Merge branch 'develop'

LICENSE.txt

-		NIBIO OPEN SOURCE LICENSE V.1.0 (2014)
-
-			PREAMBLE AND ADDITIONAL TERMS
-
-  The original licensor is the Norwegian Institute for Agricultural and 
-Environmental Research, registered in Norway with registration number 988 983 
-837, and business address NO-1430 ÅS, NORWAY, hereafter referred to as 
-"NIBIO". 
-
-  This NIBIO OPEN SOURCE LICENSE V.1.0 (2014), in short the NIBIO Open 
-Source License, is based on the GNU Affero General Public License, version 3.
-All of the terms and conditions of the GNU Affero General Public License, 
-version 3, have been set out below, save the below mentioned additional 
-prevailing terms that have priority over the terms otherwise identical to the 
-GNU Affero General Public License, version 3, and that Section 0 ("This 
-License" definition changed), 13 ("version 3 of the GNU General Public License" 
-replaced by "this License") and 14 ("The Free Software Foundation" replaced by 
-"NIBIO" and "GNU Affero General Public License" replaced by "License") have 
-been adjusted as a consequence of this.
-
-			ADDITONAL PREVAILING TERMS
-
-  (a) The NIBIO Open Source License regulates the NIBIO VIPS Platform 
-software, an Internet based system enabling prediction of infection risk of 
-plant diseases, pests and weeds. The NIBIO Open Source License DOES NOT 
-INCLUDE the specific forecasting models, neither their algorithms nor their 
-implementation to be used by the NIBIO VIPS Platform. You are free to 
-implement any other forecasting model to be used by the NIBIO VIPS Platform, 
-regardless of license terms at your own responsibility. 
-
-  (b) This license is governed by Norwegian law, as far as any party or third 
-party purports or sets forward any claim towards NIBIO. Any claims towards 
-NIBIO shall be solved by the exclusive venue of Oslo City Courts, Norway. 
-This paragraph is not applicable for claims only between any later parties to 
-this license. 
-
-  (c) By entering into this agreement you also agree to indemnify NIBIO and 
-its employees / consultants / board, for any claims of liability related to 
-this license set forward by yourself or any party deviating its rights from you. 
-
-  (d) You shall include the following in the start of each source file: 
-
-	Copyright (c) <year> <name of author> 
- 
-	This file is part of <application name>. <application name> is free 
-	software: you can redistribute it and/or modify it under the terms of 
-	the NIBIO Open Source License as published by NIBIO, either 
-	version 1 of the License, or (at your option) any later version.
-
-	<application name> is distributed in the hope that it will be useful,
-	but WITHOUT ANY WARRANTY; without even the implied warranty of
-	MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-	NIBIO Open Source License for more details.
-
-	You should have received a copy of the NIBIO Open Source License
-	along with <application name>.  If not, see 
-	<http://www.nibio.no/licenses/>.
-
-      It is also recommended that you add information on how to contact you by 
-      electronic and paper mail.
-
-			1. TERMS AND CONDITIONS
-
-  2. 0. Definitions.
-
-  "This License" refers to NIBIO Open Source License v.1.0 (2014). 
+                    GNU AFFERO GENERAL PUBLIC LICENSE
+                       Version 3, 19 November 2007
+
+ Copyright (C) 2007 Free Software Foundation, Inc. <https://fsf.org/>
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+                            Preamble
+
+  The GNU Affero General Public License is a free, copyleft license for
+software and other kinds of works, specifically designed to ensure
+cooperation with the community in the case of network server software.
+
+  The licenses for most software and other practical works are designed
+to take away your freedom to share and change the works.  By contrast,
+our General Public Licenses are intended to guarantee your freedom to
+share and change all versions of a program--to make sure it remains free
+software for all its users.
+
+  When we speak of free software, we are referring to freedom, not
+price.  Our General Public Licenses are designed to make sure that you
+have the freedom to distribute copies of free software (and charge for
+them if you wish), that you receive source code or can get it if you
+want it, that you can change the software or use pieces of it in new
+free programs, and that you know you can do these things.
+
+  Developers that use our General Public Licenses protect your rights
+with two steps: (1) assert copyright on the software, and (2) offer
+you this License which gives you legal permission to copy, distribute
+and/or modify the software.
+
+  A secondary benefit of defending all users' freedom is that
+improvements made in alternate versions of the program, if they
+receive widespread use, become available for other developers to
+incorporate.  Many developers of free software are heartened and
+encouraged by the resulting cooperation.  However, in the case of
+software used on network servers, this result may fail to come about.
+The GNU General Public License permits making a modified version and
+letting the public access it on a server without ever releasing its
+source code to the public.
+
+  The GNU Affero General Public License is designed specifically to
+ensure that, in such cases, the modified source code becomes available
+to the community.  It requires the operator of a network server to
+provide the source code of the modified version running there to the
+users of that server.  Therefore, public use of a modified version, on
+a publicly accessible server, gives the public access to the source
+code of the modified version.
+
+  An older license, called the Affero General Public License and
+published by Affero, was designed to accomplish similar goals.  This is
+a different license, not a version of the Affero GPL, but Affero has
+released a new version of the Affero GPL which permits relicensing under
+this license.
+
+  The precise terms and conditions for copying, distribution and
+modification follow.
+
+                       TERMS AND CONDITIONS
+
+  0. Definitions.
+
+  "This License" refers to version 3 of the GNU Affero General Public License.
 
   "Copyright" also means copyright-like laws that apply to other kinds of
 works, such as semiconductor masks.
@@ -100,7 +97,7 @@ work under this License, and how to view a copy of this License.  If
 the interface presents a list of user commands or options, such as a
 menu, a prominent item in the list meets this criterion.
 
-  3. 1. Source Code.
+  1. Source Code.
 
   The "source code" for a work means the preferred form of the work
 for making modifications to it.  "Object code" means any non-source
@@ -142,7 +139,7 @@ Source.
   The Corresponding Source for a work in source code form is that
 same work.
 
-  4. 2. Basic Permissions.
+  2. Basic Permissions.
 
   All rights granted under this License are granted for the term of
 copyright on the Program, and are irrevocable provided the stated
@@ -167,7 +164,7 @@ your copyrighted material outside their relationship with you.
 the conditions stated below.  Sublicensing is not allowed; section 10
 makes it unnecessary.
 
-  5. 3. Protecting Users' Legal Rights From Anti-Circumvention Law.
+  3. Protecting Users' Legal Rights From Anti-Circumvention Law.
 
   No covered work shall be deemed part of an effective technological
 measure under any applicable law fulfilling obligations under article
@@ -183,7 +180,7 @@ modification of the work as a means of enforcing, against the work's
 users, your or third parties' legal rights to forbid circumvention of
 technological measures.
 
-  6. 4. Conveying Verbatim Copies.
+  4. Conveying Verbatim Copies.
 
   You may convey verbatim copies of the Program's source code as you
 receive it, in any medium, provided that you conspicuously and
@@ -196,7 +193,7 @@ recipients a copy of this License along with the Program.
   You may charge any price or no price for each copy that you convey,
 and you may offer support or warranty protection for a fee.
 
-  7. 5. Conveying Modified Source Versions.
+  5. Conveying Modified Source Versions.
 
   You may convey a work based on the Program, or the modifications to
 produce it from the Program, in the form of source code under the
@@ -233,7 +230,7 @@ beyond what the individual works permit.  Inclusion of a covered work
 in an aggregate does not cause this License to apply to the other
 parts of the aggregate.
 
-  8. 6. Conveying Non-Source Forms.
+  6. Conveying Non-Source Forms.
 
   You may convey a covered work in object code form under the terms
 of sections 4 and 5, provided that you also convey the
@@ -331,7 +328,7 @@ documented (and with an implementation available to the public in
 source code form), and must require no special password or key for
 unpacking, reading or copying.
 
-  9. 7. Additional Terms.
+  7. Additional Terms.
 
   "Additional permissions" are terms that supplement the terms of this
 License by making exceptions from one or more of its conditions.
@@ -395,7 +392,7 @@ where to find the applicable terms.
 form of a separately written license, or stated as exceptions;
 the above requirements apply either way.
 
-  10. 8. Termination.
+  8. Termination.
 
   You may not propagate or modify a covered work except as expressly
 provided under this License.  Any attempt otherwise to propagate or
@@ -423,7 +420,7 @@ this License.  If your rights have been terminated and not permanently
 reinstated, you do not qualify to receive new licenses for the same
 material under section 10.
 
-  11. 9. Acceptance Not Required for Having Copies.
+  9. Acceptance Not Required for Having Copies.
 
   You are not required to accept this License in order to receive or
 run a copy of the Program.  Ancillary propagation of a covered work
@@ -434,7 +431,7 @@ modify any covered work.  These actions infringe copyright if you do
 not accept this License.  Therefore, by modifying or propagating a
 covered work, you indicate your acceptance of this License to do so.
 
-  12. 10. Automatic Licensing of Downstream Recipients.
+  10. Automatic Licensing of Downstream Recipients.
 
   Each time you convey a covered work, the recipient automatically
 receives a license from the original licensors, to run, modify and
@@ -459,7 +456,7 @@ rights granted under this License, and you may not initiate litigation
 any patent claim is infringed by making, using, selling, offering for
 sale, or importing the Program or any portion of it.
 
-  13. 11. Patents.
+  11. Patents.
 
   A "contributor" is a copyright holder who authorizes use under this
 License of the Program or a work on which the Program is based.  The
@@ -528,7 +525,7 @@ or that patent license was granted, prior to 28 March 2007.
 any implied license or other defenses to infringement that may
 otherwise be available to you under applicable patent law.
 
-  14. 12. No Surrender of Others' Freedom.
+  12. No Surrender of Others' Freedom.
 
   If conditions are imposed on you (whether by court order, agreement or
 otherwise) that contradict the conditions of this License, they do not
@@ -540,7 +537,7 @@ to collect a royalty for further conveying from those to whom you convey
 the Program, the only way you could satisfy both those terms and this
 License would be to refrain entirely from conveying the Program.
 
-  15. 13. Remote Network Interaction; Use with the GNU General Public License.
+  13. Remote Network Interaction; Use with the GNU General Public License.
 
   Notwithstanding any other provision of this License, if you modify the
 Program, your modified version must prominently offer all users
@@ -549,8 +546,9 @@ supports such interaction) an opportunity to receive the Corresponding
 Source of your version by providing access to the Corresponding Source
 from a network server at no charge, through some standard or customary
 means of facilitating copying of software.  This Corresponding Source
-shall include the Corresponding Source for any work covered by This License 
-that is incorporated pursuant to the following paragraph.
+shall include the Corresponding Source for any work covered by version 3
+of the GNU General Public License that is incorporated pursuant to the
+following paragraph.
 
   Notwithstanding any other provision of this License, you have
 permission to link or combine any covered work with a work licensed
@@ -560,30 +558,33 @@ License will continue to apply to the part which is the covered work,
 but the work with which it is combined will remain governed by version
 3 of the GNU General Public License.
 
-  16. 14. Revised Versions of this License.
+  14. Revised Versions of this License.
 
-  NIBIO may publish revised and/or new versions of the License from time to 
-time. Such new versions will be similar in spirit to the present version, but 
-may differ in detail to address new problems or concerns.
+  The Free Software Foundation may publish revised and/or new versions of
+the GNU Affero General Public License from time to time.  Such new versions
+will be similar in spirit to the present version, but may differ in detail to
+address new problems or concerns.
 
   Each version is given a distinguishing version number.  If the
-Program specifies that a certain numbered version of the License "or any later 
-version" applies to it, you have the option of following the terms and 
-conditions either of that numbered version or of any later version published by 
-NIBIO. If the Program does not specify a version number of the License, you 
-may choose any version ever published by the NIBIO.
+Program specifies that a certain numbered version of the GNU Affero General
+Public License "or any later version" applies to it, you have the
+option of following the terms and conditions either of that numbered
+version or of any later version published by the Free Software
+Foundation.  If the Program does not specify a version number of the
+GNU Affero General Public License, you may choose any version ever published
+by the Free Software Foundation.
 
   If the Program specifies that a proxy can decide which future
-versions of the License can be used, that proxy's public statement of 
-acceptance of a version permanently authorizes you to choose that version for 
-the Program.
+versions of the GNU Affero General Public License can be used, that proxy's
+public statement of acceptance of a version permanently authorizes you
+to choose that version for the Program.
 
   Later license versions may give you additional or different
 permissions.  However, no additional obligations are imposed on any
 author or copyright holder as a result of your choosing to follow a
 later version.
 
-  17. 15. Disclaimer of Warranty.
+  15. Disclaimer of Warranty.
 
   THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY
 APPLICABLE LAW.  EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT
@@ -594,7 +595,7 @@ PURPOSE.  THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM
 IS WITH YOU.  SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF
 ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
 
-  18. 16. Limitation of Liability.
+  16. Limitation of Liability.
 
   IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
 WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS
@@ -606,7 +607,7 @@ PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),
 EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
 SUCH DAMAGES.
 
-  19. 17. Interpretation of Sections 15 and 16.
+  17. Interpretation of Sections 15 and 16.
 
   If the disclaimer of warranty and limitation of liability provided
 above cannot be given local legal effect according to their terms,
@@ -615,4 +616,46 @@ an absolute waiver of all civil liability in connection with the
 Program, unless a warranty or assumption of liability accompanies a
 copy of the Program in return for a fee.
 
-                     END OF TERMS AND CONDITIONS
+                     END OF TERMS AND CONDITIONS
\ No newline at end of file
+
+            How to Apply These Terms to Your New Programs
+
+  If you develop a new program, and you want it to be of the greatest
+possible use to the public, the best way to achieve this is to make it
+free software which everyone can redistribute and change under these terms.
+
+  To do so, attach the following notices to the program.  It is safest
+to attach them to the start of each source file to most effectively
+state the exclusion of warranty; and each file should have at least
+the "copyright" line and a pointer to where the full notice is found.
+
+    <one line to give the program's name and a brief idea of what it does.>
+    Copyright (C) <year>  <name of author>
+
+    This program is free software: you can redistribute it and/or modify
+    it under the terms of the GNU Affero General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+
+    This program is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU Affero General Public License for more details.
+
+    You should have received a copy of the GNU Affero General Public License
+    along with this program.  If not, see <https://www.gnu.org/licenses/>.
+
+Also add information on how to contact you by electronic and paper mail.
+
+  If your software can interact with users remotely through a computer
+network, you should also make sure that it provides a way for users to
+get its source.  For example, if your program is a web application, its
+interface could display a "Source" link that leads users to an archive
+of the code.  There are many ways you could offer source, and different
+solutions will be better for different programs; see section 13 for the
+specific requirements.
+
+  You should also get your employer (if you work as a programmer) or school,
+if any, to sign a "copyright disclaimer" for the program, if necessary.
+For more information on this, and how to apply and follow the GNU AGPL, see
+<https://www.gnu.org/licenses/>.

README.md

@@ -55,6 +55,7 @@ Add the model jar file, and edit module.xml accordingly.
 		<module name="com.fasterxml.jackson.core.jackson-databind" export="false"/>
 		<module name="com.vividsolutions.jts" export="false"/>
 		<module name="org.renjin" export="false"/>
+                <module name="org.slf4j" export="false"/>
     </dependencies>
     
 </module>

docs/create_client.md

@@ -2,25 +2,28 @@
 
 Running a model is a matter of creating a client that is able to send a POST request to a common endpoint, and provide Json in the request body and consume the standard Json that is returned from the model.
 
-The endpoint for running a model is:
+The **endpoint for running a model** is:
 
 ```
-{{vipslogic_url}}/models/{{MODEL_ID}}/run
+{{vipscore_url}}/models/{{MODEL_ID}}/run
 ```
 
-Get the model ID by simply connecting to
+**Get the model ID** by simply connecting to
 
 ```
-{{vipslogic_url}}/models/
+{{vipscore_url}}/models/
 ```
 
-So you must create a model configuration object and pass it in the request body. Each model has its own set of input data. To se a configuration example for a specific model, query
+So you must create a model configuration object and pass it in the request body. Each model has its own set of input data. 
+To see a **configuration example for a specific model**, query
 
 ```
-{{vipslogic_url}}/models/{{MODEL_ID}}/sampleconfig
+{{vipscore_url}}/models/{{MODEL_ID}}/sampleconfig
 ```
 
 Here's a sample for the Carrot rust fly temperature model (PSILARTEMP)
+**NOTE: Not all models are properly documented. If you find models with missing information, get in touch and we'll 
+help you out**
 
 ```
 {
@@ -47,7 +50,7 @@ The `"loginInfo"` property is only relevant when running the model through the V
 An explanation of the input parameters should be provided for each model from this endpoint:
 
 ```
-{{vipslogic_url}}/models/{{MODEL_ID}}/sampleconfig
+{{vipscore_url}}/models/{{MODEL_ID}}/usage
 ```
 
 If not, please contact the model provider and notify them.
@@ -109,7 +112,7 @@ Each model has its own output parameters, given in "allValues". They all provide
 The exact interpretation of the warningStatus is provided by the model, and can be read from this endpoint: 
 
 ```
-{{vipslogic_url}}/models/{{MODEL_ID}}/warningstatusinterpretation
+{{vipscore_url}}/models/{{MODEL_ID}}/warningstatusinterpretation
 ```
 
 Example from the PSILARTEMP model:

src/main/java/no/nibio/vips/core/service/ModelResourceImpl.java

@@ -74,7 +74,7 @@ public class ModelResourceImpl implements ModelResource{
     @Override
     public Response defaultResponse() 
     {
-        return Response.ok().entity("<html><head></head><body><a href=\"" + servletRequest.getContextPath() + "/models/\">Models</a></body></html>").build();
+        return Response.ok().entity("<html><head></head><body><a href=\"/models/\">Models</a></body></html>").build();
     }
     
     /**
@@ -88,7 +88,7 @@ public class ModelResourceImpl implements ModelResource{
     public Response printModelListJSON()
     {
         
-        return this.printModelListJSON(null);
+        return this.printModelListJSON(Model.DEFAULT_LANGUAGE);
     }
     
     /**
@@ -327,8 +327,7 @@ public class ModelResourceImpl implements ModelResource{
             if(config.getConfigParameter("fieldObservations") != null && List.class.isAssignableFrom(config.getConfigParameter("fieldObservations").getClass()))
             {
                 config.setConfigParameter("pestObservations", dt.getVIPSPestObservations(
-                        (List) config.getConfigParameter("fieldObservations"),
-                        (List) config.getConfigParameter("fieldObservationQuantifications")
+                        (List) config.getConfigParameter("fieldObservations")
                         )
                 );
             }
@@ -336,6 +335,10 @@ public class ModelResourceImpl implements ModelResource{
             {
             	throw new ConfigValidationException("ERROR: fieldObservations must be of type array");
             }
+            else if(config.getConfigParameter("fieldObservations") == null)
+            {
+                config.setConfigParameter("pestObservations",new ArrayList<>());
+            }
             Model calledModel = ModelFactory.getInstance().getModelInstance(modelId);
             calledModel.setConfiguration(config);
             List<Result> results = calledModel.getResult();