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edges.sqlite
When I saved a static html page for each edge (e.g., http://118.25.96.118/static/edges/AT1G20910_AT1G30100_0.html), it took
5GB disk space for saving 1 million html pages. Not very disk space efficient.
An alternative is to save all edge information in a database table (i.e., edge), and query this database table for a
particular edge.
The database file edges.sqlite takes less than 200MB for 1 million edges, requiring 10 times smaller space than the static
approach. The reason is that we do not have a lot of HTML tags in the database. Quite happy about that, though it seems
that filling a database is a bit slower (2 hours??? for 1 million rows).
Also updated two files that were affected: update_network.py and update_network_by_force.py. Now instead of copying 1 million
static html page to the Webapp, I just need to copy edges.sqlite to static/edges/. Faster.
In the Webapp, I updated start_webapp.py and added a file templates/edge.html for handling dynamic page generation.
-Hui
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If there is no enough space left in the disk, download_and_map.py will refuse to download any data.
This can be quite mysterious for a maintainer.
So, write the reason to the network log file.
The reason is something like:
"[download_and_map.py] home directory does not have enough space (only 13 G available)."
-Hui
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The purpose of duniq is to avoid duplicated edge lines.
Now, just make sure we don't insert the same tuple.
-Hui
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It would be interesting to see how edges' association strengths change over time, as time is an input variable for the
function that computes the association strength.
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Define a function copy_and_backup_file(src_file, dest_dir) to do backup and compression work.
The function copy_and_backup_file is used in update_network_by_force.py.
-Hui
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Fixed a bug.
Now I close figure (plt.close()) before creating a new one, to avoid that the current figure is drawn
on top of the old one.
-Hui
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might be responsible for thermomorphogenesis
Use networkx and matplotlib.
Reference:
Quint et al. (2016) Molecular and genetic control of plant thermomorphogenesis. Nature Plants.
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the head comments.
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