Merge remote-tracking branch 'origin/afterdjango2' into afterdjango2

Author: miguelcleon

.travis.yml

@@ -16,6 +16,14 @@ env:
 before_cache:
   - rm -rf $HOME/miniconda/envs/TEST
 
+services:
+  - postgresql
+addons:
+  postgresql: "9.5"
+  apt:
+    packages:
+      - postgresql-9.5-postgis-2.3
+
 matrix:
   fast_finish: true
   include:
@@ -29,6 +37,8 @@ matrix:
 
 
 before_install:
+  - psql -U postgres -c "create extension postgis"
+  - psql -c "CREATE DATABASE test;" -U postgres
   - |
     URL="http://bit.ly/miniconda"
     echo ""
@@ -42,17 +52,14 @@ before_install:
   - conda config --set always_yes yes --set changeps1 no --set show_channel_urls true
   - conda update conda
   - conda config --add channels conda-forge --force
-  - conda config --add channels odm2 --force
-  - conda create --name TEST python=$TRAVIS_PYTHON_VERSION libgdal boost --file requirements.txt --file requirements-dev.txt
+  - conda create --name TEST python=$TRAVIS_PYTHON_VERSION libgdal --file requirements.txt --file requirements-dev.txt
   - source activate TEST
-  - pip install --upgrade http://github.com/miguelcleon/django-admin-shortcuts/zipball/master
+#   - pip install --upgrade http://github.com/miguelcleon/django-admin-shortcuts/zipball/master
+
 
 install:
   - python setup.py sdist && version=$(python setup.py --version) && pushd dist  && pip install odm2admin-${version}.tar.gz && popd
 
-before_script:
-- psql -c "CREATE DATABASE test;" -U postgres
-
 script:
   - if [[ $TEST_TARGET == 'default' ]]; then
       python $TRAVIS_BUILD_DIR/manage.py test tests/;

docker/odm2admin/startup.sh

@@ -3,7 +3,7 @@
 echo "Activating environment..."
 source activate odm2adminenv
 conda install --yes -c conda-forge sqlalchemy
-pip install git+git://github.com/miguelcleon/django-admin-shortcuts --upgrade
+# pip install git+git://github.com/miguelcleon/django-admin-shortcuts --upgrade
 
 #echo "Building database..."
 #su - postgres -c 'pg_restore -d odm2_db -1 -v "/ODM2-Admin/ODM2AdminDBBlank"'
@@ -18,4 +18,4 @@ wget https://raw.githubusercontent.com/ODM2/ODM2/master/src/load_cvs/cvload.py
 python cvload.py postgresql+psycopg2://postgres:test@db:5432/odm2
 
 echo "Running server..."
-python manage.py runserver 0.0.0.0:8000
+python manage.py runserver 0.0.0.0:8000

docs/source/DataQAQC.rst

@@ -39,12 +39,12 @@ Our Annotated data will then look something like this:
 
 You can also add or subtract an offset value to a set of points or drift correct them. Drift correcting points will
 apply a linear correction so that the first or last point (depending if you select forward or backward) will have the
-value entered. the remaining values you selected will have an offset added to them proportional to their position in the
-set of points selected.
+value entered. The remaining values you selected will have an offset added to them. This offset is proportional to the
+points position in the set of points selected.
 
   .. image:: /images/offsetanddriftcorrect.png
 
 :ref:`5) Data visualization and URL parameters <Data-Visualization>`
 
 * :ref:`ODM2 Admin docs home page<ODM2-Admin>`
-* :ref:`Search the docs <search>`
+* :ref:`Search the docs <search>`

docs/source/DataVisualizationTips.rst

@@ -3,7 +3,7 @@
 Data Visualization and URL parameters
 =====================================
 
-Graphs presenting ODM2 Time Series can be easily shared with formatted URL parameters. if we return to the example we
+Graphs presenting ODM2 Time Series can be easily shared with formatted URL parameters. Let's we return to the example we
 used in :ref:`Data QAQC doc<Data-QA-QC>`
 
 * We looked at a timeseries with the following link: https://dev-odm2admin.cuahsi.org/Sandbox/graphfa/samplingfeature=776/resultidu=16657/popup=Anno/

docs/source/ManagingODM2WithTheDjangoORM.rst

@@ -3,13 +3,13 @@
 The Django ORM and WOFpy
 ========================
 
-While not all of the ODM2 entities are exposed through the ODM2 Admin interface all of the entities can be managed
-using Python scripts using either ODM2PythonAPI or the Django ORM using the models in ODM2 Admin. Two examples using
-the Django ORM come with the source code of ODM2 Admin.
+While not all of the ODM2 entities are exposed through the ODM2 Admin interface they can all be managed using Python
+scripts using either ODM2PythonAPI or the Django ORM using the models in ODM2 Admin. Two examples using the Django ORM
+ are included with the source code of ODM2 Admin.
 
 The ODM2PythonAPI can be found here: https://github.com/ODM2/ODM2PythonAPI
 
-An example merging data from a csv file to  fill a gap in a time series can be found here:
+An example of merging data from a csv file to  fill a gap in a time series can be found here:
 https://github.com/ODM2/ODM2-Admin/blob/master/example_scripts/SonadoraNitrateFill.py
 
 An example creating soil profile result values from a file can be found here:
@@ -20,8 +20,8 @@ WOFpy
 
 ODM2 Admin can also be used with WOFpy and water one flow webservices can be registered with CUAHSI HIS central.
 
-WOFpy REST API test page:
-http://odm2admin.cuahsi.org/wofpy/odm2lczo/rest_1_1/
+WOFpy REST API test page for the Luquillo CZO:
+http://dev-odm2admin.cuahsi.org/odm2lczo/odm2lczo/rest_1_1/
 
 This is still in testing an initial implementation has been registered with the HIS central QA system:
 

docs/source/ODM2AdminAdministration.rst

@@ -23,7 +23,7 @@ Many of the below entities use controlled vocabularies which can be found here h
 People and Organizations
 ------------------------
 
-* **Organizations:** Observations and other Actions can be associated with  the Organization responsible for creating
+* **Organizations:** Observations, Sensor deployments retrievals and other Actions can be associated with  the Organization responsible for creating
    or performing them. `see here for ODM2 Organizations doc <https://github.com/ODM2/ODM2/blob/master/doc/ODM2Docs/core_organizations.md>`_
 * **People:** ODM2 Core people details can be found `here ODM2 people doc <https://github.com/ODM2/ODM2/blob/master/doc/ODM2Docs/core_people.md>`_
 * **Affiliation:** Relates people and organizations
@@ -47,6 +47,8 @@ Methods and Actions
     * Sample preparation methods
     * Sample analysis methods
     * Observation methods
+    * Instrument calibration
+    *Instrument Maintenance
 
     See the `ODM2 Methods doc <https://github.com/ODM2/ODM2/blob/master/doc/ODM2Docs/core_methods.md>`_
 * **Actions:** ODM2 Core Action details can be found at the `ODM2 Actions doc  <https://github.com/ODM2/ODM2/blob/master/doc/ODM2Docs/core_actions.md>`_
@@ -88,7 +90,8 @@ Sampling Features and Sites
 Results
 -------
 
-* **Results:** labeled as data results in ODM2 Admin.
+* **Results:** The outcome of an action, such as sensor deployment or specimen observation. These are labeled as data
+results in ODM2 Admin. For more see `ODM2 Results doc https://github.com/ODM2/ODM2/blob/master/doc/ODM2Docs/core_results.md`_
 
 * **Datasets:** The Datasets entity is used to encode information about groups of Results that are logically related.
   A Dataset has a type, title, an abstract, and is the entity in ODM2 that would receive a citation.
@@ -178,7 +181,7 @@ External identifier systems
 
 * **External identifier systems:** Such as an IGSN or ORCiD.
 
-:ref:`2) Using Data Logger Files <DataLoggerFiles>`
+:ref:`2) ODM2 Admin Site Management <ODM2AdminSiteManagement>`
 
 * :ref:`ODM2 Admin docs home page <ODM2-Admin>`
 * :ref:`Search the docs <search>`

docs/source/ODM2AdminDemo.rst

@@ -40,6 +40,12 @@ ODM2 Admin site administration dashboard
 
 .. image:: /images/AdminDashboard.png
 
+The recent actions block of the site administration dashboard shows changes you have recently completed in ODM2 Admin
+such as adding or editing an item in the forms. In the example above we can see that a method, a data result and a
+variable were recently changed.
+
+The Authentication and Authorization link will allow you to create users and groups so others can login to the system.
+
 The ODM2 Admin Administration link will take you to a list of all 44 ODM2 entities that can be directly managed in
 ODM2 Admin. See the ODM2 Admin Forms for details about the ODM2 Admin Forms :ref:`ODM2-Administration`.
 
@@ -58,13 +64,13 @@ ORM with ODM2 databases.
    :maxdepth: 1
 
    1) The ODM2 Admin Forms <ODM2AdminAdministration>
-   2) Using Data Logger Files <DataLoggerFiles>
-   3) Managing Profile Results With ODM2 Admin <ProfileResults>
-   4) Time series QA/QC <DataQAQC>
-   5) Data visualization and URL parameters <DataVisualizationTips>
-   6) Using the Django ORM <ManagingODM2WithTheDjangoORM>
+   2) ODM2 Admin Field Site Management <ODM2AdminSiteManagement>
+   3) Using Data Logger Files <DataLoggerFiles>
+   4) Managing Profile Results With ODM2 Admin <ProfileResults>
+   5) Time series QA/QC <DataQAQC>
+   6) Data visualization and URL parameters <DataVisualizationTips>
+   7) Using the Django ORM <ManagingODM2WithTheDjangoORM>
 
 
 * :ref:`ODM2 Admin docs home page <ODM2-Admin>`
 * :ref:`Search the docs <search>`
-

docs/source/ODM2AdminSettings.rst

@@ -123,8 +123,9 @@ where your data are viewable.
         "featureactionids": [1699, 1784,1782,1780,1701,1707,1778,1779],
     }
 
-Add sampling feature actions to the sensor dashboard. Feature actions listed here will be present in a drop down list on
-the sensor dashboard page.
+In the Sensor dashboard configuration "featureactionids" add sampling feature actions, related to sensor time series
+results, to the sensor dashboard. Feature actions listed here will be present in a drop down list on the sensor
+dashboard page.
 
 The sensor dashboard can be found by visiting 'Graph My Data' -> 'Sensor Dashboard'.
 

docs/source/ODM2AdminSiteManagement.rst

@@ -0,0 +1,26 @@
+ODM2 Admin Site Management
+==========================
+
+One of the principal ways ODM2 improves on the original ODM information model is in accounting for a field sites needs
+for managing field sites. In ODM2 Admin users can track instrument deployments, equipment maintenance, sample collection
+and methods used for these tasks. Users can also track who performed the task, called actions in ODM2, along with field
+or lab notes from the performance of the task.
+
+Record an Action
+----------------
+
+While logged into the ODM2 Admin demo, click the record an action shortcut, then select add a new method.
+
+.. image:: /images/methods.png
+
+Here we will see a list of methods for our site. Along with the method name, and method type is a link to documentation.
+This link might be to a web page, dropbox, box or other hosted file describing the method. Types of methods listed here
+include equipment maintenance, specimen analysis, and Instrument deployment. Let's look at the first method "A quick
+temp-accuracy check (ice bath)". We can see the documentation link will take us to webpage from an equipment
+manufacturer onset. The Method Type link will take us to the ODM2 controlled vocabulary page for equipment maintenance.
+Click on the method name, this will show us the details about this method.
+
+Here we have a method description, and at the bottom actions. The actions listed here used this method, we can also add
+a new action.
+
+:ref:`3) Using Data Logger Files <DataLoggerFiles>`

docs/source/ODM2Adminbackground.rst

@@ -6,15 +6,15 @@ Why ODM2 Admin was developed
 
 ODM2 Admin is an application for site level data management of environmental observations using Observation Data Model 2
 (ODM2). The application was designed for management of observations generated by the Luquillo Critical Zone Observatory
-(LCZO), an NSF funded Observatory established in 2009, located in northeastern Puerto Rico. The LCZO is one of NSF
-funded nine critical zone observatories, it features a dynamic tropical rainforest, with a long history of scientific
+(LCZO), an NSF funded Observatory established in 2009, located in northeastern Puerto Rico. The LCZO is one of nine NSF
+funded critical zone observatories, it features a dynamic tropical rainforest, with a long history of scientific
 inquiry and natural resource management. The LCZO manages in situ stream, groundwater, atmospheric, and soil sensors at
 53 locations throughout the Luquillo Mountains. The LCZO also supports a number of field campaigns where samples of
 soils, rocks, and water are taken and analyzed in a laboratory. The results of these analyzes inform LCZO researchers on
 rates of weathering, sources and sinks of carbon, nitrogen and phosphorus, riparian zone dynamics among many other
 subjects of inquiry.
 
-Managing the diverse range of data and associated metadata generated from studies of the LCZO requires a robust
+Managing the diverse range of data, and associated metadata, generated from studies of the LCZO requires a robust
 information model. To meet this requirement the LCZO adopted Observation data model 2 (ODM2) which serves as the
 foundation of ODM2 Admin. ODM2 is designed to manage data generated from discreet earth observations across many
 disciplines such as those made through the CZO program. Once the LCZO began using ODM2 it became clear, that due to the