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<h1 class="title">Package <code>mongiris</code></h1>
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<section id="section-intro">
The package <code>mongiris</code> consists of two modules:
<ul>
<li><a href="api.html">api</a>, for manipulating IRIS data.</li>
<li><a href="integrator.html">integrator</a>, for integrating data sources. There should be no need to run this module since the MongoDB dumps are provided.</li>
</ul>
</section>
</article>
<nav id="sidebar">
<h1>Index</h1>
<div class="toc">
<ul></ul>
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<ul id="index">
<li><h3><a href="#header-modules">Modules</a></h3>
<ul>
<li>
<h4><code><a title="api" href="api.html">api</a></code></h4>
</li>
<li><h4><code><a title="integrator" href="integrator.html">integrator</a></code></h4>
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<article id="content">
<header>
<h1 class="title">Module <code>integrator</code></h1>
</header>
<section id="section-intro">
<details class="source">
<summary>Source code</summary>
<pre><code class="python">#!/usr/bin/env python
# encoding: utf-8
# =============================================================================
# Integrator: perform the integration of different data sources to produce MongoDB documents (GeoJSON format) containing
# IRIS information (~640 or ~350 INSEE indicators, depending on the IRIS).
# This file does not need to be run because the MongoDB dump is provided (unless for integrating new data sources).
# =============================================================================
# Path to MongoDB tools (under MacOS): /Applications/MongoDB.app/Contents/Resources/Vendor/mongodb/bin/
# Export and import a local database (metadata/indexes included, option dryRun for testing, several files):
# mongodump --db dbinsee --verbose -o dump/
# mongorestore --db dbinsee --dir dump/dbinsee --verbose --dryRun
# Export and import a local database (metadata/indexes included, option dryRun for testing, single binary file):
# mongodump --db dbinsee --verbose --archive=dbinsee.bin
# mongorestore --archive=dbinsee.bin --verbose
# Export and import in JSON:
# ./mongoexport --db dbinsee --out ~/dump-iris.json
# ./mongoimport --db dbinsee --file ~/dump-iris.json
# =============================================================================
import os
import logging
from mongiris import config
from mongiris import xls_utils
from mongiris import api
def get_all_xlsx_files(dir_sources):
&#34;&#34;&#34;
Returns a list of spreadsheets files to be integrated.
Args:
dir_sources: path to a directory containing data sources (spreadsheets from INSEE)
Returns:
insee_files: a list of filepaths (to xls files)
&#34;&#34;&#34;
insee_files = list()
for file in os.listdir(dir_sources):
filepath = os.path.join(config.insee_dir, file)
if os.path.isfile(filepath) and filepath.endswith(&#34;.xls&#34;):
insee_files.append(filepath)
return insee_files
def integrate_xls_file(connection, xls_file):
&#34;&#34;&#34;
Integrates data from an xsl file : the 3 collections may be updated. First, extracts information about the source
(e.g., title, date) and inserts a document for that source in &#39;collsources&#39;. Next extracts information about the
indicators (e.g., short name, long name) and updates/inserts a document in &#39;collindic&#39;. Finally for each line (IRIS)
in the spreadsheet, updates corresponding document with new indicators.
Args:
connection: an object representing the database connection
xls_file: a csv file path containing INSEE indicators
&#34;&#34;&#34;
indicator_metadata, indicators, source_metadata = xls_utils.parse_xls_to_dict(xls_file)
# add the source metadata into collection_sources
doc = connection.find_one_document(connection.collection_sources, {&#34;filename&#34;: xls_file})
if doc is None:
connection.insert_one_document(connection.collection_sources, source_metadata)
# add the indicators information into collection_indic
for ind in indicator_metadata:
short_name = ind[config.geojson_shortname_label]
doc = connection.find_one_document(connection.collection_indic, {config.geojson_shortname_label: short_name})
if doc is not None: # only update field from_insee_files, $addToSet does not add duplicate values
connection.update_one_document(connection.collection_indic, {config.geojson_shortname_label: short_name},
{&#34;$addToSet&#34;: {config.geojson_from_files_label: xls_file}})
else: # add the document
connection.insert_one_document(connection.collection_indic, ind)
# add the indicators values into collection_iris
not_found_iris = found_iris = nb_replacements = 0
for code_iris, indics in indicators.items():
doc = connection.get_iris_from_code(code_iris)
if doc is None:
not_found_iris += 1
else:
doc_id = doc[&#39;properties&#39;][&#39;CODE_IRIS&#39;]
found_iris += 1
need_replacement = False
doc_changes = {&#34;$set&#34;: dict()} # an update document containing the new fields
for ind, value in indics.items():
if ind in config.labels_dictionary_init: # main indicator, do not replace it if already there
if ind not in doc[&#39;properties&#39;]: # general information (code iris, city name, etc.)
doc_changes[&#34;$set&#34;][&#34;properties.&#34; + ind] = value
need_replacement = True
else: # raw indicator
if ind not in doc[&#39;properties&#39;][config.geojson_raw_indicators_label]: # add this value
doc_changes[&#34;$set&#34;][&#34;properties.&#34; + config.geojson_raw_indicators_label + &#34;.&#34; + ind] = value
need_replacement = True
if need_replacement: # replace the old doc by new doc
res = connection.update_one_document(connection.collection_iris, {&#39;properties.CODE_IRIS&#39;: doc_id}, doc_changes)
nb_replacements += res.modified_count
logger.info(f&#34;\t\t{xls_file}: {found_iris} found iris, {not_found_iris} not found iris, {nb_replacements} updates&#34;)
return True
def integrate(connection, dir_sources):
&#34;&#34;&#34;
Main integration method: parses a directory of data sources, and call the `integrate_xls_file` function for each
data source.
Args:
connection: an object representing the database connection
dir_sources: path to a directory containing data sources (spreadsheets from INSEE)
&#34;&#34;&#34;
logger.info(&#34;Searching xlsx files...&#34;)
insee_files = get_all_xlsx_files(dir_sources) # get the list of all xlsx files to be integrated
logger.info(f&#34;Found a total of {len(insee_files)} xlsx files to be integrated.&#34;)
# insee_files = [] # roughly 10-20 mins execution time for one data source
logger.info(f&#39;Selected {len(insee_files)} xlsx files to be integrated.&#39;)
logger.info(&#34;Integrating sources files (metadata for source and indicators, data for iris)&#34;)
for file in insee_files: # integrate each xlsx INSEE file (both indicators in IRIS and indicators dict)
logger.info(f&#34;\t- INSEE xlsx file: {file}&#34;)
integrate_xls_file(connection, file)
logger.info(&#34;Done !&#34;)
def check_properties(connection):
&#34;&#34;&#34;
Computes and prints statistics on the IRIS collection, mainly the number of indicators per document.
Args:
connection: an object representing the database connection
&#34;&#34;&#34;
docs = connection.find_documents(connection.collection_iris, {}, )
counts = dict()
for doc in docs:
nb = len(doc[&#39;properties&#39;][config.geojson_raw_indicators_label])
if nb not in counts:
counts[nb] = 0
counts[nb] += 1
print(counts)
#########################
# main integration script
#########################
if __name__ == &#39;__main__&#39;:
logging.basicConfig(format=&#39;[%(levelname)s] - %(name)s - %(asctime)s : %(message)s&#39;)
logger = logging.getLogger()
logger.setLevel(logging.INFO)
connection = api.Mongiris() # database connection
integrate(connection, config.insee_dir) # integrating data sources
check_properties(connection) # stats about properties 5min execution {350: 36530, 638: 11738, 615: 1057, 373: 79}</code></pre>
</details>
</section>
<section>
</section>
<section>
</section>
<section>
<h2 class="section-title" id="header-functions">Functions</h2>
<dl>
<dt id="integrator.check_properties"><code class="name flex">
<span>def <span class="ident">check_properties</span></span>(<span>connection)</span>
</code></dt>
<dd>
<section class="desc"><p>Computes and prints statistics on the IRIS collection, mainly the number of indicators per document.</p>
<h2 id="args">Args</h2>
<dl>
<dt><strong><code>connection</code></strong></dt>
<dd>an object representing the database connection</dd>
</dl></section>
<details class="source">
<summary>Source code</summary>
<pre><code class="python">def check_properties(connection):
&#34;&#34;&#34;
Computes and prints statistics on the IRIS collection, mainly the number of indicators per document.
Args:
connection: an object representing the database connection
&#34;&#34;&#34;
docs = connection.find_documents(connection.collection_iris, {}, )
counts = dict()
for doc in docs:
nb = len(doc[&#39;properties&#39;][config.geojson_raw_indicators_label])
if nb not in counts:
counts[nb] = 0
counts[nb] += 1
print(counts)</code></pre>
</details>
</dd>
<dt id="integrator.get_all_xlsx_files"><code class="name flex">
<span>def <span class="ident">get_all_xlsx_files</span></span>(<span>dir_sources)</span>
</code></dt>
<dd>
<section class="desc"><p>Returns a list of spreadsheets files to be integrated.</p>
<h2 id="args">Args</h2>
<dl>
<dt><strong><code>dir_sources</code></strong></dt>
<dd>path to a directory containing data sources (spreadsheets from INSEE)</dd>
</dl>
<h2 id="returns">Returns</h2>
<dl>
<dt><strong><code>insee_files</code></strong></dt>
<dd>a list of filepaths (to xls files)</dd>
</dl></section>
<details class="source">
<summary>Source code</summary>
<pre><code class="python">def get_all_xlsx_files(dir_sources):
&#34;&#34;&#34;
Returns a list of spreadsheets files to be integrated.
Args:
dir_sources: path to a directory containing data sources (spreadsheets from INSEE)
Returns:
insee_files: a list of filepaths (to xls files)
&#34;&#34;&#34;
insee_files = list()
for file in os.listdir(dir_sources):
filepath = os.path.join(config.insee_dir, file)
if os.path.isfile(filepath) and filepath.endswith(&#34;.xls&#34;):
insee_files.append(filepath)
return insee_files</code></pre>
</details>
</dd>
<dt id="integrator.integrate"><code class="name flex">
<span>def <span class="ident">integrate</span></span>(<span>connection, dir_sources)</span>
</code></dt>
<dd>
<section class="desc"><p>Main integration method: parses a directory of data sources, and call the <a title="integrator.integrate_xls_file" href="#integrator.integrate_xls_file"><code>integrate_xls_file()</code></a> function for each
data source.</p>
<h2 id="args">Args</h2>
<dl>
<dt><strong><code>connection</code></strong></dt>
<dd>an object representing the database connection</dd>
<dt><strong><code>dir_sources</code></strong></dt>
<dd>path to a directory containing data sources (spreadsheets from INSEE)</dd>
</dl></section>
<details class="source">
<summary>Source code</summary>
<pre><code class="python">def integrate(connection, dir_sources):
&#34;&#34;&#34;
Main integration method: parses a directory of data sources, and call the `integrate_xls_file` function for each
data source.
Args:
connection: an object representing the database connection
dir_sources: path to a directory containing data sources (spreadsheets from INSEE)
&#34;&#34;&#34;
logger.info(&#34;Searching xlsx files...&#34;)
insee_files = get_all_xlsx_files(dir_sources) # get the list of all xlsx files to be integrated
logger.info(f&#34;Found a total of {len(insee_files)} xlsx files to be integrated.&#34;)
# insee_files = [] # roughly 10-20 mins execution time for one data source
logger.info(f&#39;Selected {len(insee_files)} xlsx files to be integrated.&#39;)
logger.info(&#34;Integrating sources files (metadata for source and indicators, data for iris)&#34;)
for file in insee_files: # integrate each xlsx INSEE file (both indicators in IRIS and indicators dict)
logger.info(f&#34;\t- INSEE xlsx file: {file}&#34;)
integrate_xls_file(connection, file)
logger.info(&#34;Done !&#34;)</code></pre>
</details>
</dd>
<dt id="integrator.integrate_xls_file"><code class="name flex">
<span>def <span class="ident">integrate_xls_file</span></span>(<span>connection, xls_file)</span>
</code></dt>
<dd>
<section class="desc"><p>Integrates data from an xsl file : the 3 collections may be updated. First, extracts information about the source
(e.g., title, date) and inserts a document for that source in 'collsources'. Next extracts information about the
indicators (e.g., short name, long name) and updates/inserts a document in 'collindic'. Finally for each line (IRIS)
in the spreadsheet, updates corresponding document with new indicators.</p>
<h2 id="args">Args</h2>
<dl>
<dt><strong><code>connection</code></strong></dt>
<dd>an object representing the database connection</dd>
<dt><strong><code>xls_file</code></strong></dt>
<dd>a csv file path containing INSEE indicators</dd>
</dl></section>
<details class="source">
<summary>Source code</summary>
<pre><code class="python">def integrate_xls_file(connection, xls_file):
&#34;&#34;&#34;
Integrates data from an xsl file : the 3 collections may be updated. First, extracts information about the source
(e.g., title, date) and inserts a document for that source in &#39;collsources&#39;. Next extracts information about the
indicators (e.g., short name, long name) and updates/inserts a document in &#39;collindic&#39;. Finally for each line (IRIS)
in the spreadsheet, updates corresponding document with new indicators.
Args:
connection: an object representing the database connection
xls_file: a csv file path containing INSEE indicators
&#34;&#34;&#34;
indicator_metadata, indicators, source_metadata = xls_utils.parse_xls_to_dict(xls_file)
# add the source metadata into collection_sources
doc = connection.find_one_document(connection.collection_sources, {&#34;filename&#34;: xls_file})
if doc is None:
connection.insert_one_document(connection.collection_sources, source_metadata)
# add the indicators information into collection_indic
for ind in indicator_metadata:
short_name = ind[config.geojson_shortname_label]
doc = connection.find_one_document(connection.collection_indic, {config.geojson_shortname_label: short_name})
if doc is not None: # only update field from_insee_files, $addToSet does not add duplicate values
connection.update_one_document(connection.collection_indic, {config.geojson_shortname_label: short_name},
{&#34;$addToSet&#34;: {config.geojson_from_files_label: xls_file}})
else: # add the document
connection.insert_one_document(connection.collection_indic, ind)
# add the indicators values into collection_iris
not_found_iris = found_iris = nb_replacements = 0
for code_iris, indics in indicators.items():
doc = connection.get_iris_from_code(code_iris)
if doc is None:
not_found_iris += 1
else:
doc_id = doc[&#39;properties&#39;][&#39;CODE_IRIS&#39;]
found_iris += 1
need_replacement = False
doc_changes = {&#34;$set&#34;: dict()} # an update document containing the new fields
for ind, value in indics.items():
if ind in config.labels_dictionary_init: # main indicator, do not replace it if already there
if ind not in doc[&#39;properties&#39;]: # general information (code iris, city name, etc.)
doc_changes[&#34;$set&#34;][&#34;properties.&#34; + ind] = value
need_replacement = True
else: # raw indicator
if ind not in doc[&#39;properties&#39;][config.geojson_raw_indicators_label]: # add this value
doc_changes[&#34;$set&#34;][&#34;properties.&#34; + config.geojson_raw_indicators_label + &#34;.&#34; + ind] = value
need_replacement = True
if need_replacement: # replace the old doc by new doc
res = connection.update_one_document(connection.collection_iris, {&#39;properties.CODE_IRIS&#39;: doc_id}, doc_changes)
nb_replacements += res.modified_count
logger.info(f&#34;\t\t{xls_file}: {found_iris} found iris, {not_found_iris} not found iris, {nb_replacements} updates&#34;)
return True</code></pre>
</details>
</dd>
</dl>
</section>
<section>
</section>
</article>
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<h1>Index</h1>
<div class="toc">
<ul></ul>
</div>
<ul id="index">
<li><h3><a href="#header-functions">Functions</a></h3>
<ul class="">
<li><code><a title="integrator.check_properties" href="#integrator.check_properties">check_properties</a></code></li>
<li><code><a title="integrator.get_all_xlsx_files" href="#integrator.get_all_xlsx_files">get_all_xlsx_files</a></code></li>
<li><code><a title="integrator.integrate" href="#integrator.integrate">integrate</a></code></li>
<li><code><a title="integrator.integrate_xls_file" href="#integrator.integrate_xls_file">integrate_xls_file</a></code></li>
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setup.py
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View file @ 96df1036
#!/usr/bin/env python
# mongiris setup.py (uses setup.cfg)
# pdoc --force --html mongiris/main.py mongiris/integrator.py
# pdoc mongiris/api.py -o doc
# pandoc paper.md --filter pandoc-citeproc -o paper.pdf
# python3 -m setup bdist_wheel sdist
# python3 -m pip install -e mongiris/
......
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