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!

Author: josenavas

.travis.yml

@@ -40,9 +40,10 @@ script:
   - qiita-env start_cluster qiita-general
   - qiita-env make --no-load-ontologies
   - if [ ${TEST_ADD_STUDIES} == "True" ]; then test_data_studies/commands.sh ; fi
+  - if [ ${TEST_ADD_STUDIES} == "True" ]; then qiita-cron-job ; fi
   - if [ ${TEST_ADD_STUDIES} == "False" ]; then qiita-test-install ; fi
   - if [ ${TEST_ADD_STUDIES} == "False" ]; then nosetests --with-doctest --with-coverage -v --cover-package=qiita_db,qiita_pet,qiita_core,qiita_ware; fi
-  - flake8 qiita_* setup.py scripts/qiita scripts/qiita-env scripts/qiita-test-install
+  - flake8 qiita_* setup.py scripts/*
   - ls -R /home/travis/miniconda3/envs/qiita/lib/python2.7/site-packages/qiita_pet/support_files/doc/
   - qiita pet webserver
 addons:

qiita_core/support_files/server.crt

@@ -1,15 +1,15 @@
 -----BEGIN CERTIFICATE-----
-MIICQzCCAawCCQDD7K/frIbu8DANBgkqhkiG9w0BAQUFADBmMQswCQYDVQQGEwJV
+MIICRTCCAa4CCQDPGmrQ4bra7TANBgkqhkiG9w0BAQUFADBmMQswCQYDVQQGEwJV
 UzELMAkGA1UECBMCQ0ExEjAQBgNVBAcTCVNhbiBEaWVnbzENMAsGA1UEChMEVUNT
-RDETMBEGA1UECxMKS25pZ2h0IExhYjESMBAGA1UEAxMJbG9jYWxob3N0MB4XDTE2
-MTIxOTE2MDA1NFoXDTE3MDExODE2MDA1NFowZjELMAkGA1UEBhMCVVMxCzAJBgNV
-BAgTAkNBMRIwEAYDVQQHEwlTYW4gRGllZ28xDTALBgNVBAoTBFVDU0QxEzARBgNV
-BAsTCktuaWdodCBMYWIxEjAQBgNVBAMTCWxvY2FsaG9zdDCBnzANBgkqhkiG9w0B
-AQEFAAOBjQAwgYkCgYEAq6ChN/5vk1fn45Ys5inttHe8IntBQtU31oKy+2IR+znT
-GBvG/iht0veG5sbjlkm+Hn4auk5lR9EOmnTy+fl44LJ81rZuYmy3mjLSAHwmx7ee
-ZTJ2lNjH/Blq5vC4VmPQ3Ka7zMusOTZSBDw6k8r6bxbMgarXc+rQtDvQfv2QITsC
-AwEAATANBgkqhkiG9w0BAQUFAAOBgQBBir71K7HdTbU7129ZYLDyeXJfAjzCsSxj
-evSqa6PJuh5PODdPyO01Hyxb5J/aHzmE5FRZKMLdgOTlqCpQjyMMvVc6UJzX5bZo
-x6Y5gvoTNeCfaD0N6eZxxd7BqFGq+gmqk5U1cyKf+QjIhu/Q4p/Ga+Cx9b3t/Sk+
-/iUPu/otBw==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 -----END CERTIFICATE-----

qiita_db/artifact.py

@@ -420,6 +420,15 @@ def _associate_with_analysis(instance, analysis_id):
                 sql_args = [(instance.id, p.id) for p in parents]
                 qdb.sql_connection.TRN.add(sql, sql_args, many=True)
 
+                # inheriting visibility
+                visibilities = {a.visibility for a in instance.parents}
+                # set based on the "lowest" visibility
+                if 'sandbox' in visibilities:
+                    instance.visibility = 'sandbox'
+                elif 'private' in visibilities:
+                    instance.visibility = 'private'
+                else:
+                    instance.visibility = 'public'
             elif prep_template:
                 # This artifact is uploaded by the user in the
                 # processing pipeline