XML import to Oracle with SQL Developer

You're trying to update two columns from a subquery, but your syntax is wrong; it should be more like:

update tablename set (col1 = val1, col2 = val2)
select (val1, val 2 from ...)

In your case something like this, assuming you're inserting and updating the same table, and passing the (modified) raw XML as an SQL*Plus var for my testing:

create table spectraexchange(sv_sv_id varchar2(15), ss_ss_id varchar2(15),
    ap_name varchar2(15), ap_prj_ident varchar2(15),
    tcs_name varchar2(15), tcs_call varchar2(15));

Table created.

insert into spectraexchange(sv_sv_id, ss_ss_id, ap_name, ap_prj_ident)
select extractvalue(value(x), 'APPLICATION/SV_SV_ID') sv_sv_id,
    extractvalue(value(x), 'APPLICATION/SS_SS_ID') ss_ss_id,
    extractvalue(value(x), 'APPLICATION/AP_NAME') ap_name,
    extractvalue(value(x), 'APPLICATION/AP_PRJ_IDENT') ap_prj_ident
from (
    select xmltype(:raw_xml) xmlcol from dual
) t
cross join table(XMLSequence(extract(t.xmlcol,
    '/SPECTRAEXCHANGE/APPLICATION'))) x;

1 row created.

select * from spectraexchange;

SV_SV_ID        SS_SS_ID        AP_NAME         AP_PRJ_IDENT    TCS_NAME        TCS_CALL
--------------- --------------- --------------- --------------- --------------- ---------------
kClong          kClong          kCstring (64)   kCstring (32)

Then the update could be:

update spectraexchange
set (tcs_name, tcs_call) = (
    select extractvalue(value(x), 'STATION/TCS_NAME'),
        extractvalue(value(x), 'STATION/TCS_CALL')
    from (
        select xmltype(:raw_xml) xmlcol from dual
    ) t
    cross join table(XMLSequence(extract(t.xmlcol,
        '/SPECTRAEXCHANGE/APPLICATION/STATION'))) x
);

1 row updated.

select * from spectraexchange;

SV_SV_ID        SS_SS_ID        AP_NAME         AP_PRJ_IDENT    TCS_NAME        TCS_CALL
--------------- --------------- --------------- --------------- --------------- ---------------
kClong          kClong          kCstring (64)   kCstring (32)   kCstring (64)   kCstring (256)

If course this also assumes one station per application, otherwise you'll need multiple joined tables to hold the relationships I guess; and only one application or your update would need to be correlated somehow. But then the update seems pointless, you could do it all on insert:

insert into spectraexchange(sv_sv_id, ss_ss_id, ap_name, ap_prj_ident,
    tcs_name, tcs_call)
select extractvalue(value(x), 'APPLICATION/SV_SV_ID') sv_sv_id,
    extractvalue(value(x), 'APPLICATION/SS_SS_ID') ss_ss_id,
    extractvalue(value(x), 'APPLICATION/AP_NAME') ap_name,
    extractvalue(value(x), 'APPLICATION/AP_PRJ_IDENT') ap_prj_ident,
    extractvalue(value(x), 'APPLICATION/STATION/TCS_NAME') tcs_name,
    extractvalue(value(x), 'APPLICATION/STATION/TCS_CALL') tcs_call
from (
    select xmltype(:raw_xml) xmlcol from dual
) t
cross join table(XMLSequence(extract(t.xmlcol,
    '/SPECTRAEXCHANGE/APPLICATION'))) x;

... (which only works with one-to-one relationships) so clearly I'm missing something from the picture.

Based on your comments that you have one-to-many relationships and you're inserting everything into one table (!?), you can do this instead:

insert into spectra exchange ( ... columns ... )
select a.sv_sv_id, a.ss_ss_id, a.ap_name, a.ap_prj_ident,
    s.tcs_name, s.tcs_call,
    t.eqp_equip_name, t.eqp_equip_type
from (select xmltype(:raw_xml) xmlcol from dual) r
cross join xmltable('/SPECTRAEXCHANGE/APPLICATION' passing r.xmlcol
        columns sv_sv_id varchar2(15) path 'SV_SV_ID',
            ss_ss_id varchar2(15) path 'SS_SS_ID',
            ap_name varchar2(15) path 'AP_NAME',
            ap_prj_ident varchar2(15) path 'AP_PRJ_IDENT',
            stations xmltype path 'STATION'
    ) (+) a
cross join xmltable('/STATION' passing a.stations
        columns tcs_name varchar2(15) path 'TCS_NAME',
            tcs_call varchar2(15) path 'TCS_CALL',
            transmitter xmltype path 'TRANSMITTER'
    ) (+) s
cross join xmltable('/TRANSMITTER' passing s.transmitter
        columns eqp_equip_name varchar2(15) path 'EQP_EQUIP_NAME',
            eqp_equip_type varchar2(15) path 'EQP_EQUIP_TYPE',
            frequency xmltype path 'FREQUENCY'
    ) (+) t
/

I've gone down an extra level to transmitter, and you can just repeat the pattern to add more, passing the relevant node down each time. The outer joins (+) will allow for some things not existing, e.g. if you have a transmitter that hasn't been given a frequency yet, or whatever - you'll get a null in the relevant columns.