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IHTSDO / snomed-owl-toolkit

The official SNOMED CT OWL Toolkit. OWL conversion, classification and authoring support.
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Not all rows loaded from user created file. (Originally: Not all stated relationships taken into account) #27

Closed trudiger closed 5 years ago

trudiger commented 5 years ago

Dear providers,

I am trying to classify a Snomed extension with the toolkit commandline.

(java -jar "C:\Users\thoma\Documents\PuffinPathology\Classifier\snomed-owl-toolkit-2.6.0-executable.jar" -classify -rf2-snapshot-archives "C:\Users\thoma\Documents\PuffinPathology\Classifier\SnomedCT_InternationalRF2_PRODUCTION_20190131T120000Z.zip" -rf2-authoring-delta-archive "C:\Users\thoma\Documents\PuffinPathology\Classifier\TR_Delta\SnomedCT_InternationalRF2_PRODUCTION_20190131T120000Z.zip")

The input is provided by the "-rf2-authoring-delta-archive " parameter. There are no other relevant files in the archive. For a reason, that I cannot understand, the last of the stated attribute relationships does not appear in the inferred relationsships and appropriate is-A relationships from this last grouped attribute relationship are not inferred. If I change the order of the attribute relationships, always the last one seems not to be taken into account. What am I doing wrong?

5 rf2-files attached (3 input, 2 output)

Best regards Thomas

sct2_Concept_Delta_INT_20190131.txt sct2_StatedRelationship_Delta_INT_20190131.txt sct2_TextDefinition_Delta-en_INT_20190131.txt

trudiger commented 5 years ago

classification-results-2019-07-14_13-59-54.zip SnomedCT_InternationalRF2_PRODUCTION_20190131T120000Z.zip

... attaching failed in the previous comment Here are the relavant zip-archives

kaicode commented 5 years ago

Hi @trudiger,

Please make sure every line in your RF2 ends with a ends with a carriage return and line feed character. The concept delta you attached does not have these characters at the end so it's quite possible that the last line will not be loaded. It's worth checking all the lines of the rest of your files too. Let us know how it goes.

Kind regards, Kai

RF2 docs for reference: https://confluence.ihtsdotools.org/display/DOCRELFMT/3.1.1+General+Structure+of+Release+Files

trudiger commented 5 years ago

Hi Kai, Thank you very much. I will try and keep you informed. Yours Thomas

Von meinem iPhone gesendet

Am 15.07.2019 um 12:57 schrieb Kai Kewley notifications@github.com<mailto:notifications@github.com>:

Hi @trudigerhttps://github.com/trudiger,

Please make sure every line in your RF2 ends with a ends with a carriage return and line feed character. The concept delta you attached does not have these characters at the end so it's quite possible that the last line will not be loaded. It's worth checking all the lines of the rest of your files too. Let us know how it goes.

Kind regards, Kai

RF2 docs for reference: https://confluence.ihtsdotools.org/display/DOCRELFMT/3.1.1+General+Structure+of+Release+Files

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/IHTSDO/snomed-owl-toolkit/issues/27?email_source=notifications&email_token=AMTOZVLAXDBFUQF2FO3XGK3P7RJYVA5CNFSM4IDNMTDKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODZ5LB7Q#issuecomment-511357182, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AMTOZVKZE6PEFW2P3VE564TP7RJYVANCNFSM4IDNMTDA.

kaicode commented 5 years ago

Closing this one for now. Please reopen if the issue is not yet resolved.

trudiger commented 5 years ago

Dear Kai Kewley,

you were completely right! Thank you very much for your help. Thomas

Von: Kai Kewley notifications@github.com Gesendet: Donnerstag, 15. August 2019 15:52 An: IHTSDO/snomed-owl-toolkit snomed-owl-toolkit@noreply.github.com Cc: Prof. Dr. med. Thomas Rüdiger thomas.ruediger@iap-bonn.de; Mention mention@noreply.github.com Betreff: Re: [IHTSDO/snomed-owl-toolkit] Not all rows loaded from user created file. (Originally: Not all stated relationships taken into account) (#27)

Closed #27https://github.com/IHTSDO/snomed-owl-toolkit/issues/27.

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kaicode commented 5 years ago

Thanks for the good news Thomas 👍. I hope your data is behaving now 😄.