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View Code? Open in Web Editor NEWA utility constructing bio.tools entries from publications
License: GNU General Public License v3.0
A utility constructing bio.tools entries from publications
License: GNU General Public License v3.0
Hi, when using the JSON file from an API call of bio.tools
e.g. https://bio.tools/api/t/?collectionID=%22VIB%22&format=json&page=1
I encounter parsing errors like the one below.
It seems to be that several properties (e.g. publication type or rorid of persons etc) present in the JSON are not accepted by the parser of pub2tools.
Any feedback is appreciated.
Cheers, Alex
$ java -jar target/pub2tools-1.0.0.jar -pass2 output
2020-08-13 22:04:35,817 INFO This is Pub2Tools 1.0.0 (https://github.com/bio-tools/pub2tools) pub2tools.Pub2Tools main
2020-08-13 22:04:36,242 INFO Loading IDF from output\tf.idf pub2tools.Pass2 main
2020-08-13 22:04:39,320 INFO Loading all bio.tools content from output\biotools.json pub2tools.Pass2 main
2020-08-13 22:04:39,822 ERROR Exception! pub2tools.Pub2Tools main
com.fasterxml.jackson.databind.exc.MismatchedInputException: Cannot deserialize instance of `org.edamontology.edammap.core.input.json.DocumentationType` out of START_ARRAY token
at [Source: (FileInputStream); line: 134, column: 19] (through reference chain: org.edamontology.edammap.core.input.json.Biotools["list"]->java.util.ArrayList[0]->org.edamontology.edammap.core.input.json.Tool["documentation"]->java.util.ArrayList[0]->org.edamontology.edammap.core.input.json.Link["type"])
at com.fasterxml.jackson.databind.exc.MismatchedInputException.from(MismatchedInputException.java:59) ~[jackson-databind-2.10.2.jar:2.10.2]
at com.fasterxml.jackson.databind.DeserializationContext.reportInputMismatch(DeserializationContext.java:1442) ~[jackson-databind-2.10.2.jar:2.10.2]
at com.fasterxml.jackson.databind.DeserializationContext.handleUnexpectedToken(DeserializationContext.java:1216) ~[jackson-databind-2.10.2.jar:2.10.2]
at com.fasterxml.jackson.databind.deser.std.StdDeserializer._deserializeFromArray(StdDeserializer.java:714) ~[jackson-databind-2.10.2.jar:2.10.2]
at com.fasterxml.jackson.databind.deser.std.EnumDeserializer._deserializeOther(EnumDeserializer.java:265) ~[jackson-databind-2.10.2.jar:2.10.2]
at com.fasterxml.jackson.databind.deser.std.EnumDeserializer.deserialize(EnumDeserializer.java:206) ~[jackson-databind-2.10.2.jar:2.10.2]
at com.fasterxml.jackson.databind.deser.impl.MethodProperty.deserializeAndSet(MethodProperty.java:129) ~[jackson-databind-2.10.2.jar:2.10.2]
at com.fasterxml.jackson.databind.deser.BeanDeserializer.vanillaDeserialize(BeanDeserializer.java:288) ~[jackson-databind-2.10.2.jar:2.10.2]
at com.fasterxml.jackson.databind.deser.BeanDeserializer.deserialize(BeanDeserializer.java:151) ~[jackson-databind-2.10.2.jar:2.10.2]
at com.fasterxml.jackson.databind.deser.std.CollectionDeserializer.deserialize(CollectionDeserializer.java:286) ~[jackson-databind-2.10.2.jar:2.10.2]
at com.fasterxml.jackson.databind.deser.std.CollectionDeserializer.deserialize(CollectionDeserializer.java:245) ~[jackson-databind-2.10.2.jar:2.10.2]
at com.fasterxml.jackson.databind.deser.std.CollectionDeserializer.deserialize(CollectionDeserializer.java:27) ~[jackson-databind-2.10.2.jar:2.10.2]
at com.fasterxml.jackson.databind.deser.impl.MethodProperty.deserializeAndSet(MethodProperty.java:129) ~[jackson-databind-2.10.2.jar:2.10.2]
at com.fasterxml.jackson.databind.deser.BeanDeserializer.vanillaDeserialize(BeanDeserializer.java:288) ~[jackson-databind-2.10.2.jar:2.10.2]
at com.fasterxml.jackson.databind.deser.BeanDeserializer.deserialize(BeanDeserializer.java:151) ~[jackson-databind-2.10.2.jar:2.10.2]
at com.fasterxml.jackson.databind.deser.std.CollectionDeserializer.deserialize(CollectionDeserializer.java:286) ~[jackson-databind-2.10.2.jar:2.10.2]
at com.fasterxml.jackson.databind.deser.std.CollectionDeserializer.deserialize(CollectionDeserializer.java:245) ~[jackson-databind-2.10.2.jar:2.10.2]
at com.fasterxml.jackson.databind.deser.std.CollectionDeserializer.deserialize(CollectionDeserializer.java:27) ~[jackson-databind-2.10.2.jar:2.10.2]
at com.fasterxml.jackson.databind.deser.impl.MethodProperty.deserializeAndSet(MethodProperty.java:129) ~[jackson-databind-2.10.2.jar:2.10.2]
at com.fasterxml.jackson.databind.deser.BeanDeserializer.vanillaDeserialize(BeanDeserializer.java:288) ~[jackson-databind-2.10.2.jar:2.10.2]
at com.fasterxml.jackson.databind.deser.BeanDeserializer.deserialize(BeanDeserializer.java:151) ~[jackson-databind-2.10.2.jar:2.10.2]
at com.fasterxml.jackson.databind.ObjectMapper._readMapAndClose(ObjectMapper.java:4202) ~[jackson-databind-2.10.2.jar:2.10.2]
at com.fasterxml.jackson.databind.ObjectMapper.readValue(ObjectMapper.java:3242) ~[jackson-databind-2.10.2.jar:2.10.2]
at org.edamontology.edammap.core.input.Json.load(Json.java:49) ~[edammap-core-1.0.0.jar:?]
at tools.bio.pub2tools.Pass2.run(Pass2.java:1217) ~[pub2tools-1.0.0.jar:?]
at tools.bio.pub2tools.Pub2Tools.pass2(Pub2Tools.java:261) ~[pub2tools-1.0.0.jar:?]
at tools.bio.pub2tools.Pub2Tools.run(Pub2Tools.java:473) ~[pub2tools-1.0.0.jar:?]
at tools.bio.pub2tools.Pub2Tools.main(Pub2Tools.java:613) [pub2tools-1.0.0.jar:?]
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