From ce160e61fffbc3370497a1adc299dad230411b72 Mon Sep 17 00:00:00 2001 From: zsloan Date: Fri, 5 Aug 2016 20:53:38 +0000 Subject: Fixed issue that caused some interval mapping results to be wrong; the cause seems to be related to some strains being renamed in the genofiles Added a message to the Add to Collection page warning users that anonymous collections will only be stored for 5 days Updated genofiles --- wqflask/base/webqtlCaseData.py | 4 ++++ 1 file changed, 4 insertions(+) (limited to 'wqflask/base') diff --git a/wqflask/base/webqtlCaseData.py b/wqflask/base/webqtlCaseData.py index c80fcb65..8df9939e 100644 --- a/wqflask/base/webqtlCaseData.py +++ b/wqflask/base/webqtlCaseData.py @@ -52,6 +52,10 @@ class webqtlCaseData(object): str += " variance=%2.3f" % self.variance if self.num_cases != None: str += " ndata=%d" % self.num_cases + if self.name != None: + str += " name=%s" % self.name + if self.name2 != None: + str += " name2=%s" % self.name2 return str @property -- cgit v1.2.3 From e695e8d162ca04f41694a525e93ced1b9d23a85b Mon Sep 17 00:00:00 2001 From: zsloan Date: Tue, 16 Aug 2016 20:30:38 +0000 Subject: Users can now select specific traits from collection when using collection tools (correlation matrix, wgcna, etc) To do the above, changed the way form submission worked for those features; previously each feature had its own form, but that was dumb so instead I wrote a javascript function that just changed a single form's target url Duplicate traits can no longer by added to collections Fixed the digits for a few table columns in collection (additive effect, etc). --- wqflask/base/trait.py | 1 - wqflask/utility/helper_functions.py | 16 +- wqflask/wqflask/collect.py | 41 +--- wqflask/wqflask/model.py | 2 - wqflask/wqflask/templates/collections/add.html | 11 - wqflask/wqflask/templates/collections/view.html | 235 ++++++++++++---------- wqflask/wqflask/templates/search_result_page.html | 2 +- 7 files changed, 149 insertions(+), 159 deletions(-) (limited to 'wqflask/base') diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py index 9566c192..f18481a8 100644 --- a/wqflask/base/trait.py +++ b/wqflask/base/trait.py @@ -116,7 +116,6 @@ class GeneralTrait(object): return stringy - def display_name(self): stringy = "" if self.dataset and self.name: diff --git a/wqflask/utility/helper_functions.py b/wqflask/utility/helper_functions.py index 15f60765..149ee553 100644 --- a/wqflask/utility/helper_functions.py +++ b/wqflask/utility/helper_functions.py @@ -4,6 +4,8 @@ from base.trait import GeneralTrait from base import data_set from base.species import TheSpecies +from wqflask import user_manager + def get_species_dataset_trait(self, start_vars): #assert type(read_genotype) == type(bool()), "Expecting boolean value for read_genotype" @@ -23,13 +25,15 @@ def get_species_dataset_trait(self, start_vars): def get_trait_db_obs(self, trait_db_list): - + if isinstance(trait_db_list, basestring): + trait_db_list = trait_db_list.split(",") + self.trait_list = [] - for i, trait_db in enumerate(trait_db_list): - if i == (len(trait_db_list) - 1): - break - trait_name, dataset_name = trait_db.split(":") - #print("dataset_name:", dataset_name) + for trait in trait_db_list: + data, _separator, hmac = trait.rpartition(':') + data = data.strip() + assert hmac==user_manager.actual_hmac_creation(data), "Data tampering?" + trait_name, dataset_name = data.split(":") dataset_ob = data_set.create_dataset(dataset_name) trait_ob = GeneralTrait(dataset=dataset_ob, name=trait_name, diff --git a/wqflask/wqflask/collect.py b/wqflask/wqflask/collect.py index 5484633b..7e7aba89 100644 --- a/wqflask/wqflask/collect.py +++ b/wqflask/wqflask/collect.py @@ -165,12 +165,19 @@ class UserCollection(object): return create_new("Default") else: uc = model.UserCollection.query.get(params['existing_collection']) - members = uc.members_as_set() #set(json.loads(uc.members)) + members = list(uc.members_as_set()) #set(json.loads(uc.members)) len_before = len(members) traits = process_traits(params['traits']) - - members_now = list(members | traits) + + members_now = members + for trait in traits: + if trait in members: + continue + else: + members_now.append(trait) + + #members_now = list(members | traits) len_now = len(members_now) uc.members = json.dumps(members_now) @@ -184,28 +191,6 @@ class UserCollection(object): # Probably have to change that return redirect(url_for('view_collection', uc_id=uc.id)) - def remove_traits(self, params): - - #params = request.form - print("params are:", params) - uc_id = params['uc_id'] - uc = model.UserCollection.query.get(uc_id) - traits_to_remove = params.getlist('traits[]') - print("traits_to_remove are:", traits_to_remove) - traits_to_remove = process_traits(traits_to_remove) - print("\n\n after processing, traits_to_remove:", traits_to_remove) - all_traits = uc.members_as_set() - print(" all_traits:", all_traits) - members_now = all_traits - traits_to_remove - print(" members_now:", members_now) - print("Went from {} to {} members in set.".format(len(all_traits), len(members_now))) - uc.members = json.dumps(list(members_now)) - uc.changed_timestamp = datetime.datetime.utcnow() - db_session.commit() - - # We need to return something so we'll return this...maybe in the future - # we can use it to check the results - return str(len(members_now)) def report_change(len_before, len_now): new_length = len_now - len_before @@ -218,8 +203,6 @@ def report_change(len_before, len_now): print("No new traits were added.") - - @app.route("/collections/add") def collections_add(): traits=request.args['traits'] @@ -329,7 +312,6 @@ def list_collections(): @app.route("/collections/remove", methods=('POST',)) def remove_traits(): - params = request.form print("params are:", params) @@ -337,14 +319,11 @@ def remove_traits(): uc_id = params['uc_id'] uc = model.UserCollection.query.get(uc_id) traits_to_remove = params.getlist('traits[]') - print("traits_to_remove are:", traits_to_remove) traits_to_remove = process_traits(traits_to_remove) print("\n\n after processing, traits_to_remove:", traits_to_remove) all_traits = uc.members_as_set() - print(" all_traits:", all_traits) members_now = all_traits - traits_to_remove print(" members_now:", members_now) - print("Went from {} to {} members in set.".format(len(all_traits), len(members_now))) uc.members = json.dumps(list(members_now)) uc.changed_timestamp = datetime.datetime.utcnow() db_session.commit() diff --git a/wqflask/wqflask/model.py b/wqflask/wqflask/model.py index 17343186..5321e420 100644 --- a/wqflask/wqflask/model.py +++ b/wqflask/wqflask/model.py @@ -177,12 +177,10 @@ class UserCollection(Base): except: return 0 - #@property #def display_num_members(self): # return display_collapsible(self.num_members) - def members_as_set(self): return set(json.loads(self.members)) diff --git a/wqflask/wqflask/templates/collections/add.html b/wqflask/wqflask/templates/collections/add.html index c5598e84..47b87d73 100644 --- a/wqflask/wqflask/templates/collections/add.html +++ b/wqflask/wqflask/templates/collections/add.html @@ -6,16 +6,6 @@
- -
Create a new named collection @@ -28,7 +18,6 @@ {% endif %}
-
Or add to an existing collection diff --git a/wqflask/wqflask/templates/collections/view.html b/wqflask/wqflask/templates/collections/view.html index 68d2886f..6a11600c 100644 --- a/wqflask/wqflask/templates/collections/view.html +++ b/wqflask/wqflask/templates/collections/view.html @@ -21,64 +21,41 @@
- - {% if uc %} - - {% else %} - - {% endif %} -
- -
- -
- {% if uc %} - - {% endif %} - -
- -
-
-
- {% if uc %} - - {% endif %} - -
- -
-
-
- {% if uc %} - - {% endif %} - -
- -
-
-
- {% if uc %} - - {% endif %} - -
- -
-
+
+ {% if uc %} + + {% endif %} + + +
+ +
+
+ +
+
+ +
+
+ +
+
+ +
+
@@ -92,53 +69,54 @@

-
- - - - - - - - - - - - - - - - - {% for this_trait in trait_obs %} - - - - - - - - - - - - - - {% endfor %} - - -
IndexRecordDescriptionLocationMeanMax LRS ?Max LRS LocationAdditive Effect ?
- - {{ loop.index }} - - {{ this_trait.name }} - - {{ this_trait.description_display }}{{ this_trait.location_repr }}{{ this_trait.mean }}{{ this_trait.LRS_score_repr }}{{ this_trait.LRS_location_repr }}{{ this_trait.additive }}
-
-
+
+ + + + + + + + + + + + + + + + + + {% for this_trait in trait_obs %} + + + + + + + + + + + + + + {% endfor %} + + +
IndexDatasetRecordDescriptionLocationMeanMax LRS ?Max LRS LocationAdditive Effect ?
+ + {{ loop.index }}{{ this_trait.dataset.name }} + + {{ this_trait.name }} + + {{ this_trait.description_display }}{{ this_trait.location_repr }}{{ '%0.3f' % this_trait.mean|float }}{{ '%0.3f' % this_trait.LRS_score_repr|float }}{{ this_trait.LRS_location_repr }}{{ '%0.3f' % this_trait.additive|float }}
+
+
@@ -175,13 +153,14 @@ { "type": "natural" }, { "type": "natural" }, { "type": "natural" }, + { "type": "natural" }, { "type": "natural", "width": "35%" }, { "type": "natural", "width": "15%" }, { "type": "cust-txt" }, { "type": "natural", - "width": "12%" }, + "width": "9%" }, { "type": "natural", "width": "15%" }, { "type": "natural" } @@ -193,7 +172,7 @@ title: 'collection', fieldBoundary: '"', exportOptions: { - columns: [1, 2, 3, 4, 5, 6, 7, 8] + columns: [1, 2, 3, 4, 5, 6, 7, 8, 9] } } ], @@ -208,6 +187,48 @@ } ); console.timeEnd("Creating table"); + submit_special = function(url) { + $("#collection_form").attr("action", url); + return $("#collection_form").submit(); + }; + + $("#delete").on("click", function() { + url = $(this).data("url") + return submit_special(url) + }); + + $("#corr_matrix").on("click", function() { + traits = $("#trait_table input:checked").map(function() { + return $(this).val(); + }).get(); + $("#trait_list").val(traits) + url = $(this).data("url") + return submit_special(url) + }); + $("#wgcna_setup").on("click", function() { + traits = $("#trait_table input:checked").map(function() { + return $(this).val(); + }).get(); + $("#trait_list").val(traits) + url = $(this).data("url") + return submit_special(url) + }); + $("#ctl_setup").on("click", function() { + traits = $("#trait_table input:checked").map(function() { + return $(this).val(); + }).get(); + $("#trait_list").val(traits) + url = $(this).data("url") + return submit_special(url) + }); + $("#heatmap").on("click", function() { + traits = $("#trait_table input:checked").map(function() { + return $(this).val(); + }).get(); + $("#trait_list").val(traits) + url = $(this).data("url") + return submit_special(url) + }); }); diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html index 02c97862..bf1475ff 100644 --- a/wqflask/wqflask/templates/search_result_page.html +++ b/wqflask/wqflask/templates/search_result_page.html @@ -122,7 +122,7 @@ {{ this_trait.pubmed_text }} - {{ this_trait.LRS_score_repr }} + {{ '%0.3f' % this_trait.LRS_score_repr|float }} {{ this_trait.LRS_location_repr }} {{ '%0.3f' % this_trait.additive|float }} {% elif dataset.type == 'Geno' %} -- cgit v1.2.3 From 4695840f6100d566c251eaa09498a60f6d7cfe29 Mon Sep 17 00:00:00 2001 From: zsloan Date: Wed, 24 Aug 2016 19:01:20 +0000 Subject: Replaced post-publication description with pre-publication description for confidential phenotype traits in search results and trait pages Fixed table style for mapping results and interval analyst tables and added additive/dominance effect columns to the former Fixed mapping figure X-axis to accurately label Centimorgans vs Megabases (previously it would always say Megabases) Removed the "Sequence Site" marker from mapping result figure when mapping with genetics (centimorgans) scale Removed some unused javascript libary imports from search/global search pages --- wqflask/base/trait.py | 15 +++-- .../wqflask/marker_regression/marker_regression.py | 2 - .../marker_regression/marker_regression_gn1.py | 13 ++-- wqflask/wqflask/templates/gsearch_gene.html | 2 +- wqflask/wqflask/templates/gsearch_pheno.html | 2 +- .../wqflask/templates/marker_regression_gn1.html | 77 ++++++++++++++++------ wqflask/wqflask/templates/search_result_page.html | 2 - 7 files changed, 78 insertions(+), 35 deletions(-) (limited to 'wqflask/base') diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py index f18481a8..900e050c 100644 --- a/wqflask/base/trait.py +++ b/wqflask/base/trait.py @@ -322,7 +322,7 @@ class GeneralTrait(object): #phenotype traits, then display the pre-publication description instead #of the post-publication description if self.confidential: - self.description_display = "" + self.description_display = self.pre_publication_description #if not webqtlUtil.hasAccessToConfidentialPhenotypeTrait( # privilege=self.dataset.privilege, @@ -330,11 +330,11 @@ class GeneralTrait(object): # authorized_users=self.authorized_users): # # description = self.pre_publication_description - - if description: - self.description_display = description.strip() else: - self.description_display = "" + if description: + self.description_display = description.strip() + else: + self.description_display = "" if not self.year.isdigit(): self.pubmed_text = "N/A" @@ -612,7 +612,10 @@ class GeneralTrait(object): if self.probe_target_description: formatted += "; " + self.probe_target_description elif self.dataset.type == 'Publish': - formatted = self.post_publication_description + if self.confidential: + formatted = self.pre_publication_description + else: + formatted = self.post_publication_description else: formatted = "Not available" return formatted.capitalize() diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py index 89af856e..a53afd5a 100644 --- a/wqflask/wqflask/marker_regression/marker_regression.py +++ b/wqflask/wqflask/marker_regression/marker_regression.py @@ -702,8 +702,6 @@ class MarkerRegression(object): control = control_geno, nboot = self.num_bootstrap) else: - # reaper_results = genotype.regression(strains = self.samples, - # trait = self.vals) reaper_results = genotype.regression(strains = trimmed_samples, trait = trimmed_values) diff --git a/wqflask/wqflask/marker_regression/marker_regression_gn1.py b/wqflask/wqflask/marker_regression/marker_regression_gn1.py index 4f52bd55..f902afb7 100644 --- a/wqflask/wqflask/marker_regression/marker_regression_gn1.py +++ b/wqflask/wqflask/marker_regression/marker_regression_gn1.py @@ -810,7 +810,7 @@ class MarkerRegression(object): #draw bootstap #if self.bootChecked and not self.multipleInterval: - # self.drawBootStrapResult(canvas, self.nboot, drawAreaHeight, plotXScale, offset=newoffset) + # self.drawBootStrapResult(canvas, self.nboot, drawAreaHeight, plotXScale, offset=newoffset, zoom= zoom, startMb=startMb, endMb = endMb) # Draw clickable region and gene band if selected if self.plotScale == 'physic' and self.selectedChr > -1: @@ -857,7 +857,7 @@ class MarkerRegression(object): BootCoord = [] i = 0 startX = xLeftOffset - + if self.selectedChr == -1: #ZS: If viewing full genome/all chromosomes for j, _chr in enumerate(self.genotype): BootCoord.append( []) @@ -876,7 +876,7 @@ class MarkerRegression(object): for _locus in _chr: if _chr.name == self.ChrList[self.selectedChr][0]: if self.plotScale == 'physic': - Xc = startX + (_locus.Mb-self.startMb)*plotXScale + Xc = startX + (_locus.Mb-startMb)*plotXScale else: Xc = startX + (_locus.cM-_chr[0].cM)*plotXScale BootCoord[-1].append([Xc, self.bootResult[i]]) @@ -1017,7 +1017,7 @@ class MarkerRegression(object): else: locPixel += (Mb*(_chr[-1].cM-_chr[0].cM)/self.ChrLengthCMList[i])*plotXScale break - if locPixel >= 0: + if locPixel >= 0 and self.plotScale == 'physic': traitPixel = ((locPixel, yZero), (locPixel-6, yZero+12), (locPixel+6, yZero+12)) canvas.drawPolygon(traitPixel, edgeColor=pid.black, fillColor=self.TRANSCRIPT_LOCATION_COLOR, closed=1) @@ -1762,6 +1762,7 @@ class MarkerRegression(object): strYLoc + canvas.fontHeight(MBLabelFont)+ 10*(zoom%2) + 10, font=megabaseLabelFont, color=pid.black) pass else: + strYLoc = yZero + spacingFromLabelToAxis + canvas.fontHeight(MBLabelFont) + 8 ChrAInfo = [] preLpos = -1 distinctCount = 0.0 @@ -1847,6 +1848,10 @@ class MarkerRegression(object): if j == 0: canvas.drawLine(startPosX,yZero,startPosX,yZero+40, color=lineColor) startPosX += (self.ChrLengthDistList[j]+self.GraphInterval)*plotXScale + + centimorganLabelFont = pid.Font(ttf="verdana", size=18*zoom*1.5, bold=0) + canvas.drawString("Centimorgans", xLeftOffset + (plotWidth - canvas.stringWidth("Megabases", font=centimorganLabelFont))/2, + strYLoc + canvas.fontHeight(MBLabelFont)+ 10*(zoom%2) + 10, font=centimorganLabelFont, color=pid.black) canvas.drawLine(xLeftOffset, yZero, xLeftOffset+plotWidth, yZero, color=pid.black, width=X_AXIS_THICKNESS) # Draw the X axis itself diff --git a/wqflask/wqflask/templates/gsearch_gene.html b/wqflask/wqflask/templates/gsearch_gene.html index a50157ce..2d970b36 100644 --- a/wqflask/wqflask/templates/gsearch_gene.html +++ b/wqflask/wqflask/templates/gsearch_gene.html @@ -93,7 +93,7 @@ {% block js %} - + diff --git a/wqflask/wqflask/templates/gsearch_pheno.html b/wqflask/wqflask/templates/gsearch_pheno.html index b28a34df..be4981bb 100644 --- a/wqflask/wqflask/templates/gsearch_pheno.html +++ b/wqflask/wqflask/templates/gsearch_pheno.html @@ -86,7 +86,7 @@ {% block js %} - + diff --git a/wqflask/wqflask/templates/marker_regression_gn1.html b/wqflask/wqflask/templates/marker_regression_gn1.html index c5cb278c..7454b650 100644 --- a/wqflask/wqflask/templates/marker_regression_gn1.html +++ b/wqflask/wqflask/templates/marker_regression_gn1.html @@ -169,14 +169,16 @@
-
- {% if selectedChr == -1 %} + {% if selectedChr == -1 %} +

Results

+
- + + {% if plotScale == "centimorgan" %} @@ -184,7 +186,12 @@ {% else %} {% endif %} - + {% if 'additive' in trimmed_markers[0] %} + + {% endif %} + {% if 'dominance' in trimmed_markers[0] %} + + {% endif %} @@ -196,6 +203,7 @@ value="{{ marker.name }}" checked="checked"> + {% if LRS_LOD == "LOD" %} {% if 'lod_score' in marker %} @@ -211,13 +219,22 @@ {% endif %} - + {% if 'additive' in marker %} + + {% endif %} + {% if 'dominance' in marker %} + + {% endif %} {% endfor %}
IndexRowLocus {{ LRS_LOD }} ChrMbLocusAdd EffDom Eff
{{ loop.index }}{{ marker.name }}{{ '%0.2f' | format(marker.lod_score|float) }}{{marker.chr}} {{ '%0.6f' | format(marker.Mb|float) }}{{ marker.name }}{{ '%0.3f' | format(marker.additive|float) }}{{ '%0.2f' | format(marker.dominance|float) }}
- {% else %} +
+
+ {% else %} +

Interval Analyst

+
@@ -236,8 +253,9 @@ {% endfor %}
- {% endif %} +
+ {% endif %}
@@ -251,7 +269,7 @@ - + @@ -274,26 +292,35 @@ - @@ -171,7 +170,6 @@ - + + + + + + + + + + + +{% endblock %} diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index 63dceb42..41e2c7be 100644 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -38,6 +38,7 @@ from wqflask.show_trait import export_trait_data from wqflask.heatmap import heatmap from wqflask.marker_regression import marker_regression from wqflask.marker_regression import marker_regression_gn1 +from wqflask.network_graph import network_graph from wqflask.correlation import show_corr_results from wqflask.correlation_matrix import show_corr_matrix from wqflask.correlation import corr_scatter_plot @@ -530,6 +531,22 @@ def export_pdf(): response.headers["Content-Disposition"] = "attachment; filename=%s"%filename return response +@app.route("/network_graph", methods=('POST',)) +def network_graph_page(): + logger.info("In network_graph, request.form is:", pf(request.form)) + + start_vars = request.form + traits = [trait.strip() for trait in start_vars['trait_list'].split(',')] + if traits[0] != "": + template_vars = network_graph.NetworkGraph(start_vars) + template_vars.js_data = json.dumps(template_vars.js_data, + default=json_default_handler, + indent=" ") + + return render_template("network_graph.html", **template_vars.__dict__) + else: + return render_template("empty_collection.html", **{'tool':'Network Graph'}) + @app.route("/corr_compute", methods=('POST',)) def corr_compute_page(): logger.info("In corr_compute, request.form is:", pf(request.form)) -- cgit v1.2.3 From ec7d4e1198bc8d2f83ce99b41e2084fbce6a0be7 Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Sat, 10 Sep 2016 11:43:21 +0200 Subject: Support for running maintenance scripts so they can pick up all webserver settings Run with ./bin/genenetwork2 ~/my_settings.py -c ./wqflask/maintenance/gen_select_dataset.py --- bin/genenetwork2 | 27 ++++++++++++++++++++++++--- wqflask/base/data_set.py | 2 +- wqflask/base/webqtlConfig.py | 1 - wqflask/maintenance/gen_select_dataset.py | 26 +++++++++++++++++--------- wqflask/utility/tools.py | 1 + 5 files changed, 43 insertions(+), 14 deletions(-) (limited to 'wqflask/base') diff --git a/bin/genenetwork2 b/bin/genenetwork2 index d3bf3299..3a8c3ff4 100755 --- a/bin/genenetwork2 +++ b/bin/genenetwork2 @@ -1,6 +1,14 @@ #! /bin/bash # -# This will run the GN2 server (with default settings if none supplied). +# This will run the GN2 server (with default settings if none supplied). Pass in +# your own settings file, e.g. +# +# ./bin/genenetwork2 ~/my_settings.py +# +# To run a maintenance script with settings (instead of the webserver) add that with +# a -c switch, e.g. +# +# ./bin/genenetwork2 ~/my_settings.py -c ./wqflask/maintenance/gen_select_dataset.py # # Environment settings can be used to preconfigure as well as a # settings.py file. @@ -18,7 +26,12 @@ echo $GN2_BASE_PATH # Handle settings parameter settings=$1 -if [ -z $settings ]; then settings=$GN2_BASE_PATH/etc/default_settings.py ; fi +if [ -z $settings ]; then + # get default + settings=$GN2_BASE_PATH/etc/default_settings.py +else + shift +fi if [ ! -e $settings ]; then echo "ERROR: can not locate settings file - pass it in the command line" exit 1 @@ -32,7 +45,15 @@ export PYTHONPATH=$GN2_BASE_PATH/wqflask:$PYTHONPATH if [ -z $TEMPDIR ]; then TEMPDIR="/tmp" fi - + +# Now handle command parameter -c +if [ $1 = '-c' ] ; then + echo PYTHONPATH=$PYTHONPATH + echo RUNNING COMMAND $2 + /usr/bin/env python $2 + exit 0 +fi + echo "Starting the redis server:" echo -n "dir $TEMPDIR dbfilename gn2.rdb diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index 1b4e1195..6cd3c8e6 100644 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -91,7 +91,7 @@ Publish or ProbeSet. E.g. if USE_GN_SERVER: data = menu_main() else: - file_name = "wqflask/static/new/javascript/dataset_menu_structure.json" + file_name = "wqflask/wqflask/static/new/javascript/dataset_menu_structure.json" with open(file_name, 'r') as fh: data = json.load(fh) diff --git a/wqflask/base/webqtlConfig.py b/wqflask/base/webqtlConfig.py index f76d8140..8c67a6fd 100644 --- a/wqflask/base/webqtlConfig.py +++ b/wqflask/base/webqtlConfig.py @@ -80,4 +80,3 @@ PORTADDR = "http://50.16.251.170" INFOPAGEHREF = '/dbdoc/%s.html' CGIDIR = '/webqtl/' #XZ: The variable name 'CGIDIR' should be changed to 'PYTHONDIR' SCRIPTFILE = 'main.py' - diff --git a/wqflask/maintenance/gen_select_dataset.py b/wqflask/maintenance/gen_select_dataset.py index d39bf4a5..5c25c15b 100644 --- a/wqflask/maintenance/gen_select_dataset.py +++ b/wqflask/maintenance/gen_select_dataset.py @@ -1,7 +1,9 @@ """Script that generates the data for the main dropdown menus on the home page Writes out data as /static/new/javascript/dataset_menu_structure.json -It needs to be run manually when database has been changed. +It needs to be run manually when database has been changed. Run it as + + python gen_select_dataset.py """ @@ -37,9 +39,15 @@ from __future__ import print_function, division #print("cdict is:", cdict) import sys -# import zach_settings # no hard code paths! -# import MySQLdb +# NEW: Note we prepend the current path - otherwise a guix instance of GN2 is used instead +sys.path.insert(0,'./wqflask') +# NEW: import app to avoid a circular dependency on utility.tools +from wqflask import app + +from utility.tools import locate, locate_ignore_error, TEMPDIR, SQL_URI + +import MySQLdb # import simplejson as json import urlparse @@ -55,14 +63,13 @@ from pprint import pformat as pf #conn = Engine.connect() -print('ERROR: This conversion is now OBSOLETE as the menu gets built from the database in Javascript using GN_SERVER instead!') -sys.exit() +print('WARNING: This conversion is now OBSOLETE as the menu gets built from the database in Javascript using GN_SERVER instead!') def parse_db_uri(db_uri): """Converts a database URI to the db name, host name, user name, and password""" - parsed_uri = urlparse.urlparse(zach_settings.DB_URI) + parsed_uri = urlparse.urlparse(SQL_URI) db_conn_info = dict( db = parsed_uri.path[1:], @@ -70,6 +77,7 @@ def parse_db_uri(db_uri): user = parsed_uri.username, passwd = parsed_uri.password) + print(db_conn_info) return db_conn_info @@ -258,7 +266,7 @@ def build_datasets(species, group, type_name): def main(): """Generates and outputs (as json file) the data for the main dropdown menus on the home page""" - parse_db_uri(zach_settings.SQL_URI) + parse_db_uri(SQL_URI) species = get_species() groups = get_groups(species) @@ -281,7 +289,7 @@ def main(): #print("data:", data) - output_file = """../wqflask/static/new/javascript/dataset_menu_structure.json""" + output_file = """./wqflask/wqflask/static/new/javascript/dataset_menu_structure.json""" with open(output_file, 'w') as fh: json.dump(data, fh, indent=" ", sort_keys=True) @@ -297,6 +305,6 @@ def _test_it(): #print("build_datasets:", pf(datasets)) if __name__ == '__main__': - Conn = MySQLdb.Connect(**parse_db_uri(zach_settings.SQL_URI)) + Conn = MySQLdb.Connect(**parse_db_uri(SQL_URI)) Cursor = Conn.cursor() main() diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py index bb8241f5..2c8cc5c5 100644 --- a/wqflask/utility/tools.py +++ b/wqflask/utility/tools.py @@ -3,6 +3,7 @@ import os import sys + from wqflask import app # Use the standard logger here to avoid a circular dependency -- cgit v1.2.3 From f399b3bf514b396de67644d4b1e2018886cecac2 Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Tue, 13 Sep 2016 09:09:21 +0200 Subject: Run scripts from ./wqflask - just like the webserver --- bin/genenetwork2 | 9 +++++---- wqflask/base/data_set.py | 2 +- wqflask/maintenance/gen_select_dataset.py | 4 ++-- 3 files changed, 8 insertions(+), 7 deletions(-) (limited to 'wqflask/base') diff --git a/bin/genenetwork2 b/bin/genenetwork2 index 3a8c3ff4..d926d6a1 100755 --- a/bin/genenetwork2 +++ b/bin/genenetwork2 @@ -13,13 +13,12 @@ # Environment settings can be used to preconfigure as well as a # settings.py file. -# Absolute path to this script, e.g. /home/user/bin/foo.sh SCRIPT=$(readlink -f "$0") -# Absolute path this script is in, thus /home/user/bin GN2_BASE_PATH=$(dirname $(dirname "$SCRIPT")) GN2_GUIX_PATH=$GN2_BASE_PATH/lib/python2.7/site-packages/genenetwork2-2.0-py2.7.egg if [ -d $GN2_GUIX_PATH ]; then + echo GN2 is running from GUIX GN2_BASE_PATH=$GN2_GUIX_PATH fi echo $GN2_BASE_PATH @@ -48,9 +47,11 @@ fi # Now handle command parameter -c if [ $1 = '-c' ] ; then + cd $GN2_BASE_PATH/wqflask + cmd=${2#wqflask/} echo PYTHONPATH=$PYTHONPATH - echo RUNNING COMMAND $2 - /usr/bin/env python $2 + echo RUNNING COMMAND $cmd + /usr/bin/env python $cmd exit 0 fi diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index 6cd3c8e6..1b4e1195 100644 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -91,7 +91,7 @@ Publish or ProbeSet. E.g. if USE_GN_SERVER: data = menu_main() else: - file_name = "wqflask/wqflask/static/new/javascript/dataset_menu_structure.json" + file_name = "wqflask/static/new/javascript/dataset_menu_structure.json" with open(file_name, 'r') as fh: data = json.load(fh) diff --git a/wqflask/maintenance/gen_select_dataset.py b/wqflask/maintenance/gen_select_dataset.py index f2f0830f..23adc4f9 100644 --- a/wqflask/maintenance/gen_select_dataset.py +++ b/wqflask/maintenance/gen_select_dataset.py @@ -40,8 +40,8 @@ from __future__ import print_function, division import sys -# NEW: Note we prepend the current path - otherwise a guix instance of GN2 is used instead -sys.path.insert(0,'./wqflask') +# NEW: Note we prepend the current path - otherwise a guix instance of GN2 may be used instead +sys.path.insert(0,'./') # NEW: import app to avoid a circular dependency on utility.tools from wqflask import app -- cgit v1.2.3 From e7693e53821747d294452c9bff7e8b0f38a0eb8e Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Sat, 24 Sep 2016 07:41:39 +0000 Subject: tools: export GENENETWORK_FILES and move cache into TMPDIR/gn2 --- etc/default_settings.py | 13 ++++++++----- wqflask/base/webqtlConfig.py | 5 +++-- wqflask/utility/tools.py | 7 +++++-- 3 files changed, 16 insertions(+), 9 deletions(-) (limited to 'wqflask/base') diff --git a/etc/default_settings.py b/etc/default_settings.py index df734f7c..9dddd0ad 100644 --- a/etc/default_settings.py +++ b/etc/default_settings.py @@ -22,7 +22,7 @@ SQLALCHEMY_DATABASE_URI = 'mysql://gn2:mysql_password@localhost/db_webqtl_s' SQLALCHEMY_POOL_RECYCLE = 3600 GN_SERVER_URL = "http://localhost:8880/" -# Flask configuration (see website) +# ---- Flask configuration (see website) TRAP_BAD_REQUEST_ERRORS = True SECURITY_CONFIRMABLE = True SECURITY_TRACKABLE = True @@ -34,8 +34,8 @@ SECURITY_POST_LOGIN_VIEW = "/thank_you" SERVER_PORT = 5003 SECRET_HMAC_CODE = '\x08\xdf\xfa\x93N\x80\xd9\\H@\\\x9f`\x98d^\xb4a;\xc6OM\x946a\xbc\xfc\x80:*\xebc' -# Behavioural settings (defaults) note that logger and log levels can -# be overridden at the module level and with enviroment settings +# ---- Behavioural settings (defaults) note that logger and log levels can +# be overridden at the module level and with enviroment settings WEBSERVER_MODE = 'DEV' # Python webserver mode (DEBUG|DEV|PROD) WEBSERVER_BRANDING = None # Set the branding (nyi) WEBSERVER_DEPLOY = None # Deployment specifics (nyi) @@ -49,10 +49,13 @@ LOG_BENCH = True # Log bench marks USE_REDIS = True # REDIS caching (note that redis will be phased out) USE_GN_SERVER = 'False' # Use GN_SERVER SQL calls -# Path overrides for Genenetwork +# ---- Path overrides for Genenetwork +# TMPDIR is normally picked up from the environment HOME=os.environ['HOME'] LOGFILE = HOME+"/genenetwork2.log" -GENENETWORK_FILES = HOME+"/gn2_data" +GENENETWORK_FILES = HOME+"/gn2_data" # base dir for all static data files + +# ---- GN2 Executables PYLMM_COMMAND = str.strip(os.popen("which pylmm_redis").read()) PLINK_COMMAND = str.strip(os.popen("which plink2").read()) GEMMA_COMMAND = str.strip(os.popen("which gemma").read()) diff --git a/wqflask/base/webqtlConfig.py b/wqflask/base/webqtlConfig.py index 8c67a6fd..6bbabdec 100644 --- a/wqflask/base/webqtlConfig.py +++ b/wqflask/base/webqtlConfig.py @@ -60,9 +60,10 @@ ENSEMBLETRANSCRIPT_URL="http://useast.ensembl.org/Mus_musculus/Lucene/Details?sp # HTMLPATH is replaced by GENODIR # IMGDIR is replaced by GENERATED_IMAGE_DIR -# Temporary storage: +# Temporary storage (note that this TMPDIR is not the same directory +# as the UNIX TMPDIR) TMPDIR = mk_dir(TEMPDIR+'/gn2/') -CACHEDIR = mk_dir(TEMPDIR+'/cache/') +CACHEDIR = mk_dir(TMPDIR+'/cache/') # We can no longer write into the git tree: GENERATED_IMAGE_DIR = mk_dir(TMPDIR+'/generated/') GENERATED_TEXT_DIR = mk_dir(TMPDIR+'/generated_text/') diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py index 2c8cc5c5..907b0d6a 100644 --- a/wqflask/utility/tools.py +++ b/wqflask/utility/tools.py @@ -147,7 +147,10 @@ def locate_ignore_error(name, subdir=None): return None def tempdir(): - return valid_path(get_setting("TEMPDIR","/tmp")) + """ + Get UNIX TMPDIR by default + """ + return valid_path(get_setting("TMPDIR","/tmp")) BLUE = '\033[94m' GREEN = '\033[92m' @@ -184,9 +187,9 @@ LOG_BENCH = get_setting_bool('LOG_BENCH') LOG_FORMAT = "%(message)s" # not yet in use USE_REDIS = get_setting_bool('USE_REDIS') USE_GN_SERVER = get_setting_bool('USE_GN_SERVER') +GENENETWORK_FILES = get_setting_bool('GENENETWORK_FILES') PYLMM_COMMAND = pylmm_command() GEMMA_COMMAND = gemma_command() PLINK_COMMAND = plink_command() -FLAT_FILES = flat_files() TEMPDIR = tempdir() -- cgit v1.2.3