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https://issues.apache.org/jira/browse/GOBBLIN-1367?focusedWorklogId=539673&page=com.atlassian.jira.plugin.system.issuetabpanels:worklog-tabpanel#worklog-539673
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ASF GitHub Bot logged work on GOBBLIN-1367:
-------------------------------------------
Author: ASF GitHub Bot
Created on: 22/Jan/21 05:59
Start Date: 22/Jan/21 05:59
Worklog Time Spent: 10m
Work Description: codecov-io edited a comment on pull request #3209:
URL:
https://github.com/apache/incubator-gobblin/pull/3209#issuecomment-764450255
#
[Codecov](https://codecov.io/gh/apache/incubator-gobblin/pull/3209?src=pr&el=h1)
Report
> Merging
[#3209](https://codecov.io/gh/apache/incubator-gobblin/pull/3209?src=pr&el=desc)
(07d9511) into
[master](https://codecov.io/gh/apache/incubator-gobblin/commit/2fa3553c75775d2d2a3a98f51c92b5c758c7abc9?el=desc)
(2fa3553) will **decrease** coverage by `0.00%`.
> The diff coverage is `100.00%`.
[](https://codecov.io/gh/apache/incubator-gobblin/pull/3209?src=pr&el=tree)
```diff
@@ Coverage Diff @@
## master #3209 +/- ##
============================================
- Coverage 46.23% 46.23% -0.01%
- Complexity 9788 9797 +9
============================================
Files 2019 2019
Lines 77439 77504 +65
Branches 8602 8606 +4
============================================
+ Hits 35807 35837 +30
- Misses 38300 38334 +34
- Partials 3332 3333 +1
```
| [Impacted
Files](https://codecov.io/gh/apache/incubator-gobblin/pull/3209?src=pr&el=tree)
| Coverage Δ | Complexity Δ | |
|---|---|---|---|
|
[...pache/gobblin/source/jdbc/PostgresqlExtractor.java](https://codecov.io/gh/apache/incubator-gobblin/pull/3209/diff?src=pr&el=tree#diff-Z29iYmxpbi1tb2R1bGVzL2dvYmJsaW4tc3FsL3NyYy9tYWluL2phdmEvb3JnL2FwYWNoZS9nb2JibGluL3NvdXJjZS9qZGJjL1Bvc3RncmVzcWxFeHRyYWN0b3IuamF2YQ==)
| `50.00% <100.00%> (+20.17%)` | `14.00 <0.00> (+2.00)` | |
|
[...obblin/yarn/YarnAppSecurityManagerWithKeytabs.java](https://codecov.io/gh/apache/incubator-gobblin/pull/3209/diff?src=pr&el=tree#diff-Z29iYmxpbi15YXJuL3NyYy9tYWluL2phdmEvb3JnL2FwYWNoZS9nb2JibGluL3lhcm4vWWFybkFwcFNlY3VyaXR5TWFuYWdlcldpdGhLZXl0YWJzLmphdmE=)
| `8.33% <0.00%> (-13.55%)` | `1.00% <0.00%> (-1.00%)` | |
|
[...he/gobblin/source/PartitionAwareFileRetriever.java](https://codecov.io/gh/apache/incubator-gobblin/pull/3209/diff?src=pr&el=tree#diff-Z29iYmxpbi1jb3JlL3NyYy9tYWluL2phdmEvb3JnL2FwYWNoZS9nb2JibGluL3NvdXJjZS9QYXJ0aXRpb25Bd2FyZUZpbGVSZXRyaWV2ZXIuamF2YQ==)
| `48.14% <0.00%> (-7.41%)` | `0.00% <0.00%> (ø%)` | |
|
[...in/java/org/apache/gobblin/cluster/HelixUtils.java](https://codecov.io/gh/apache/incubator-gobblin/pull/3209/diff?src=pr&el=tree#diff-Z29iYmxpbi1jbHVzdGVyL3NyYy9tYWluL2phdmEvb3JnL2FwYWNoZS9nb2JibGluL2NsdXN0ZXIvSGVsaXhVdGlscy5qYXZh)
| `32.23% <0.00%> (-5.79%)` | `12.00% <0.00%> (-2.00%)` | |
|
[...a/org/apache/gobblin/cluster/GobblinHelixTask.java](https://codecov.io/gh/apache/incubator-gobblin/pull/3209/diff?src=pr&el=tree#diff-Z29iYmxpbi1jbHVzdGVyL3NyYy9tYWluL2phdmEvb3JnL2FwYWNoZS9nb2JibGluL2NsdXN0ZXIvR29iYmxpbkhlbGl4VGFzay5qYXZh)
| `58.06% <0.00%> (-2.16%)` | `6.00% <0.00%> (ø%)` | |
|
[...n/java/org/apache/gobblin/yarn/YarnHelixUtils.java](https://codecov.io/gh/apache/incubator-gobblin/pull/3209/diff?src=pr&el=tree#diff-Z29iYmxpbi15YXJuL3NyYy9tYWluL2phdmEvb3JnL2FwYWNoZS9nb2JibGluL3lhcm4vWWFybkhlbGl4VXRpbHMuamF2YQ==)
| `32.69% <0.00%> (-2.01%)` | `8.00% <0.00%> (ø%)` | |
|
[...rg/apache/gobblin/yarn/GobblinYarnAppLauncher.java](https://codecov.io/gh/apache/incubator-gobblin/pull/3209/diff?src=pr&el=tree#diff-Z29iYmxpbi15YXJuL3NyYy9tYWluL2phdmEvb3JnL2FwYWNoZS9nb2JibGluL3lhcm4vR29iYmxpbllhcm5BcHBMYXVuY2hlci5qYXZh)
| `24.10% <0.00%> (-0.06%)` | `12.00% <0.00%> (ø%)` | |
|
[...ava/org/apache/gobblin/util/hadoop/TokenUtils.java](https://codecov.io/gh/apache/incubator-gobblin/pull/3209/diff?src=pr&el=tree#diff-Z29iYmxpbi11dGlsaXR5L3NyYy9tYWluL2phdmEvb3JnL2FwYWNoZS9nb2JibGluL3V0aWwvaGFkb29wL1Rva2VuVXRpbHMuamF2YQ==)
| `0.00% <0.00%> (ø)` | `0.00% <0.00%> (ø%)` | |
|
[...e/gobblin/yarn/AbstractYarnAppSecurityManager.java](https://codecov.io/gh/apache/incubator-gobblin/pull/3209/diff?src=pr&el=tree#diff-Z29iYmxpbi15YXJuL3NyYy9tYWluL2phdmEvb3JnL2FwYWNoZS9nb2JibGluL3lhcm4vQWJzdHJhY3RZYXJuQXBwU2VjdXJpdHlNYW5hZ2VyLmphdmE=)
| `49.47% <0.00%> (+1.19%)` | `7.00% <0.00%> (+1.00%)` | |
|
[...a/management/copy/publisher/CopyDataPublisher.java](https://codecov.io/gh/apache/incubator-gobblin/pull/3209/diff?src=pr&el=tree#diff-Z29iYmxpbi1kYXRhLW1hbmFnZW1lbnQvc3JjL21haW4vamF2YS9vcmcvYXBhY2hlL2dvYmJsaW4vZGF0YS9tYW5hZ2VtZW50L2NvcHkvcHVibGlzaGVyL0NvcHlEYXRhUHVibGlzaGVyLmphdmE=)
| `75.33% <0.00%> (+1.33%)` | `32.00% <0.00%> (+1.00%)` | |
| ... and [6
more](https://codecov.io/gh/apache/incubator-gobblin/pull/3209/diff?src=pr&el=tree-more)
| |
------
[Continue to review full report at
Codecov](https://codecov.io/gh/apache/incubator-gobblin/pull/3209?src=pr&el=continue).
> **Legend** - [Click here to learn
more](https://docs.codecov.io/docs/codecov-delta)
> `Δ = absolute <relative> (impact)`, `ø = not affected`, `? = missing data`
> Powered by
[Codecov](https://codecov.io/gh/apache/incubator-gobblin/pull/3209?src=pr&el=footer).
Last update
[2fa3553...07d9511](https://codecov.io/gh/apache/incubator-gobblin/pull/3209?src=pr&el=lastupdated).
Read the [comment docs](https://docs.codecov.io/docs/pull-request-comments).
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Issue Time Tracking
-------------------
Worklog Id: (was: 539673)
Time Spent: 1h (was: 50m)
> Fix PostgresqlExtractor's unnecessary string replacement
> --------------------------------------------------------
>
> Key: GOBBLIN-1367
> URL: https://issues.apache.org/jira/browse/GOBBLIN-1367
> Project: Apache Gobblin
> Issue Type: Bug
> Components: gobblin-sql
> Reporter: Kengo Seki
> Assignee: Shirshanka Das
> Priority: Major
> Time Spent: 1h
> Remaining Estimate: 0h
>
> I tried to run PostgreSQL Source/Extractor with the following minimal config,
> {code}
> $ psql
> psql (12.5 (Ubuntu 12.5-0ubuntu0.20.04.1))
> Type "help" for help.
> sekikn=# \c
> You are now connected to database "sekikn" as user "sekikn".
> sekikn=# \d
> public | t | table | sekikn
> sekikn=# \d t
> c | character varying | | |
> {code}
> {code}
> $ cat ~/postgres_to_console.job
> source.class=org.apache.gobblin.source.extractor.extract.jdbc.PostgresqlSource
> source.conn.driver=org.postgresql.Driver
> source.conn.username=sekikn
> source.conn.password=********
> source.conn.host=localhost
> source.conn.port=5432
> source.conn.database=sekikn
> source.querybased.schema=public
> source.entity=t
> extract.table.type=SNAPSHOT_APPEND
> writer.builder.class=org.apache.gobblin.writer.ConsoleWriterBuilder
> data.publisher.type=org.apache.gobblin.publisher.NoopPublisher
> {code}
> but came across the following error.
> {code}
> $ bin/gobblin cli run -jobName postgres_to_console -jobFile
> ~/postgres_to_console.job
> (snip)
> 2021-01-21 07:45:40 JST INFO [gobblin-instance-driver]
> org.apache.gobblin.source.jdbc.JdbcExtractor [public_t_1611182740226_0] -
> Extract metadata using JDBC
> 2021-01-21 07:45:40 JST INFO [gobblin-instance-driver]
> org.apache.gobblin.source.jdbc.JdbcExtractor [public_t_1611182740226_0] -
> Executing query:select col.column_name, col.data_type, case when
> CHARACTER_OCTET_LENGTH is null then 0 else 0 end as length, case when
> NUMERIC_PRECISION is null then 0 else NUMERIC_PRECISION end as precesion,
> case when NUMERIC_SCALE is null then 0 else NUMERIC_SCALE end as scale, case
> when is_nullable='NO' then 'false' else 'true' end as nullable, '' as format,
> '' as comment from information_schema.COLUMNS col WHERE
> upper(col.table_name)=upper(?) AND upper(col.table_schema)=upper(?) order by
> col.ORDINAL_POSITION
> 2021-01-21 07:45:40 JST INFO [gobblin-instance-driver]
> org.apache.gobblin.source.jdbc.JdbcExtractor [public_t_1611182740226_0] -
> Schema:[{"columnName":"c","dataType":{"type":"string"},"isWaterMark":false,"primaryKey":0,"length":0,"precision":0,"scale":0,"isNullable":true,"format":"","comment":"","isUnique":false}]
> 2021-01-21 07:45:40 JST INFO [gobblin-instance-driver]
> org.apache.gobblin.source.jdbc.JdbcExtractor [public_t_1611182740226_0] -
> Extract query: SELECT c FROM public.t where ('$WATERMARK')
> 2021-01-21 07:45:40 JST INFO [gobblin-instance-driver]
> org.apache.gobblin.source.jdbc.JdbcExtractor [public_t_1611182740226_0] - Get
> source record count using JDBC
> 2021-01-21 07:45:40 JST INFO [gobblin-instance-driver]
> org.apache.gobblin.source.jdbc.JdbcExtractor [public_t_1611182740226_0] -
> Executing query:SELECT COUNT(1) FROM publiCOUNT(1).t where (1=1)
> 2021-01-21 07:45:40 JST ERROR [gobblin-instance-driver]
> org.apache.gobblin.source.jdbc.JdbcExtractor [public_t_1611182740226_0] -
> Failed to execute sql:SELECT COUNT(1) FROM publiCOUNT(1).t where (1=1)
> ;error-ERROR: syntax error at or near "."
> Position: 35
> org.postgresql.util.PSQLException: ERROR: syntax error at or near "."
> Position: 35
> at
> org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2477)
> at
> org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:2190)
> at
> org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:300)
> at org.postgresql.jdbc.PgStatement.executeInternal(PgStatement.java:428)
> at org.postgresql.jdbc.PgStatement.execute(PgStatement.java:354)
> at
> org.postgresql.jdbc.PgStatement.executeWithFlags(PgStatement.java:301)
> at
> org.postgresql.jdbc.PgStatement.executeCachedSql(PgStatement.java:287)
> at
> org.postgresql.jdbc.PgStatement.executeWithFlags(PgStatement.java:264)
> at org.postgresql.jdbc.PgStatement.execute(PgStatement.java:260)
> at
> org.apache.commons.dbcp.DelegatingStatement.execute(DelegatingStatement.java:264)
> at
> org.apache.commons.dbcp.DelegatingStatement.execute(DelegatingStatement.java:264)
> at
> org.apache.gobblin.source.jdbc.JdbcExtractor.executeSql(JdbcExtractor.java:666)
> at
> org.apache.gobblin.source.jdbc.JdbcExtractor.getSourceCount(JdbcExtractor.java:797)
> at
> org.apache.gobblin.source.extractor.extract.QueryBasedExtractor.build(QueryBasedExtractor.java:326)
> at
> org.apache.gobblin.source.extractor.extract.jdbc.PostgresqlSource.getExtractor(PostgresqlSource.java:47)
> at
> org.apache.gobblin.runtime.TaskContext.getExtractor(TaskContext.java:120)
> at org.apache.gobblin.runtime.Task.<init>(Task.java:196)
> at
> org.apache.gobblin.runtime.GobblinMultiTaskAttempt.createTaskRunnable(GobblinMultiTaskAttempt.java:485)
> at
> org.apache.gobblin.runtime.GobblinMultiTaskAttempt.access$100(GobblinMultiTaskAttempt.java:86)
> at
> org.apache.gobblin.runtime.GobblinMultiTaskAttempt$2.call(GobblinMultiTaskAttempt.java:511)
> at
> org.apache.gobblin.runtime.GobblinMultiTaskAttempt$2.call(GobblinMultiTaskAttempt.java:505)
> at
> com.github.rholder.retry.AttemptTimeLimiters$NoAttemptTimeLimit.call(AttemptTimeLimiters.java:78)
> at com.github.rholder.retry.Retryer.call(Retryer.java:160)
> at
> org.apache.gobblin.runtime.GobblinMultiTaskAttempt.createTaskWithRetry(GobblinMultiTaskAttempt.java:505)
> at
> org.apache.gobblin.runtime.GobblinMultiTaskAttempt.runWorkUnits(GobblinMultiTaskAttempt.java:421)
> at
> org.apache.gobblin.runtime.GobblinMultiTaskAttempt.run(GobblinMultiTaskAttempt.java:157)
> at
> org.apache.gobblin.runtime.GobblinMultiTaskAttempt.runAndOptionallyCommitTaskAttempt(GobblinMultiTaskAttempt.java:521)
> at
> org.apache.gobblin.runtime.GobblinMultiTaskAttempt.runWorkUnits(GobblinMultiTaskAttempt.java:563)
> at
> org.apache.gobblin.runtime.local.LocalJobLauncher.runWorkUnitStream(LocalJobLauncher.java:156)
> at
> org.apache.gobblin.runtime.AbstractJobLauncher.launchJob(AbstractJobLauncher.java:508)
> at
> org.apache.gobblin.runtime.job_exec.JobLauncherExecutionDriver$DriverRunnable.call(JobLauncherExecutionDriver.java:164)
> at
> org.apache.gobblin.runtime.job_exec.JobLauncherExecutionDriver$DriverRunnable.call(JobLauncherExecutionDriver.java:152)
> at java.util.concurrent.FutureTask.run(FutureTask.java:266)
> at java.lang.Thread.run(Thread.java:748)
> 2021-01-21 07:45:40 JST ERROR [gobblin-instance-driver]
> org.apache.gobblin.source.extractor.extract.jdbc.PostgresqlSource
> [public_t_1611182740226_0] - Failed to prepare extractor: error - Failed to
> get record count; error - Failed to get source record count using JDBC; error
> - Failed to get source record count from database; error - null
> {code}
> This is because the target schema and table (publi"c".t) contains the name of
> column (c), so it was replaced wrongly. PostgresqlExtractor should replace
> only the first occurrence of the target substring here.
>
> [https://github.com/apache/incubator-gobblin/blob/release-0.15.0/gobblin-modules/gobblin-sql/src/main/java/org/apache/gobblin/source/jdbc/PostgresqlExtractor.java#L134]
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