diff --git a/README.md b/README.md index 8bef94f..5886c36 100644 --- a/README.md +++ b/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 `/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 ` 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. diff --git a/app/src/main/resources/logback.xml b/app/src/main/resources/logback.xml new file mode 100644 index 0000000..d22daf8 --- /dev/null +++ b/app/src/main/resources/logback.xml @@ -0,0 +1,20 @@ + + + + + + %d [%thread] %X{run.id} %-5level %logger{36} - %msg%n + + + + + + + + + + + + + + diff --git a/lib/src/main/resources/de/uni_halle/informatik/biodata/mp/resolver/identifiersorg/IdentifiersOrg-Registry.json b/lib/src/main/resources/de/uni_halle/informatik/biodata/mp/resolver/identifiersorg/IdentifiersOrg-Registry.json index 972ed16..23dbb0a 100644 --- a/lib/src/main/resources/de/uni_halle/informatik/biodata/mp/resolver/identifiersorg/IdentifiersOrg-Registry.json +++ b/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", diff --git a/lib/src/test/java/de/uni_halle/informatik/biodata/mp/annotation/bigg/BiGGSpeciesAnnotatorTest.java b/lib/src/test/java/de/uni_halle/informatik/biodata/mp/annotation/bigg/BiGGSpeciesAnnotatorTest.java index e61ca9d..185c4e0 100644 --- a/lib/src/test/java/de/uni_halle/informatik/biodata/mp/annotation/bigg/BiGGSpeciesAnnotatorTest.java +++ b/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,