Removed svg.py, which I know isn't used, and webqtlFormData, which I'm pretty sure also isn't used any more.

Also removed some other unused code from the files listed
author: zsloan 2018-04-09 23:07:33 +0000
committer: zsloan 2018-04-09 23:07:33 +0000
commit: 23ef6a91c1dce4c9258dfb2bc24ee7e0004f509d (patch)
tree: 15c04aaa974e8b6eea087c0fab5947763d774795 /wqflask/wqflask
parent: bd6d36ddb366a3ee427a0c237ebf8f672606ff19 (diff)
download: genenetwork2-23ef6a91c1dce4c9258dfb2bc24ee7e0004f509d.tar.gz
3 files changed, 22 insertions, 126 deletions
diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py
index 73072423..abf9fc89 100644
--- a/wqflask/wqflask/correlation/show_corr_results.py
+++ b/wqflask/wqflask/correlation/show_corr_results.py
@@ -296,60 +296,8 @@ class CorrelationResults(object):
             if self.corr_type != "tissue" and self.dataset.type == "ProbeSet" and self.target_dataset.type == "ProbeSet":
                 self.do_tissue_correlation_for_trait_list()
 
-            #print("self.correlation_results: ", pf(self.correlation_results))
-
         self.json_results = generate_corr_json(self.correlation_results, self.this_trait, self.dataset, self.target_dataset)
 
-        #XZ, 09/18/2008: get all information about the user selected database.
-        #target_db_name = fd.corr_dataset
-        #self.target_db_name = start_vars['corr_dataset']
-
-        # Zach said this is ok
-        # Auth if needed
-        #try:
-        #    auth_user_for_db(self.db, self.cursor, self.target_db_name, self.privilege, self.userName)
-        #except AuthException as e:
-        #    detail = [e.message]
-        #    return self.error(detail)
-
-        #XZ, 09/18/2008: filter out the strains that have no value.
-        #self.sample_names, vals, vars, N = fd.informativeStrains(sample_list)
-
-        #print("samplenames is:", pf(self.sample_names))
-        #CF - If less than a minimum number of strains/cases in common, don't calculate anything
-        #if len(self.sample_names) < self.corr_min_informative:
-        #    detail = ['Fewer than %d strain data were entered for %s data set. No calculation of correlation has been attempted.' % (self.corr_min_informative, fd.RISet)]
-        #    self.error(heading=None, detail=detail)
-
-        #correlation_method = self.CORRELATION_METHODS[self.method]
-        #rankOrder = self.RANK_ORDERS[self.method]
-
-        # CF - Number of results returned
-        # Todo: Get rid of self.returnNumber
-
-        #self.record_count = 0
-
-        #myTrait = get_custom_trait(fd, self.cursor)
-
-
-        # We will not get Literature Correlations if there is no GeneId because there is nothing
-        # to look against
-        #self.geneid = self.this_trait.geneid
-
-        # We will not get Tissue Correlations if there is no gene symbol because there is nothing to look against
-        #self.trait_symbol = myTrait.symbol
-
-
-        #XZ, 12/12/2008: if the species is rat or human, translate the geneid to mouse geneid
-        #self.input_trait_mouse_gene_id = self.translateToMouseGeneID(self.dataset.group.species, self.geneid)
-
-        #XZ: As of Nov/13/2010, this dataset is 'UTHSC Illumina V6.2 RankInv B6 D2 average CNS GI average (May 08)'
-        #self.tissue_probeset_freeze_id = 1
-
-        #traitList = self.correlate()
-
-        #print("Done doing correlation calculation")
-
 ############################################################################################################################################
 
     def get_formatted_corr_type(self):
diff --git a/wqflask/wqflask/marker_regression/marker_regression_gn1.py b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
index 632c2f8f..81da8976 100644
--- a/wqflask/wqflask/marker_regression/marker_regression_gn1.py
+++ b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
@@ -190,21 +190,6 @@ class MarkerRegression(object):
             self.js_data = start_vars['js_data']
         self.trimmed_markers = start_vars['trimmed_markers'] #Top markers to display in table
 
-        #ZS: Think I can just get all this from dataset object now
-        #RISet and Species
-        #if not fd.genotype:
-        #    fd.readGenotype()
-        #
-        #fd.parentsf14regression = fd.formdata.getvalue('parentsf14regression')
-        #
-        #if ((fd.parentsf14regression == 'on') and fd.genotype_2):
-        #    fd.genotype = fd.genotype_2
-        #else:
-        #    fd.genotype = fd.genotype_1
-        #fd.strainlist = list(fd.genotype.prgy)
-        #
-        #self.species = webqtlDatabaseFunction.retrieveSpecies(cursor=self.cursor, RISet=fd.RISet)
-
         if self.dataset.group.species == "rat":
             self._ucscDb = "rn3"
         elif self.dataset.group.species == "mouse":
@@ -212,7 +197,6 @@ class MarkerRegression(object):
         else:
             self._ucscDb = ""
 
-
         #####################################
         # Options
         #####################################
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 3c2cca94..8ff359a7 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -57,7 +57,6 @@ from utility import temp_data
 from utility.tools import SQL_URI,TEMPDIR,USE_REDIS,USE_GN_SERVER,GN_SERVER_URL,GN_VERSION,JS_TWITTER_POST_FETCHER_PATH,JS_GUIX_PATH, CSS_PATH
 from utility.helper_functions import get_species_groups
 
-from base import webqtlFormData
 from base.webqtlConfig import GENERATED_IMAGE_DIR
 from utility.benchmark import Bench
 
@@ -163,62 +162,37 @@ def css(filename):
 def twitter(filename):
     return send_from_directory(JS_TWITTER_POST_FETCHER_PATH, filename)
 
-#@app.route("/data_sharing")
-#def data_sharing_page():
-#    logger.info("In data_sharing")
-#    fd = webqtlFormData.webqtlFormData(request.args)
-#    logger.info("1Have fd")
-#    sharingInfoObject = SharingInfo.SharingInfo(request.args['GN_AccessionId'], None)
-#    info, htmlfilelist = sharingInfoObject.getBody(infoupdate="")
-#    logger.info("type(htmlfilelist):", type(htmlfilelist))
-#    htmlfilelist = htmlfilelist.encode("utf-8")
-#    #template_vars = SharingInfo.SharingInfo(request.args['GN_AccessionId'], None)
-#    logger.info("1 Made it to rendering")
-#    return render_template("data_sharing.html",
-#                            info=info,
-#                            htmlfilelist=htmlfilelist)
-
-
 @app.route("/search", methods=('GET',))
 def search_page():
     logger.info("in search_page")
     logger.info(request.url)
-    if 'info_database' in request.args:
-        logger.info("Going to sharing_info_page")
-        template_vars = sharing_info_page()
-        if template_vars.redirect_url:
-            logger.info("Going to redirect")
-            return flask.redirect(template_vars.redirect_url)
-        else:
-            return render_template("data_sharing.html", **template_vars.__dict__)
+    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:
-        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("Skipping Redis cache (USE_REDIS=False)")
 
-        logger.info("request.args is", request.args)
-        the_search = search_results.SearchResultPage(request.args)
-        result = the_search.__dict__
-        valid_search = result['search_term_exists']
+    logger.info("request.args is", request.args)
+    the_search = search_results.SearchResultPage(request.args)
+    result = the_search.__dict__
+    valid_search = result['search_term_exists']
 
-        logger.debugf("result", result)
+    logger.debugf("result", result)
 
-        if USE_REDIS and valid_search:
-            Redis.set(key, pickle.dumps(result, pickle.HIGHEST_PROTOCOL))
-            Redis.expire(key, 60*60)
+    if USE_REDIS and valid_search:
+        Redis.set(key, pickle.dumps(result, pickle.HIGHEST_PROTOCOL))
+        Redis.expire(key, 60*60)
 
-        if valid_search:
-            return render_template("search_result_page.html", **result)
-        else:
-            return render_template("search_error.html")
+    if valid_search:
+        return render_template("search_result_page.html", **result)
+    else:
+        return render_template("search_error.html")
 
 @app.route("/gsearch", methods=('GET',))
 def gsearchact():
@@ -741,7 +715,6 @@ def network_graph_page():
 def corr_compute_page():
     logger.info("In corr_compute, request.form is:", pf(request.form))
     logger.info(request.url)
-    #fd = webqtlFormData.webqtlFormData(request.form)
     template_vars = show_corr_results.CorrelationResults(request.form)
     return render_template("correlation_page.html", **template_vars.__dict__)
 
@@ -777,15 +750,6 @@ def submit_bnw():
     template_vars = get_bnw_input(request.form)
     return render_template("empty_collection.html", **{'tool':'Correlation Matrix'})
 
-# Todo: Can we simplify this? -Sam
-def sharing_info_page():
-    """Info page displayed when the user clicks the "Info" button next to the dataset selection"""
-    logger.info("In sharing_info_page")
-    logger.info(request.url)
-    fd = webqtlFormData.webqtlFormData(request.args)
-    template_vars = SharingInfoPage.SharingInfoPage(fd)
-    return template_vars
-
 # Take this out or secure it before putting into production
 @app.route("/get_temp_data")
 def get_temp_data():
author	zsloan	2018-04-09 23:07:33 +0000
committer	zsloan	2018-04-09 23:07:33 +0000
commit	23ef6a91c1dce4c9258dfb2bc24ee7e0004f509d (patch)
tree	15c04aaa974e8b6eea087c0fab5947763d774795 /wqflask/wqflask
parent	bd6d36ddb366a3ee427a0c237ebf8f672606ff19 (diff)
download	genenetwork2-23ef6a91c1dce4c9258dfb2bc24ee7e0004f509d.tar.gz