java.lang.NoClassDefFoundError: bioc/BioCSentence

[soulofshadow]

i download the "MetaMapLite 3.6.2rc8 and UMLS 2022", and also the dataset [2022AA UMLS Level 0+4+9 DataSet].
when i run ./metamaplite.sh. it failed to run.

[willjrogers]

If you have cloned MetaMapLite using git you’ll need to first run maven and update the configuration file: config/metamaplite.properties: Compile MetaMapLite using Maven: $ mvn package Make sure MML_VERSION matches version of standalone jar file in target: MML_VERSION=3.6.2rc8 Should match file in metamaplite directory: target/metamaplite-3.6.2rc8-standalone.jar

…

-- Willie Rogers, Contractor, Lister Hill Center, National Library of Medicine, NIH Rogers, Willie (NIH/NLM/LHC) [C] email: ***@***.******@***.***> From: 奚斤 ***@***.***> Date: Wednesday, October 18, 2023 at 3:51 PM To: lhncbc/metamaplite ***@***.***> Cc: Subscribed ***@***.***> Subject: [EXTERNAL] [lhncbc/metamaplite] java.lang.NoClassDefFoundError: bioc/BioCSentence (Issue #36) i download the "MetaMapLite 3.6.2rc8 and UMLS 2022", and also the dataset [2022AA UMLS Level 0+4+9 DataSet]. when i run ./metamaplite.sh. it failed to run. — Reply to this email directly, view it on GitHub<#36>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AHOVZBMTTRAXDXBIUTIDMYTYAAXMFAVCNFSM6AAAAAA6GB3FFGVHI2DSMVQWIX3LMV43ASLTON2WKOZRHE2TANJTGUZDCNY>. You are receiving this because you are subscribed to this thread.Message ID: ***@***.***> CAUTION: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and are confident the content is safe.

[soulofshadow]

If you have cloned MetaMapLite using git you’ll need to first run maven and update the configuration file: config/metamaplite.properties: Compile MetaMapLite using Maven: $ mvn package Make sure MML_VERSION matches version of standalone jar file in target: MML_VERSION=3.6.2rc8 Should match file in metamaplite directory: target/metamaplite-3.6.2rc8-standalone.jar
…
-- Willie Rogers, Contractor, Lister Hill Center, National Library of Medicine, NIH Rogers, Willie (NIH/NLM/LHC) [C] email: @.@.> From: 奚斤 @.> Date: Wednesday, October 18, 2023 at 3:51 PM To: lhncbc/metamaplite @.> Cc: Subscribed @.> Subject: [EXTERNAL] [lhncbc/metamaplite] java.lang.NoClassDefFoundError: bioc/BioCSentence (Issue #36) i download the "MetaMapLite 3.6.2rc8 and UMLS 2022", and also the dataset [2022AA UMLS Level 0+4+9 DataSet]. when i run ./metamaplite.sh. it failed to run. — Reply to this email directly, view it on GitHub<#36>, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AHOVZBMTTRAXDXBIUTIDMYTYAAXMFAVCNFSM6AAAAAA6GB3FFGVHI2DSMVQWIX3LMV43ASLTON2WKOZRHE2TANJTGUZDCNY. You are receiving this because you are subscribed to this thread.Message ID: @.> CAUTION: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and are confident the content is safe.

If you have cloned MetaMapLite using git you’ll need to first run maven and update the configuration file: config/metamaplite.properties: Compile MetaMapLite using Maven: $ mvn package Make sure MML_VERSION matches version of standalone jar file in target: MML_VERSION=3.6.2rc8 Should match file in metamaplite directory: target/metamaplite-3.6.2rc8-standalone.jar
…
-- Willie Rogers, Contractor, Lister Hill Center, National Library of Medicine, NIH Rogers, Willie (NIH/NLM/LHC) [C] email: @.@.> From: 奚斤 @.> Date: Wednesday, October 18, 2023 at 3:51 PM To: lhncbc/metamaplite @.> Cc: Subscribed @.> Subject: [EXTERNAL] [lhncbc/metamaplite] java.lang.NoClassDefFoundError: bioc/BioCSentence (Issue #36) i download the "MetaMapLite 3.6.2rc8 and UMLS 2022", and also the dataset [2022AA UMLS Level 0+4+9 DataSet]. when i run ./metamaplite.sh. it failed to run. — Reply to this email directly, view it on GitHub<#36>, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AHOVZBMTTRAXDXBIUTIDMYTYAAXMFAVCNFSM6AAAAAA6GB3FFGVHI2DSMVQWIX3LMV43ASLTON2WKOZRHE2TANJTGUZDCNY. You are receiving this because you are subscribed to this thread.Message ID: @.> CAUTION: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and are confident the content is safe.

Hi, Thanks for the reply, but I download it from the lhncbc website also with the dataset overthere.
and I didn't use Maven, cause I just wanna test it first using some terminal command line and them use a python wrapper to combine the metamaplite tool to a pipeline of my NLP model.
is there any instructions on how to run it without maven? when I downloaded it, i run the install.sh and then metamaplite.sh gives me the error I mentioned on the title.

[willjrogers]

The following sequence of commands should be all that is needed to install MetaMapLite: $ unzip public_mm_lite_3.6.2rc8_binaryonly.zip … $ unzip public_mm_data_lite_usabase_2022aa.zip … And a simple run to lookup one term as follows: $ cd public_mm_lite $ echo "hiv" | ./metamaplite.sh -- 00000000.tx|MMI|14.27|HIV Infections|C0019693|[dsyn]|"HIV"-text-0-"hiv"-NN-0|text|0/3|C01.221.250.875;C01.221.812.640.400;C01.778.640.400;C01.925.782.815.616.400;C01.925.813.400;C12.100.937.640.400;C20.673.480| 00000000.tx|MMI|2.76|HIV|C0019682|[virs]|"HIV"-text-0-"hiv"-NN-0|text|0/3|B04.820.650.589.650.350| 00000000.tx|MMI|0.46|Human Immunodeficiency Virus Measurement|C5202935|[lbpr]|"HIV"-text-0-"hiv"-NN-0|text|0/3|| I was wondering which version of Java are you using? I’ve run it on Java 1.8, 11, 12, and Java 18. Sincerely, Willie Rogers -- Willie Rogers, Contractor, Lister Hill Center, National Library of Medicine, NIH email: ***@***.******@***.***> Rogers, Willie (NIH/NLM/LHC) [C] From: 奚斤 ***@***.***> Date: Thursday, October 19, 2023 at 11:42 AM To: lhncbc/metamaplite ***@***.***> Cc: Rogers, Willie (NIH/NLM/LHC) [C] ***@***.***>, Comment ***@***.***> Subject: [EXTERNAL] Re: [lhncbc/metamaplite] java.lang.NoClassDefFoundError: bioc/BioCSentence (Issue #36) If you have cloned MetaMapLite using git you’ll need to first run maven and update the configuration file: config/metamaplite.properties: Compile MetaMapLite using Maven: $ mvn package Make sure MML_VERSION matches version of standalone jar file in target: MML_VERSION=3.6.2rc8 Should match file in metamaplite directory: target/metamaplite-3.6.2rc8-standalone.jar … -- Willie Rogers, Contractor, Lister Hill Center, National Library of Medicine, NIH Rogers, Willie (NIH/NLM/LHC) [C] email: @.@.> From: 奚斤 @.> Date: Wednesday, October 18, 2023 at 3:51 PM To: lhncbc/metamaplite @.> Cc: Subscribed @.> Subject: [EXTERNAL] [lhncbc/metamaplite] java.lang.NoClassDefFoundError: bioc/BioCSentence (Issue #36<#36>) i download the "MetaMapLite 3.6.2rc8 and UMLS 2022", and also the dataset [2022AA UMLS Level 0+4+9 DataSet]. when i run ./metamaplite.sh. it failed to run. — Reply to this email directly, view it on GitHub<#36<#36>>, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AHOVZBMTTRAXDXBIUTIDMYTYAAXMFAVCNFSM6AAAAAA6GB3FFGVHI2DSMVQWIX3LMV43ASLTON2WKOZRHE2TANJTGUZDCNY. You are receiving this because you are subscribed to this thread.Message ID: @.> CAUTION: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and are confident the content is safe. If you have cloned MetaMapLite using git you’ll need to first run maven and update the configuration file: config/metamaplite.properties: Compile MetaMapLite using Maven: $ mvn package Make sure MML_VERSION matches version of standalone jar file in target: MML_VERSION=3.6.2rc8 Should match file in metamaplite directory: target/metamaplite-3.6.2rc8-standalone.jar … -- Willie Rogers, Contractor, Lister Hill Center, National Library of Medicine, NIH Rogers, Willie (NIH/NLM/LHC) [C] email: @.@.> From: 奚斤 @.> Date: Wednesday, October 18, 2023 at 3:51 PM To: lhncbc/metamaplite @.> Cc: Subscribed @.> Subject: [EXTERNAL] [lhncbc/metamaplite] java.lang.NoClassDefFoundError: bioc/BioCSentence (Issue #36<#36>) i download the "MetaMapLite 3.6.2rc8 and UMLS 2022", and also the dataset [2022AA UMLS Level 0+4+9 DataSet]. when i run ./metamaplite.sh. it failed to run. — Reply to this email directly, view it on GitHub<#36<#36>>, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AHOVZBMTTRAXDXBIUTIDMYTYAAXMFAVCNFSM6AAAAAA6GB3FFGVHI2DSMVQWIX3LMV43ASLTON2WKOZRHE2TANJTGUZDCNY. You are receiving this because you are subscribed to this thread.Message ID: @.> CAUTION: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and are confident the content is safe. Hi, Thanks for the reply, but I download it from the lhncbc website also with the dataset overthere. and I didn't use Maven, cause I just wanna test it first using some terminal command line and them use a python wrapper to combine the metamaplite tool to a pipeline of my NLP model. is there any instructions on how to run it without maven? when I downloaded it, i run the install.sh and then metamaplite.sh gives me the error I mentioned on the title. [Image removed by sender. 005b2260e91b5671e9f10161c2b326631144b8882d3f9c0c650c1693d0f208b3]<https://user-images.githubusercontent.com/95683271/276672489-fbd98e71-ff8d-4b39-9ea5-776ece96ca01.png> — Reply to this email directly, view it on GitHub<#36 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AHOVZBL3OROW2IFAGUIPYC3YAFC7PAVCNFSM6AAAAAA6GB3FFGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTONZRGI2DQOBWHA>. You are receiving this because you commented.Message ID: ***@***.***> CAUTION: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and are confident the content is safe.