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Tethys fixes Pre rel V2.02.15b
Fix some issues in Tethys 3.2 which was putting a \n at the beginning of some reurned field names, particularly document names, which was messing up document matching in PAMGuard.
This commit is contained in:
Douglas Gillespie
parent
b1e34b6dd9
commit
a213762e4e
171
README.html
171
README.html
@ -438,23 +438,34 @@ name="_2.02.15_December_2014"></a><a name="_Version_2.02.16_February"></a>Versio
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<h2>New Features</h2>
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<p class=MsoNormal>Updates to Tethys to make export of data (Calibrations,
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Deployments, Detections, and Localisations) available as ‘offline tasks’. This
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is not useful when running Tethys on a single dataset, since all tasks can be
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easily performed using ‘Export’ buttons on the main Tethys interface. However,
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this change means that these export tasks become available to the batch
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processor (Version ?? or above) which can be used to export data from multiple
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similar datasets without having to personally go into each one individually. See
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Tethys online help pages and help pages for the Batch processor for details.</p>
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<p class=MsoNormal><b>Updates to Tethys</b></p>
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<p class=MsoNormal>Similar addition of offline click event data integrity
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checking, so that this can be run prior to exporting data to Tethys. </p>
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<p class=MsoNormal>Updates to compatibility with Tethys Server 3.2 and Nilus
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3.2. No longer compatible with 3.1, the pre-release version. </p>
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<p class=MsoNormal>Made export of data (Calibrations, Deployments, Detections,
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and Localisations) available as ‘offline tasks’. This is not useful when
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running Tethys on a single dataset, since all tasks can be easily performed
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using ‘Export’ buttons on the main Tethys interface. However, this change means
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that these export tasks become available to the batch processor (Version 2.0 or
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above) which can be used to export data from multiple similar datasets without
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having to personally go into each one individually. See Tethys online help
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pages and help pages for the Batch processor for details.</p>
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<p class=MsoNormal><b>Other</b></p>
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<p class=MsoNormal>Made click detector offline click event data integrity
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checking available as offline task, so that this can be run prior to exporting
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data to Tethys. </p>
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<p class=MsoNormal>Multiple management changes to support batch processing of
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offline tasks. Compatible with batch processor 2.0. </p>
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<h2>Bug Fixes</h2>
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<p class=MsoNormal>Issue 190. Array Files exported from array manager were not
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automatically getting the correct file end, making the exported files impossible
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to use. This is fixed and files will get the correct .paf end.</p>
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automatically getting the correct file end, making the exported files
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impossible to use. This is fixed and files will get the correct .paf end.</p>
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<p class=MsoNormal>Issue 167. File counter not resetting when restarting
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PAMGuard if it was paused during processing of folders of offline files. This
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@ -469,6 +480,9 @@ time, meaning you got an invalid file path. This has been fixed. </p>
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channel list from acquisition module and automatically removes channels that
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were selected in the FFT module, but are not available from the acquisition. </p>
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<p class=MsoNormal>Dealt with issue in Tethys module looking up IT IS species
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codes where the progress dialog would not close. </p>
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<p class=MsoNormal>Project Information abstract field was not saving /
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reloading correctly in the configuration file. Fixed.</p>
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@ -575,9 +589,9 @@ Visualiser, Audacity etc.)</p>
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<h2>Tethys Database</h2>
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<p class=MsoNormal>Many users will be aware that we're integrating an interface
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to the <a href="https://tethys.sdsu.edu/">Tethys Database</a> into PAMGuard. Some
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basic features are available for testing. If interested, please contact the
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PAMGuard support team. </p>
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to the <a href="https://tethys.sdsu.edu/">Tethys Database</a> into PAMGuard.
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Some basic features are available for testing. If interested, please contact
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the PAMGuard support team. </p>
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<h2>Bug Fixes</h2>
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@ -871,8 +885,8 @@ audio files. </span></p>
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binary files even if DWV file doesn‚'t exist (which is correct behavior in
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quiet conditions when no clicks were detected). </span></p>
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<p class=MsoNormal><span lang=EN-US>Spectrogram. Changes to stop occasional crashing
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when restarting processing of wav files. </span></p>
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<p class=MsoNormal><span lang=EN-US>Spectrogram. Changes to stop occasional
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crashing when restarting processing of wav files. </span></p>
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<p class=MsoNormal><span lang=EN-US>Sizing of dialogs on ultra high definition
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monitors so that data fields are sized correctly. </span></p>
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@ -1128,11 +1142,11 @@ understand the notes listed for <a href="#_Latest_Beta_Version_2.00.10">Beta
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Version 2.00.10</a> before proceeding with installation and use of this
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version.</b></p>
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<p class=MsoNormal>This version of PAMGuard has been bundled with Java 13 (release
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13.0.1). PSFX files generated in previous beta releases (2.xx.xx) should be
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compatible with this version, and vice-versa. PSF files generated in core
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releases (1.15.xx) can be loaded in this version, but will be converted to PSFX
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files when PAMGuard exits.</p>
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<p class=MsoNormal>This version of PAMGuard has been bundled with Java 13
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(release 13.0.1). PSFX files generated in previous beta releases (2.xx.xx)
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should be compatible with this version, and vice-versa. PSF files generated in
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core releases (1.15.xx) can be loaded in this version, but will be converted to
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PSFX files when PAMGuard exits.</p>
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<p class=MsoNormal><b><span lang=EN-US>Bug Fixes</span></b></p>
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@ -1235,11 +1249,11 @@ understand the notes listed for <a href="#_Latest_Beta_Version_2.00.10">Beta
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Version 2.00.10</a> before proceeding with installation and use of this
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version.</b></p>
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<p class=MsoNormal>This version of PAMGuard has been bundled with Java 13 (release
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13.0.1). PSFX files generated in previous beta releases (2.xx.xx) should be
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compatible with this version, and vice-versa. PSF files generated in core
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releases (1.15.xx) can be loaded in this version, but will be converted to PSFX
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files when PAMGuard exits.</p>
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<p class=MsoNormal>This version of PAMGuard has been bundled with Java 13
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(release 13.0.1). PSFX files generated in previous beta releases (2.xx.xx)
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should be compatible with this version, and vice-versa. PSF files generated in
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core releases (1.15.xx) can be loaded in this version, but will be converted to
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PSFX files when PAMGuard exits.</p>
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<p class=MsoNormal><b><span lang=EN-US>Bug Fixes</span></b></p>
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@ -1408,9 +1422,9 @@ correctly on each call rather then recycling old data. Makes the output more
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spectrally flat. </p>
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<p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>14. </span><span
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lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'> </span>
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Changes to FX Display to make it more intuitive - menu options, button
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placement, etc.</p>
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lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'> </span><span
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lang=EN-US> </span>Changes to FX Display to make it more intuitive - menu
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options, button placement, etc.</p>
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<!-- ************************************************************************************************************************** --><!-- ************************************************************************************************************************** -->
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@ -1507,8 +1521,9 @@ lang=EN-US> </span>Bug 448. Detection Group Localiser data units not being
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loaded in Viewer mode.</p>
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<p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>17. </span><span
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lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'> </span>
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Bug 449. Rocca Encounter Stats output file calculating incorrect values.</p>
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lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'> </span><span
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lang=EN-US> </span>Bug 449. Rocca Encounter Stats output file calculating
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incorrect values.</p>
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<p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>18. </span><span
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lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'> </span><span
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@ -1611,8 +1626,8 @@ lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'> &nb
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Bug 428. Decimator crashing in viewer mode</p>
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<p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>3. </span><span
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lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'> </span>
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Bug 429. Click Bearings at 180 degrees</p>
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lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'> </span><span
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lang=EN-US> </span>Bug 429. Click Bearings at 180 degrees</p>
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<p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>4. </span><span
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lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'> </span><span
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@ -1902,9 +1917,9 @@ lang=EN-US> </span>Added decimal degrees option to latitude/longitude dialog.</p
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<p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>2. </span><span
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lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'> </span><span
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lang=EN-US> </span>Added option in the Click Delay parameters to restrict the
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number of initial samples used in the calculation. This can be useful for
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cleaning up delays in the presence of echoes and small time delays.</p>
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lang=EN-US> </span>Added option in the Click Delay parameters to restrict the number
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of initial samples used in the calculation. This can be useful for cleaning up
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delays in the presence of echoes and small time delays.</p>
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<p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>3. </span><span
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lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'> </span>
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@ -2017,10 +2032,10 @@ lang=EN-US> </span>Added ability to read differential GPS data.</p>
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<p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>5. </span><span
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lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'> </span><span
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lang=EN-US> </span>Added check for duplicate settings in the psf file when
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exiting PAMGuard. If duplicate settings are found, user is given the option to
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leave them in the psf or get rid of them. Duplicate settings are ignored by
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PAMGuard, but can cause the psf file to grow large over time.</p>
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lang=EN-US> </span>Added check for duplicate settings in the psf file when exiting
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PAMGuard. If duplicate settings are found, user is given the option to leave
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them in the psf or get rid of them. Duplicate settings are ignored by PAMGuard,
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but can cause the psf file to grow large over time.</p>
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<p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>6. </span><span
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lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'> </span>
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@ -2434,8 +2449,8 @@ to colour them by the colour assigned to the group. </span></p>
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<h3><span lang=EN-US>Using Old PAMGuard Configurations</span></h3>
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<p class=MsoNormal><span lang=EN-US>Old PAMGuard configurations will work with
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the new version. However please note the following:</span></p>
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<p class=MsoNormal><span lang=EN-US>Old PAMGuard configurations will work with the
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new version. However please note the following:</span></p>
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<p class=MsoListParagraph style='margin-left:54.0pt;text-indent:-36.0pt'><span
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lang=EN-US>1.</span><span lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>
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@ -2600,8 +2615,8 @@ dependencies)</span></p>
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<p class=MsoNormal><b><span lang=EN-US>Other Changes</span></b></p>
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<p class=MsoNormal><span lang=EN-US>The installer has been updated to handle
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both 64 bit and 32 bit installations. PAMGuard psf files are now registered in
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the Windows Registry, so double-clicking on a psf file should run PAMGuard in
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both 64 bit and 32 bit installations. PAMGuard psf files are now registered in the
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Windows Registry, so double-clicking on a psf file should run PAMGuard in
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normal mode (as opposed to Viewer or Mixed modes). Note that the Windows
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Registry can only hold a single executable reference for psf files; therefore,
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for users with multiple installations of PAMGuard, double-clicking on a psf
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@ -2886,10 +2901,10 @@ GUI instead. This has been Fixed.</p>
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<p class=MsoListParagraph style='margin-left:38.25pt;text-indent:-20.25pt'>8.<span
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style='font-size:7.0pt;font-family:"Times New Roman",serif'>
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</span>Bug 280. Recorder control option to automatically restart recording were
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causing confusion. It was working in that the recorder would return to its previous
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state, but it was sometimes difficult for users to set it so that recording
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would always start as soon as PAMGuard started. More sensible and easy to
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understand options have been developed in a new options dialog.</p>
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causing confusion. It was working in that the recorder would return to its
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previous state, but it was sometimes difficult for users to set it so that
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recording would always start as soon as PAMGuard started. More sensible and
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easy to understand options have been developed in a new options dialog.</p>
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<p class=MsoListParagraph style='margin-left:38.25pt;text-indent:-20.25pt'>9.<span
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style='font-size:7.0pt;font-family:"Times New Roman",serif'>
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@ -3060,9 +3075,9 @@ the PAMGuard help file for further details. </p>
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lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>
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</span><span lang=EN-US>Feature Request 45.</span><span lang=EN-US
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style='font-size:7.0pt;font-family:"Times New Roman",serif'> </span><span
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lang=EN-US>Module settings import. Functions have been provided which enable users
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to import the settings for individual modules into new configurations. See the
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help file for details.</span></p>
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lang=EN-US>Module settings import. Functions have been provided which enable
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users to import the settings for individual modules into new configurations.
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See the help file for details.</span></p>
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<p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>2.</span><span
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lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>
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@ -3679,9 +3694,9 @@ databases.</p>
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<p class=MsoNormal style='margin-left:36.0pt'>National Instruments cards: Added
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code in support of the new x-series devices. </p>
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<p class=MsoNormal style='margin-left:36.0pt'>ASIO sound cards: Added support
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for a new open source ASIO driver system (jasiohost). The old system has been
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left in place for now while we assess users response to the newer system. </p>
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<p class=MsoNormal style='margin-left:36.0pt'>ASIO sound cards: Added support for
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a new open source ASIO driver system (jasiohost). The old system has been left
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in place for now while we assess users response to the newer system. </p>
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<p class=MsoNormal style='margin-left:36.0pt'><i>AIS</i></p>
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@ -3756,9 +3771,9 @@ have implemented database storage for output of these modules. </p>
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<p class=MsoListParagraph style='text-indent:-18.0pt'><span style='font-family:
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Symbol'>'</span><span style='font-size:7.0pt;font-family:"Times New Roman",serif'>
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</span>Radar Display: A bug which stopped the radar display from correctly
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displaying bearings to whistles from arrays containing more than two hydrophone
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elements has been fixed. </p>
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</span>Radar Display: A bug which stopped the radar display from correctly displaying
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bearings to whistles from arrays containing more than two hydrophone elements
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has been fixed. </p>
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<p class=MsoListParagraph style='text-indent:-18.0pt'><span style='font-family:
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Symbol'>'</span><span style='font-size:7.0pt;font-family:"Times New Roman",serif'>
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@ -4101,9 +4116,9 @@ example channel 0 and 1 on two different devices, so to uniquely identify
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channels in the rest of PAMGuard, the only rational thing to do was to re-label
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those channels 0,1,2,3. </p>
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<p class=MsoNormal>There have been other annoyances with the ASIO channel numbering
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scheme. For instance, if you had a configuration which worked in real time
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using channels 7 and 8 of a sound card, you could not use that same
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<p class=MsoNormal>There have been other annoyances with the ASIO channel
|
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numbering scheme. For instance, if you had a configuration which worked in real
|
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time using channels 7 and 8 of a sound card, you could not use that same
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configuration to analyse wav files, which would always read their data as
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channels 0 and 1. Similarly if you switched sound cards, you may have to
|
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reconfigure every detector and several of the displays to handle the changes in
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@ -4468,11 +4483,11 @@ now been fixed. </p>
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<p class=MsoNormal><b>Bug Fixes</b></p>
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<p class=MsoNormal>Decimator was calculating incorrect filter coefficients
|
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(coefficients were based on the output sample rate, not the input sample rate,
|
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so it's likely that actual filtering of data was minimal). This is now
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rectified. Ishmael matched filter. Would crash if template file not correctly
|
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loaded. Now issues a warning message to the terminal and does not crash. </p>
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<p class=MsoNormal>Decimator was calculating incorrect filter coefficients (coefficients
|
||||
were based on the output sample rate, not the input sample rate, so it's likely
|
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that actual filtering of data was minimal). This is now rectified. Ishmael
|
||||
matched filter. Would crash if template file not correctly loaded. Now issues a
|
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warning message to the terminal and does not crash. </p>
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<p class=MsoNormal>Spelling correction on user input form (Sumbit - Submit)</p>
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@ -4601,11 +4616,11 @@ Utilities. This will not affect how existing settings files are loaded. </p>
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|
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<p class=MsoNormal><b>Multi-screen environments.</b></p>
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|
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<p class=MsoNormal>In previous versions, if PAMGuard was configured in a multiscreen
|
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environment and is then run on a single screen, it was possible that the
|
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display would not appear. PAMGuard now checks screen dimensions at start up and
|
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ensures that the main display is visible. Consequently, program start-up takes
|
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slightly longer than previously. </p>
|
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<p class=MsoNormal>In previous versions, if PAMGuard was configured in a
|
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multiscreen environment and is then run on a single screen, it was possible
|
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that the display would not appear. PAMGuard now checks screen dimensions at
|
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start up and ensures that the main display is visible. Consequently, program
|
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start-up takes slightly longer than previously. </p>
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<p class=MsoNormal><b>Outstanding bugs</b></p>
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@ -4698,9 +4713,9 @@ a serial port </p>
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||||
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||||
<p class=MsoNormal>New Likelihood detector. </p>
|
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|
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<p class=MsoNormal>The likelihood detector module is an implementation of a
|
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likelihood ratio test with flexible algorithms and configuration to estimate
|
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likelihood. It is </p>
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<p class=MsoNormal>The likelihood detector module is an implementation of a likelihood
|
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ratio test with flexible algorithms and configuration to estimate likelihood.
|
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It is </p>
|
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|
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<p class=MsoNormal>suitable for detecting both short duration Odontocete clicks
|
||||
(Sperm, Beaked, etc.) as well as moderate duration Mysticete calls (Humpback,
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@ -4825,8 +4840,8 @@ drawn in red on the marked panel and in green on other panels. </p>
|
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|
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<p class=MsoListParagraph style='text-indent:-18.0pt'><span style='font-family:
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Symbol'>'</span><span style='font-size:7.0pt;font-family:"Times New Roman",serif'>
|
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</span>Spectrogram. Frequency information displayed in a 'hover' box when the mouse
|
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is moved over the display. Choice of colour maps for display. </p>
|
||||
</span>Spectrogram. Frequency information displayed in a 'hover' box when the
|
||||
mouse is moved over the display. Choice of colour maps for display. </p>
|
||||
|
||||
<p class=MsoListParagraph style='text-indent:-18.0pt'><span style='font-family:
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Symbol'>'</span><span style='font-size:7.0pt;font-family:"Times New Roman",serif'>
|
||||
@ -5026,8 +5041,8 @@ Symbol'>'</span><span style='font-size:7.0pt;font-family:"Times New Roman",serif
|
||||
<p class=MsoNormal> </p>
|
||||
|
||||
<p class=MsoNormal><a name="_Toc312065304"></a><a name="_Toc312063949"></a><span
|
||||
class=Heading2Char><span style='font-size:13.0pt'>1.0Beta 22 Jan 2008 -
|
||||
PAMGuard starts two releases, core and beta release</span></span>, </p>
|
||||
class=Heading2Char><span style='font-size:13.0pt'>1.0Beta 22 Jan 2008 - PAMGuard
|
||||
starts two releases, core and beta release</span></span>, </p>
|
||||
|
||||
<p class=MsoNormal>this is the beta release</p>
|
||||
|
||||
|
||||
9420
README.html.mht
9420
README.html.mht
File diff suppressed because it is too large
Load Diff
@ -1034,7 +1034,8 @@ public class PamUtils {
|
||||
}
|
||||
|
||||
/**
|
||||
* Trim a string, checking it's not null first.
|
||||
* Trim a string of leading and trailing blanks AND carriage returns, checking it's not null first.
|
||||
* But leave any other carriage returns within the string itself in place.
|
||||
* @param string
|
||||
* @return
|
||||
*/
|
||||
@ -1042,7 +1043,37 @@ public class PamUtils {
|
||||
if (string == null) {
|
||||
return null;
|
||||
}
|
||||
return string.trim();
|
||||
int startSkip = 0;
|
||||
int endSkip = 0;
|
||||
for (int i = 0; i < string.length(); i++) {
|
||||
char ch = string.charAt(i);
|
||||
if (ch == '\n' || ch == ' ') {
|
||||
startSkip ++;
|
||||
}
|
||||
else {
|
||||
break;
|
||||
}
|
||||
}
|
||||
/* need to do the start and end separately in case the
|
||||
* entire string is spaces which would lead to an overlap
|
||||
* of the starts and ends.
|
||||
*/
|
||||
if (startSkip > 0) {
|
||||
string = string.substring(startSkip);
|
||||
}
|
||||
for (int i = string.length()-1; i >= 0; i--) {
|
||||
char ch = string.charAt(i);
|
||||
if (ch == '\n' || ch == ' ') {
|
||||
endSkip ++;
|
||||
}
|
||||
else {
|
||||
break;
|
||||
}
|
||||
}
|
||||
if (endSkip > 0) {
|
||||
string = string.substring(0, string.length()-endSkip);
|
||||
}
|
||||
return string;
|
||||
}
|
||||
|
||||
|
||||
|
||||
@ -1,5 +1,7 @@
|
||||
package tethys;
|
||||
|
||||
import PamUtils.PamUtils;
|
||||
|
||||
/**
|
||||
* Basic information about a document that can be used to
|
||||
* make document lists.
|
||||
@ -19,8 +21,8 @@ public class DocumentInfo implements Comparable<DocumentInfo> {
|
||||
*/
|
||||
public DocumentInfo(Collection collection, String documentName, String documentId) {
|
||||
this.collection = collection;
|
||||
this.documentName = documentName;
|
||||
this.documentId = documentId;
|
||||
this.documentName = PamUtils.trimString(documentName);
|
||||
this.documentId = PamUtils.trimString(documentId);
|
||||
}
|
||||
@Override
|
||||
public int compareTo(DocumentInfo o) {
|
||||
|
||||
@ -111,7 +111,7 @@ public class CalibrationsTable extends TethysGUIPanel {
|
||||
JPopupMenu popMenu = new JPopupMenu();
|
||||
JMenuItem menuItem;
|
||||
if (n == 1) {
|
||||
menuItem = new JMenuItem("Show document " + doc.getDocumentName());
|
||||
menuItem = new JMenuItem("Display document " + doc.getDocumentName());
|
||||
menuItem.addActionListener(new ActionListener() {
|
||||
@Override
|
||||
public void actionPerformed(ActionEvent e) {
|
||||
|
||||
@ -660,7 +660,10 @@ Returns something like this:
|
||||
}
|
||||
catch (NumberFormatException ne) {
|
||||
}
|
||||
String vS = vData.substring(sp1+1);
|
||||
String vS = null;
|
||||
if (sp1+1<vData.length()) {
|
||||
vData.substring(sp1+1);
|
||||
}
|
||||
|
||||
return new ServerVersion(vn, vS);
|
||||
}
|
||||
|
||||
@ -11,6 +11,7 @@ import javax.xml.parsers.DocumentBuilder;
|
||||
import javax.xml.parsers.DocumentBuilderFactory;
|
||||
import javax.xml.parsers.ParserConfigurationException;
|
||||
|
||||
import org.w3c.dom.Attr;
|
||||
import org.w3c.dom.Document;
|
||||
import org.w3c.dom.Element;
|
||||
import org.w3c.dom.Node;
|
||||
@ -19,6 +20,7 @@ import org.xml.sax.InputSource;
|
||||
import org.xml.sax.SAXException;
|
||||
|
||||
import PamController.settings.output.xml.PamguardXMLWriter;
|
||||
import PamUtils.PamUtils;
|
||||
import PamguardMVC.PamDataBlock;
|
||||
import dbxml.JerseyClient;
|
||||
import dbxml.Queries;
|
||||
@ -147,6 +149,7 @@ public class DBXMLQueries {
|
||||
|
||||
}
|
||||
catch (Exception e) {
|
||||
System.out.println(e.getMessage());
|
||||
throw new TethysQueryException("Error running JSON query", jsonQueryString);
|
||||
|
||||
}
|
||||
@ -180,6 +183,7 @@ public class DBXMLQueries {
|
||||
* @return list of all documents in a collection, or null if no collection.
|
||||
*/
|
||||
public ArrayList<DocumentInfo> getCollectionDocumentList(Collection collection) {
|
||||
|
||||
if (collection == null) {
|
||||
return null;
|
||||
}
|
||||
@ -229,27 +233,83 @@ public class DBXMLQueries {
|
||||
int n = returns.getLength();
|
||||
String toStrip = "dbxml:///"+collection.collectionName()+"/";
|
||||
for (int i = 0; i < n; i++) {
|
||||
// if (i == 24) {
|
||||
// int b = 4-6;
|
||||
// }
|
||||
Node aNode = returns.item(i);
|
||||
String nameStr = null;
|
||||
String id = null;
|
||||
NodeList kids = aNode.getChildNodes();
|
||||
for (int k = 0; k < kids.getLength(); k++) {
|
||||
int nKids = kids.getLength();
|
||||
// System.out.printf("Node %d is type %d\n", i, aNode.getNodeType());
|
||||
// String nodeName = aNode.getNodeName();
|
||||
// nameStr = aNode.getTextContent();
|
||||
// nameStr = nameStr.replaceFirst(toStrip, "");
|
||||
// if (nameStr.length() > 60 && collection == Collection.Calibrations) {
|
||||
// System.out.println("Long name: " + nameStr);
|
||||
// }
|
||||
// id = aNode.get
|
||||
if (aNode instanceof Element) {
|
||||
Element el = (Element) aNode;
|
||||
// nameStr = el.getLocalName();
|
||||
// nameStr = el.getNodeName(); // gets doc
|
||||
// nameStr = el.getNodeValue(); // gets null
|
||||
// nameStr = el.getTagName(); // gets doc
|
||||
// nameStr = el.getTextContent(); // gets concatenation of everything
|
||||
// nameStr = el.get
|
||||
NodeList ids = el.getElementsByTagName("Id");
|
||||
if (ids.getLength() > 0) {
|
||||
Node idEl = ids.item(0);
|
||||
id = idEl.getTextContent();
|
||||
}
|
||||
|
||||
}
|
||||
/**
|
||||
* For some reason, this is now getting four kid nodes when
|
||||
* really there should only be two and as a result it's getting
|
||||
* the #text one twice, the second of which was empty, so
|
||||
* was overwriting the correct data
|
||||
*/
|
||||
for (int k = 0; k < nKids; k++) {
|
||||
Node kidNode = kids.item(k);
|
||||
// kidNode.get
|
||||
String name = kidNode.getNodeName();
|
||||
String cont = kidNode.getTextContent();
|
||||
cont = PamUtils.trimString(cont);
|
||||
if (cont == null || cont.length() == 0) {
|
||||
continue;
|
||||
}
|
||||
switch(name) {
|
||||
case "#text":
|
||||
nameStr = cont;
|
||||
nameStr = nameStr.replaceFirst(toStrip, "");
|
||||
if (nameStr == null) {
|
||||
nameStr = cont;
|
||||
}
|
||||
break;
|
||||
case "Id":
|
||||
id = kidNode.getTextContent();
|
||||
if (id == null) {
|
||||
id = cont;
|
||||
}
|
||||
break;
|
||||
default:
|
||||
System.out.printf("Uknonwn node in Collection list %s item %d, Node %d name %s content %s\n",
|
||||
collection, i, k, name, cont);
|
||||
}
|
||||
}
|
||||
nameStr = nameStr.replaceFirst(toStrip, "");
|
||||
id = PamUtils.trimString(id);
|
||||
/**
|
||||
* Put in a bit fat bodge to see if the xml has concattenated
|
||||
* the name and id values into a stupid long name ...
|
||||
*
|
||||
*/
|
||||
nameStr = PamUtils.trimString(nameStr);
|
||||
id = PamUtils.trimString(id);
|
||||
if (nameStr.endsWith(id)) {
|
||||
if (nameStr.length() - id.length() > id.length()-5) {
|
||||
// seems to genuinely be that problem of concatenations
|
||||
nameStr = nameStr.substring(0, nameStr.length()-id.length());
|
||||
}
|
||||
}
|
||||
// if (i > 428) {
|
||||
// System.out.println("MARU cal doc");
|
||||
// }
|
||||
@ -1077,6 +1137,13 @@ public class DBXMLQueries {
|
||||
|
||||
public Document convertStringToXMLDocument(String xmlString) {
|
||||
//Parser that produces DOM object trees from XML content
|
||||
if (xmlString == null) {
|
||||
return null;
|
||||
}
|
||||
xmlString = xmlString.trim();
|
||||
if (xmlString.length() == 0) {
|
||||
return null;
|
||||
}
|
||||
DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
|
||||
|
||||
//API to obtain DOM Document instance
|
||||
@ -1093,6 +1160,7 @@ public class DBXMLQueries {
|
||||
}
|
||||
return null;
|
||||
}
|
||||
|
||||
|
||||
/**
|
||||
* Get the basic information about a Detections document. This is basically everything apart from
|
||||
@ -1103,6 +1171,12 @@ public class DBXMLQueries {
|
||||
public Detections getDetectionsDocInfo(String detectionsDocName) {
|
||||
// String oldqueryBase = "{\"species\":{\"query\":{\"op\":\"lib:abbrev2tsn\",\"optype\":\"function\",\"operands\":[\"%s\",\"SIO.SWAL.v1\"]},\"return\":{\"op\":\"lib:tsn2abbrev\",\"optype\":\"function\",\"operands\":[\"%s\",\"SIO.SWAL.v1\"]}},\"return\":[\"Detections/Id\",\"Detections/Description\",\"Detections/DataSource\",\"Detections/Algorithm\"],\"select\":[{\"op\":\"=\",\"operands\":[\"Detections/Id\",\"DetectionsDocName\"],\"optype\":\"binary\"}],\"enclose\":1}";
|
||||
// updated May 23
|
||||
// seems like this docName now may have a \n at the start, so it needs correclty trimming:
|
||||
// detectionsDocName = detectionsDocName.replace((char) 10, ' ');
|
||||
// detectionsDocName = detectionsDocName.trim();
|
||||
detectionsDocName = PamUtils.trimString(detectionsDocName);
|
||||
|
||||
|
||||
String queryBase = "{\"species\":{\"query\":{\"op\":\"lib:completename2tsn\",\"optype\":\"function\",\"operands\":[\"%s\"]},\"return\":{\"op\":\"lib:tsn2completename\",\"optype\":\"function\",\"operands\":[\"%s\"]}},\"return\":[\"Detections/Id\",\"Detections/Description\",\"Detections/DataSource\",\"Detections/Algorithm\",\"Detections/QualityAssurance\",\"Detections/UserId\",\"Detections/MetadataInfo\",\"Detections/Effort\"],\"select\":[{\"op\":\"=\",\"operands\":[\"Detections/Id\",\"DetectionsDocName\"],\"optype\":\"binary\"}],\"enclose\":1}";
|
||||
String query = queryBase.replace("DetectionsDocName", detectionsDocName);
|
||||
DBQueryResult queryResult;
|
||||
|
||||
@ -33,7 +33,12 @@ public class ServerVersion {
|
||||
@Override
|
||||
public String toString() {
|
||||
Float f = versionNo;
|
||||
return String.format("%s %s", f.toString(), versionName);
|
||||
if (versionName == null) { // not always set, so don't want to write it.
|
||||
return f.toString();
|
||||
}
|
||||
else {
|
||||
return String.format("%s %s", f.toString(), versionName);
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
|
||||
Loading…
Reference in New Issue
Block a user