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425 lines
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425 lines
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HTML
6 years ago
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</head>
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<body>
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<p>It may be useful to download data from openSenseMap only once.
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For reproducible results, the data could be saved to disk, and reloaded at a
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later point.</p>
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<p>This avoids..</p>
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<ul>
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<li>changed results for queries without date parameters,</li>
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<li>unnecessary wait times,</li>
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<li>risk of API changes / API unavailability,</li>
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<li>stress on the openSenseMap-server.</li>
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</ul>
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<p>This vignette shows how to use this built in <code>opensensmapr</code> feature, and
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how to do it yourself, if you want to store to other data formats.</p>
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<h2>Using openSensMapr Caching Feature</h2>
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<p>All data retrieval functions of <code>opensensmapr</code> have a built in caching feature,
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which serializes an API response to disk.
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Subsequent identical requests will then return the serialized data instead of making
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another request.
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To do so, each request is given a unique ID based on its parameters.</p>
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<p>To use this feature, just add a path to a directory to the <code>cache</code> parameter:</p>
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<pre><code class="r">b = osem_boxes(cache = tempdir())
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list.files(tempdir(), pattern = 'osemcache\\..*\\.rds')
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</code></pre>
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<pre><code>## [1] "osemcache.c54710f66b662e29dd86b089962b0f598e47eddb.rds"
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</code></pre>
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<pre><code class="r"># the next identical request will hit the cache only!
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b = osem_boxes(cache = tempdir())
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# requests without the cache parameter will still be performed normally
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b = osem_boxes()
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</code></pre>
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<p>You can maintain multiple caches simultaneously which allows to store only
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serialized data related to a script in its directory:</p>
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<pre><code class="r">cacheDir = getwd() # current working directory
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b = osem_boxes(cache = cacheDir)
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# the next identical request will hit the cache only!
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b = osem_boxes(cache = cacheDir)
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</code></pre>
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<p>To get fresh results again, just call <code>osem_clear_cache()</code> for the respective cache:</p>
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<pre><code class="r">osem_clear_cache() # clears default cache
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</code></pre>
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<pre><code>## [1] TRUE
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</code></pre>
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<pre><code class="r">osem_clear_cache(getwd()) # clears a custom cache
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</code></pre>
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<pre><code>## [1] TRUE
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</code></pre>
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<h2>Custom (De-) Serialization</h2>
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<p>If you want to roll your own serialization method to support custom data formats,
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here's how:</p>
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<pre><code class="r"># this section requires:
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library(opensensmapr)
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library(jsonlite)
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library(readr)
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# first get our example data:
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boxes = osem_boxes(grouptag = 'ifgi')
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measurements = osem_measurements(boxes, phenomenon = 'PM10')
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</code></pre>
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<p>If you are paranoid and worry about <code>.rds</code> files not being decodable anymore
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in the (distant) future, you could serialize to a plain text format such as JSON.
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This of course comes at the cost of storage space and performance.</p>
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<pre><code class="r"># serializing senseBoxes to JSON, and loading from file again:
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write(jsonlite::serializeJSON(measurements), 'boxes.json')
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boxes_from_file = jsonlite::unserializeJSON(readr::read_file('boxes.json'))
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</code></pre>
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<p>Both methods also persist the R object metadata (classes, attributes).
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If you were to use a serialization method that can't persist object metadata, you
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could re-apply it with the following functions:</p>
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<pre><code class="r"># note the toJSON call
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write(jsonlite::toJSON(measurements), 'boxes_bad.json')
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boxes_without_attrs = jsonlite::fromJSON('boxes_bad.json')
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boxes_with_attrs = osem_as_sensebox(boxes_without_attrs)
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class(boxes_with_attrs)
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</code></pre>
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<pre><code>## [1] "sensebox" "data.frame"
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</code></pre>
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<p>The same goes for measurements via <code>osem_as_measurements()</code>.</p>
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<h2>Workflow for reproducible code</h2>
|
||
|
|
|
||
|
|
<p>For truly reproducible code you want it to work and return the same results –
|
||
|
|
no matter if you run it the first time or a consecutive time, and without making
|
||
|
|
changes to it.</p>
|
||
|
|
|
||
|
|
<p>Therefore we need a wrapper around the save-to-file & load-from-file logic.
|
||
|
|
The following examples show a way to do just that, and where inspired by
|
||
|
|
<a href="https://github.com/nuest/sensebox-binder">this reproducible analysis by Daniel Nuest</a>.</p>
|
||
|
|
|
||
|
|
<pre><code class="r"># offline logic
|
||
|
|
osem_offline = function (func, file, format='rds', ...) {
|
||
|
|
# deserialize if file exists, otherwise download and serialize
|
||
|
|
if (file.exists(file)) {
|
||
|
|
if (format == 'json')
|
||
|
|
jsonlite::unserializeJSON(readr::read_file(file))
|
||
|
|
else
|
||
|
|
readRDS(file)
|
||
|
|
} else {
|
||
|
|
data = func(...)
|
||
|
|
if (format == 'json')
|
||
|
|
write(jsonlite::serializeJSON(data), file = file)
|
||
|
|
else
|
||
|
|
saveRDS(data, file)
|
||
|
|
data
|
||
|
|
}
|
||
|
|
}
|
||
|
|
|
||
|
|
# wrappers for each download function
|
||
|
|
osem_measurements_offline = function (file, ...) {
|
||
|
|
osem_offline(opensensmapr::osem_measurements, file, ...)
|
||
|
|
}
|
||
|
|
osem_boxes_offline = function (file, ...) {
|
||
|
|
osem_offline(opensensmapr::osem_boxes, file, ...)
|
||
|
|
}
|
||
|
|
osem_box_offline = function (file, ...) {
|
||
|
|
osem_offline(opensensmapr::osem_box, file, ...)
|
||
|
|
}
|
||
|
|
osem_counts_offline = function (file, ...) {
|
||
|
|
osem_offline(opensensmapr::osem_counts, file, ...)
|
||
|
|
}
|
||
|
|
</code></pre>
|
||
|
|
|
||
|
|
<p>Thats it! Now let's try it out:</p>
|
||
|
|
|
||
|
|
<pre><code class="r"># first run; will download and save to disk
|
||
|
|
b1 = osem_boxes_offline('mobileboxes.rds', exposure='mobile')
|
||
|
|
|
||
|
|
# consecutive runs; will read from disk
|
||
|
|
b2 = osem_boxes_offline('mobileboxes.rds', exposure='mobile')
|
||
|
|
class(b1) == class(b2)
|
||
|
|
</code></pre>
|
||
|
|
|
||
|
|
<pre><code>## [1] TRUE TRUE
|
||
|
|
</code></pre>
|
||
|
|
|
||
|
|
<pre><code class="r"># we can even omit the arguments now (though thats not really the point here)
|
||
|
|
b3 = osem_boxes_offline('mobileboxes.rds')
|
||
|
|
nrow(b1) == nrow(b3)
|
||
|
|
</code></pre>
|
||
|
|
|
||
|
|
<pre><code>## [1] TRUE
|
||
|
|
</code></pre>
|
||
|
|
|
||
|
|
<pre><code class="r"># verify that the custom sensebox methods are still working
|
||
|
|
summary(b2)
|
||
|
|
</code></pre>
|
||
|
|
|
||
|
|
<pre><code>## boxes total: 55
|
||
|
|
##
|
||
|
|
## boxes by exposure:
|
||
|
|
## mobile
|
||
|
|
## 55
|
||
|
|
##
|
||
|
|
## boxes by model:
|
||
|
|
## custom homeEthernet homeWifi
|
||
|
|
## 7 2 8
|
||
|
|
## homeWifiFeinstaub luftdaten_pms5003_bme280 luftdaten_sds011_bme280
|
||
|
|
## 6 2 9
|
||
|
|
## luftdaten_sds011_dht11 luftdaten_sds011_dht22
|
||
|
|
## 1 20
|
||
|
|
##
|
||
|
|
## $last_measurement_within
|
||
|
|
## 1h 1d 30d 365d never
|
||
|
|
## 16 18 24 43 12
|
||
|
|
##
|
||
|
|
## oldest box: 2017-05-24 08:16:36 (Feinstaub Hauptstrasse Steampunk-Design)
|
||
|
|
## newest box: 2018-05-24 07:08:32 (Josi Test)
|
||
|
|
##
|
||
|
|
## sensors per box:
|
||
|
|
## Min. 1st Qu. Median Mean 3rd Qu. Max.
|
||
|
|
## 1.000 4.000 4.000 4.618 5.000 22.000
|
||
|
|
</code></pre>
|
||
|
|
|
||
|
|
<pre><code class="r">plot(b3)
|
||
|
|
</code></pre>
|
||
|
|
|
||
|
|
<p><img src="data:image/png;base64,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
|
||
|
|
|
||
|
|
<p>To re-download the data, just clear the files that were created in the process:</p>
|
||
|
|
|
||
|
|
<pre><code class="r">file.remove('mobileboxes.rds', 'boxes_bad.json', 'boxes.json', 'measurements.rds')
|
||
|
|
</code></pre>
|
||
|
|
|
||
|
|
<pre><code>## Warning in file.remove("mobileboxes.rds", "boxes_bad.json", "boxes.json", :
|
||
|
|
## cannot remove file 'measurements.rds', reason 'No such file or directory'
|
||
|
|
</code></pre>
|
||
|
|
|
||
|
|
<p>A possible extension to this scheme comes to mind: Omit the specification of a
|
||
|
|
filename, and assign a unique ID to the request instead.
|
||
|
|
For example, one could calculate the SHA-1 hash of the parameters, and use it
|
||
|
|
as filename.</p>
|
||
|
|
|
||
|
|
</body>
|
||
|
|
|
||
|
|
</html>
|