Merge 761ffa0 into 2e1d684

.travis.yml

@@ -20,12 +20,27 @@ before_install:
   # Update conda itself
   - conda update --yes conda
 install:
+  - travis_retry conda create --yes -n qiita_env python=2.7 pip nose flake8 pyzmq
+    networkx pyparsing natsort mock future libgfortran 'pandas>=0.18' 'scipy>0.13.0'
+    'numpy>=1.7' 'h5py>=2.3.1'
+  - source activate qiita_env
+  - pip install sphinx sphinx-bootstrap-theme coveralls ipython[all]==2.4.1
+  - pip install https://github.com/biocore/qiita/archive/master.zip --process-dependency-links
+  - ipython profile create qiita-general --parallel
+  - export QIITA_SERVER_CERT=$HOME/miniconda3/envs/qiita_env/lib/python2.7/site-packages/qiita_core/support_files/server.crt
+  - export MOI_CONFIG_FP=$HOME/miniconda3/envs/qiita_env/lib/python2.7/site-packages/qiita_core/support_files/config_test.cfg
+  - qiita-env start_cluster qiita-general
+  - qiita-env make --no-load-ontologies
+  - source deactivate
   - travis_retry conda create --yes -n labadmin python=2.7 pip
   - source activate labadmin
   - pip install -U pip
   - pip install -U click natsort coverage coveralls
   - travis_retry pip install -U .[test]
 before_script:
+  - source activate qiita_env
+  - qiita pet webserver --no-build-docs start &
+  - source activate labadmin
   # installing jira locally for testing
   - wget https://marketplace.atlassian.com/download/plugins/atlassian-plugin-sdk-tgz
   - tar zxvf atlassian-plugin-sdk-tgz
@@ -43,19 +58,22 @@ before_script:
   # </dev/zero 2>&1 & --> https://goo.gl/n7BYnh
   # this will install the latest version of JIRA but we could install other ones
   # via --version 6.4.7
-  - atlas-run --product jira -DskipAllPrompts=true </dev/zero 2>&1 &
+  - atlas-run --product jira -DskipAllPrompts=true </dev/zero 2>&1 > /dev/null &
   - sleep 560
 script:
-  - git clone https://github.com/biocore/american-gut-web.git ~/build/biocore/american-gut-web
+  - source activate labadmin
+  - git clone -b plate-mapper-jose https://github.com/biocore/american-gut-web.git ~/build/biocore/american-gut-web
   - cd /home/travis/build/biocore/american-gut-web
   - export AG_CONFIG=`pwd`/ag_config.txt.example
   - export PYTHONPATH=/home/travis/build/biocore/american-gut-web:$PYTHONPATH
   - ./scripts/ag make test
   - export PYTHONPATH=
   - $PYTHONPATH
   - cd $TRAVIS_BUILD_DIR
-  - cp $TRAVIS_BUILD_DIR/knimin/config.txt.example $TRAVIS_BUILD_DIR/knimin/config.txt
+  # We need to add the Qiita server cert path to the config file
+  - sed "s:SERVER_CERT =:SERVER_CERT = $QIITA_SERVER_CERT:g" $TRAVIS_BUILD_DIR/knimin/config.txt.example > $TRAVIS_BUILD_DIR/knimin/config.txt
   - nosetests --verbose --with-doctest --with-coverage
   - flake8 knimin setup.py scripts
+  - phantomjs knimin/tests/javascript/runner.js knimin/tests/javascript/index.html
 after_success:
   - coveralls

LICENSE.md

@@ -0,0 +1,153 @@
+License
+=======
+
+labadmin makes usage of all of the following copyrighted packages; their licenses have been centralized in this document.
+
+--------------------------------------------------------------------------------
+
+#### Chosen (v1.4.2)
+- by Patrick Filler for [Harvest](http://getharvest.com)
+- Copyright (c) 2011-2014 by Harvest
+
+Available for use under the [MIT License](http://en.wikipedia.org/wiki/MIT_License)
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.
+
+--------------------------------------------------------------------------------
+
+### DataTables ([1.10.12](https://github.com/DataTables/DataTables/releases/tag/1.10.12)) is released under the MIT License
+
+Copyright (c) 2008-2015 SpryMedia Limited
+http://datatables.net
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.
+
+--------------------------------------------------------------------------------
+
+### jQuery ([1.9.1](https://github.com/jquery/jquery/releases/tag/1.9.1)) is released under the MIT License
+
+Copyright 2012 jQuery Foundation and other contributors
+http://jquery.com/
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+
+--------------------------------------------------------------------------------
+
+### QUnit [2.0.1](https://github.com/jquery/qunit/releases/tag/2.0.1)
+
+Copyright jQuery Foundation and other contributors, https://jquery.org/
+
+This software consists of voluntary contributions made by many
+individuals. For exact contribution history, see the revision history
+available at https://github.com/jquery/qunit
+
+The following license applies to all parts of this software except as
+documented below:
+
+====
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+
+====
+
+All files located in the node_modules directory are externally maintained
+libraries used by this software which have their own licenses; we
+recommend you read them, as their terms may differ from the terms above.
+
+--------------------------------------------------------------------------------
+
+### Font Awesome [4.6.3](https://github.com/FortAwesome/Font-Awesome/releases/tag/v4.6.3)
+
+- by Dave Gandy - [http://fontawesome.io](http://fontawesome.io)
+
+Font License
+Applies to all desktop and webfont files in the following directory: font-awesome/fonts/.
+License: SIL OFL 1.1
+URL: http://scripts.sil.org/OFL
+
+====
+
+Code License
+Applies to all CSS and LESS files in the following directories: font-awesome/css/, font-awesome/less/, and font-awesome/scss/.
+License: MIT License
+URL: [http://opensource.org/licenses/mit-license.html](http://opensource.org/licenses/mit-license.html)
+
+====
+
+Documentation License
+Applies to all Font Awesome project files that are not a part of the Font or Code licenses.
+License: CC BY 3.0
+URL: [http://creativecommons.org/licenses/by/3.0/](http://creativecommons.org/licenses/by/3.0/)
+
+====
+
+Brand Icons
+All brand icons are trademarks of their respective owners.
+The use of these trademarks does not indicate endorsement of the trademark holder by Font Awesome, nor vice versa.
+Brand icons should only be used to represent the company or product to which they refer.

knimin/__init__.py

@@ -1,9 +1,20 @@
-#!/usr/bin/env python
+# -----------------------------------------------------------------------------
+# Copyright (c) 2014--, The LabAdmin Development Team.
+#
+# Distributed under the terms of the BSD 3-clause License.
+#
+# The full license is in the file LICENSE, distributed with this software.
+# -----------------------------------------------------------------------------
+
 from knimin.lib.configuration import config
 from knimin.lib.data_access import KniminAccess
 from knimin.lib.ag_jira import create_jira_handler
+from knimin.lib.qiita_client import QiitaClient
 
 db = KniminAccess(config)
 jira_handler = create_jira_handler(config)
+qiita_client = QiitaClient(config.qiita_host, config.qiita_client_id,
+                           config.qiita_client_secret,
+                           server_cert=config.qiita_server_cert)
 
-__all__ = ['db', 'jira_handler']
+__all__ = ['db', 'jira_handler', 'qiita_client']

knimin/config.txt.example

@@ -29,3 +29,13 @@ HOST = http://127.0.0.1:2990/jira
 USERNAME = admin
 PASSWORD = admin
 PASSKEY =
+
+[qiita]
+# SERVER_CERT is only needed if the Qiita server doesn't have a valid certificate
+HOST = https://localhost:21174
+CLIENT_ID = 19ndkO3oMKsoChjVVWluF7QkxHRfYhTKSFbAVt8IhK7gZgDaO4
+CLIENT_SECRET = J7FfQ7CQdOxuKhQAf1eoGgBAE81Ns8Gu3EKaWFm3IO2JKhAmmCWZuabe0O5Mp28s1
+SERVER_CERT =
+
+[platemapper]
+SAMPLE_SHEET_DIR = /tmp

knimin/handlers/ag_search.py

@@ -49,11 +49,8 @@ def post(self):
                     barcode_info[ag_barcode['barcode']]['ag_info'] = ag_barcode
                     lab_barcode_info = db.get_barcode_details(
                         ag_barcode['barcode'])
-                    plate = db.get_plate_for_barcode(
-                        ag_barcode['barcode'])
                     barcode_info[ag_barcode['barcode']]['barcode_info'] = \
                         lab_barcode_info
-                    barcode_info[ag_barcode['barcode']]['plate'] = plate
                 kit['barcode_info'] = barcode_info
             display_results.append(login_display)
 

knimin/handlers/pm_condense.py

@@ -0,0 +1,47 @@
+# -----------------------------------------------------------------------------
+# Copyright (c) 2014--, The LabAdmin Development Team.
+#
+# Distributed under the terms of the BSD 3-clause License.
+#
+# The full license is in the file LICENSE, distributed with this software.
+# -----------------------------------------------------------------------------
+
+from tornado.web import authenticated
+
+from knimin.handlers.base import BaseHandler
+from knimin.handlers.access_decorators import set_access
+from knimin import db
+
+
+@set_access(['Admin'])
+class PMCondensePlatesHandler(BaseHandler):
+    @authenticated
+    def get(self):
+        dna_plates = db.get_dna_plate_list()
+        for plate in dna_plates:
+            plate['date'] = plate['date'].isoformat()
+
+        self.render("pm_condense.html",
+                    plates=dna_plates,
+                    robots=db.get_property_options("processing_robot"))
+
+    @authenticated
+    def post(self):
+        plate1 = self.get_argument('plate-1')
+        plate2 = self.get_argument('plate-2')
+        plate3 = self.get_argument('plate-3')
+        plate4 = self.get_argument('plate-4')
+        name = self.get_argument('name')
+        robot = self.get_argument('robot')
+        volume = self.get_argument('volume')
+
+        dna_plates = [(plate1, 0), (plate2, 1), (plate3, 2), (plate4, 3)]
+        plates = [plate1, plate2, plate3, plate4]
+        pos = [0, 1, 2, 3]
+        dna_plates = [(p, idx) for p, idx in zip(plates, pos) if p]
+        # Magic number 2 -> The only supported plate type here is
+        # a 384-well plate
+        plate_id = db.condense_dna_plates(
+            dna_plates, name, self.get_current_user(), robot, 2, volume)
+
+        self.redirect("/pm_quantify/?plate=%s" % plate_id)

knimin/handlers/pm_create_study.py

@@ -0,0 +1,47 @@
+# -----------------------------------------------------------------------------
+# Copyright (c) 2014--, The LabAdmin Development Team.
+#
+# Distributed under the terms of the BSD 3-clause License.
+#
+# The full license is in the file LICENSE, distributed with this software.
+# -----------------------------------------------------------------------------
+
+from tornado.web import authenticated
+from tornado.escape import json_decode, json_encode
+
+from knimin.handlers.base import BaseHandler
+from knimin.handlers.access_decorators import set_access
+from knimin.lib.qiita_jira_util import create_study
+from knimin import qiita_client, db
+
+
+@set_access(['Admin'])
+class PMCreateStudyHandler(BaseHandler):
+    @authenticated
+    def get(self):
+        _, qiita_persons = qiita_client.get('/api/v1/person')
+        # We don't have an id for each person. "Create" one by jsonizing
+        # the information of each person
+        for q in qiita_persons:
+            q['json'] = json_encode(q)
+
+        self.render("pm_create_study.html", currentuser=self.current_user,
+                    qiita_persons=qiita_persons)
+
+    @authenticated
+    def post(self):
+        qiita_user = self.get_argument('qiita-user')
+        jira_user = self.get_argument('jira-user')
+        title = self.get_argument('study-title')
+        alias = self.get_argument('study-alias')
+        description = self.get_argument('study-description')
+        abstract = self.get_argument('study-abstract')
+        qiita_pi = json_decode(self.get_argument('qiita-pi'))
+        qiita_lp = json_decode(self.get_argument('qiita-lp'))
+
+        study_id = create_study(title, abstract, description, alias,
+                                qiita_user, qiita_pi, qiita_lp, jira_user)
+        study = db.read_study(study_id)
+
+        self.render("pm_study_created.html", current_user=self.current_user,
+                    title=title, study_id=study_id, jira_key=study['jira_id'])