Closed mandywil closed 9 years ago
goksel
commented
10 years ago Hi Mandy,
Ideally, the api should have merged the content for the DnaComponent entity causing this problem. Currently, the validation fails when a DnaComponent entity does not have the displayId, even if the entity has this property when included in other parts of the same document! For now, I would suggest including all the details for DNA components. Does anyone have any opinion? Goksel
drdozer
commented
10 years ago Hi all,
Right now the combination of validation by xsd and by code used for the v1 serialization means that some data must be duplicated at each point in the file. This is an inherent limitation, and can't be fixed until we move to the v2 serialization, with its explicit distinction between data representation and data referencing. So while it is a Bad Thing that we've had badly-formed example data files for years, it is one symptom among many that will be fixed when we move to the new file format.
Looking forward to discussing this on Sunday.
Matthew
On 16 August 2014 13:58, Goksel Misirli notifications@github.com wrote:
Hi Mandy,
Ideally, the api should have merged the content for the DnaComponent entity causing this problem. Currently, the validation fails when a DnaComponent entity does not have the displayId, even if the entity has this property when included in other parts of the same document! For now, I would suggest including all the details for DNA components. Does anyone has any opinion? Goksel
— Reply to this email directly or view it on GitHub https://github.com/SynBioDex/libSBOLj/issues/61#issuecomment-52392410.
Dr Matthew Pocock Turing ate my hamster LTD mailto: turingatemyhamster@gmail.com
Integrative Bioinformatics Group, School of Computing Science, Newcastle University mailto: matthew.pocock@ncl.ac.uk
gchat: turingatemyhamster@gmail.com msn: matthew_pocock@yahoo.co.uk irc.freenode.net: drdozer skype: matthew.pocock tel: (0191) 2566550 mob: +447535664143
mandywil
commented
10 years ago Do you know when you will be moving to the new format? We are writing a paper, and Dr. Peccoud wants to release the data in SBOL format, but we probably don't want to release it just in time for it to become obsolete :)
Thanks! Mandy Wilson
On Sat, Aug 16, 2014 at 9:23 AM, Matthew Pocock notifications@github.com wrote:
Hi all,
Right now the combination of validation by xsd and by code used for the v1 serialization means that some data must be duplicated at each point in the file. This is an inherent limitation, and can't be fixed until we move to the v2 serialization, with its explicit distinction between data representation and data referencing. So while it is a Bad Thing that we've had badly-formed example data files for years, it is one symptom among many that will be fixed when we move to the new file format.
Looking forward to discussing this on Sunday.
Matthew
On 16 August 2014 13:58, Goksel Misirli notifications@github.com wrote:
Hi Mandy,
Ideally, the api should have merged the content for the DnaComponent entity causing this problem. Currently, the validation fails when a DnaComponent entity does not have the displayId, even if the entity has this property when included in other parts of the same document! For now, I would suggest including all the details for DNA components. Does anyone has any opinion? Goksel
— Reply to this email directly or view it on GitHub https://github.com/SynBioDex/libSBOLj/issues/61#issuecomment-52392410.
Dr Matthew Pocock Turing ate my hamster LTD mailto: turingatemyhamster@gmail.com
Integrative Bioinformatics Group, School of Computing Science, Newcastle University mailto: matthew.pocock@ncl.ac.uk
gchat: turingatemyhamster@gmail.com msn: matthew_pocock@yahoo.co.uk irc.freenode.net: drdozer skype: matthew.pocock tel: (0191) 2566550 mob: +447535664143
— Reply to this email directly or view it on GitHub https://github.com/SynBioDex/libSBOLj/issues/61#issuecomment-52392928.
nroehner
commented
10 years ago Hi Mandy,
You should be okay releasing data in the old format. We are definitely implementing backwards compatibility in the new library so that tools using it can read files in the old format files and convert them to the new format.
Best,
Nic
On Monday, August 18, 2014, Mandy Wilson notifications@github.com wrote:
Do you know when you will be moving to the new format? We are writing a paper, and Dr. Peccoud wants to release the data in SBOL format, but we probably don't want to release it just in time for it to become obsolete :)
Thanks! Mandy Wilson
On Sat, Aug 16, 2014 at 9:23 AM, Matthew Pocock notifications@github.com wrote:
Hi all,
Right now the combination of validation by xsd and by code used for the v1 serialization means that some data must be duplicated at each point in the file. This is an inherent limitation, and can't be fixed until we move to the v2 serialization, with its explicit distinction between data representation and data referencing. So while it is a Bad Thing that we've had badly-formed example data files for years, it is one symptom among many that will be fixed when we move to the new file format.
Looking forward to discussing this on Sunday.
Matthew
On 16 August 2014 13:58, Goksel Misirli notifications@github.com wrote:
Hi Mandy,
Ideally, the api should have merged the content for the DnaComponent entity causing this problem. Currently, the validation fails when a DnaComponent entity does not have the displayId, even if the entity has this property when included in other parts of the same document! For now, I would suggest including all the details for DNA components. Does anyone has any opinion? Goksel
— Reply to this email directly or view it on GitHub <https://github.com/SynBioDex/libSBOLj/issues/61#issuecomment-52392410 .
Dr Matthew Pocock Turing ate my hamster LTD mailto: turingatemyhamster@gmail.com
Integrative Bioinformatics Group, School of Computing Science, Newcastle University mailto: matthew.pocock@ncl.ac.uk
gchat: turingatemyhamster@gmail.com msn: matthew_pocock@yahoo.co.uk irc.freenode.net: drdozer skype: matthew.pocock tel: (0191) 2566550 mob: +447535664143
— Reply to this email directly or view it on GitHub https://github.com/SynBioDex/libSBOLj/issues/61#issuecomment-52392928.
When I try to validate SBOL files, I am consistently getting errors like the following: C:\Users\mandywil\Documents\GitHub\libSBOLj2\libSBOLj\core\target>java -jar lib BOLj-core-1.0.0-SNAPSHOT.jar ....\BBa_T9002.xml Validation failed, error: org.xml.sax.SAXParseException; lineNumber: 233; colum Number: 23; cvc-complex-type.2.4.b: The content of element 's:DnaComponent' is ot complete. One of '{"http://www.w3.org/1999/02/22-rdf-syntax-ns#":type, "http //sbols.org/v1#":displayId}' is expected.
I get this with files I converted using the j5 SBOL XML converter as well as files I found in the examples directory (specifically BBa_T9002.xml.)
Any help would be appreciated!