BOX - beginning of expedition
EOX - end of expedition
The DBA is responsible for shore EOX processing.
...
This expedition is ended. Within two weeks, science participants expect to have moratorium access to LIMS content. DBA, Systems/MCS, and sometimes Programmers need to coordinate to help this happen. The Database Librarian needs to know when these changes occur too.
Make sure we are getting as a complete a copy of the shipboard data to be warehoused on shore as we can.
0. Notify that the data load is in progress
Lot's of folks want to know: Systems, Data Librarian, Programmers, EPMs, Managers, selected TAS staff.
It is helpful to chat with Curation. If there is a sampling party or post-cruise meeting in progress, it is preferrable to post-pone the Copy the content step to a less busy time. Otherwise activities up to that point can be completed without any production impact.
1. Retrieve data content from tape
Distribute it Subsets of the EOX tapes are distributed to Publications, Data Librarian, DBA, Operations, and public access storage locations. - Systems
A copy of the shipboard database export is stage for DBA use at OEM:/backup/eox/
- The database dump is backed up to tape via the host
OEMJR:/backup/eox/. TBD--confirm location and match in DEV and MCS SOPs. - When restored, the file is copied to
OEM:/backup/eox/.
There should be one data dump file and an accompanying log of the export activity.
- When the file contains a full shipboard database export the naming pattern is like
limsjr_full-398.dmpdp - When the file contains selected schema exports it is named like
limsjr_schemas-398.dmpdp
For the shore EOX work, the filename is typically shortened to the expedition designation, e.g. 398.dmpdp.
2. Restore and review
Restore routinely selected database content from the full backup to the shore production transfer schema. - DBA
| Info |
|---|
Nota bene. The expectation is that the data staged will contain the new expedition, QAQC, and 999 (operational test expedition). In some cases, data is included from a prior expedition.
Presently a common edge case with poor automation. Tread lightly. Check your work. |
Once staged extract, transfer, and load scripts may be run.
- DBA scripting for the EOX (and other) processes are hosted at
OEM:/backup/scripts/rci_work/exp/Please create a subdirectory for expedition-specific outputs. - This scripting is designed to be run from an ODA command-prompt.
- Privilege to sudo to the ODA oracle user is required.
Other pre-requisites.
- What database instance are you connecting to? You must be at a command-line for that ODA instance.
As the OS oracle user specify which database instance you are using with this syntax
Code Block . oraenv ORACLE_SID = [oracle] ? LIMSHQ (or RTLIMS or LIMS19)
From that command-line, the following shell and SQL scripts (bold header) are run. In the order shown.
import_transfer.ksh
When executed, this script
- Prompts for the local name (and extension) of the database export file. Upon <Enter>
- Shipboard content is imported into the TRANSFER schema. Indexes are created for the largest rowcount tables: new_sample, new_test, new_result.
- The script now prompts for the expedition of interest, e.g. 398, 397T, etc. Upon <Enter>
- The script imports reference copies of GEODCAT (renamed to include the expedition) and GEODP### schemas.
On completion--of the schema imports above--a variety of SQL statements are run to highlight what data was brought back and how many rows.
- This script imported 398 content over multiple tests between 30 and 40 minutes.
Additional data review scripts take another 10-15 minutes to run. - The script requires no TRANSFER schema preparation--all the tables required are present, the import methodology truncates the tables before importing new content.
- The content is imported directly from SCHEMAS exported on ship (LIMS, DESCINFO2, OPS, GEODCAT, GEODP###, etc.).
There is no duplication of keys incurred by the ETL cycle now in use.
| Code Block | ||||
|---|---|---|---|---|
| ||||
EOX_EXP_DIR=`sqlplus -s / as sysdba << EOT
set pages 0 feedback off
SELECT directory_path FROM dba_directories WHERE directory_name = 'EOX_EXP_DIR';
exit
EOT`
# DIRECTORY_PATH
# --------------------------------------------------------------------------------
# /backup/eox
if [ ! -d $EOX_EXP_DIR ]
then
echo $EOX_EXP_DIR not found...
exit 1
fi
if [ $# -ne 1 ]
then
echo Enter dump file name
read DUMP_FILE_NAME
else
DUMP_FILE_NAME=$1
fi
if [ ! -r $EOX_EXP_DIR/$DUMP_FILE_NAME ]
then
echo $EOX_EXP_DIR/$DUMP_FILE_NAME not found
exit 2
fi
DT=`date +"%m%d%Y"`
SCHEMA_NAME=transfer
LOG_FILE_NAME=${SCHEMA_NAME}_import_${DT}.log
# Import LIMS, DESCINFO2, and OPS tables into target TRANSFER schema.
impdp system/$s directory=eox_exp_dir DUMPFILE=$DUMP_FILE_NAME LOGFILE=${LOG_FILE_NAME} VERSION=LATEST PARFILE=eox_impdp_to_transfer.par
while [ ${EOX}1 == "1" ]
do
echo Enter EOX#
read EOX
done
if [ ${EOX}1 == "1" ]
then
echo EOX is not set.
exit 1
fi
sql / as sysdba <<+++
drop user geodcat${EOX} cascade;
drop user geodp${EOX} cascade;
exit;
+++
# Import GEODCAT to an GEODCAT### where ### is the expedition being processed.
SCHEMA_NAME=geodcat${EOX}
LOG_FILE_NAME=${SCHEMA_NAME}_import_${DT}.log
impdp system/$s directory=eox_exp_dir DUMPFILE=$DUMP_FILE_NAME LOGFILE=${LOG_FILE_NAME} VERSION=LATEST CONTENT=ALL SCHEMAS=GEODCAT REMAP_SCHEMA=GEODCAT:${SCHEMA_NAME}
# Import GEODP### where ### is the expedition being processed.
SCHEMA_NAME=geodp${EOX}
LOG_FILE_NAME=${SCHEMA_NAME}_import_${DT}.log
impdp system/$s directory=eox_exp_dir DUMPFILE=$DUMP_FILE_NAME LOGFILE=${LOG_FILE_NAME} VERSION=LATEST CONTENT=ALL SCHEMAS=${SCHEMA_NAME}
# TBD--revise to log this output to a single file for reference after data modifications and copying.
sql / as sysdba <<+++
set newpage 0
set linesize 100
set pagesize 0
set timing on
set time on
set feedback on
set heading on
set trimspool on
set trimout on
set tab off
/* These indexes help speed up later bulk data manipulation and merge activites. */
drop index transfer.new_result_idx;
drop index transfer.new_result_result_number;
drop index transfer.new_test_idx;
drop index transfer.new_test_test_number;
drop index transfer.new_sample_sample_number;
create bitmap index transfer.new_result_idx on transfer.new_result ( sample_number, test_number, result_number ) tablespace transfer parallel;
create unique index transfer.new_result_result_number on transfer.new_result (result_number) tablespace transfer parallel;
create bitmap index transfer.new_test_idx on transfer.new_test ( sample_number, test_number ) tablespace transfer parallel;
create unique index transfer.new_test_test_number on transfer.new_test (test_number) tablespace transfer parallel;
create unique index transfer.new_sample_sample_number on transfer.new_sample (sample_number) tablespace transfer parallel;
/* Review the content loaded in TRANSFER in finer detail than the import activity. */
-- Review the sample, test, result content just loaded to TRANSFER
alter session set current_schema=transfer;
select 'REVIEW TRANSFER.NEW_SAMPLE' from dual;
select s.group_name, s.x_expedition, s.status, count(*) from transfer.new_sample s where s.x_expedition in ('${EOX}', 'QAQC', '999') group by s.group_name, s.x_expedition, s.status order by s.x_expedition, s.group_name, s.status;
select 'REVIEW TRANSFER.NEW_TEST' from dual;
select t.group_name, s.x_expedition, t.status, count(*) from transfer.new_sample s, transfer.new_test t where s.sample_number=t.sample_number and s.x_expedition in ('${EOX}', 'QAQC', '999') group by t.group_name, s.x_expedition, t.status order by s.x_expedition, t.group_name, t.status;
select 'REVIEW TRANSFER.NEW_RESULT' from dual;
select r.group_name, s.x_expedition, r.status, count(*) from transfer.new_sample s, transfer.new_result r where s.sample_number=r.sample_number and s.x_expedition in ('${EOX}', 'QAQC', '999') group by r.group_name, s.x_expedition, r.status order by s.x_expedition, r.group_name, r.status;
-- Compare to content in LIMS
alter session set current_schema=lims;
select 'REVIEW LIMS.SAMPLE' from dual;
select s.group_name, s.x_expedition, s.status, count(*) from lims.sample s where s.x_expedition in ('${EOX}', 'QAQC', '999') group by s.group_name, s.x_expedition, s.status order by s.x_expedition, s.group_name, s.status;
select 'REVIEW LIMS.TEST' from dual;
select t.group_name, s.x_expedition, t.status, count(*) from lims.sample s, lims.test t where s.sample_number=t.sample_number and s.x_expedition in ('${EOX}', 'QAQC', '999') group by t.group_name, s.x_expedition, t.status order by s.x_expedition, t.group_name, t.status;
select 'REVIEW LIMS.RESULT' from dual;
select r.group_name, s.x_expedition, r.status, count(*) from lims.sample s, lims.result r where s.sample_number=r.sample_number and s.x_expedition in ('${EOX}', 'QAQC', '999') group by r.group_name, s.x_expedition, r.status order by s.x_expedition, r.group_name, r.status;
-- Gather stats for the TRANSFER schema
exec dbms_stats.gather_schema_stats('TRANSFER', cascade=>TRUE);
-- Show info about tables imported from data pump export
select table_name, num_rows, avg_row_len, blocks, empty_blocks, owner from all_tables where owner='TRANSFER' order by owner, num_rows desc;
exit
+++ |
and its companion
| Code Block | ||||
|---|---|---|---|---|
| ||||
CONTENT=DATA_ONLY
TABLE_EXISTS_ACTION=TRUNCATE
# Fully load all tables required.
# Complex filtering was problematic, so handling it post import.
# Nota bene--DESCINFO2 tables on ship will be retired within 2023.
# LIMS
TABLES=LIMS.FILES, LIMS.SAMPLE, LIMS.TEST, LIMS.RESULT, LIMS.X_EXTERNAL_KEYS, LIMS.X_SCALE, LIMS.X_HOLE_TO_SCALE, LIMS.X_SAMPLE_DEPTH, LIMS.SCORS_AFFINE, LIMS.SCORS_AFFINE_DETAIL, LIMS.SCORS_SPLICE, LIMS.SCORS_SPLICE_DETAIL, LIMS.X_LIME_AUDIT_MAIN, LIMS.X_LIME_AUDIT_DETAIL, LIMS.GEOD_METADATA, LIMS.GEOD_DATA
REMAP_SCHEMA=LIMS:TRANSFER
REMAP_TABLE=LIMS.FILES:NEW_FILES, LIMS.SAMPLE:NEW_SAMPLE, LIMS.TEST:NEW_TEST, LIMS.RESULT:NEW_RESULT, LIMS.X_EXTERNAL_KEYS:NEW_X_EXTERNAL_KEYS, LIMS.X_SCALE:NEW_X_SCALE, LIMS.X_HOLE_TO_SCALE:NEW_X_HOLE_TO_SCALE, LIMS.X_SAMPLE_DEPTH:NEW_X_SAMPLE_DEPTH, LIMS.SCORS_AFFINE:NEW_SCORS_AFFINE, LIMS.SCORS_AFFINE_DETAIL:NEW_SCORS_AFFINE_DETAIL, LIMS.SCORS_SPLICE:NEW_SCORS_SPLICE, LIMS.SCORS_SPLICE_DETAIL:NEW_SCORS_SPLICE_DETAIL, LIMS.X_LIME_AUDIT_MAIN:NEW_X_LIME_AUDIT_MAIN, LIMS.X_LIME_AUDIT_DETAIL:NEW_X_LIME_AUDIT_DETAIL, LIMS.GEOD_METADATA:NEW_GEOD_METADATA, LIMS.GEOD_DATA:NEW_GEOD_DATA
# OPS
#TABLES=OPS.RIS_DATA
#REMAP_SCHEMA=OPS:TRANSFER
#REMAP_TABLE=OPS.RIS_DATA:NEW_RIS_DATA |
3. Establish moratorium credentials and controls
For the new expedition data. - DBA
The credential is selected by the Director of the Staff Scientist group. Enquire with Leah Levay--or see the password safe for entries provided for FY2024. The moratorium name follows this pattern: EXP###--examples EXP399, EXP400T, EXP398, EXP398P, etc.
The account is shared by a science party for the moratorium period (typically 18 months)--it enables specific support for SDRM; it enables access to data in moratorium within the web-based LORE reporting system.
The moratorium name is generally selected and specified by the operator of this process.
eox_gen_in_moratorium_script.ksh [moratorium-group]
This script accepts a moratorium name, e.g. SHACKLETON, SANTORINI, etc. Restrictions on that name are listed below.
The script (below) is generated by the above. It writes the SQL to specifically modify NEW_TEST, NEW_RESULT, and NEW_GEOD_DATA tables for moratorium concerns.
- If a moratorium group is not provided, the script will prompt.
- The script does not check these requirement
- The GROUP_NAME field that this string populates is 10 characters or less.
- The string must also be a valid name for a ROLE. Example: should not start with a number; must be valid for naming a Unix file. By convention we stick with names using A to Z uppercase only, no symbols or special characters.
| Code Block | ||||
|---|---|---|---|---|
| ||||
DT=`date +"%Y%m%d_%H%M%S"`
LOG1=upd1_result_grp_name_${DT}.txt
LOG2=upd2_result_grp_name_${DT}.txt
echo "Started at `date`"
if [ $# -ne 1 ]
then
echo Enter GRP_NM
read GRP_NM
else
GRP_NM=$1
fi
KSH_SCRIPT=in_moratorium_${GRP_NM}.ksh
echo "sql / as sysdba <<+++" >${KSH_SCRIPT}
echo "alter session set current_schema=transfer;" >>${KSH_SCRIPT}
echo "set echo on" >>${KSH_SCRIPT}
echo "set pagesize 0" >>${KSH_SCRIPT}
echo "set linesize 132" >>${KSH_SCRIPT}
echo "set timing on" >>${KSH_SCRIPT}
echo "set heading off" >>${KSH_SCRIPT}
echo "spool in_moratorium_${GRP_NM}.log" >>${KSH_SCRIPT}
echo "update transfer.new_result set group_name='${GRP_NM}' where group_name='DEFAULT' and analysis not in ('BHA','BIT','DEPLETED','DRILLING','LATLONG','ORIGDEPTH','ROUTING','SCALINPUTS') and sample_number in (select sample_number from transfer.new_sample where x_expedition='${EOX}');" >>${KSH_SCRIPT}
echo "commit;" >>${KSH_SCRIPT}
echo "update transfer.new_test set group_name='${GRP_NM}' where group_name='DEFAULT' and analysis not in ('BHA','BIT','DEPLETED','DRILLING','LATLONG','ORIGDEPTH','ROUTING','SCALINPUTS') and sample_number in (select sample_number from transfer.new_sample where x_expedition='${EOX}');" >>${KSH_SCRIPT}
echo "commit;" >>${KSH_SCRIPT}
echo "update transfer.new_result set group_name='DEFAULT' where rowid in (select t.rowid from transfer.new_sample s, transfer.new_result t where s.sample_number=t.sample_number and s.x_expedition in ('QAQC','999'));" >>${KSH_SCRIPT}
echo "commit;" >>${KSH_SCRIPT}
echo "update transfer.new_test set group_name='DEFAULT' where rowid in (select t.rowid from transfer.new_sample s, transfer.new_test t where s.sample_number=t.sample_number and s.x_expedition in ('QAQC','999'));" >>${KSH_SCRIPT}
echo "commit;" >>${KSH_SCRIPT}
echo "select 'REVIEW CHANGED ROWS' from dual;" >>${KSH_SCRIPT}
echo "select count(*), r.group_name, s.x_expedition from transfer.new_sample s, transfer.new_result r where s.sample_number=r.sample_number group by r.group_name, s.x_expedition;" >>${KSH_SCRIPT}
echo "select count(*), t.group_name, s.x_expedition from transfer.new_sample s, transfer.new_test t where s.sample_number=t.sample_number group by t.group_name, s.x_expedition;" >>${KSH_SCRIPT}
echo "exit;" >>${KSH_SCRIPT}
echo "+++" >>${KSH_SCRIPT}
chmod 777 ${KSH_SCRIPT}
echo "Completed at `date`" |
in_moratorium_[moratorium-group].ksh
Running this script
- Ensures the current expedition content is tagged for moratorium control.
- Do review the script. Sometimes the EOX expedition number is cleared before running
eox_gen_in_moratorium_script.ksh.
Upon running the script--wait.
- The NEW_RESULT table typically contains 20-30 million rows. This update takes the longest.
- The NEW_TEST and NEW_SAMPLE table are much faster due to being 3 orders of magnitude smaller.
- Timing is turned on--the scripts will show how long they took to run.
The result table took 2-5 minutes to complete (with indexes in place) for each of ORTLIMS, LIMS19, RTLIMS, and LIMSHQ.
| Code Block | ||||
|---|---|---|---|---|
| ||||
sql -s / as sysdba <<+++
alter session set current_schema=transfer;
set echo on
set pagesize 0
set linesize 132
set timing on
set heading off
spool in_moratorium_GROUPNAME.log
update transfer.new_result set group_name='GROUPNAME' where group_name='DEFAULT' and analysis not in ('BHA','BIT','DEPLETED','DRILLING','LATLONG','ORIGDEPTH','ROUTING','SCALINPUTS') and sample_number in (select sample_number from transfer.new_sample where x_expedition='###');
commit;
update transfer.new_test set group_name='GROUPNAME' where group_name='DEFAULT' and analysis not in ('BHA','BIT','DEPLETED','DRILLING','LATLONG','ORIGDEPTH','ROUTING','SCALINPUTS') and sample_number in (select sample_number from transfer.new_sample where x_expedition='###');
commit;
update transfer.new_result set group_name='DEFAULT' where rowid in (select t.rowid from transfer.new_sample s, transfer.new_result t where s.sample_number=t.sample_number and s.x_expedition in ('QAQC','999'));
commit;
update transfer.new_test set group_name='DEFAULT' where rowid in (select t.rowid from transfer.new_sample s, transfer.new_test t where s.sample_number=t.sample_number and s.x_expedition in ('QAQC','999'));
commit;
select 'REVIEW CHANGED ROWS' from dual;
select count(*), r.group_name, s.x_expedition from transfer.new_sample s, transfer.new_result r where s.sample_number=r.sample_number group by r.group_name, s.x_expedition;
select count(*), t.group_name, s.x_expedition from transfer.new_sample s, transfer.new_test t where s.sample_number=t.sample_number group by t.group_name, s.x_expedition;
exit;
+++ |
crt_user_exp.sql
Review the script.
- Make a copy of it specifically for the expedition you are processing--e.g.
crt_user_398.sql - As of expedition 401, the user credential will apply LONG_PASSWORD requirements--edit the file accordingly. Use the credential provided by the EPM.
Run the script via SQL.
Provide an explicit path to the script to run it.
Pass the expedition as a parameter to the script. The pattern to follow based on expedition 398 activity
| Code Block |
|---|
sql / as sysdba
SQL>@/backup/scripts/rci_work/exp/crt_user_398.sql 398 |
Note that this script may be run at any time. It is free of any dependencies on other scripts here.
This credential needs to be distributed to the following email distributions for filing: EPM for the expedition in processing, it_ops@iodp.tamu.edu, programmers@iodp.tamu.edu, database@iodp.tamu.edu (Data Librarian), webmaster@iodp.tamu.edu
| Code Block | ||||
|---|---|---|---|---|
| ||||
set echo on
create user exp&1 identified by "secret-secure" default tablespace labware profile LONG_PASSWORD;
grant connect to exp&1;
create role "GROUPNAME";
grant "GROUPNAME" to exp&1;
exit; |
The above script must be run for the test database instance selected, and for the production instance to which the data is merged.
4. Copy the content
Into the publicly accessible LIMS. - DBA
The data is first imported into a test database instance in the transfer schema. After the data has been remediated to support moratorium concerns, a snapshot of this data may be exported for re-use. The export will be re-imported into the production database.
| Code Block |
|---|
sql my_dba@instance
dp export -directory dmpdir -dumpfile ###-transfer.dmpdp -schemas transfer -filesize 15gb |
After completing the above export from the selected test instance, complete these commands at the production instance (LIMSHQ).
| Code Block |
|---|
sql my_dba@limshq
call transfer.util_cleanout_transfer_new_tables();
dp import -directory dmpdir -dumpfile ###-transfer.dmpdp -schemas transfer -nameexpr table="like 'NEW__%'" -includemetadata false -includerows true |
chk_tablespace_free.ksh
Review the space available in LABWARE, LABWAREIDX.
| Code Block | ||||
|---|---|---|---|---|
| ||||
DT=`date +"%Y%m%d_%H%M%S"`
OUT=chk_tablespace_free_${DT}.txt
TMP=chk_tablespace_free_${DT}.tmp
sqlplus -s "/ as sysdba" 2>/dev/null 1>$TMP <<+++
set newpage 0
set linesize 150
set pagesize 0
set echo off
set feedback off
set tab off
column TABLESPACE_NAME FORMAT A15 HEADING 'Tablespace';
column file_name FORMAT A45 HEADING 'File Name ';
COLUMN allocated_mb FORMAT 999,999,999,999 HEADING 'Tablespace|Pieces';
cOLUMN free_mb FORMAT 999,999,999,999 HEADING 'Free|Mbytes';
cOLUMN free_mb_per FORMAT 999.99 HEADING 'Free ';
SELECT
a.tablespace_name,
a.file_name,
(a.bytes/1024) allocated_mb,
(b.free_bytes/1024) free_mb,
(b.free_bytes/a.bytes)*100 free_mb_per
FROM
dba_data_files a,
(SELECT file_id, SUM(bytes) free_bytes
FROM dba_free_space b GROUP BY file_id) b
WHERE
a.file_id=b.file_id
ORDER BY
a.tablespace_name;
exit;
+++
grep -v "^$" $TMP >$OUT
rm $TMP
egrep "LABWARE |LABWAREIDX |UNDOTBS1|TRANSFER|TEMP" $OUT
#cat $OUT |
grp_cnt_transfer.ksh, grp_cnt_lims.ksh
Run these scripts to obtain row counts by moratorium group, expedition, and record status after the moratorium remediation is complete. Preparatory step before data is merged. The output of these scripts are text files. Review them. File the info in the expedition-specific directory.
| Code Block | ||||
|---|---|---|---|---|
| ||||
DT=`date +"%Y%m%d_%H%M%S"`
OUT=grp_cnt_transfer_${DT}.txt
sql -s "/ as sysdba" 2>>$OUT 1>>$OUT <<+++
alter session set current_schema=transfer;
--connect transfer/HQtransfer:dbashare.hhhhh;
set newpage 0
set linesize 100
set pagesize 0
set echo on
set timing on
set time on
set feedback off
set heading off
set tab off
select 'REVIEW TRANSFER.TEST' from dual;
select t.group_name, s.x_expedition, t.status, count(*) from transfer.new_sample s, transfer.new_test t where s.sample_number=t.sample_number group by t.group_name, s.x_expedition, t.status order by s.x_expedition, t.group_name, t.status;
select 'REVIEW TRANSFER.RESULT' from dual;
select r.group_name, s.x_expedition, r.status, count(*) from transfer.new_sample s, transfer.new_result r where s.sample_number=r.sample_number group by r.group_name, s.x_expedition, r.status order by s.x_expedition, r.group_name, r.status;
exit;
+++ |
| Code Block | ||||
|---|---|---|---|---|
| ||||
DT=`date +"%Y%m%d_%H%M%S"`
OUT=grp_cnt_lims_${DT}.txt
sql -s "/ as sysdba" 2>>$OUT 1>>$OUT <<+++
alter session set current_schema=lims;
set newpage 0
set linesize 100
set pagesize 0
set timing on
set time on
set feedback off
set heading off
set tab off
select 'REVIEW LIMS.TEST' from dual;
select t.group_name, s.x_expedition, t.status, count(*) from lims.sample s, lims.test t where s.sample_number=t.sample_number and s.x_expedition in ('${EOX}', 'QAQC', '999') group by t.group_name, s.x_expedition, t.status order by s.x_expedition, t.group_name, t.status;
select 'REVIEW LIMS.RESULT' from dual;
select r.group_name, s.x_expedition, r.status, count(*) from lims.sample s, lims.result r where s.sample_number=r.sample_number and s.x_expedition in ('${EOX}', 'QAQC', '999') group by r.group_name, s.x_expedition, r.status order by s.x_expedition, r.group_name, r.status;
exit;
+++ |
call transfer.eox_shore_merge_transfer_new_to_lims()
This procedure merges TRANSFER schema NEW_* table content into LIMS. Including
- scales, depth, samples, tests, results; and
- two (recently added) GEODESC tables.
Please review the procedure. To run it
| Code Block |
|---|
sql / as sysdba
SQL>
call transfer.eox_shore_merge_transfer_new_to_lims() |
Noted
- Without a unique result_number index, the bulk merging of the NEW_RESULT content took upwards of 6 hours.
- With a unique index on NEW_RESULT.RESULT_NUMBER the bulk merge was observed to complete in 4 hours (this for ~26 million rows).
- Support is no longer provided for merging content from the DESCINFO2 schema. No new data is being generated for that product.
- Script operation does briefly disable triggers on the LIMS.SAMPLE, LIMS.TEST tables. For this reason, it is best run outside of business hours where samples and tests are being modified. The script is preferred. It does not forget to re-enable triggers.
- The triggers being enabled/disabled are owned by the LIMS schema. To enable the TRANSFER schema to effect changes, simple procedures owned by the LIMS schema manage enable/disable support. The TRANSFER schema is granted permission to execute these LIMS-owned procedures.
grp_cnt_lims.ksh
Re-run this script for review purposes. Data formerly only in the TRANSFER schema should now be present in the same numbers in the LIMS schema.
5. Miscellaneous: Update the Database Overview, Ensure Moratorium User privileges are set
Configuration updates provide summary of the expedition data for participants and future users. - DBA
...
call transfer.dbo_compute_exp('###')
Run this script to compute new expedition summaries for display in the database OVERVIEW application. Substitute the desired expedition number.
| Code Block |
|---|
sql / as sysdba
SQL>
set serveroutput on
call transfer.dbo_compute_exp('398'); |
Upon completion, review the database overview application from a browser: : https://web.iodp.tamu.edu/OVERVIEW/
A new column of summary statistics should be visible for the new expedition.
DEV - The moratorium user must be modified within the https://web.iodp.tamu.edu/Auther/ application.
- The moratorium user must be added to the account list (match the pattern of other moratorium accounts).
- The moratorium user requires the roles: MORATORIUM USER and ALL_SPLAT.
DEV - When moratorium and all major sampling parties are complete for this data, the Auther configurations may be removed. This tends to lag behind moving data out of moratorium.
6. Test
Spot-check and test availability and completeness.
- Confirm that moratorium access is functioning by running LORE reports. - TAS, DEV
- Can the EXP### moratorium account login to https://web.iodp.tamu.edu/LORE?
- Can the EXP### moratorium account see LIMS data for the expedition--images, etc. Spotcheck.
- Can the EXP### actually download some of the file content?
- Confirm that moratorium access and account permissions are functioning for GEODESC data products. - TAS, DEV
- Can the EXP### moratorium account login to https://web.iodp.tamu.edu/DataAccess?
- Can the EXP### moratorium account see the GEODESC Final Product files via DataAccess?
- Can EXP### actually download some of those files?
7. Notify interested parties
Notify interested parties that new moratorium data is available in LIMS
- EPM
- DBA - RCI
- Data Librarian
- Web Master
- Programmers
- IT OPS
Shore EOX process applied by the DBA prior to expedition 398.
Re-worked below into process above--polishing and efficiency improvements welcome.
The scripts below are equivalent to steps 2. thru 5.
EOX load and merge - rci_work/exp
The collection of scripts in this location is used to automate the shore components of EOX processing: retrieve last expedition content from the database dump, create and apply moratorium supports, merge the data into production; provide statistics which give quality assurance/quality control on the process.
These are the scripts (in-order) that are typically used
|