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    <p>Ok, here's my stab at the problem. </p> <p>Here's a sketch of the nodes and edges tables:</p> <pre><code>[nodes] node : varchar(xx) [edges] outputNode : varchar(xx) inputNode : varchar(xx) </code></pre> <p>Assuming your db has support for CTEs, then a query structured like this will bring together the relationships and concatenate results:</p> <pre><code>/* pair output nodes with a topic, assigned sequentially */ WITH OutputTopics(node, topicNumber) AS ( SELECT outputNode, ROW_NUMBER() (ORDER BY outputNode) AS topicNumber FROM (SELECT DISTINCT outputNode FROM edges) AS outputNodes ), /* pair input nodes to the topic of associated output nodes */ InputTopicNumbers(inputNode, topicNumber) AS ( SELECT edges.inputNode, ot.topicNumber FROM edges INNER JOIN OutputTopics AS ot ON ot.node=edges.outputNode ), /* Recursive CTE to concat all topics together */ InputTopics(inputNode, topics, topicNumber) AS ( /* The seed for the recursion - all input nodes */ SELECT inputNode, CAST ('' AS nvarchar(max)), 0 /* max topic handled for node */ FROM InputTopicNumbers GROUP BY inputNode UNION ALL /* Add topics that are greater than those processed */ /* recursively concat topic numbers in ascending order */ SELECT i.inputNode, CONCAT(c.topics, ' --input-topic=T',i.topicNumber), i.topicNumber FROM InputTopics AS c INNER JOIN InputTopicNumbers i ON i.inputNode=c.inputNode WHERE i.topicNumber &gt; c.topicNumber ), /* Bring it all together - append each node with '.exe', list the output topic, if present Use the recursive CTE to concat all inputTopics */ NodeCommands(node, exe, input, output) AS ( SELECT nodes.node, CONCAT(nodes.node,'.exe'), CONCAT(' --output_topic=T',ot.topicNumber), /* NULL if no output node */ it.topics FROM nodes LEFT OUTER JOIN OutputTopics AS ot ON ot.node=nodes.node LEFT OUTER JOIN InputTopics AS it ON it.inputNode=nodes.node ) /* finally our top-level query concatenates the parts to arrive at a single command line */ SELECT CONCAT( exe, ISNULL(input, ''), ISNULL(output, '')) FROM NodeCommands ORDER BY node </code></pre> <p>I'm doing this off the bat, so surely a few syntax errors in there. I hope the comments explain the intent.</p>
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    1. POHow to perform undirected graph processing from SQL data
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    1. COThanks a lot mdma! I'm a novice in SQL, but some Googling showed that MySQL, which is what we're using, doesn't support CTE (http://stackoverflow.com/questions/1382573/how-do-you-use-the-with-clause-in-mysql). Is this technique easy to replace with other approaches supported by MySQL you think? BTW, we're controlling MySQL using Hibernate.
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    2. COPitty you didn't mention these details at the start. You could probably rewrite most of this without CTE, although I'm not sure how you'd do the recursive concatenation. If you're using hibernate, a better appraoch is to read the nodes/edges in hibernate and code some java logic to produce the command lines.
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