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add a job/task manager #1505

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antgonza opened this issue Oct 15, 2015 · 9 comments
Closed

add a job/task manager #1505

antgonza opened this issue Oct 15, 2015 · 9 comments
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@antgonza
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Alpha 0.3

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@antgonza
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It will be great so we can keep track of everything is running and their state.
@antgonza antgonza added this to the Beta milestone Oct 15, 2015
@josenavas
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Should this be part of MOI as it is the one that manages the firing of the jobs?

@antgonza
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Perhaps but we will need also a way to display it via CLI/WEB.

@wasade
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wasade commented Oct 15, 2015

moi has a cli and the js to display a joblist was part of the initial design

On Thu, Oct 15, 2015 at 2:24 PM, Antonio Gonzalez notifications@github.com
wrote:

Perhaps but we will need also a way to display it via CLI/WEB.

—
Reply to this email directly or view it on GitHub
#1505 (comment).

@josenavas
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Agree - @antgonza the interface for the analysis jobs lives in moi, so we can do something similar here - and have an Admin site that loads such moi interface.

@antgonza
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Makes sense ...

@colinbrislawn
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This should include a 'Clear failed jobs' option (that way when you are troubleshooting Prep Info Files, you can clear all the errors you accumulate along the way.)

@jwdebelius
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Bumping this as something to expose to users.

It would be really awesome if this could let you see the job, runtime, and possibly who spawned it for sandbox/private studies. I'd also like to be able to stop, bump, or delete jobs. (If, maybe, I accidentally spawned off a job I hadn't meant to start).

Also 👍 on Colin's suggestion to clear failed jobs.

@colinbrislawn
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and possibly who spawned it for sandbox/private studies

👍 Also a very good idea. Today I discovered an artifact locked by old job that I'm not sure who started.

@antgonza antgonza modified the milestones: Alpha 0.3, Beta Dec 7, 2016
@antgonza
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antgonza commented Dec 7, 2016

We will use moi lists and the DB to generate the tasks.

@antgonza antgonza self-assigned this Dec 7, 2016
antgonza pushed a commit that referenced this issue 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 issue 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 issue 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 issue 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 issue 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 issue 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 issue 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 issue 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 issue 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 issue 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 issue 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 issue 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 issue 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 issue 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 issue 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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@antgonza antgonza

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@wasade @antgonza @josenavas @jwdebelius @colinbrislawn