

* fix #1959

* addressing @josenavas comments

* addressing @josenavas comments

* fixing error

* fixed?

* addressing @josenavas comments

* addressing @wasade comments

* fix flake8

* generate biom and metadata release (#2066)

* initial commit

* adding portal

* addressing @josenavas comments

* pid -> qiita_artifact_id

* addressing @josenavas comments

* addressing @ElDeveloper comments

* rm 50.sql

* database changes to fix 969

* adding delete

* addressing @josenavas comments

* addressing @ElDeveloper comments

* duh!

* fix generate_biom_and_metadata_release (#2072)

* fix generate_biom_and_metadata_release

* addressing @ElDeveloper comment

* Removing qiita ware code that will not be used anymore

* Organizing the handlers and new analysis description page

* Connecting the analysis creation and making interface responsive

* Addressing @antgonza's comments

* Initial artifact GUI refactor

* Removing unused code

* Adding can_edit call to the analysis

* Fixing artifact rest API since not all artifacts have study

* Adding can_be_publicized call to analysis

* Adding QiitaHTTPError to handle errors gracefully

* Adding safe_execution contextmanager

* Fixing typo

* Adding qiita test checker

* Adapting some artifact handlers

* Abstracting the graph reloading and adding some documentation

* Fixing typo

* Fixing changing artifact visibility

* Fixing delete

* Fixing artifact deletion

* Analysis refactor gui part5 (#2115)

* fix #1505

* improving some GUI stuff

* improving some GUI stuff - missing lines

* addressing all comments

* ready for review

* fix #1987

* initial commit

* requested changes

* fix filter job list

* Fixing server cert (#2051)

* fix get_studies

* flake8

* fix #503

* fix #2010

* fix #1913

* fix errors

* addressing @josenavas comment

* flake8

* fix #1010

* fix #1066 (#2058)

* addressing @josenavas comments

* fix #1961

* fix #1837

* Automatic jobs & new stats (#2057)

* fix #814, fix #1636

* fixing error in test-env

* fixing stats.html call

* adding img

* addressing @josenavas comments

* rm for loops

* addresssing @ElDeveloper comments

* generalizing this functionality

* fix #1816

* fix #1959

* addressing @josenavas comments

* addressing @josenavas comments

* fixing error

* fixed?

* addressing @josenavas comments

* addressing @wasade comments

* fix flake8

* generate biom and metadata release (#2066)

* initial commit

* adding portal

* addressing @josenavas comments

* pid -> qiita_artifact_id

* addressing @josenavas comments

* addressing @ElDeveloper comments

* rm 50.sql

* database changes to fix 969

* adding delete

* addressing @josenavas comments

* addressing @ElDeveloper comments

* duh!

* fix generate_biom_and_metadata_release (#2072)

* fix generate_biom_and_metadata_release

* addressing @ElDeveloper comment

* Removing qiita ware code that will not be used anymore

* Organizing the handlers and new analysis description page

* Connecting the analysis creation and making interface responsive

* Addressing @antgonza's comments

* Initial artifact GUI refactor

* Removing unused code

* Adding can_edit call to the analysis

* Fixing artifact rest API since not all artifacts have study

* Adding can_be_publicized call to analysis

* Adding QiitaHTTPError to handle errors gracefully

* Adding safe_execution contextmanager

* Fixing typo

* Adding qiita test checker

* Adapting some artifact handlers

* Abstracting the graph reloading and adding some documentation

* Fixing typo

* Fixing changing artifact visibility

* Fixing delete

* Fixing artifact deletion

* Adding default parameters to the commands

* Fixing processing page

* Fixing variable name

* Changing bdiv metrics to single choice

* Fixing patch

* Various small fixes to be able to run tests on the plugins

* Addressing @antgonza's comments

* Analysis refactor gui part6 (#2116)

* fix #1505

* improving some GUI stuff

* improving some GUI stuff - missing lines

* addressing all comments

* ready for review

* fix #1987

* initial commit

* requested changes

* fix filter job list

* Fixing server cert (#2051)

* fix get_studies

* flake8

* fix #503

* fix #2010

* fix #1913

* fix errors

* addressing @josenavas comment

* flake8

* fix #1010

* fix #1066 (#2058)

* addressing @josenavas comments

* fix #1961

* fix #1837

* Automatic jobs & new stats (#2057)

* fix #814, fix #1636

* fixing error in test-env

* fixing stats.html call

* adding img

* addressing @josenavas comments

* rm for loops

* addresssing @ElDeveloper comments

* generalizing this functionality

* fix #1816

* fix #1959

* addressing @josenavas comments

* addressing @josenavas comments

* fixing error

* fixed?

* addressing @josenavas comments

* addressing @wasade comments

* fix flake8

* generate biom and metadata release (#2066)

* initial commit

* adding portal

* addressing @josenavas comments

* pid -> qiita_artifact_id

* addressing @josenavas comments

* addressing @ElDeveloper comments

* rm 50.sql

* database changes to fix 969

* adding delete

* addressing @josenavas comments

* addressing @ElDeveloper comments

* duh!

* fix generate_biom_and_metadata_release (#2072)

* fix generate_biom_and_metadata_release

* addressing @ElDeveloper comment

* Removing qiita ware code that will not be used anymore

* Organizing the handlers and new analysis description page

* fixing timestamp

* rm formats

* st -> pt

* Connecting the analysis creation and making interface responsive

* Addressing @antgonza's comments

* Initial artifact GUI refactor

* Removing unused code

* moving to ISO 8601 - wow :'(

* fix errors

* addressing @wasade comments

* Adding can_edit call to the analysis

* Fixing artifact rest API since not all artifacts have study

* Adding can_be_publicized call to analysis

* Adding QiitaHTTPError to handle errors gracefully

* Adding safe_execution contextmanager

* Fixing typo

* Adding qiita test checker

* Adapting some artifact handlers

* Abstracting the graph reloading and adding some documentation

* Fixing typo

* Fixing changing artifact visibility

* Fixing delete

* Fixing artifact deletion

* Adding default parameters to the commands

* Fixing processing page

* Fixing variable name

* fixing private/public studies

* Changing bdiv metrics to single choice

* sanbox-to-sandbox

* flake8

* Fixing patch

* fixing other issues

* adding share documentation

* psycopg2 <= 2.7

* psycopg2 < 2.7

* Various small fixes to be able to run tests on the plugins

* Solving merge conflicts

* Adding processing handlers

* Fixing url and bug on processing job workflow

* Adding the private script runner

* Adding is_analysis column to the command

* Adding retrieval of commands excluding analysis commands

* Addressing bug on retrieving information from redis

* Enabling the command register endpoint to provide if the command is analysis only

* Addressing @antgonza's comments

* Addressing @wasade's comments

* Supporting multiple choice

* Adding documentation

* Analysis refactor gui part7 (#2117)

* fix #1505

* improving some GUI stuff

* improving some GUI stuff - missing lines

* addressing all comments

* ready for review

* fix #1987

* initial commit

* requested changes

* fix filter job list

* Fixing server cert (#2051)

* fix get_studies

* flake8

* fix #503

* fix #2010

* fix #1913

* fix errors

* addressing @josenavas comment

* flake8

* fix #1010

* fix #1066 (#2058)

* addressing @josenavas comments

* fix #1961

* fix #1837

* Automatic jobs & new stats (#2057)

* fix #814, fix #1636

* fixing error in test-env

* fixing stats.html call

* adding img

* addressing @josenavas comments

* rm for loops

* addresssing @ElDeveloper comments

* generalizing this functionality

* fix #1816

* fix #1959

* addressing @josenavas comments

* addressing @josenavas comments

* fixing error

* fixed?

* addressing @josenavas comments

* addressing @wasade comments

* fix flake8

* generate biom and metadata release (#2066)

* initial commit

* adding portal

* addressing @josenavas comments

* pid -> qiita_artifact_id

* addressing @josenavas comments

* addressing @ElDeveloper comments

* rm 50.sql

* database changes to fix 969

* adding delete

* addressing @josenavas comments

* addressing @ElDeveloper comments

* duh!

* fix generate_biom_and_metadata_release (#2072)

* fix generate_biom_and_metadata_release

* addressing @ElDeveloper comment

* Removing qiita ware code that will not be used anymore

* Organizing the handlers and new analysis description page

* fixing timestamp

* rm formats

* st -> pt

* Connecting the analysis creation and making interface responsive

* Addressing @antgonza's comments

* Initial artifact GUI refactor

* Removing unused code

* moving to ISO 8601 - wow :'(

* fix errors

* addressing @wasade comments

* Adding can_edit call to the analysis

* Fixing artifact rest API since not all artifacts have study

* Adding can_be_publicized call to analysis

* Adding QiitaHTTPError to handle errors gracefully

* Adding safe_execution contextmanager

* Fixing typo

* Adding qiita test checker

* Adapting some artifact handlers

* Abstracting the graph reloading and adding some documentation

* Fixing typo

* Fixing changing artifact visibility

* Fixing delete

* Fixing artifact deletion

* Adding default parameters to the commands

* Fixing processing page

* Fixing variable name

* fixing private/public studies

* Changing bdiv metrics to single choice

* sanbox-to-sandbox

* flake8

* Fixing patch

* fixing other issues

* adding share documentation

* psycopg2 <= 2.7

* psycopg2 < 2.7

* Various small fixes to be able to run tests on the plugins

* Adding private module

* Fixing processing job completion

* Fixing patch 52

* Fixing call

* Fixing complete

* small fixes

* Adding processing handlers

* Fixing url and bug on processing job workflow

* Adding the private script runner

* Adding is_analysis column to the command

* Adding retrieval of commands excluding analysis commands

* Addressing bug on retrieving information from redis

* Enabling the command register endpoint to provide if the command is analysis only

* Addressing @antgonza's comments

* Addressing @wasade's comments

* Modifying handler to pass allow_change_optionals

* returning optional parameters

* Addressing bug found by @antgonza

* Enabling changing the default parameters

* Adding correct class

* Allowing user to change default parameters

* Fixing bug with commands listing

* Enabling arbitrary htmls in the summary

* Prepping for merge hell

* Addressing @wasade's comments

* Fixing qiita_db tests

* Analysis refactor allow users change dflt params (#2136)

* fix #1505

* improving some GUI stuff

* improving some GUI stuff - missing lines

* addressing all comments

* ready for review

* fix #1987

* initial commit

* requested changes

* fix filter job list

* Fixing server cert (#2051)

* fix get_studies

* flake8

* fix #503

* fix #2010

* fix #1913

* fix errors

* addressing @josenavas comment

* flake8

* fix #1010

* fix #1066 (#2058)

* addressing @josenavas comments

* fix #1961

* fix #1837

* Automatic jobs & new stats (#2057)

* fix #814, fix #1636

* fixing error in test-env

* fixing stats.html call

* adding img

* addressing @josenavas comments

* rm for loops

* addresssing @ElDeveloper comments

* generalizing this functionality

* fix #1816

* fix #1959

* addressing @josenavas comments

* addressing @josenavas comments

* fixing error

* fixed?

* addressing @josenavas comments

* addressing @wasade comments

* fix flake8

* generate biom and metadata release (#2066)

* initial commit

* adding portal

* addressing @josenavas comments

* pid -> qiita_artifact_id

* addressing @josenavas comments

* addressing @ElDeveloper comments

* rm 50.sql

* database changes to fix 969

* adding delete

* addressing @josenavas comments

* addressing @ElDeveloper comments

* duh!

* fix generate_biom_and_metadata_release (#2072)

* fix generate_biom_and_metadata_release

* addressing @ElDeveloper comment

* Removing qiita ware code that will not be used anymore

* Organizing the handlers and new analysis description page

* fixing timestamp

* rm formats

* st -> pt

* Connecting the analysis creation and making interface responsive

* Addressing @antgonza's comments

* Initial artifact GUI refactor

* Removing unused code

* moving to ISO 8601 - wow :'(

* fix errors

* addressing @wasade comments

* Adding can_edit call to the analysis

* Fixing artifact rest API since not all artifacts have study

* Adding can_be_publicized call to analysis

* Adding QiitaHTTPError to handle errors gracefully

* Adding safe_execution contextmanager

* Fixing typo

* Adding qiita test checker

* Adapting some artifact handlers

* Abstracting the graph reloading and adding some documentation

* Fixing typo

* Fixing changing artifact visibility

* Fixing delete

* Fixing artifact deletion

* Adding default parameters to the commands

* Fixing processing page

* Fixing variable name

* fixing private/public studies

* Changing bdiv metrics to single choice

* sanbox-to-sandbox

* flake8

* Fixing patch

* fixing other issues

* adding share documentation

* psycopg2 <= 2.7

* psycopg2 < 2.7

* Various small fixes to be able to run tests on the plugins

* Adding private module

* Fixing processing job completion

* Fixing patch 52

* Fixing call

* Fixing complete

* small fixes

* Adding processing handlers

* Fixing url and bug on processing job workflow

* Adding the private script runner

* Adding is_analysis column to the command

* Adding retrieval of commands excluding analysis commands

* Addressing bug on retrieving information from redis

* Enabling the command register endpoint to provide if the command is analysis only

* Addressing @antgonza's comments

* Addressing @wasade's comments

* Supporting multiple choice

* Adding documentation

* Modifying handler to pass allow_change_optionals

* returning optional parameters

* Addressing bug found by @antgonza

* Enabling changing the default parameters

* Adding correct class

* Allowing user to change default parameters

* Fixing bug with commands listing

* Addressing @wasade's comments

* Addressing @antgonza's comment

* Solving a few more tests

* Arbitrary summary HTML (#2138)

* fix #1505

* improving some GUI stuff

* improving some GUI stuff - missing lines

* addressing all comments

* ready for review

* fix #1987

* initial commit

* requested changes

* fix filter job list

* Fixing server cert (#2051)

* fix get_studies

* flake8

* fix #503

* fix #2010

* fix #1913

* fix errors

* addressing @josenavas comment

* flake8

* fix #1010

* fix #1066 (#2058)

* addressing @josenavas comments

* fix #1961

* fix #1837

* Automatic jobs & new stats (#2057)

* fix #814, fix #1636

* fixing error in test-env

* fixing stats.html call

* adding img

* addressing @josenavas comments

* rm for loops

* addresssing @ElDeveloper comments

* generalizing this functionality

* fix #1816

* fix #1959

* addressing @josenavas comments

* addressing @josenavas comments

* fixing error

* fixed?

* addressing @josenavas comments

* addressing @wasade comments

* fix flake8

* generate biom and metadata release (#2066)

* initial commit

* adding portal

* addressing @josenavas comments

* pid -> qiita_artifact_id

* addressing @josenavas comments

* addressing @ElDeveloper comments

* rm 50.sql

* database changes to fix 969

* adding delete

* addressing @josenavas comments

* addressing @ElDeveloper comments

* duh!

* fix generate_biom_and_metadata_release (#2072)

* fix generate_biom_and_metadata_release

* addressing @ElDeveloper comment

* Removing qiita ware code that will not be used anymore

* Organizing the handlers and new analysis description page

* fixing timestamp

* rm formats

* st -> pt

* Connecting the analysis creation and making interface responsive

* Addressing @antgonza's comments

* Initial artifact GUI refactor

* Removing unused code

* moving to ISO 8601 - wow :'(

* fix errors

* addressing @wasade comments

* Adding can_edit call to the analysis

* Fixing artifact rest API since not all artifacts have study

* Adding can_be_publicized call to analysis

* Adding QiitaHTTPError to handle errors gracefully

* Adding safe_execution contextmanager

* Fixing typo

* Adding qiita test checker

* Adapting some artifact handlers

* Abstracting the graph reloading and adding some documentation

* Fixing typo

* Fixing changing artifact visibility

* Fixing delete

* Fixing artifact deletion

* Adding default parameters to the commands

* Fixing processing page

* Fixing variable name

* fixing private/public studies

* Changing bdiv metrics to single choice

* sanbox-to-sandbox

* flake8

* Fixing patch

* fixing other issues

* adding share documentation

* psycopg2 <= 2.7

* psycopg2 < 2.7

* Various small fixes to be able to run tests on the plugins

* Adding private module

* Fixing processing job completion

* Fixing patch 52

* Fixing call

* Fixing complete

* small fixes

* Adding processing handlers

* Fixing url and bug on processing job workflow

* Adding the private script runner

* Adding is_analysis column to the command

* Adding retrieval of commands excluding analysis commands

* Addressing bug on retrieving information from redis

* Enabling the command register endpoint to provide if the command is analysis only

* Addressing @antgonza's comments

* Addressing @wasade's comments

* Supporting multiple choice

* Adding documentation

* Modifying handler to pass allow_change_optionals

* returning optional parameters

* Addressing bug found by @antgonza

* Enabling changing the default parameters

* Adding correct class

* Allowing user to change default parameters

* Fixing bug with commands listing

* Enabling arbitrary htmls in the summary

* Addressing @wasade's comments

* Addressing @antgonza's comment

* Analysis refactor sync with master - DEPENDS ON #2138 (#2139)

* fix #1505

* improving some GUI stuff

* improving some GUI stuff - missing lines

* addressing all comments

* ready for review

* fix #1987

* initial commit

* requested changes

* fix filter job list

* Fixing server cert (#2051)

* fix get_studies

* flake8

* fix #503

* fix #2010

* fix #1913

* fix errors

* addressing @josenavas comment

* flake8

* fix #1010

* fix #1066 (#2058)

* addressing @josenavas comments

* fix #1961

* fix #1837

* Automatic jobs & new stats (#2057)

* fix #814, fix #1636

* fixing error in test-env

* fixing stats.html call

* adding img

* addressing @josenavas comments

* rm for loops

* addresssing @ElDeveloper comments

* generalizing this functionality

* fix #1805

* adding button

* fix errors

* fix #1816

* fixing failures tests

* fix #1959

* addressing @josenavas comments

* addressing @josenavas comments

* fixing error

* fixed?

* addressing @josenavas comments

* addressing @wasade comments

* fix flake8

* generate biom and metadata release (#2066)

* initial commit

* adding portal

* addressing @josenavas comments

* pid -> qiita_artifact_id

* addressing @josenavas comments

* addressing @ElDeveloper comments

* rm 50.sql

* database changes to fix 969

* adding delete

* addressing @josenavas comments

* addressing @ElDeveloper comments

* duh!

* fix generate_biom_and_metadata_release (#2072)

* fix generate_biom_and_metadata_release

* addressing @ElDeveloper comment

* Removing qiita ware code that will not be used anymore

* Organizing the handlers and new analysis description page

* fixing timestamp

* rm formats

* st -> pt

* Connecting the analysis creation and making interface responsive

* Addressing @antgonza's comments

* Initial artifact GUI refactor

* Removing unused code

* moving to ISO 8601 - wow :'(

* fix errors

* addressing @wasade comments

* Adding can_edit call to the analysis

* Fixing artifact rest API since not all artifacts have study

* Adding can_be_publicized call to analysis

* Adding QiitaHTTPError to handle errors gracefully

* Adding safe_execution contextmanager

* Fixing typo

* Adding qiita test checker

* Adapting some artifact handlers

* Abstracting the graph reloading and adding some documentation

* Fixing typo

* Fixing changing artifact visibility

* Fixing delete

* Fixing artifact deletion

* Adding default parameters to the commands

* Fixing processing page

* Fixing variable name

* fixing private/public studies

* Changing bdiv metrics to single choice

* sanbox-to-sandbox

* flake8

* Fixing patch

* fixing other issues

* adding share documentation

* psycopg2 <= 2.7

* psycopg2 < 2.7

* Various small fixes to be able to run tests on the plugins

* Adding private module

* Fixing processing job completion

* Fixing patch 52

* Fixing call

* Fixing complete

* small fixes

* init commit

* fixing errors

* fixing errors due to update

* Making the download work

* Fixing tests

* working status

* adding tags, the right way!

* fix error

* Addressing @antgonza's comments

* Adding missing test

* Ignoring tgz - thanks @antgonza

* addressing @josenavas comments

* list study tags

* fix error

* adding tags to public

* adding docs

* addressing @wasade comment

* addressing @josenavas and @wasade comments

* addressing @wasade request

* fix #2091

* option 2: @ElDeveloper and @josenavas

* A minimal REST API for Qiita (#2094)

* TST: Add initial test cases for study handler

* ENH: Add initial study rest api

* API: test if a study exists

* ENH: oauth2 forced

* Get back basic study deets

* TST: test for samples collection

* API: rest get sample IDs from a study

* ENH: samples/info handler

* broken routes

* API: request sample metadata

* ENH/API: Add methods to check for a study person

* ENH/API: Add POST methods for study person

* TST: Add tests for from_name_and_affiliation

* TST: study creation

* BUG: Add headers to tests

* ENH: create study

* Adjust GET on study description

* API: Add endpoints for preparation creation

* TST: 200 :D

* TST: Correctly verify study instantiation

* TST: prep artifact creation

* ENH/API: associate artifacts with a preparation

* TST: test study statys

* ENH: study status

* Removed trailing whitespace

* STY: PEP8

* MAINT: refactor, centralize setup boilerplate

* REFACTOR: Remove repeated code

* DOC: Remove unnecessary comments

* REFACTOR: Missing removal of pattern

* STY: Fix PEP8 errors

* BUG: Incorrectly changed error code

* BUG/TST: Fix typo in tests

* Addressing an @antgonza comment

* Another @antgonza comment

* RVW: Address review comments

* ENH: Cleanup webserver and name-spaces

* ENH: Improve error messages

* ENH: Add more descriptive error message

* TST: Exercise different argument types

* DOC: Add documentation for REST API

* ENH: Remove extra comma

* ENH/DOC: update/add samples to sample information via rest (#2097)

* Changing how artifact visibility works (#2098)

* changing how artifact visibility works

* fixing code

* fix errors

* fixing edit check access

* fix

* fix #2086

* flak8

* addressing @ElDeveloper comments + fixes

* adding the final changes

* fix failures

* get_qiita_version -> generate_biom_and_metadata_release

* download raw data

* adding missing empty files

* Adding endpoint to retrieve list of person (#2103)

* Adding missing endpoint

* Addressing @ElDeveloper comment

* fix #2086 (#2102)

* fix #2086

* flak8

* addressing @ElDeveloper comments + fixes

* adding the final changes

* fix failures

* get_qiita_version -> generate_biom_and_metadata_release

* addressing @wasade comments and fix errors

* fix error?

* rm vfabu + addressing @wasade and @josenavas comments + fix errors

* just being dumb!

* Deblur quality mention (#2107)

* Revised rst values used for section headers (#2108)

* Adding processing handlers

* Fixing latlongs (#2120)

* public studies are being shown in the user own studies

* fix #2069 - adding tests

* flake8

* Fixing url and bug on processing job workflow

* Adding the private script runner

* Adding is_analysis column to the command

* Adding retrieval of commands excluding analysis commands

* Addressing bug on retrieving information from redis

* Enabling the command register endpoint to provide if the command is analysis only

* Improving study list speed (#2123)

* init commit

* reading if ...

* fixing tests

* rethinking listint

* split SQL

* reseting sql

* ignoring prep_total_samples

* finishing changes

* adding comment: @ElDeveloper

* adding message: @josenavas

* addressing @ElDeveloper, @josenavas @jdereus comments

* fixing download buttons show (#2127)

* fixing download buttons show

* addressing @ElDeveloper comment

* connecting tutorials to CMI

* adding link in main page

* fixing prep getting-started

* mv complex designs

* fix idents

* Addressing @antgonza's comments

* Addressing @wasade's comments

* Supporting multiple choice

* Adding documentation

* limiting number of jobs retrieved

* Modifying handler to pass allow_change_optionals

* returning optional parameters

* Addressing bug found by @antgonza

* Enabling changing the default parameters

* Adding correct class

* Allowing user to change default parameters

* Fixing bug with commands listing

* Enabling arbitrary htmls in the summary

* Prepping for merge hell

* Addressing @wasade's comments

* Addressing @antgonza's comment

* Moving tests around and deleting unused code

* Analysis refactor sync w master 2 (#2141)

* fix #1505

* improving some GUI stuff

* improving some GUI stuff - missing lines

* addressing all comments

* ready for review

* fix #1987

* initial commit

* requested changes

* fix filter job list

* Fixing server cert (#2051)

* fix get_studies

* flake8

* fix #503

* fix #2010

* fix #1913

* fix errors

* addressing @josenavas comment

* flake8

* fix #1010

* fix #1066 (#2058)

* addressing @josenavas comments

* fix #1961

* fix #1837

* Automatic jobs & new stats (#2057)

* fix #814, fix #1636

* fixing error in test-env

* fixing stats.html call

* adding img

* addressing @josenavas comments

* rm for loops

* addresssing @ElDeveloper comments

* generalizing this functionality

* fix #1805

* adding button

* fix errors

* fix #1816

* fixing failures tests

* fix #1959

* addressing @josenavas comments

* addressing @josenavas comments

* fixing error

* fixed?

* addressing @josenavas comments

* addressing @wasade comments

* fix flake8

* generate biom and metadata release (#2066)

* initial commit

* adding portal

* addressing @josenavas comments

* pid -> qiita_artifact_id

* addressing @josenavas comments

* addressing @ElDeveloper comments

* rm 50.sql

* database changes to fix 969

* adding delete

* addressing @josenavas comments

* addressing @ElDeveloper comments

* duh!

* fix generate_biom_and_metadata_release (#2072)

* fix generate_biom_and_metadata_release

* addressing @ElDeveloper comment

* fixing timestamp

* rm formats

* st -> pt

* moving to ISO 8601 - wow :'(

* fix errors

* addressing @wasade comments

* fixing private/public studies

* sanbox-to-sandbox

* flake8

* fixing other issues

* adding share documentation

* psycopg2 <= 2.7

* psycopg2 < 2.7

* init commit

* fixing errors

* fixing errors due to update

* Making the download work

* Fixing tests

* working status

* adding tags, the right way!

* fix error

* Addressing @antgonza's comments

* Adding missing test

* Ignoring tgz - thanks @antgonza

* addressing @josenavas comments

* list study tags

* fix error

* adding tags to public

* adding docs

* addressing @wasade comment

* addressing @josenavas and @wasade comments

* addressing @wasade request

* fix #2091

* option 2: @ElDeveloper and @josenavas

* A minimal REST API for Qiita (#2094)

* TST: Add initial test cases for study handler

* ENH: Add initial study rest api

* API: test if a study exists

* ENH: oauth2 forced

* Get back basic study deets

* TST: test for samples collection

* API: rest get sample IDs from a study

* ENH: samples/info handler

* broken routes

* API: request sample metadata

* ENH/API: Add methods to check for a study person

* ENH/API: Add POST methods for study person

* TST: Add tests for from_name_and_affiliation

* TST: study creation

* BUG: Add headers to tests

* ENH: create study

* Adjust GET on study description

* API: Add endpoints for preparation creation

* TST: 200 :D

* TST: Correctly verify study instantiation

* TST: prep artifact creation

* ENH/API: associate artifacts with a preparation

* TST: test study statys

* ENH: study status

* Removed trailing whitespace

* STY: PEP8

* MAINT: refactor, centralize setup boilerplate

* REFACTOR: Remove repeated code

* DOC: Remove unnecessary comments

* REFACTOR: Missing removal of pattern

* STY: Fix PEP8 errors

* BUG: Incorrectly changed error code

* BUG/TST: Fix typo in tests

* Addressing an @antgonza comment

* Another @antgonza comment

* RVW: Address review comments

* ENH: Cleanup webserver and name-spaces

* ENH: Improve error messages

* ENH: Add more descriptive error message

* TST: Exercise different argument types

* DOC: Add documentation for REST API

* ENH: Remove extra comma

* ENH/DOC: update/add samples to sample information via rest (#2097)

* Changing how artifact visibility works (#2098)

* changing how artifact visibility works

* fixing code

* fix errors

* fixing edit check access

* fix

* fix #2086

* flak8

* addressing @ElDeveloper comments + fixes

* adding the final changes

* fix failures

* get_qiita_version -> generate_biom_and_metadata_release

* download raw data

* adding missing empty files

* Adding endpoint to retrieve list of person (#2103)

* Adding missing endpoint

* Addressing @ElDeveloper comment

* fix #2086 (#2102)

* fix #2086

* flak8

* addressing @ElDeveloper comments + fixes

* adding the final changes

* fix failures

* get_qiita_version -> generate_biom_and_metadata_release

* addressing @wasade comments and fix errors

* fix error?

* rm vfabu + addressing @wasade and @josenavas comments + fix errors

* just being dumb!

* Deblur quality mention (#2107)

* Revised rst values used for section headers (#2108)

* Fixing latlongs (#2120)

* public studies are being shown in the user own studies

* fix #2069 - adding tests

* flake8

* Improving study list speed (#2123)

* init commit

* reading if ...

* fixing tests

* rethinking listint

* split SQL

* reseting sql

* ignoring prep_total_samples

* finishing changes

* adding comment: @ElDeveloper

* adding message: @josenavas

* addressing @ElDeveloper, @josenavas @jdereus comments

* fixing download buttons show (#2127)

* fixing download buttons show

* addressing @ElDeveloper comment

* connecting tutorials to CMI

* adding link in main page

* fixing prep getting-started

* mv complex designs

* fix idents

* limiting number of jobs retrieved

* Deleting unused code

* Fixing travis

* Flake8-ing

* Fixing travis

* Removing unused code

* Trying one thing on travis

* Trying one thing on travis

* Trying to debug

* Still debugging

* ...

* Config biom plugin

* Creating the dir

* Speed up server by not building the docs

* More playing with travis

* Fixing config file

* Trying with a diff conf file

* Fixing path

* Adding a print to see the error

* Adding another print

* Removing debugging bits

* Runnning webserver only if running tests

* Fixing last failing errors

* Removing debugging bits

* Fixing tests

* fixing config

* Fixing stochastic tests

* Fixing tests (#2142)

* Removing qiita ware code that will not be used anymore

* Organizing the handlers and new analysis description page

* Connecting the analysis creation and making interface responsive

* Addressing @antgonza's comments

* Initial artifact GUI refactor

* Removing unused code

* Adding can_edit call to the analysis

* Fixing artifact rest API since not all artifacts have study

* Adding can_be_publicized call to analysis

* Adding QiitaHTTPError to handle errors gracefully

* Adding safe_execution contextmanager

* Fixing typo

* Adding qiita test checker

* Adapting some artifact handlers

* Abstracting the graph reloading and adding some documentation

* Fixing typo

* Fixing changing artifact visibility

* Fixing delete

* Fixing artifact deletion

* Adding default parameters to the commands

* Fixing processing page

* Fixing variable name

* Changing bdiv metrics to single choice

* Fixing patch

* Various small fixes to be able to run tests on the plugins

* Adding private module

* Fixing processing job completion

* Fixing patch 52

* Fixing call

* Fixing complete

* small fixes

* Adding processing handlers

* Fixing url and bug on processing job workflow

* Adding the private script runner

* Adding is_analysis column to the command

* Adding retrieval of commands excluding analysis commands

* Addressing bug on retrieving information from redis

* Enabling the command register endpoint to provide if the command is analysis only

* Addressing @antgonza's comments

* Addressing @wasade's comments

* Supporting multiple choice

* Adding documentation

* Modifying handler to pass allow_change_optionals

* returning optional parameters

* Addressing bug found by @antgonza

* Enabling changing the default parameters

* Adding correct class

* Allowing user to change default parameters

* Fixing bug with commands listing

* Enabling arbitrary htmls in the summary

* Prepping for merge hell

* Addressing @wasade's comments

* Fixing qiita_db tests

* Addressing @antgonza's comment

* Solving a few more tests

* Moving tests around and deleting unused code

* Deleting unused code

* Fixing travis

* Flake8-ing

* Fixing travis

* Removing unused code

* Trying one thing on travis

* Trying one thing on travis

* Trying to debug

* Still debugging

* ...

* Config biom plugin

* Creating the dir

* Speed up server by not building the docs

* More playing with travis

* Fixing config file

* Trying with a diff conf file

* Fixing path

* Adding a print to see the error

* Adding another print

* Removing debugging bits

* Runnning webserver only if running tests

* Fixing last failing errors

* Removing debugging bits

* Fixing tests

* fixing config

* Fixing stochastic tests

* Extending post test call to accept analysis

* Extending post test call to accept analysis (#2144)

* some minor fixes

* adding timer

* nose-timer to pip command

* nose-timer to pip command

* active_children test

* improving study listing // artifact info

* adding code to both list

* fix js length

* 300000

* multiprocessing->active_children

* 2400000

* 600000

* Trying to fix the tests

* Submit the job on commit

* Reverting last change

* improving sql and display

* improving sql

* adding some of the requested improvements

* addressing comments

* addressing @ElDeveloper and @wasade comments

* Registering commands after updating plugins (#2156)

* Adding codecov (#2157)

* Testing codecov for speeding up tests

* Fixing test

* Fixing ware test

* Adding codecov badge

* Removing coveralls

* Trying to fix the failing test

* Expand html summary setter (#2150)

* Changing the HTML setter to add support dirs

* Extending the patch operation

* Fixing remaining calls to html_summary_fp set

* Fixing test

* Deleting unused function

* Removing unused import

* Fixing tests

* Fixing failing test

* Fix artifact type creation (#2158)

* Changing the HTML setter to add support dirs

* Extending the patch operation

* Fixing remaining calls to html_summary_fp set

* Fixing test

* Deleting unused function

* Removing unused import

* Fixing tests

* Fixing failing test

* Creating the mountpoint of the new type

* Cleaning up patch and fixing bug

* Fixing tests

* Adding analysis to the list of acceptable parameter types

* Adding the provenance parameter automatically

* Adding qzv fileapth type (#2159)

* Adding qzv fileapth type

* Fixing test

* fixing tests

* adding ORDER

* to debug

* splitting the plugin registration

* Analysis refactor misc (#2161)

* Fixing race condition

* Removing unused code and fixing typo

* Hiding job step if success

* Showing loading gif and fixing typo

* fix tests

* to debug

* improving delete speed (#2165)

* improving delete speed

* more sleep!

* fix artifact summary issue (#2163)

* fix artifact summary issue

* sleep

* fixing errors 1

* missing ]

* fix error

* barcode_type 8, defaults

* WIP: using new info to merge bioms (#2167)

* using new info to merge bioms

* fix errors

* flake8

* fix 55.py (#2168)

* fix 55.py

* fixing small bug in test env

* addressing @ElDeveloper comments

* config_test.cfg

* rm /test_data/ from folders

* fixing

* releases

* working_dir/releases

* working_dir/

* Fix analysis artifact name (#2169)

* fix analysis artifact name

* fix analysis artifact name

* params -> md5

* ignoring params and target subfragment

* flake8

* remonving parent_processing

* Improving analysis listing (#2170)

* improving analysis listing

* addressing @ElDeveloper comments

* Improving analysis listing b (#2175)

* improving analysis listing

* addressing @ElDeveloper comments

* adding list artifacts

* changing names

* fixing . -> ,

* only_biom

* actually using only_biom

* sleep

* moving sleep

* import sleep

* sleep(0.8)

* sleep(1)

* addressing @ElDeveloper comments

* flake8

* is_qiita_job

* job_info -> ji

* addressing @ElDeveloper comments

* Fix branch (#2176)

* improving analysis listing

* addressing @ElDeveloper comments

* adding list artifacts

* changing names

* fixing . -> ,

* only_biom

* actually using only_biom

* sleep

* moving sleep

* import sleep

* sleep(0.8)

* sleep(1)

* addressing @ElDeveloper comments

* flake8

* is_qiita_job

* job_info -> ji

* addressing @ElDeveloper comments

* fixing branch
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@ElDeveloper ElDeveloper ElDeveloper approved these changes

@josenavas josenavas josenavas approved these changes

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@antgonza @coveralls @wasade @ElDeveloper @josenavas