[jira] [Resolved] (BEAM-3416) File is not properly closed in VcfSource when exception is thrown
[ https://issues.apache.org/jira/browse/BEAM-3416?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Asha Rostamianfar resolved BEAM-3416. - Resolution: Fixed Fix Version/s: 2.3.0 > File is not properly closed in VcfSource when exception is thrown > - > > Key: BEAM-3416 > URL: https://issues.apache.org/jira/browse/BEAM-3416 > Project: Beam > Issue Type: Bug > Components: sdk-py-core >Reporter: Asha Rostamianfar >Assignee: Asha Rostamianfar >Priority: Minor > Fix For: 2.3.0 > > > Files are not properly closed when an exception is thrown in VcfSource > (apache_beam/io/vcfio.py). > This is because the file is opened within TextSource (using a 'with' > statement), but the exception in VcfSource is thrown outside of that scope. > This only causes an issue in Windows unit tests where files cannot be deleted > if they're used by another process. -- This message was sent by Atlassian JIRA (v7.6.3#76005)
[jira] [Updated] (BEAM-3416) File is not properly closed in VcfSource when exception is thrown
[ https://issues.apache.org/jira/browse/BEAM-3416?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Asha Rostamianfar updated BEAM-3416: Summary: File is not properly closed in VcfSource when exception is thrown (was: File is not properly close in VcfSource when exception is thrown) > File is not properly closed in VcfSource when exception is thrown > - > > Key: BEAM-3416 > URL: https://issues.apache.org/jira/browse/BEAM-3416 > Project: Beam > Issue Type: Bug > Components: sdk-py-core >Reporter: Asha Rostamianfar >Assignee: Asha Rostamianfar >Priority: Minor > > Files are not properly closed when an exception is thrown in VcfSource > (apache_beam/io/vcfio.py). > This is because the file is opened within TextSource (using a 'with' > statement), but the exception in VcfSource is thrown outside of that scope. > This only causes an issue in Windows unit tests where files cannot be deleted > if they're used by another process. -- This message was sent by Atlassian JIRA (v6.4.14#64029)
[jira] [Created] (BEAM-3416) File is not properly close in VcfSource when exception is thrown
Asha Rostamianfar created BEAM-3416: --- Summary: File is not properly close in VcfSource when exception is thrown Key: BEAM-3416 URL: https://issues.apache.org/jira/browse/BEAM-3416 Project: Beam Issue Type: Bug Components: sdk-py-core Reporter: Asha Rostamianfar Assignee: Asha Rostamianfar Priority: Minor Files are not properly closed when an exception is thrown in VcfSource (apache_beam/io/vcfio.py). This is because the file is opened within TextSource (using a 'with' statement), but the exception in VcfSource is thrown outside of that scope. This only causes an issue in Windows unit tests where files cannot be deleted if they're used by another process. -- This message was sent by Atlassian JIRA (v6.4.14#64029)
[jira] [Closed] (BEAM-2774) Add I/O source for VCF files (python)
[ https://issues.apache.org/jira/browse/BEAM-2774?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Asha Rostamianfar closed BEAM-2774. --- Resolution: Fixed Fix Version/s: 2.3.0 The main code is done. Additional features (e.g. ReadAllFromVcf to handle massive number of files) will be done in separate issues. > Add I/O source for VCF files (python) > - > > Key: BEAM-2774 > URL: https://issues.apache.org/jira/browse/BEAM-2774 > Project: Beam > Issue Type: New Feature > Components: sdk-py-core >Reporter: Asha Rostamianfar >Assignee: Miles Saul > Fix For: 2.3.0 > > Original Estimate: 336h > Remaining Estimate: 336h > > A new I/O source for reading (and eventually writing) VCF files [1] for > Python. The design doc is available at > https://docs.google.com/document/d/1jsdxOPALYYlhnww2NLURS8NKXaFyRSJrcGbEDpY9Lkw/edit > [1] http://samtools.github.io/hts-specs/VCFv4.3.pdf -- This message was sent by Atlassian JIRA (v6.4.14#64029)
[jira] [Created] (BEAM-2774) Add I/O source for VCF files (python)
Asha Rostamianfar created BEAM-2774: --- Summary: Add I/O source for VCF files (python) Key: BEAM-2774 URL: https://issues.apache.org/jira/browse/BEAM-2774 Project: Beam Issue Type: New Feature Components: sdk-py Reporter: Asha Rostamianfar Assignee: Ahmet Altay A new I/O source for reading (and eventually writing) VCF files [1] for Python. The design doc is available at https://docs.google.com/document/d/1jsdxOPALYYlhnww2NLURS8NKXaFyRSJrcGbEDpY9Lkw/edit [1] http://samtools.github.io/hts-specs/VCFv4.3.pdf -- This message was sent by Atlassian JIRA (v6.4.14#64029)
