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| author | BonfaceKilz | 2020-10-27 01:18:38 +0300 |
|---|---|---|
| committer | GitHub | 2020-10-27 01:18:38 +0300 |
| commit | 37c391bc62e9080effcf83c6ff0056ab8841b7fb (patch) | |
| tree | 1e794c5616c25e82869314a2f4e91f64c4d40ea9 /wqflask/db | |
| parent | 85896707ef1f9e214b45298f6b5b1a9dc37bc839 (diff) | |
| parent | b369489e6c075eee3f58bb33e493c901b052b0a1 (diff) | |
| download | genenetwork2-37c391bc62e9080effcf83c6ff0056ab8841b7fb.tar.gz | |
Merge pull request #422 from BonfaceKilz/build/python3-migration
Build/python3 migration
Diffstat (limited to 'wqflask/db')
| -rw-r--r-- | wqflask/db/call.py | 21 | ||||
| -rw-r--r-- | wqflask/db/webqtlDatabaseFunction.py | 8 |
2 files changed, 18 insertions, 11 deletions
diff --git a/wqflask/db/call.py b/wqflask/db/call.py index 1a1b3adc..0971d2a2 100644 --- a/wqflask/db/call.py +++ b/wqflask/db/call.py @@ -3,7 +3,10 @@ from flask import g import string -import urllib2 +try: # Python2 support + import urllib.request, urllib.error, urllib.parse +except: + import urllib2 import json from utility.tools import USE_GN_SERVER, LOG_SQL, GN_SERVER_URL from utility.benchmark import Bench @@ -26,8 +29,8 @@ GN_SERVER result when set (which should return a Tuple) else: res2 = result, if LOG_SQL: - logger.debug("Replaced SQL call",query) - logger.debug(path,res2) + logger.debug("Replaced SQL call", query) + logger.debug(path, res2) return res2 else: return fetchone(query) @@ -37,7 +40,7 @@ def fetchone(query): original fetchone, but with logging) """ - with Bench("SQL",LOG_SQL): + with Bench("SQL", LOG_SQL): def helper(query): res = g.db.execute(query) return res.fetchone() @@ -48,7 +51,7 @@ def fetchall(query): original fetchall, but with logging) """ - with Bench("SQL",LOG_SQL): + with Bench("SQL", LOG_SQL): def helper(query): res = g.db.execute(query) return res.fetchall() @@ -58,8 +61,12 @@ def gn_server(path): """Return JSON record by calling GN_SERVER """ - with Bench("GN_SERVER",LOG_SQL): - res = urllib2.urlopen(GN_SERVER_URL+path) + with Bench("GN_SERVER", LOG_SQL): + res = () + try: + res = urllib.request.urlopen(GN_SERVER_URL+path) + except: + res = urllib2.urlopen(GN_SERVER_URL+path) rest = res.read() res2 = json.loads(rest) logger.debug(res2) diff --git a/wqflask/db/webqtlDatabaseFunction.py b/wqflask/db/webqtlDatabaseFunction.py index 8a9dc79d..2805febd 100644 --- a/wqflask/db/webqtlDatabaseFunction.py +++ b/wqflask/db/webqtlDatabaseFunction.py @@ -35,13 +35,13 @@ def retrieve_species(group): """Get the species of a group (e.g. returns string "mouse" on "BXD" """ - result = fetch1("select Species.Name from Species, InbredSet where InbredSet.Name = '%s' and InbredSet.SpeciesId = Species.Id" % (group),"/cross/"+group+".json",lambda r: (r["species"],))[0] - logger.debug("retrieve_species result:",result) + result = fetch1("select Species.Name from Species, InbredSet where InbredSet.Name = '%s' and InbredSet.SpeciesId = Species.Id" % (group), "/cross/"+group+".json", lambda r: (r["species"],))[0] + logger.debug("retrieve_species result:", result) return result def retrieve_species_id(group): - result = fetch1("select SpeciesId from InbredSet where Name = '%s'" % (group),"/cross/"+group+".json",lambda r: (r["species_id"],))[0] - logger.debug("retrieve_species_id result:",result) + result = fetch1("select SpeciesId from InbredSet where Name = '%s'" % (group), "/cross/"+group+".json", lambda r: (r["species_id"],))[0] + logger.debug("retrieve_species_id result:", result) return result |