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<div style="direction: ltr;">Hi Peter</div>
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<div style="direction: ltr;">Yes, where possible I’m using BioSQL—especially BioSeqDatabase—which has been perfectly fine for all my scripts (so far just data ingestion and output) but am having a particularly difficult time with data replacement.
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<div style="direction: ltr;">The goal is to be able to extract some records, modify them, and push them back in under the same name with an updated version number and bioentry_id, such that whenever those records are next extracted it is the latest version
that is pulled by default. </div>
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<div style="direction: ltr;">I am very new to all of this (just about to start my masters) so this is no doubt just a shortcoming in my understanding, but it feels like I must be missing something very simple, as this is surely something that most users would
need!</div>
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<div style="direction: ltr;">Can you think of anything that could help?</div>
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<div style="direction: ltr;">Very much appreciated </div>
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<div style="direction: ltr;">Luke </div>
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<div id="divRplyFwdMsg" dir="dir="ltr""><font face="Calibri, sans-serif" style="font-size:11pt"><b>From:</b> Peter Cock <p.j.a.cock@googlemail.com><br>
<b>Sent:</b> Monday, August 3, 2020 9:39 am<br>
<b>To:</b> Luke Swaby<br>
<b>Cc:</b> biosql-l@mailman.open-bio.org<br>
<b>Subject:</b> Re: [BioSQL-l] Versioning in BioSQL Database
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<div dir="ltr">Hello Luke,
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<div>It has been some time since I looked at the tables in BioSQL, but just to be clear - you are not using the Biopthon BioSQL wrapper, are you?</div>
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<div><a href="https://github.com/biopython/biopython/tree/master/BioSQL/">https://github.com/biopython/biopython/tree/master/BioSQL/</a><br>
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<div>Peter</div>
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<div dir="ltr" class="gmail_attr">On Mon, Aug 3, 2020 at 2:36 AM Luke Swaby <<a href="mailto:lukeswabypetts@gmail.com">lukeswabypetts@gmail.com</a>> wrote:<br>
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<div dir="ltr"><span style="color:rgb(0,0,0); font-family:Helvetica; font-size:12px">Hello</span><br style="color:rgb(0,0,0); font-family:Helvetica; font-size:12px">
<br style="color:rgb(0,0,0); font-family:Helvetica; font-size:12px">
<span style="color:rgb(0,0,0); font-family:Helvetica; font-size:12px">I’m currently writing a load of Python scripts to interact with a slightly modified version of your BioSQL database (pretty much identical, with an additional table for metadata), and am
having a lot of trouble working out how to implement record versioning in it.</span><br style="color:rgb(0,0,0); font-family:Helvetica; font-size:12px">
<br style="color:rgb(0,0,0); font-family:Helvetica; font-size:12px">
<span style="color:rgb(0,0,0); font-family:Helvetica; font-size:12px">Comments in the schema—and the version field in the bioentry table—suggest a particular method of doing this was in mind when the schema was written, but I can’t find any documentation on
how this is to be done.<span> </span></span><br style="color:rgb(0,0,0); font-family:Helvetica; font-size:12px">
<br style="color:rgb(0,0,0); font-family:Helvetica; font-size:12px">
<span style="color:rgb(0,0,0); font-family:Helvetica; font-size:12px">In sum, I need it to be able to hold multiple versions of the same record in the same table, and a means of accessing (ideally by default) only the latest version of each record when it is
requested. It would ideally also automatically add a new version of a record whenever any change is made to it, either internally by direct MySQL queries or externally by ingestion of newly modified .gb/.csv files. I’ve thought of numerous ways of doing this,
including creating a new table which points to the unique bioentry_id/metadata_id of the latest version of each record, but am very stuck on how to do this.</span><br style="color:rgb(0,0,0); font-family:Helvetica; font-size:12px">
<br style="color:rgb(0,0,0); font-family:Helvetica; font-size:12px">
<span style="color:rgb(0,0,0); font-family:Helvetica; font-size:12px">Do you have any suggestions? I’m sure there is a relatively basic answer that I am totally missing, but I’m pressed for time now and am finding nothing anywhere!</span><br style="color:rgb(0,0,0); font-family:Helvetica; font-size:12px">
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<span style="color:rgb(0,0,0); font-family:Helvetica; font-size:12px">Very much appreciated if so</span><br style="color:rgb(0,0,0); font-family:Helvetica; font-size:12px">
<br style="color:rgb(0,0,0); font-family:Helvetica; font-size:12px">
<span style="color:rgb(0,0,0); font-family:Helvetica; font-size:12px">Luke</span><br>
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