From 096dd5b59fc37f8587329387864a2d8afeabcd11 Mon Sep 17 00:00:00 2001
From: Duchateau Fabien <fabien.duchateau@univ-lyon1.fr>
Date: Sun, 14 Mar 2021 14:07:52 +0100
Subject: [PATCH] [AM] update for Docker use
---
Dockerfile-db-predihood | 13 +
import-data.sh | 27 +
mongiris/api.py | 23 +-
mongiris/data/dumps/dump-bird-indicators.json | 3 +
.../data/dumps/dump-bird-neighbourhoods.json | 769 ++++++++++++++++++
.../data/{dump => dumps}/dump-dbinsee.bin | Bin
mongiris/tests/api_tests.py | 12 +-
requirements.txt | 2 +
8 files changed, 838 insertions(+), 11 deletions(-)
create mode 100644 Dockerfile-db-predihood
create mode 100644 import-data.sh
create mode 100644 mongiris/data/dumps/dump-bird-indicators.json
create mode 100644 mongiris/data/dumps/dump-bird-neighbourhoods.json
rename mongiris/data/{dump => dumps}/dump-dbinsee.bin (100%)
mode change 100644 => 100755 mongiris/tests/api_tests.py
create mode 100755 requirements.txt
diff --git a/Dockerfile-db-predihood b/Dockerfile-db-predihood
new file mode 100644
index 0000000..d403621
--- /dev/null
+++ b/Dockerfile-db-predihood
@@ -0,0 +1,13 @@
+FROM mongo
+#RUN mkdir /mongodata
+COPY ./mongiris-v2/mongiris/data/dumps/ /tmp/dumps/
+COPY ./mongiris-v2/import-data.sh /docker-entrypoint-initdb.d/import-data.sh
+EXPOSE 27017
+#CMD chmod 777 /docker-entrypoint-initdb.d/import-data.sh # not needed
+#VOLUME /mongodata
+
+# CMD mongod --fork --logpath /var/log/mongodb.log; \
+# mongorestore --archive=/tmp/dump/dump-dbinsee.bin; \
+# mongod --shutdown; \
+# docker-entrypoint.sh mongod
+
diff --git a/import-data.sh b/import-data.sh
new file mode 100644
index 0000000..e4953c4
--- /dev/null
+++ b/import-data.sh
@@ -0,0 +1,27 @@
+# import-data.sh: restores mongodata if needed
+# mongod should be already launched by the container
+
+echo "Executing import-data.sh"
+
+dbs=$(mongo --eval 'db.getMongo().getDBNames()')
+echo "$dbs";
+
+# teste si la BD dbinsee existe, et importe les données du dataset dbinsee si besoin
+if [ $(mongo --eval 'db.getMongo().getDBNames().indexOf("dbinsee")' --quiet) -lt 0 ]; then
+ echo "Database dbinsee does not exist, restoring dbinsee."
+ mongorestore --archive=/tmp/dumps/dump-dbinsee.bin;
+else
+ echo "Database dbinsee already exists, not restoring data."
+fi
+
+# teste si la BD dbmigration existe, et importe les données du dataset bird migration si besoin
+if [ $(mongo --eval 'db.getMongo().getDBNames().indexOf("dbmigration")' --quiet) -lt 0 ]; then
+ echo "Database dbmigration does not exist, importing collections in dbmigration."
+ mongoimport --db=dbmigration -c=collmigration --file=/tmp/dumps/dump-bird-neighbourhoods.json
+ mongoimport --db=dbmigration -c=collindic --file=/tmp/dumps/dump-bird-indicators.json
+else
+ echo "Database dbmigration already exists, not restoring data."
+fi
+
+echo "End of script import-data.sh"
+
diff --git a/mongiris/api.py b/mongiris/api.py
index e1ca9c2..81ae8a7 100755
--- a/mongiris/api.py
+++ b/mongiris/api.py
@@ -11,7 +11,7 @@ from bson import json_util # used to convert BSON to JSON (especially ObjectId
import json
import logging
-max_timeout = 3 # delay before connection timeout
+max_timeout = 30000 # delay before connection timeout in milliseconds
class Mongiris:
"""
@@ -32,9 +32,11 @@ class Mongiris:
An example of neighbourhood following the GeoJSON format is provided in `data/example-neighbourhood.json`.
Args:
+ host: the server hosting MongoDB (string, default to 'localhost')
+ port: the port number on which MongoDB listens to (integer, default tp 27017)
db: the MongoDB database name to connect to (string)
- coll_neighbourhoods: the name of the neighbourhoods collection, inside database db (string)
- coll_indic: the name of the indicators collection, inside database db (string)
+ coll_neighbourhoods: the name of the neighbourhoods collection, inside database db (string)
+ coll_indic: the name of the indicators collection, inside database db (string)
Additional resources:
@@ -46,11 +48,14 @@ class Mongiris:
"""
- def __init__(self, db, coll_neighbourhoods, coll_indic='collindic'):
+ def __init__(self, host='localhost', port=27017, db='dbinsee', coll_neighbourhoods='colliris', coll_indic='collindic'):
logging.basicConfig(format='[%(levelname)s] - %(name)s - %(asctime)s : %(message)s')
self.logger = logging.getLogger()
self.logger.setLevel(logging.INFO)
- self.connection, self.connection_status = self.init_connection() # default connection on 'localhost', 27017
+ self.host = host
+ self.port = port
+ self.connection, self.connection_status = self.init_connection()
+ self.dbname = db
self.database = self.connection[db] # link to database
self.collection_neighbourhoods = self.database[coll_neighbourhoods] # link to neighbourhoods collection
self.collection_indicators = self.database[coll_indic] # link to indicators collection (used for prediction)
@@ -71,8 +76,9 @@ class Mongiris:
def init_connection(self):
"""
- Tries to connect to MongoDB. The output connection object do not provide reliable connection status, only the
- boolean connection_status indicates whether the connection is working or not.
+ Tries to connect to MongoDB (default on localhost:27017). The output connection object do not provide
+ reliable connection status, only the boolean connection_status indicates whether the connection is
+ working or not.
Returns:
connection: an object with information about the connection
@@ -80,8 +86,9 @@ class Mongiris:
"""
connection_status = True # by default, connection is ok
connection = None
+ self.logger.info(f'Trying to connect to MongoDB server ({self.host}:{self.port})...')
try:
- connection = pymongo.MongoClient(serverSelectionTimeoutMS=max_timeout) # default localhost:27017
+ connection = pymongo.MongoClient(self.host, self.port, serverSelectionTimeoutMS=max_timeout)
connection.server_info() # forces a query to MongoDB (for checking the connection)
except pymongo.errors.ServerSelectionTimeoutError as e:
self.logger.error('Could not connect to the MongoDB database ! Have you launched MongoDB ? ' + str(e))
diff --git a/mongiris/data/dumps/dump-bird-indicators.json b/mongiris/data/dumps/dump-bird-indicators.json
new file mode 100644
index 0000000..4062b0f
--- /dev/null
+++ b/mongiris/data/dumps/dump-bird-indicators.json
@@ -0,0 +1,3 @@
+{"_id":{"$oid":"5ff1e6e6b0c86c7361a2637c"},"short_label":"percent_greens","full_label":"Percentage of greens areas"}
+{"_id":{"$oid":"5ff1e6eeb0c86c7361a2637d"},"short_label":"percent_built","full_label":"Percentage of building areas"}
+{"_id":{"$oid":"5ff1e6f3b0c86c7361a2637e"},"short_label":"human_pressure","full_label":"The human pressure on the area"}
\ No newline at end of file
diff --git a/mongiris/data/dumps/dump-bird-neighbourhoods.json b/mongiris/data/dumps/dump-bird-neighbourhoods.json
new file mode 100644
index 0000000..5a45748
--- /dev/null
+++ b/mongiris/data/dumps/dump-bird-neighbourhoods.json
@@ -0,0 +1,769 @@
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diff --git a/mongiris/data/dump/dump-dbinsee.bin b/mongiris/data/dumps/dump-dbinsee.bin
similarity index 100%
rename from mongiris/data/dump/dump-dbinsee.bin
rename to mongiris/data/dumps/dump-dbinsee.bin
diff --git a/mongiris/tests/api_tests.py b/mongiris/tests/api_tests.py
old mode 100644
new mode 100755
index 83bad1f..bcde16e
--- a/mongiris/tests/api_tests.py
+++ b/mongiris/tests/api_tests.py
@@ -4,11 +4,17 @@
# Unit tests for mongiris.
# =============================================================================
-from mongiris.api import Mongiris
+# eternal hack for python imports (here to access parent directory)
+import sys, os
+sys.path.append(os.path.join(os.path.dirname(__file__), '..'))
+
+from api import Mongiris
import unittest
import random
import re
+host="db-mongihood"
+port=27017
class TestCase(unittest.TestCase):
"""
@@ -18,7 +24,7 @@ class TestCase(unittest.TestCase):
def setUp(self):
# a setup (connection to MongoDB) executed before each test
- self.db = Mongiris('dbinsee', 'colliris')
+ self.db = Mongiris(host=host, port=port, db='dbinsee', coll_neighbourhoods='colliris')
def test_count(self):
# test for counting the number of documents
@@ -113,7 +119,7 @@ class TestCase(unittest.TestCase):
assert (doc is None), 'Coordinates (79.333879, -49.016200) should return no document (no corresponding neighbourhood)'
def test_switch_db(self):
- self.db = Mongiris('dbmigration', 'collmigration')
+ self.db = Mongiris(host=host, port=port, db='dbmigration', coll_neighbourhoods='collmigration')
self.db.logger.info("Connection to another database (dbmigration).")
count = self.db.count_documents(self.db.collection_neighbourhoods, {})
assert (count == 769), f'Error: expecting 769 neighbourhoods stored in datase dbmigration, but found {count}'
diff --git a/requirements.txt b/requirements.txt
new file mode 100755
index 0000000..c673119
--- /dev/null
+++ b/requirements.txt
@@ -0,0 +1,2 @@
+pymongo~=3.7.2
+xlrd~=1.2.0
--
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