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* 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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