FTP into Xdb

I am using
ELSDV01> select * from v$version;
BANNER
Oracle Database 11g Enterprise Edition Release 11.2.0.2.0 - 64bit Production
PL/SQL Release 11.2.0.2.0 - Production
CORE    11.2.0.2.0      Production
TNS for Solaris: Version 11.2.0.2.0 - Production
NLSRTL Version 11.2.0.2.0 - ProductionI have a need to populate an XDB repository with a number of xml (shredded) documents for testing purposes. This I can do via a shell script (windows or solaris). But perhaps easier would be to use an FTP client. But there is a problem.
After each document put I would also need to create an accompanying history folder and finally a symbolic link that points to the latest (even if only one exist) version.
I have done a little research, but I cannot find any explicit information about logging in via an FTP client (like C:\WIndows\system32\ftp.exe) and then creating a symbolic link from within that FTP session. It is at all doable? Thank you.

After each document put I would also need to create an accompanying history folder and finally a symbolic link that points to the latest (even if only one exist) version. A couple of options :
- using the versioning capabilities of the XDB repository
- using XDB events to trigger the creation of the folder and the sym link whenever a document is dropped in a specific location

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  • Error while loading valid, schema-related document into xdb

    Hi Mark.
    I tried to load other xml documents (ftp://ftp.tigr.org/pub/data/a_thaliana/ath1/PSEUDOCHROMOSOMES/) into the xdb.
    The documents are related to the same schema as the documents i used until now.
    I had to change the schema a bit. Three elements (protein_sequence, cds_sequence, transcript_sequence) are now stored as CLOB instead of VARCHAR2.
    My first idea was, that the new documents are not valid, but they are.
    The old documents still work. I get an ORA-00600 everytime.
    I tried to get some information from the trace file but this did not help really.
    I don't believe this will help you but i post it anyway:
    Dump file d:\oracle\admin\pdw\udump\pdw_s000_6388.trc
    Mon Jan 02 09:21:36 2006
    ORACLE V9.2.0.7.0 - Production vsnsta=0
    vsnsql=12 vsnxtr=3
    Windows 2000 Version 5.0 Service Pack 4, CPU type 586
    Oracle9i Enterprise Edition Release 9.2.0.7.0 - Production
    With the Partitioning, OLAP and Oracle Data Mining options
    JServer Release 9.2.0.7.0 - Production
    Windows 2000 Version 5.0 Service Pack 4, CPU type 586
    Instance name: pdw
    Redo thread mounted by this instance: 1
    Oracle process number: 10
    Windows thread id: 6388, image: ORACLE.EXE
    *** 2006-01-02 09:21:36.218
    *** SESSION ID:(23.9078) 2006-01-02 09:21:36.187
    QMHD escaped text too long: dstlen=0 dstbuf=/
    QMHD escaped text too long: dstlen=0 dstbuf=home
    QMHD escaped text too long: dstlen=0 dstbuf=public
    QMHD escaped text too long: dstlen=0 dstbuf=sys
    QMHD escaped text too long: dstlen=0 dstbuf=xdbconfig.xml
    QMHD escaped text too long: dstlen=0 dstbuf=/
    QMHD escaped text too long: dstlen=0 dstbuf=home
    QMHD escaped text too long: dstlen=0 dstbuf=public
    QMHD escaped text too long: dstlen=0 dstbuf=sys
    QMHD escaped text too long: dstlen=0 dstbuf=xdbconfig.xml
    QMHD escaped text too long: dstlen=0 dstbuf=home
    QMHD escaped text too long: dstlen=0 dstbuf=RSCHULZE
    QMHD escaped text too long: dstlen=0 dstbuf=PDV70
    QMHD escaped text too long: dstlen=0 dstbuf=SCOTT
    QMHD escaped text too long: dstlen=0 dstbuf=SCOTT1
    QMHD escaped text too long: dstlen=0 dstbuf=SCOTT2
    QMHD escaped text too long: dstlen=0 dstbuf=hbachman
    QMHD escaped text too long: dstlen=0 dstbuf=pdw_biowh31
    QMHD escaped text too long: dstlen=0 dstbuf=pdw_stage
    QMHD escaped text too long: dstlen=0 dstbuf=pdw_tigr_chromosome
    QMHD escaped text too long: dstlen=0 dstbuf=uniprot
    QMHD escaped text too long: dstlen=0 dstbuf=pdw_tigr_chromosome
    QMHD escaped text too long: dstlen=0 dstbuf=data
    QMHD escaped text too long: dstlen=0 dstbuf=xsd
    QMHD escaped text too long: dstlen=0 dstbuf=data
    QMHD escaped text too long: dstlen=0 dstbuf=seq1.txt
    QMHD escaped text too long: dstlen=0 dstbuf=seq2.txt
    QMHD escaped text too long: dstlen=0 dstbuf=seq3.txt
    QMHD escaped text too long: dstlen=0 dstbuf=seq4.txt
    QMHD escaped text too long: dstlen=0 dstbuf=seq5.txt
    *** 2006-01-02 09:36:57.421
    ksedmp: internal or fatal error
    ORA-00600: internal error code, arguments: [kokbgcip1], [196609], [63], [], [], [], [], []
    Current SQL statement for this session:
    INSERT /*+ NO_REF_CASCADE */ INTO "PDW_TIGR_CHROMOSOME"."SYS_NT0upV7+xbRnu3KquZIaRFgQ=="("NESTED_TABLE_ID","ARRAY_INDEX","SYS_NC_ROWINFO$") VALUES(:1,:2,:3)
    ----- Call Stack Trace -----
    calling call entry argument values in hex
    location type point (? means dubious value)
    ksedmp+327          CALLrel  ksedst+0
    ksfdmp.108+14       CALLrel  ksedmp+0 3
    _kgerinv+131         CALLreg  00000000             D3E4368 3
    kgeasnmierr+19      CALLrel  kgerinv+0 D3E4368 4BE2A94 1AF86D4 2
    4B56B40
    kokbgcip+343        CALLrel  kgeasnmierr+0 D3E4368 4BE2A94 1AF86D4 2 4
    30001 4 3F
    qerocImageIterStar  CALLrel  kokbgcip+0
    t+160
    qerocStart+265      CALLrel  qerocImageIterStar 237701B4 D3E41E0
    t+0
    _kokbint+242         CALL???  00000000             81DFD20 1
    kokbeva+338         CALLrel  kokbint+0 237700B8 237700FC
    ..1.42_2.filter.9+1 CALLreg 00000000 D3E41E0
    101
    insolev.73+164      CALLrel  evaopn2+0 237700B8
    insbrp.73+1558      CALLrel  insolev.73+0 2374A8B4 81DDFF8 1
    insrow+173          CALLrel  insbrp.73+0
    insdrv.73+1302      CALLrel  insrow+0 81DDFF8 4B584E4 0
    ..1.6_1.filter.73+2 CALLrel _insdrv.73+0         81DDFF8
    28
    ..1.5_2.except.29+1 CALLrel _insexe+0            2374A8B4 4B58730
    6740
    ..1.2_1.filter.25+3 CALLrel _opiexe+0            4 3 4B58B24
    347
    opikpr+512          CALLrel  opiall0+0 65 22 4B58D20 0 0 4B58DB8 9C
    20 0 0 0 0 0
    ..1.1_1.filter.34+1 CALLreg 00000000 65 14 4B59980
    356
    rpidrus.43+167      CALLrel  opiodr+0 65 14 4B59980 0
    _skgmstack+113       CALLreg  00000000             4B590A0
    rpidru+109          CALLrel  skgmstack+0 4B590B8 D3E41F0 F618 59941C
    4B590A0
    _rpiswu2+839         CALLreg  00000000             4B59498
    kprball+1537        CALLrel  rpiswu2+0 1EA8DD18 102 4B59414 4
    1E833D34 102 4B59414 0 59932C
    5991DC 4B59498 8
    kokbint+1766        CALLrel  kprball+0 4B59980 500
    kokbeva+338         CALLrel  kokbint+0 2374E498 2374E4DC
    ..1.42_2.filter.9+1 CALLreg 00000000 D3E41E0
    101
    insolev.73+164      CALLrel  evaopn2+0 2374E498
    insbrp.73+1558      CALLrel  insolev.73+0 25EC7468 7D0BD90 1
    insrow+173          CALLrel  insbrp.73+0
    insdrv.73+1302      CALLrel  insrow+0 7D0BD90 4B5AD78 0
    ..1.6_1.filter.73+2 CALLrel _insdrv.73+0         7D0BD90
    28
    ..1.5_2.except.29+1 CALLrel _insexe+0            25EC7468 4B5AFC4
    6740
    ..1.2_1.filter.25+3 CALLrel _opiexe+0            4 3 4B5B3B8
    347
    opikpr+512          CALLrel  opiall0+0 65 22 4B5B5B4 0 0 4B5B64C 77
    20 0 0 0 0 0
    ..1.1_1.filter.34+1 CALLreg 00000000 65 14 4B5BE70
    356
    rpidrus.43+167      CALLrel  opiodr+0 65 14 4B5BE70 0
    _skgmstack+113       CALLreg  00000000             4B5B934
    rpidru+109          CALLrel  skgmstack+0 4B5B94C D3E41F0 F618 59941C
    4B5B934
    _rpiswu2+839         CALLreg  00000000             4B5BD2C
    kprball+1537        CALLrel  rpiswu2+0 1EA8DD18 102 1EA891BC 4
    1E833D34 102 1EA8923C 0
    59932C 5991DC 4B5BD2C 9
    qmskInsertXmlType+  CALLrel  kprball+0 4B5BE70 180
    1203
    qmskStoreXobWithIm  CALLrel  qmskInsertXmlType+
    age+526 0
    qmskStoreXob+16     CALLrel  qmskStoreXobWithIm
    age+0
    qmskFlushXob+22     CALLrel  qmskStoreXob+0 4BFCFCC 4BE6698 0
    _qmeSaveContents+44  CALLreg  00000000            
    6
    qmePreSave+2417     CALLrel  qmeSaveContents+0 4BFE790 2 1
    _qmtEventFire+259    CALLreg  00000000             D3E4368 3 4BFE8B0
    qmxiWriteXobToImag  CALLrel  qmtEventFire+0 D3E4368 3 4BFE8B0
    eInternal+60
    qmxiWriteXobToImag  CALLrel  qmxiWriteXobToImag D3E4368 4B5D418 0 4BFE8B0
    eWithHeap+82 eInternal+0 700ECBC 4B5D398 4B5D364
    4B5D384 60A09FC 4B5C37C 0 6
    D3E4368 C 4B5D418
    qmxtgGetOpqImageFr  CALLrel  qmxiWriteXobToImag D3E4368 4B5D418 0 4BFE8B0
    omXob+430 eWithHeap+0 700ECBC 4B5D398 4B5D364
    4B5D384 4B5D470 C 6 700ECF8
    4B5D418
    qmskStoreXobWithIm  CALLrel  qmxtgGetOpqImageFr
    age+370 omXob+0
    qmskStoreXob+16     CALLrel  qmskStoreXobWithIm
    age+0
    qmskFlushXob+22     CALLrel  qmskStoreXob+0 4BFE8B0 4BFF740 4B5D6FC
    _qmeInsertResRow+22  CALLreg  00000000            
    5
    qmeInsertRes+1831   CALLrel  qmeInsertResRow+0
    qmeLinkInternal+47  CALLrel  qmeInsertRes+0
    12
    qmeCreOrBindRes+33  CALLrel  qmeLinkInternal+0 4BFE790 60A5D14 1DFE0323 1D 0
    1 1 0 4B5D7A0 4B5D85C 0 0
    qmeCreateRes+115    CALLrel  qmeCreOrBindRes+0 4BFE790 60A5D14 1DFE0304 1F
    1DFE0323 1D 0 1 0 4B5D85C 0 0
    4B5D85C 0
    qmeuCreateOrUpdate  CALLrel  qmeCreateRes+0 4BFE790 1DFE0304 1F 1DFE0323
    Res+2232 1D 0 0 0
    qmhput+393 CALLrel _qmeuCreateOrUpdate 
    Res+0
    _qmhProcessRequestD  CALLreg  00000000             1DFE4398
    ata+2576
    qmpsrun+1220 CALL??? 00000000
    opitsk+838          CALLrel  qmps_run+0 D3E4368
    opiino+698          CALLrel  opitsk+0 0 0 D3EA5C8 278A650 3 0
    ..1.1_1.filter.34+1 CALLreg 00000000 3C 4 4B5F448
    356
    opirip+662          CALLrel  opiodr+0 3C 4 4B5F448 0
    opidrv+654          CALLrel  opirip+0 32 0 0
    sou2o+25            CALLrel  opidrv+0
    opimai+336          CALLrel  sou2o+0 4B5FE1C 32 0 0
    BackgroundThreadSt  CALLrel  opimai+0
    art@4+356
    77E7B385 CALLreg 00000000
    --------------------- Binary Stack Dump ---------------------
    ========== FRAME [1] (_ksedmp+327 -> _ksedst+0) ==========
    Dump of memory from 0x04B56A68 to 0x04B56AE0
    4B56A60 04B56AE0 00522AC8 [.j...*R.]
    4B56A70 00000000 00000000 00000000 00000000 [................]
    4B56A80 FFFFFFFF 0000003F 0D3E4444 01AF86D4 [....?...DD>.....]
    4B56A90 0D3E444C 04B56ADC 0283676E 0D3E4444 [LD>..j..ng..DD>.]
    4B56AA0 0D3E444C 00000000 00000000 01AF86D4 [LD>.............]
    4B56AB0 00000002 00000009 0D3E4368 04BE2A94 [........hC>..*..]
    4B56AC0 01A89F00 0D3E41E0 04B56A74 0D3E4368 [.....A>.tj..hC>.]
    4B56AD0 04B571F8 015DDE00 02775F44 FFFFFFFF [.q....].D_w.....]
    ========== FRAME [2] (_ksfdmp.108+14 -> _ksedmp+0) ==========
    Dump of memory from 0x04B56AE0 to 0x04B56AEC
    4B56AE0 04B56AEC 0078468B 00000003 [.j...Fx.....]
    ========== FRAME [3] (_kgerinv+131 -> 00000000) ==========
    Dump of memory from 0x04B56AEC to 0x04B56B0C
    4B56AE0 04B56B0C [.k..]
    4B56AF0 02836849 0D3E4368 00000003 081B3444 [Ih..hC>.....D4..]
    4B56B00 0D3E41E0 081B3444 081B3444 [.A>.D4..D4..]
    ========== FRAME [4] (_kgeasnmierr+19 -> _kgerinv+0) ==========
    Dump of memory from 0x04B56B0C to 0x04B56B28

    I have a new problem:
    Due to the changes of the schema ( transcript_sequence ... stored as clob) i got an error in a view.
    ORA-00932 : incosistent datatypes
    The error occurs in V007 in the following rows
    extractValue(value(tu),'/TU/TRANSCRIPT_SEQUENCE'),
    extractValue(value(model),'/MODEL/CDS_SEQUENCE'),
    extractValue(value(model),'/MODEL/PROTEIN_SEQUENCE')
    But in V005 there is no error althought there is the row extractValue(value(tu),'/TU/TRANSCRIPT_SEQUENCE'),
    the views
    create or replace view V007_MODEL(FEAT_NAME,
                                                           GENE_SYNONYM,
                                                           GENE_SYNONYM_SYN_TYPE,
                                                           CHROMO_LINK,
                                                           TU_DATE,
                                                           TU_COORDSET_END5,
                                                           TU_COORDSET_END3,
                                                      TRANSCRIPT_SEQUENCE,
                                                           URL,
                                                           URL_URLNAME,
                                                           CURATED,
                                                           MODEL_COMMENT,
                                                           MODEL_FEAT_NAME,
                                                           PUB_LOCUS,
                                                           CDNA_SUPPORT_ACCESSION,
                                                           CDNA_SUPPORT_ACCESSION_DBXREF,
                                                           CDNA_SUPPORT_ACCESSION_IS_FLI,
                                                           CDNA_SA_UNIQUE_TO_ISOFORM,
                                                           CDNA_SA_ANNOT_INCORP,                                             
                                                           MODEL_GENE_SYNONYM,
                                                           MODEL_GENE_SYNONYM_SYN_TYPE,
                                                           MODEL_CHROMO_LINK,
                                                           MODEL_DATE,
                                                           MODEL_COORDSET_END5,
                                                           MODEL_COORDSET_END3,
                                                           MA_AT_METHOD,
                                                           MA_AT_ATT_SCORE,
                                                           MA_AT_ATT_SCORE_DESC)
                                                           CDS_SEQUENCE,
                                                           PROTEIN_SEQUENCE)
    as
    select
         distinct
         extractValue(value(tu)           ,'/TU/FEAT_NAME'),
         extractValue(value(tu_gene_synonym)     ,'/GENE_SYNONYM/text()'),
         extractValue(value(tu_gene_synonym)     ,'/GENE_SYNONYM/@SYN_TYPE'),
         extractValue(value(tu_chromo_link)      ,'/CHROMO_LINK/text()'),
         extractValue(value(tu)           ,'/TU/DATE'),
         extractValue(value(tu)           ,'/TU/COORDSET/END5'),
         extractValue(value(tu)           ,'/TU/COORDSET/END3'),
         extractValue(value(tu)      ,'/TU/TRANSCRIPT_SEQUENCE'),
         extractValue(value(url)           ,'/URL/text()'),
         extractValue(value(url)           ,'/URL/@URLNAME'),
         extractValue(value(model)                    ,'/MODEL/@CURATED'),
         extractValue(value(model)                    ,'/MODEL/@COMMENT'),
         extractValue(value(model)                    ,'/MODEL/FEAT_NAME'),
         extractValue(value(model)                    ,'/MODEL/PUB_LOCUS'),
         extractValue(value(accession)      ,'/ACCESSION/text()'),
         extractValue(value(accession)      ,'/ACCESSION/@DBXREF'),
         extractValue(value(accession)           ,'/ACCESSION/@IS_FLI'),
         extractValue(value(accession)           ,'/ACCESSION/@UNIQUE_TO_ISOFORM'),
         extractValue(value(accession)           ,'/ACCESSION/@ANNOT_INCORP'),
         extractValue(value(model_gene_synonym),'/GENE_SYNONYM/text()'),
         extractValue(value(model_gene_synonym),'/GENE_SYNONYM/@SYN_TYPE'),
         extractValue(value(model_chromo_link) ,'/CHROMO_LINK/text()'),
         extractValue(value(model)                    ,'/MODEL/DATE'),
         extractValue(value(model)                    ,'/MODEL/COORDSET/END5'),
         extractValue(value(model)                    ,'/MODEL/COORDSET/END3'),
         extractValue(value(attribute_type)     ,'/ATTRIBUTE_TYPE/@METHOD'),
         extractValue(value(att_score)               ,'/ATT_SCORE/text()'),
         extractValue(value(att_score)               ,'/ATT_SCORE/@DESC')--,
         extractValue(value(model)                    ,'/MODEL/CDS_SEQUENCE'),
         extractValue(value(model)                    ,'/MODEL/PROTEIN_SEQUENCE')
    from TIGR t,
         table(xmlsequence(extract(value(t)                    ,'/TIGR/PSEUDOCHROMOSOME')))                               p,
         table(xmlsequence(extract(value(p)                ,'/PSEUDOCHROMOSOME/ASSEMBLY/GENE_LIST/PROTEIN_CODING/TU')))           tu,
         table(xmlsequence(extract(value(tu)                    ,'/TU/GENE_SYNONYM'))) (+) tu_gene_synonym,
         table(xmlsequence(extract(value(tu)                    ,'/TU/CHROMO_LINK'))) (+) tu_chromo_link,
         table(xmlsequence(extract(value(tu)                    ,'/TU/URL'))) (+) url,
         table(xmlsequence(extract(value(tu)                ,'/TU/MODEL')))                                                                       model,
         table(xmlsequence(extract(value(model)               ,'/MODEL/CDNA_SUPPORT/ACCESSION')))                                         (+) accession,
         table(xmlsequence(extract(value(model)               ,'/MODEL/GENE_SYNONYM'))) (+) model_gene_synonym,
         table(xmlsequence(extract(value(model)               ,'/MODEL/CHROMO_LINK'))) (+) model_chromo_link,
         table(xmlsequence(extract(value(model)               ,'/MODEL/MODEL_ATTRIBUTE/ATTRIBUTE_TYPE'))) (+) attribute_type,
         table(xmlsequence(extract(value(attribute_type),'/ATTRIBUTE_TYPE/ATT_SCORE')))                         (+) att_score,
         table(xmlsequence(extract(value(model)               ,'/MODEL/EXON')))                                                                            exon
    create or replace view V005_GENE_INFO(FEAT_NAME,
                                                                GENE_SYNONYM,
                                                                GENE_SYNONYM_SYN_TYPE,
                                                                CHROMO_LINK,
                                                                TU_DATE,
                                                                TU_COORDSET_END5,
                                                                TU_COORDSET_END3,
                                                                TRANSCRIPT_SEQUENCE,
                                                                URL,
                                                                URL_URLNAME,
                                                                LOCUS,
                                                                ALT_LOCUS,
                                                                PUB_LOCUS,
                                                                GENE_NAME,
                                                                GENE_NAME_IS_PRIMARY,
                                                                COM_NAME,
                                                                COM_NAME_CURATED,
                                                                COM_NAME_IS_PRIMARY,
                                                                GENE_INFO_COMMENT,
                                                                PUB_COMMENT,
                                                                EC_NUM,
                                                                EC_NUM_IS_PRIMARY,
                                                                GENE_SYM,
                                                                GENE_SYM_IS_PRIMARY,
                                                                IS_PSEUDOGENE,
                                                                FUNCT_ANNOT_EVIDENCE_TYPE,
                                                                FAE_ASSIGN_ACC,
                                                                FAE_ASSIGN_ACC_ASSIGN_METHOD,
                                                                GENE_INFO_DATE)
    as
    select
         extractValue(value(tu)                ,'/TU/FEAT_NAME'),
         extractValue(value(gene_synonym)               ,'/GENE_SYNONYM/text()'),
         extractValue(value(gene_synonym)               ,'/GENE_SYNONYM/@SYN_TYPE'),
         extractValue(value(chromo_link)                ,'/CHROMO_LINK/text()'),
         extractValue(value(tu)                ,'/TU/DATE'),
         extractValue(value(tu)                ,'/TU/COORDSET/END5'),
         extractValue(value(tu)           ,'/TU/COORDSET/END3'),
         extractValue(value(tu)                ,'/TU/TRANSCRIPT_SEQUENCE'),
         extractValue(value(url)                ,'/URL/text()'),
         extractValue(value(url)                ,'/URL/@URLNAME'),
         extractValue(value(tu)                              ,'/TU/GENE_INFO/LOCUS'),
         extractValue(value(alt_locus)                    ,'/ALT_LOCUS/text()'),
         extractValue(value(tu)                              ,'/TU/GENE_INFO/PUB_LOCUS'),
         extractValue(value(gene_name)                    ,'/GENE_NAME/text()'),
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         extractValue(value(tu)                              ,'/TU/GENE_INFO/COMMENT'),
         extractValue(value(tu)                              ,'/TU/GENE_INFO/PUB_COMMENT'),
         extractValue(value(ec_num)                     ,'/EC_NUM/text()'),
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         extractValue(value(gene_sym)                     ,'/GENE_SYM/text()'),
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    Message was edited by:
    Nick_MD

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    15" G4/1 Ghz Powerbook Mac OS X (10.3.9)
    15" G4/1 Ghz Powerbook   Mac OS X (10.3.9)  

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    Bhawna,
    Yes. I can establish a connection without defining the site root folder. The directory that I login to by default is /EH05/users/hubing. One of the other sites that I maintain is in a subdirectory of that folder and Dreamweaver CC connects to that site without any problem. It just isn't able to switch to //gs16/gs16/share/web/cvel. Dreamweaver CS5.5 and WSFTP don't seem to have any problem with this.
    Unfortunately, I can't send you the .ste file, because the password can't be shared. I appreciate your help though!

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