wqflask: views: Delete noisy logging and dead code

- Remove commented out code-blocks
- Remove calls with this pattern:
  logger.info("Sending ...")
  logger.info(request.url)

Should you want to inspect the local context of an
environment when troubleshooting, set a
breakpoint() and inspect the environment.  To view
everything in the local context, use "pp
locals()"; and to view everything in the global
context, use "pp globals()".

1 files changed, 0 insertions, 104 deletions

diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index a371d983..63f3b3bb 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -158,8 +158,6 @@ def handle_generic_exceptions(e):
                                          stack={formatted_lines},
                                          error_image=animation,
                                          version=GN_VERSION))
-
-    # logger.error("Set cookie %s with %s" % (err_msg, animation))
     resp.set_cookie(err_msg[:32], animation)
     return resp
 
@@ -171,8 +169,6 @@ def no_access_page():
 
 @app.route("/")
 def index_page():
-    logger.info("Sending index_page")
-    logger.info(request.url)
     params = request.args
     if 'import_collections' in params:
         import_collections = params['import_collections']
@@ -184,11 +180,7 @@ def index_page():
 
 @app.route("/tmp/<img_path>")
 def tmp_page(img_path):
-    logger.info("In tmp_page")
-    logger.info("img_path:", img_path)
-    logger.info(request.url)
     initial_start_vars = request.form
-    logger.info("initial_start_vars:", initial_start_vars)
     imgfile = open(GENERATED_IMAGE_DIR + img_path, 'rb')
     imgdata = imgfile.read()
     imgB64 = base64.b64encode(imgdata)
@@ -224,22 +216,14 @@ def twitter(filename):
 
 @app.route("/search", methods=('GET',))
 def search_page():
-    logger.info("in search_page")
-    logger.info(request.url)
     result = None
     if USE_REDIS:
         with Bench("Trying Redis cache"):
             key = "search_results:v1:" + \
                 json.dumps(request.args, sort_keys=True)
-            logger.debug("key is:", pf(key))
             result = Redis.get(key)
             if result:
-                logger.info("Redis cache hit on search results!")
                 result = pickle.loads(result)
-    else:
-        logger.info("Skipping Redis cache (USE_REDIS=False)")
-
-    logger.info("request.args is", request.args)
     the_search = SearchResultPage(request.args)
     result = the_search.__dict__
     valid_search = result['search_term_exists']
@@ -256,15 +240,7 @@ def search_page():
 
 @app.route("/search_table", methods=('GET',))
 def search_page_table():
-    logger.info("in search_page table")
-    logger.info(request.url)
-
-    logger.info("request.args is", request.args)
     the_search = search_results.SearchResultPage(request.args)
-
-    logger.info(type(the_search.trait_list))
-    logger.info(the_search.trait_list)
-
     current_page = server_side.ServerSideTable(
         len(the_search.trait_list),
         the_search.trait_list,
@@ -277,7 +253,6 @@ def search_page_table():
 
 @app.route("/gsearch", methods=('GET',))
 def gsearchact():
-    logger.info(request.url)
     result = GSearch(request.args).__dict__
     type = request.args['type']
     if type == "gene":
@@ -288,8 +263,6 @@ def gsearchact():
 
 @app.route("/gsearch_table", methods=('GET',))
 def gsearchtable():
-    logger.info(request.url)
-
     gsearch_table_data = GSearch(request.args)
     current_page = server_side.ServerSideTable(
         gsearch_table_data.trait_count,
@@ -303,15 +276,12 @@ def gsearchtable():
 
 @app.route("/gsearch_updating", methods=('POST',))
 def gsearch_updating():
-    logger.info("REQUEST ARGS:", request.values)
-    logger.info(request.url)
     result = UpdateGSearch(request.args).__dict__
     return result['results']
 
 
 @app.route("/docedit")
 def docedit():
-    logger.info(request.url)
     try:
         if g.user_session.record['user_email_address'] == "zachary.a.sloan@gmail.com" or g.user_session.record['user_email_address'] == "labwilliams@gmail.com":
             doc = Docs(request.args['entry'], request.args)
@@ -324,13 +294,11 @@ def docedit():
 
 @app.route('/generated/<filename>')
 def generated_file(filename):
-    logger.info(request.url)
     return send_from_directory(GENERATED_IMAGE_DIR, filename)
 
 
 @app.route("/help")
 def help():
-    logger.info(request.url)
     doc = Docs("help", request.args)
     return render_template("docs.html", **doc.__dict__)
 
@@ -338,8 +306,6 @@ def help():
 @app.route("/wgcna_setup", methods=('POST',))
 def wcgna_setup():
     # We are going to get additional user input for the analysis
-    logger.info("In wgcna, request.form is:", request.form)
-    logger.info(request.url)
     # Display them using the template
     return render_template("wgcna_setup.html", **request.form)
 
@@ -353,8 +319,6 @@ def wcgna_results():
 @app.route("/ctl_setup", methods=('POST',))
 def ctl_setup():
     # We are going to get additional user input for the analysis
-    logger.info("In ctl, request.form is:", request.form)
-    logger.info(request.url)
     # Display them using the template
     return render_template("ctl_setup.html", **request.form)
 
@@ -362,7 +326,6 @@ def ctl_setup():
 
 @app.route("/ctl_results", methods=["POST"])
 def ctl_results():
-
     ctl_results = run_ctl(request.form)
     return render_template("gn3_ctl_results.html", **ctl_results)
 
@@ -400,7 +363,6 @@ def update_page():
 
 @app.route("/submit_trait")
 def submit_trait_form():
-    logger.info(request.url)
     species_and_groups = get_species_groups()
     return render_template(
         "submit_trait.html",
@@ -411,7 +373,6 @@ def submit_trait_form():
 
 @app.route("/create_temp_trait", methods=('POST',))
 def create_temp_trait():
-    logger.info(request.url)
     doc = Docs("links")
     return render_template("links.html", **doc.__dict__)
 
@@ -422,9 +383,6 @@ def export_trait_excel():
     trait_name, sample_data = export_trait_data.export_sample_table(
         request.form)
     app.logger.info(request.url)
-    logger.info("sample_data - type: %s -- size: %s" %
-                (type(sample_data), len(sample_data)))
-
     buff = io.BytesIO()
     workbook = xlsxwriter.Workbook(buff, {'in_memory': True})
     worksheet = workbook.add_worksheet()
@@ -443,15 +401,9 @@ def export_trait_excel():
 @app.route('/export_trait_csv', methods=('POST',))
 def export_trait_csv():
     """CSV file consisting of the sample data from the trait data and analysis page"""
-    logger.info("In export_trait_csv")
-    logger.info("request.form:", request.form)
-    logger.info(request.url)
     trait_name, sample_data = export_trait_data.export_sample_table(
         request.form)
 
-    logger.info("sample_data - type: %s -- size: %s" %
-                (type(sample_data), len(sample_data)))
-
     buff = io.StringIO()
     writer = csv.writer(buff)
     for row in sample_data:
@@ -467,9 +419,6 @@ def export_trait_csv():
 @app.route('/export_traits_csv', methods=('POST',))
 def export_traits_csv():
     """CSV file consisting of the traits from the search result page"""
-    logger.info("In export_traits_csv")
-    logger.info("request.form:", request.form)
-    logger.info(request.url)
     file_list = export_traits(request.form, "metadata")
 
     if len(file_list) > 1:
@@ -501,7 +450,6 @@ def export_collection_csv():
 @app.route('/export_perm_data', methods=('POST',))
 def export_perm_data():
     """CSV file consisting of the permutation data for the mapping results"""
-    logger.info(request.url)
     perm_info = json.loads(request.form['perm_info'])
 
     now = datetime.datetime.now()
@@ -572,9 +520,6 @@ def show_trait_page():
 
 @app.route("/heatmap", methods=('POST',))
 def heatmap_page():
-    logger.info("In heatmap, request.form is:", pf(request.form))
-    logger.info(request.url)
-
     start_vars = request.form
     temp_uuid = uuid.uuid4()
 
@@ -583,18 +528,14 @@ def heatmap_page():
         version = "v5"
         key = "heatmap:{}:".format(
             version) + json.dumps(start_vars, sort_keys=True)
-        logger.info("key is:", pf(key))
         with Bench("Loading cache"):
             result = Redis.get(key)
 
         if result:
-            logger.info("Cache hit!!!")
             with Bench("Loading results"):
                 result = pickle.loads(result)
 
         else:
-            logger.info("Cache miss!!!")
-
             template_vars = heatmap.Heatmap(request.form, temp_uuid)
             template_vars.js_data = json.dumps(template_vars.js_data,
                                                default=json_default_handler,
@@ -602,12 +543,7 @@ def heatmap_page():
 
             result = template_vars.__dict__
 
-            for item in list(template_vars.__dict__.keys()):
-                logger.info(
-                    "  ---**--- {}: {}".format(type(template_vars.__dict__[item]), item))
-
             pickled_result = pickle.dumps(result, pickle.HIGHEST_PROTOCOL)
-            logger.info("pickled result length:", len(pickled_result))
             Redis.set(key, pickled_result)
             Redis.expire(key, 60 * 60)
 
@@ -623,9 +559,6 @@ def heatmap_page():
 
 @app.route("/bnw_page", methods=('POST',))
 def bnw_page():
-    logger.info("In run BNW, request.form is:", pf(request.form))
-    logger.info(request.url)
-
     start_vars = request.form
 
     traits = [trait.strip() for trait in start_vars['trait_list'].split(',')]
@@ -643,9 +576,6 @@ def bnw_page():
 
 @app.route("/webgestalt_page", methods=('POST',))
 def webgestalt_page():
-    logger.info("In run WebGestalt, request.form is:", pf(request.form))
-    logger.info(request.url)
-
     start_vars = request.form
 
     traits = [trait.strip() for trait in start_vars['trait_list'].split(',')]
@@ -663,9 +593,6 @@ def webgestalt_page():
 
 @app.route("/geneweaver_page", methods=('POST',))
 def geneweaver_page():
-    logger.info("In run WebGestalt, request.form is:", pf(request.form))
-    logger.info(request.url)
-
     start_vars = request.form
 
     traits = [trait.strip() for trait in start_vars['trait_list'].split(',')]
@@ -683,9 +610,6 @@ def geneweaver_page():
 
 @app.route("/comparison_bar_chart", methods=('POST',))
 def comp_bar_chart_page():
-    logger.info("In comp bar chart, request.form is:", pf(request.form))
-    logger.info(request.url)
-
     start_vars = request.form
 
     traits = [trait.strip() for trait in start_vars['trait_list'].split(',')]
@@ -712,7 +636,6 @@ def mapping_results_container_page():
 
 @app.route("/loading", methods=('POST',))
 def loading_page():
-    # logger.info(request.url)
     initial_start_vars = request.form
     start_vars_container = {}
     n_samples = 0  # ZS: So it can be displayed on loading page
@@ -769,7 +692,6 @@ def loading_page():
 @app.route("/run_mapping", methods=('POST',))
 def mapping_results_page():
     initial_start_vars = request.form
-    logger.info(request.url)
     temp_uuid = initial_start_vars['temp_uuid']
     wanted = (
         'trait_id',
@@ -838,18 +760,11 @@ def mapping_results_page():
         version) + json.dumps(start_vars, sort_keys=True)
     with Bench("Loading cache"):
         result = None  # Just for testing
-        #result = Redis.get(key)
-
-    #logger.info("************************ Starting result *****************")
-    #logger.info("result is [{}]: {}".format(type(result), result))
-    #logger.info("************************ Ending result ********************")
 
     if result:
-        logger.info("Cache hit!!!")
         with Bench("Loading results"):
             result = pickle.loads(result)
     else:
-        logger.info("Cache miss!!!")
         with Bench("Total time in RunMapping"):
             try:
                 template_vars = run_mapping.RunMapping(start_vars, temp_uuid)
@@ -883,8 +798,6 @@ def mapping_results_page():
 
 @app.route("/export_mapping_results", methods=('POST',))
 def export_mapping_results():
-    logger.info("request.form:", request.form)
-    logger.info(request.url)
     file_path = request.form.get("results_path")
     results_csv = open(file_path, "r").read()
     response = Response(results_csv,
@@ -908,8 +821,6 @@ def export_corr_matrix():
 
 @app.route("/export", methods=('POST',))
 def export():
-    logger.info("request.form:", request.form)
-    logger.info(request.url)
     svg_xml = request.form.get("data", "Invalid data")
     filename = request.form.get("filename", "manhattan_plot_snp")
     response = Response(svg_xml, mimetype="image/svg+xml")
@@ -920,10 +831,7 @@ def export():
 @app.route("/export_pdf", methods=('POST',))
 def export_pdf():
     import cairosvg
-    logger.info("request.form:", request.form)
-    logger.info(request.url)
     svg_xml = request.form.get("data", "Invalid data")
-    logger.info("svg_xml:", svg_xml)
     filename = request.form.get("filename", "interval_map_pdf")
     pdf_file = cairosvg.svg2pdf(bytestring=svg_xml)
     response = Response(pdf_file, mimetype="application/pdf")
@@ -933,8 +841,6 @@ def export_pdf():
 
 @app.route("/network_graph", methods=('POST',))
 def network_graph_page():
-    logger.info("In network_graph, request.form is:", pf(request.form))
-    logger.info(request.url)
     start_vars = request.form
     traits = [trait.strip() for trait in start_vars['trait_list'].split(',')]
     if traits[0] != "":
@@ -963,9 +869,6 @@ def test_corr_compute_page():
 
 @app.route("/corr_matrix", methods=('POST',))
 def corr_matrix_page():
-    logger.info("In corr_matrix, request.form is:", pf(request.form))
-    logger.info(request.url)
-
     start_vars = request.form
     traits = [trait.strip() for trait in start_vars['trait_list'].split(',')]
     if len(traits) > 1:
@@ -981,7 +884,6 @@ def corr_matrix_page():
 
 @app.route("/corr_scatter_plot")
 def corr_scatter_plot_page():
-    logger.info(request.url)
     template_vars = corr_scatter_plot.CorrScatterPlot(request.args)
     template_vars.js_data = json.dumps(template_vars.js_data,
                                        default=json_default_handler,
@@ -991,7 +893,6 @@ def corr_scatter_plot_page():
 
 @app.route("/snp_browser", methods=('GET',))
 def snp_browser_page():
-    logger.info(request.url)
     template_vars = snp_browser.SnpBrowser(request.args)
 
     return render_template("snp_browser.html", **template_vars.__dict__)
@@ -1006,7 +907,6 @@ def db_info_page():
 
 @app.route("/snp_browser_table", methods=('GET',))
 def snp_browser_table():
-    logger.info(request.url)
     snp_table_data = snp_browser.SnpBrowser(request.args)
     current_page = server_side.ServerSideTable(
         snp_table_data.rows_count,
@@ -1021,20 +921,17 @@ def snp_browser_table():
 @app.route("/tutorial/WebQTLTour", methods=('GET',))
 def tutorial_page():
     # ZS: Currently just links to GN1
-    logger.info(request.url)
     return redirect("http://gn1.genenetwork.org/tutorial/WebQTLTour/")
 
 
 @app.route("/tutorial/security", methods=('GET',))
 def security_tutorial_page():
     # ZS: Currently just links to GN1
-    logger.info(request.url)
     return render_template("admin/security_help.html")
 
 
 @app.route("/submit_bnw", methods=('POST',))
 def submit_bnw():
-    logger.info(request.url)
     return render_template("empty_collection.html", **{'tool': 'Correlation Matrix'})
 
 # Take this out or secure it before putting into production
@@ -1042,7 +939,6 @@ def submit_bnw():
 
 @app.route("/get_temp_data")
 def get_temp_data():
-    logger.info(request.url)
     temp_uuid = request.args['key']
     return flask.jsonify(temp_data.TempData(temp_uuid).get_all())