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add a select_for_update lock #76

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Dec 3, 2021
Merged

add a select_for_update lock #76

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f18e781
add a select_for_update lock
benjiec Dec 3, 2021
78bc5a8
fix typo
benjiec Dec 3, 2021
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14 changes: 14 additions & 0 deletions src/edge/models/fragment.py
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Original file line number Diff line number Diff line change
Expand Up @@ -91,8 +91,22 @@ def sorter_f(e):

return out_edges[0].to_chunk

def lock(self):
"""
Do a select for update, which, when executed inside a transaction, places
a lock on the fragment.
"""

fragments = Fragment.objects.select_for_update().filter(pk=self.id)
# Lock only happens when queryset is evaluated, therefore need to do at least fragments[0]
fragment = fragments[0]
print(f"Lock fragment {fragment.id}")
return fragment

@transaction.atomic()
def index_fragment_chunk_locations(self):
self.lock()

# remove old index
self.fragment_chunk_location_set.all().delete()

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7 changes: 6 additions & 1 deletion src/edge/recombine.py
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Expand Up @@ -510,8 +510,13 @@ def find_root_genome(genome):


def lock_genome(genome):
"""
Do a select for update, which, when executed inside a transaction, places a
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FYI I only spent two minutes poking into this, but from what I could tell, the places where you call lock_genome aren't inside transactions. Unless they're happening higher up in the call chain...

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Correct. It's upstream caller that's calling the atomic, because you need the locking and the rest of the work to happen all within a transaction. Should I change the method name to lock_genome_call_if_in_transaction? or you think the comment is sufficient.

lock on the genome.
"""

genomes = Genome.objects.select_for_update().filter(pk=find_root_genome(genome).id)
# Lock only happens when querset is evaluated, therefore need to do at least genomes[0]
# Lock only happens when queryset is evaluated, therefore need to do at least genomes[0]
genome = genomes[0]
print(f"Lock genome {genome.id}")
return genome
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