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pub2tools's Issues

issue reading biotools.json from current version of API bio.tools

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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