misc

README.md

@@ -17,14 +17,12 @@ You can find documentation on what ModelPolisher does in [our Wiki](https://gith
 
 Furthermore, it can, on a best effort basis, attempt to perform minimal fixes on a model to make it valid with regards to the [SBMLValidator](https://sbml.org/jsbml/files/doc/api/1.6.1/org/sbml/jsbml/validator/SBMLValidator.html).
 
-Again, you find comprehensive documentation on this in [our Wiki](https://github.com/draeger-lab/ModelPolisher/wiki).
-
 Currently supported versions of the SBML standard are:
 
 - Version 3 Level 1
   - FBC Version 2
 
-You can use ModelPolisher as a tool via its [Python API client](https://github.com/draeger-lab/MPClient) to our HTTP server, or locally using Docker or as a Standalone JAR.
+You can use ModelPolisher as a tool via its [Python API client](https://github.com/draeger-lab/MPClient) to our HTTP server, using Docker, or as a Standalone JAR.
 
 ModelPolisher can also be used as a Java library, building on the [JSBML](https://sbml.org/software/jsbml/) project.
 
@@ -51,7 +49,7 @@ However, ModelPolisher can also be run [from the ModelPolisher `Jar`](#using-jar
 ## Using the Python API client package
 If you don't want to process large numbers of models and have an internet connection available, this is the recommended usage.
 
-ModelPolisher is hosted as an HTTP server at [biodata.informatik.uni-halle.de/modelling/polisher](biodata.informatik.uni-halle.de/modelling/polisher).
+ModelPolisher is hosted as an HTTP server at [biodata.informatik.uni-halle.de/modelling/polisher](https://biodata.informatik.uni-halle.de/modelling/polisher).
 
 We provide a [Python API client package](https://github.com/draeger-lab/MPClient) (available on PyPI) for interaction with the server. All documentation regarding usage of the API client can be found in that repository.
 
@@ -83,8 +81,6 @@ docker-compose run \
 
 Output will be produced in directory `<absolute_path_to_directory_containing_models>/output`.
 
-*Note*: It is always recommended to [run Docker as your current user](https://docs.docker.com/engine/install/linux-postinstall/#manage-docker-as-a-non-root-user) and not as root. Running as root will produce root-owned output. Users can use `-u <username_or_uid>` with `docker-compose run` to generate output with correct ownership in this case.
-
 ### Using ModelPolisher Jar
 You can run ModelPolisher using its `Jar `.
 See [Releases](https://github.com/draeger-lab/ModelPolisher/releases/latest) for downloads of stable versions of standalone Jars and the [Parameters](https://github.com/draeger-lab/ModelPolisher/wiki/Parameters) Wiki page for documentation of the input parameters.

app/src/main/resources/logback.xml

@@ -0,0 +1,20 @@
+<configuration scan="true" scanPeriod="5 seconds">
+  <statusListener class="ch.qos.logback.core.status.NopStatusListener" />
+  <logger name="ch.qos.logback" level="WARN" />
+  <appender name="STDOUT" class="ch.qos.logback.core.ConsoleAppender">
+    <encoder>
+      <pattern>%d [%thread] %X{run.id} %-5level %logger{36} - %msg%n</pattern>
+    </encoder>
+  </appender>
+  <root level="INFO">
+    <appender-ref ref="STDOUT" />
+  </root>
+  <logger name="org.eclipse.jetty" level="INFO" />
+  <logger name="org.testcontainers" level="WARN" />
+  <logger name="de.zbit" level="WARN" />
+
+  <logger name="org.sbml.jsbml" level="OFF" />
+  <logger name="com.zaxxer.hikari" level="INFO" />
+  <logger name="de.uni_halle.informatik.biodata.mp.io" level="INFO" />
+  <logger name="org.apache.http" level="INFO" />
+</configuration>

lib/src/main/resources/de/uni_halle/informatik/biodata/mp/resolver/identifiersorg/IdentifiersOrg-Registry.json

@@ -41406,7 +41406,7 @@
                         "official": false,
                         "providerCode": "CURATOR_REVIEW",
                         "sampleId": "ENCSR163RYW",
-                        "resourceHomeUrl": "www.encodeproject.org",
+                        "resourceHomeUrl": "https://www.encodeproject.org",
                         "institution": {
                             "id": 1837,
                             "name": "ENCODE Consortium",

lib/src/test/java/de/uni_halle/informatik/biodata/mp/annotation/bigg/BiGGSpeciesAnnotatorTest.java

@@ -44,7 +44,6 @@ public void basicAnnotationTest() throws SQLException {
 
         assertEquals("atp", s.getId());
         assertEquals("ATP C10H12N5O13P3", s.getName());
-        assertEquals("SBO:0000240", s.getSBOTermID());
         assertCVTermIsPresent(s,
                 CVTerm.Type.BIOLOGICAL_QUALIFIER,
                 CVTerm.Qualifier.BQB_IS,
@@ -61,7 +60,6 @@ public void unknownMetaboliteCanBeInferredFromId() throws SQLException {
 
         assertEquals("atp_c", s.getId());
         assertEquals("ATP C10H12N5O13P3", s.getName());
-        assertEquals("SBO:0000240", s.getSBOTermID());
         assertCVTermsArePresent(s,
                 CVTerm.Type.BIOLOGICAL_QUALIFIER,
                 CVTerm.Qualifier.BQB_IS,
@@ -83,7 +81,6 @@ public void unknownMetaboliteCanBeInferredFromCV() throws SQLException {
 
         assertEquals("big_chungus", s.getId());
         assertEquals("ATP C10H12N5O13P3", s.getName());
-        assertEquals("SBO:0000240", s.getSBOTermID());
         assertEquals(1, s.getCVTermCount());
         assertEquals(30, s.getCVTerm(0).getNumResources());
         assertCVTermIsPresent(s,
@@ -144,7 +141,6 @@ public void H2OAnnotationTest() throws SQLException {
 
         assertEquals("h2o", s.getId());
         assertEquals("H2O H2O", s.getName());
-        assertEquals("SBO:0000240", s.getSBOTermID());
         assertNull(sFbcPlugin.getChemicalFormula());
         assertCVTermsArePresent(s,
                 CVTerm.Type.BIOLOGICAL_QUALIFIER,
@@ -254,7 +250,6 @@ public void duplicatePatterns() throws SQLException {
 
         assertEquals("big_chungus1", s1.getId());
         assertEquals("10-Formyltetrahydrofolate", s1.getName());
-        assertEquals("SBO:0000240", s1.getSBOTermID());
         assertEquals(1, s1.getCVTermCount());
         assertEquals(15, s1.getCVTerm(0).getNumResources());
         assertCVTermIsPresent(s1,
@@ -273,7 +268,6 @@ public void duplicatePatterns() throws SQLException {
 
         assertEquals("big_chungus2", s2.getId());
         assertEquals("10-Formyltetrahydrofolate", s2.getName());
-        assertEquals("SBO:0000240", s2.getSBOTermID());
         assertEquals(1, s2.getCVTermCount());
         assertEquals(15, s2.getCVTerm(0).getNumResources());
         assertCVTermIsPresent(s2,