Unable to install transmart - Target "clean dist deploy jboss_pre_deployment_setup" does not exist in the project "i2b2Common".

[philippeluickx]

Dear,

I am trying to install transmart and am stuck at Target "clean dist deploy jboss_pre_deployment_setup" does not exist in the project "i2b2Common". Thanks for pointing out what to do!

Executing /usr/bin/ant '-q' 'load_workdata' [exec] [echo] -----------------Loading Workdata module----------------- ------ i2b2Demodata i2b2Coreserver: Executing /usr/bin/ant 'clean dist deploy jboss_pre_deployment_setup' [exec] Buildfile: /opt/transmart/build/i2b2_1.6_postgres/coreserver/src/edu.harvard.i2b2.common/build.xml [exec] BUILD FAILED [exec] Target "clean dist deploy jboss_pre_deployment_setup" does not exist in the project "i2b2Common". [exec] Total time: 0 seconds Exception was raised: exec returned: 1

Full output:

Executing /usr/bin/psql '-U' 'postgres' '-d' 'postgres' '-c' 'select 1' [exec] psql: FATAL: Peer authentication failed for user "postgres" [exec] Result: 2 Executing sudo '-u' 'postgres' '/usr/bin/psql' '-U' 'postgres' '-d' 'postgres' '-c' 'select 1' [exec] ?column? [exec] ---------- [exec] 1 [exec](1 row) default: clean: Executing sudo '-u' 'postgres' '/usr/bin/psql' '-U' 'postgres' '-d' 'postgres' '-c' 'drop database transmart' [exec] DROP DATABASE Executing sudo '-u' 'postgres' '/usr/bin/psql' '-U' 'postgres' '-d' 'postgres' '-c' 'reassign owned by biomart, biomart_user, deapp, i2b2demodata, i2b2hive, i2b2metadata, i2b2pm, i2b2workdata, searchapp to postgres;' Executing sudo '-u' 'postgres' '/usr/bin/psql' '-U' 'postgres' '-d' 'postgres' '-c' 'drop role biomart' Executing sudo '-u' 'postgres' '/usr/bin/psql' '-U' 'postgres' '-d' 'postgres' '-c' 'drop role biomart_user' Executing sudo '-u' 'postgres' '/usr/bin/psql' '-U' 'postgres' '-d' 'postgres' '-c' 'drop role deapp' Executing sudo '-u' 'postgres' '/usr/bin/psql' '-U' 'postgres' '-d' 'postgres' '-c' 'drop role i2b2demodata' Executing sudo '-u' 'postgres' '/usr/bin/psql' '-U' 'postgres' '-d' 'postgres' '-c' 'drop role i2b2hive' Executing sudo '-u' 'postgres' '/usr/bin/psql' '-U' 'postgres' '-d' 'postgres' '-c' 'drop role i2b2metadata' Executing sudo '-u' 'postgres' '/usr/bin/psql' '-U' 'postgres' '-d' 'postgres' '-c' 'drop role i2b2pm' Executing sudo '-u' 'postgres' '/usr/bin/psql' '-U' 'postgres' '-d' 'postgres' '-c' 'drop role i2b2workdata' Executing sudo '-u' 'postgres' '/usr/bin/psql' '-U' 'postgres' '-d' 'postgres' '-c' 'drop role searchapp' [delete] Deleting directory /opt/transmart/build ------ clean install: Executing /usr/bin/git 'clone' 'git://github.com/transmart/transmartApp-DB.git' '/opt/transmart/build/transmartApp-DB' '--single-branch' '-b' 'postgresMigrate' [exec] to '/opt/transmart/build/transmartApp-DB'... createTransmartDB: About to execute SQL script /tmp/createdb645770052793739390.sql Executing sudo '-u' 'postgres' '/usr/bin/psql' '-U' 'postgres' '-f' '/tmp/createdb645770052793739390.sql' '-d' 'postgres' '--quiet' ------ createTransmartDB ensureTablespaces: Ensure /opt/transmart/db tablespace location directories are present ------ ensureTablespaces populateTransmartDB: About to execute SQL script /opt/transmart/build/transmartApp-DB/postgresql/tablespaces.sql Executing sudo '-u' 'postgres' '/usr/bin/psql' '-U' 'postgres' '-f' '/opt/transmart/build/transmartApp-DB/postgresql/tablespaces.sql' '-d' 'transmart' '--quiet' About to execute SQL script /opt/transmart/build/transmartApp-DB/postgresql/biomart_user.sql Executing sudo '-u' 'postgres' '/usr/bin/psql' '-U' 'postgres' '-f' '/opt/transmart/build/transmartApp-DB/postgresql/biomart_user.sql' '-d' 'transmart' '--quiet' About to execute SQL script /opt/transmart/build/transmartApp-DB/postgresql/searchapp/prerequisites.sql Executing sudo '-u' 'postgres' '/usr/bin/psql' '-U' 'postgres' '-f' '/opt/transmart/build/transmartApp-DB/postgresql/searchapp/prerequisites.sql' '-d' 'transmart' '--quiet' About to execute SQL script /opt/transmart/build/transmartApp-DB/postgresql/biomart/prerequisites.sql Executing sudo '-u' 'postgres' '/usr/bin/psql' '-U' 'postgres' '-f' '/opt/transmart/build/transmartApp-DB/postgresql/biomart/prerequisites.sql' '-d' 'transmart' '--quiet' About to execute SQL script /opt/transmart/build/transmartApp-DB/postgresql/deapp/prerequisites.sql Executing sudo '-u' 'postgres' '/usr/bin/psql' '-U' 'postgres' '-f' '/opt/transmart/build/transmartApp-DB/postgresql/deapp/prerequisites.sql' '-d' 'transmart' '--quiet' About to execute SQL script /opt/transmart/build/transmartApp-DB/postgresql/i2b2_prerequisites.sql Executing sudo '-u' 'postgres' '/usr/bin/psql' '-U' 'postgres' '-f' '/opt/transmart/build/transmartApp-DB/postgresql/i2b2_prerequisites.sql' '-d' 'transmart' '--quiet' Executing sudo '-u' 'postgres' '/usr/bin/psql' '-U' 'postgres' '-d' 'transmart' '-c' 'drop schema if exists biomart, deapp, searchapp, i2b2demodata, i2b2hive, i2b2metadata, i2b2pm, i2b2workdata cascade;' [exec] DROP SCHEMA Executing sudo '-u' 'postgres' '/usr/bin/pg_restore' '-U' 'postgres' '-d' 'transmart' '/opt/transmart/build/dump_f8d151a_db' [exec] WARNING: column "correl_type" has type "unknown" [exec] DETAIL: Proceeding with relation creation anyway. ------ populateTransmartDB verifyTransmartDB: verifySEARCHAPPdata: About to execute SQL script /opt/transmart/build/transmartApp-DB/postgresql/searchapp/data/check_counts.sql Executing sudo '-u' 'postgres' '/usr/bin/psql' '-U' 'postgres' '-f' '/opt/transmart/build/transmartApp-DB/postgresql/searchapp/data/check_counts.sql' '-d' 'transmart' [exec] | 105844 [exec] SEARCH_KEYWORD | 42114 [exec] SEARCH_REQUEST_MAP | 17 [exec] PLUGIN_MODULE | 11 [exec] SEARCH_ROLE_AUTH_USER | 11 [exec] SEARCH_AUTH_PRINCIPAL | 6 [exec] SEARCH_AUTH_USER | 5 [exec] SEARCH_ROLE | 5 [exec] SEARCH_GENE_SIG_FILE_SCHEMA | 3 [exec] SEARCH_SEC_ACCESS_LEVEL | 3 [exec] SEARCH_AUTH_GROUP | 1 [exec] PLUGIN | 1 [exec] SEARCH_AUTH_GROUP_MEMBER | 0 [exec] SEARCH_SECURE_OBJECT_PATH | 0 [exec] SEARCH_GENE_SIGNATURE_ITEM | 0 [exec] SEARCH_BIO_MKR_CORREL_FAST_MV | 0 [exec] SEARCH_CUSTOM_FILTER_ITEM | 0 [exec] SEARCH_APP_ACCESS_LOG | 0 [exec] SEARCH_CUSTOM_FILTER | 0 [exec] SEARCH_SECURE_OBJECT | 0 [exec] SEARCH_AUTH_USER_SEC_ACCESS | 0 [exec] SEARCH_AUTH_SEC_OBJECT_ACCESS | 0 [exec] SEARCH_GENE_SIGNATURE | 0 [exec](23 rows) checking: SEARCH_KEYWORD_TERM | 105844 = 105844 ... OK! checking: SEARCH_KEYWORD | 42114 = 42114 ... OK! checking: SEARCH_REQUEST_MAP | 17 = 17 ... OK! checking: PLUGIN_MODULE | 11 = 11 ... OK! ------ verifySEARCHAPPdata verifyDEAPPdata: About to execute SQL script /opt/transmart/build/transmartApp-DB/postgresql/deapp/data/check_counts.sql Executing sudo '-u' 'postgres' '/usr/bin/psql' '-U' 'postgres' '-f' '/opt/transmart/build/transmartApp-DB/postgresql/deapp/data/check_counts.sql' '-d' 'transmart' [exec] rows) checking: DE_SUBJECT_MICROARRAY_DATA | 54400 = 54400 ... OK! checking: DE_MRNA_ANNOTATION | 5440 = 5440 ... OK! checking: DE_SUBJECT_SAMPLE_MAPPING | 10 = 10 ... OK! checking: DE_SAVED_COMPARISON | 5 = 5 ... OK! ------ verifyDEAPPdata verifyBIOMARTdata: About to execute SQL script /opt/transmart/build/transmartApp-DB/postgresql/biomart/data/check_counts.sql Executing sudo '-u' 'postgres' '/usr/bin/psql' '-U' 'postgres' '-f' '/opt/transmart/build/transmartApp-DB/postgresql/biomart/data/check_counts.sql' '-d' 'transmart' [exec] 0 [exec] BIO_LIT_REF_DATA | 0 [exec] BIO_CLINICAL_TRIAL_DESIGN | 0 [exec] BIO_LIT_AMD_DATA | 0 [exec] CTD_DRUG_INHIB | 0 [exec] BIO_COMPOUND | 0 [exec] BIO_ASY_DATA_STATS_ALL | 0 [exec] CTD2_INHIB_DETAILS | 0 [exec] CTD_FULL | 0 [exec] CTD_DISEASE | 0 [exec] BIO_ASSAY_DATA | 0 [exec] BIO_CURATION_DATASET | 0 [exec] CTD2_STUDY | 0 [exec] BIO_PATIENT_EVENT | 0 [exec] CTD2_TRIAL_DETAILS | 0 [exec] BIO_CURATED_DATA | 0 [exec] BIO_CLINC_TRIAL_TIME_PT | 0 [exec] BIO_DATA_COMPOUND | 0 [exec] BIO_CGDCP_DATA | 0 [exec] BIO_ASSAY_DATA_STATS | 0 [exec] BIO_CELL_LINE | 0 [exec] CTD_SEC_ENDPTS | 0 [exec] BIO_STATS_EXP_MARKER | 0 [exec] BIO_CLINC_TRIAL_ATTR | 0 [exec] BIO_DATA_TAXONOMY | 0 [exec] BIO_SUBJECT | 0 [exec] BIO_DATA_LITERATURE | 0 [exec] bio_lit_int_model_mv | 0 [exec] BIO_LIT_SUM_DATA | 0 [exec] BIO_LIT_PE_DATA | 0 [exec] BIO_DATA_CORREL_DESCR | 0 [exec] CTD_ALLOWED_MEDS_TREATMENT | 0 [exec] CTD_STUDY | 0 [exec] BIO_LIT_INH_DATA | 0 [exec] CTD2_CLIN_INHIB_EFFECT | 0 [exec] BIO_LIT_ALT_DATA | 0 [exec] BIO_PATIENT | 0 [exec] CTD_INCLUSION_CRITERIA | 0 [exec] BIO_DATA_ATTRIBUTE | 0 [exec] BIO_LIT_INT_DATA | 0 [exec] CTD_PRIMARY_ENDPTS | 0 [exec] BIO_LIT_MODEL_DATA | 0 [exec] BIO_ASSAY | 0 [exec] CTD2_DISEASE | 0 [exec] BIO_DATA_CORRELATION | 0 [exec] BIO_SAMPLE | 0 [exec] CTD_BIOMARKER | 0 [exec] BIO_CLINICAL_TRIAL | 0 [exec] BIO_ASY_ANALYSIS_DATASET | 0 [exec](73 rows) checking: BIO_ASSAY_FEATURE_GROUP | 237002 = 237002 ... OK! checking: BIO_ASSAY_ANALYSIS_DATA | 184538 = 184538 ... OK! checking: BIO_DATA_EXT_CODE | 134965 = 134965 ... OK! checking: BIO_DATA_UID | 126764 = 126764 ... OK! ------ verifyBIOMARTdata ------ verifyTransmartDB downloadI2B2: [get] Getting: http://transmartproject.org/wiki/download/attachments/30441474/jboss-4.2.2.GA.tar.gz?version=1&modificationDate=1335242608000 [get] To: /opt/transmart/build/jboss.tar.gz [untar] Expanding: /opt/transmart/build/jboss.tar.gz into /opt/transmart/build [move] Moving 1208 files to /opt/transmart [get] Getting: http://jdbc.postgresql.org/download/postgresql-9.2-1002.jdbc4.jar [get] To: /opt/transmart/jboss-4.2.2.GA/server/default/lib/postgresql-9.2-1002.jdbc4.jar ------ downloadI2B2 executeI2b2ImportScripts: About to execute SQL script /opt/transmart/build/transmartApp-DB/postgresql/i2b2_prerequisites.sql Executing sudo '-u' 'postgres' '/usr/bin/psql' '-U' 'postgres' '-f' '/opt/transmart/build/transmartApp-DB/postgresql/i2b2_prerequisites.sql' '-d' 'transmart' '--quiet' Executing /usr/bin/git 'clone' 'git://github.com/transmart/i2b2_1.6_Postgres.git' '/opt/transmart/build/i2b2_1.6_postgres' [exec] Cloning into '/opt/transmart/build/i2b2_1.6_postgres'... i2b2Demodata: Executing /usr/bin/ant 'setup_db_properties' [exec] a/src/src/edu.harvard.i2b2.data/Release_1-6/NewInstall/build.xml [exec] setup_db_properties: [exec] [echo] -----------Setting property values in db.properties----------- [exec] BUILD SUCCESSFUL [exec] Total time: 0 seconds Executing /usr/bin/ant '-q' 'load_pmdata' [exec] [echo] -----------------Loading Project Management data----------------- Executing /usr/bin/ant '-q' 'load_hivedata' [exec] [echo] -----------------Loading Hive data----------------- [exec] BUILD SUCCESSFUL [exec] Total time: 1 second Executing /usr/bin/ant '-q' 'load_demodata' [exec] [echo] -----------------Loading Demodata module----------------- [exec] [echo] Loading demodata -- may take a while; over 10 min [exec] BUILD SUCCESSFUL [exec] Total time: 2 minutes 10 seconds Executing /usr/bin/ant '-q' 'load_metadata' [exec] [echo] -----------------Loading Metadata module----------------- [exec] [echo] Loading metadata -- may take a while; over 10 min [exec] BUILD SUCCESSFUL [exec] Total time: 1 minute 54 seconds Executing /usr/bin/ant '-q' 'load_workdata' [exec] [echo] -----------------Loading Workdata module----------------- ------ i2b2Demodata i2b2Coreserver: Executing /usr/bin/ant 'clean dist deploy jboss_pre_deployment_setup' [exec] Buildfile: /opt/transmart/build/i2b2_1.6_postgres/coreserver/src/edu.harvard.i2b2.common/build.xml [exec] BUILD FAILED [exec] Target "clean dist deploy jboss_pre_deployment_setup" does not exist in the project "i2b2Common". [exec] Total time: 0 seconds Exception was raised: exec returned: 1

[cataphract]

That's been fixed for some days now. Fetch the latest version.

[philippeluickx]

Fantastic, confirm it works now!