From d06fc474275306e23d96360bc183b8c484e3e42a Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Sun, 25 Sep 2016 10:42:39 +0000
Subject: Test: input parameters for mapping
---
.../input/mapping/1435395_s_at_HC_M2_0606_P.json | 140 +++++++++++++++++++++
test/lib/mapping.rb | 3 +-
2 files changed, 142 insertions(+), 1 deletion(-)
create mode 100644 test/data/input/mapping/1435395_s_at_HC_M2_0606_P.json
diff --git a/test/data/input/mapping/1435395_s_at_HC_M2_0606_P.json b/test/data/input/mapping/1435395_s_at_HC_M2_0606_P.json
new file mode 100644
index 00000000..2c4446ec
--- /dev/null
+++ b/test/data/input/mapping/1435395_s_at_HC_M2_0606_P.json
@@ -0,0 +1,140 @@
+{ "maf" : "0.01",
+ "control_marker" : "mCV24506226",
+ "dataset" : "HC_M2_0606_P",
+ "do_control" : "false",
+ "maf" : "0.01",
+ "manhattan_plot" : "False",
+ "mapmethod_rqtl_geno" : "em",
+ "mapmodel_rqtl_geno" : "normal",
+ "method" : "rqtl_geno",
+ "num_bootstrap" : "2000",
+ "num_perm" : "",
+ "pair_scan" : "false",
+ "suggestive" : "[object Object]",
+ "trait_id" : "1433387_at",
+ "value:129S1/SvImJ" : "6.920",
+ "value:A/J" : "7.437",
+ "value:AKR/J" : "7.550",
+ "value:B6D2F1" : "7.742",
+ "value:BALB/cByJ" : "6.613",
+ "value:BALB/cJ" : "6.664",
+ "value:BXD1" : "6.749",
+ "value:BXD100" : "x",
+ "value:BXD101" : "x",
+ "value:BXD102" : "x",
+ "value:BXD103" : "x",
+ "value:BXD11" : "7.398",
+ "value:BXD12" : "7.073",
+ "value:BXD13" : "8.191",
+ "value:BXD14" : "x",
+ "value:BXD15" : "7.406",
+ "value:BXD16" : "6.890",
+ "value:BXD18" : "x",
+ "value:BXD19" : "6.980",
+ "value:BXD2" : "7.248",
+ "value:BXD20" : "7.554",
+ "value:BXD21" : "7.316",
+ "value:BXD22" : "7.327",
+ "value:BXD23" : "7.605",
+ "value:BXD24" : "7.306",
+ "value:BXD24a" : "x",
+ "value:BXD25" : "x",
+ "value:BXD27" : "7.800",
+ "value:BXD28" : "7.023",
+ "value:BXD29" : "7.518",
+ "value:BXD30" : "x",
+ "value:BXD31" : "7.301",
+ "value:BXD32" : "7.161",
+ "value:BXD33" : "7.140",
+ "value:BXD34" : "8.180",
+ "value:BXD35" : "x",
+ "value:BXD36" : "x",
+ "value:BXD37" : "x",
+ "value:BXD38" : "7.350",
+ "value:BXD39" : "6.976",
+ "value:BXD40" : "7.411",
+ "value:BXD41" : "x",
+ "value:BXD42" : "7.050",
+ "value:BXD43" : "6.866",
+ "value:BXD44" : "7.246",
+ "value:BXD45" : "7.576",
+ "value:BXD48" : "7.108",
+ "value:BXD48a" : "7.192",
+ "value:BXD49" : "x",
+ "value:BXD5" : "6.771",
+ "value:BXD50" : "7.528",
+ "value:BXD51" : "7.408",
+ "value:BXD52" : "x",
+ "value:BXD53" : "x",
+ "value:BXD54" : "x",
+ "value:BXD55" : "6.720",
+ "value:BXD56" : "x",
+ "value:BXD59" : "x",
+ "value:BXD6" : "7.372",
+ "value:BXD60" : "7.178",
+ "value:BXD61" : "7.198",
+ "value:BXD62" : "7.618",
+ "value:BXD63" : "7.076",
+ "value:BXD64" : "6.576",
+ "value:BXD65" : "7.046",
+ "value:BXD65a" : "7.046",
+ "value:BXD65b" : "7.385",
+ "value:BXD66" : "7.108",
+ "value:BXD67" : "7.342",
+ "value:BXD68" : "7.668",
+ "value:BXD69" : "7.310",
+ "value:BXD70" : "7.278",
+ "value:BXD71" : "x",
+ "value:BXD72" : "x",
+ "value:BXD73" : "7.342",
+ "value:BXD73a" : "7.841",
+ "value:BXD74" : "7.298",
+ "value:BXD75" : "7.133",
+ "value:BXD76" : "7.448",
+ "value:BXD77" : "7.014",
+ "value:BXD78" : "x",
+ "value:BXD79" : "7.916",
+ "value:BXD8" : "7.148",
+ "value:BXD81" : "x",
+ "value:BXD83" : "7.322",
+ "value:BXD84" : "7.298",
+ "value:BXD85" : "7.243",
+ "value:BXD86" : "7.719",
+ "value:BXD87" : "7.145",
+ "value:BXD88" : "x",
+ "value:BXD89" : "7.162",
+ "value:BXD9" : "6.708",
+ "value:BXD90" : "7.497",
+ "value:BXD91" : "x",
+ "value:BXD93" : "7.558",
+ "value:BXD94" : "6.817",
+ "value:BXD95" : "x",
+ "value:BXD98" : "7.753",
+ "value:BXD99" : "8.076",
+ "value:C3H/HeJ" : "7.536",
+ "value:C57BL/6ByJ" : "6.940",
+ "value:C57BL/6J" : "7.309",
+ "value:CAST/EiJ" : "8.796",
+ "value:CXB1" : "6.430",
+ "value:CXB10" : "6.958",
+ "value:CXB11" : "6.182",
+ "value:CXB12" : "6.432",
+ "value:CXB13" : "6.388",
+ "value:CXB2" : "7.687",
+ "value:CXB3" : "6.312",
+ "value:CXB4" : "6.453",
+ "value:CXB5" : "6.959",
+ "value:CXB6" : "7.022",
+ "value:CXB7" : "6.334",
+ "value:CXB8" : "6.790",
+ "value:CXB9" : "6.545",
+ "value:D2B6F1" : "7.615",
+ "value:DBA/2J" : "7.816",
+ "value:KK/HlJ" : "8.035",
+ "value:LG/J" : "7.594",
+ "value:NOD/ShiLtJ" : "8.220",
+ "value:NZO/HlLtJ" : "7.629",
+ "value:PWD/PhJ" : "6.320",
+ "value:PWK/PhJ" : "7.235",
+ "value:WSB/EiJ" : "7.650"
+}
diff --git a/test/lib/mapping.rb b/test/lib/mapping.rb
index 08b6b5da..bd88b88e 100644
--- a/test/lib/mapping.rb
+++ b/test/lib/mapping.rb
@@ -1,6 +1,5 @@
# In these tests we navigate from the main page to a specific trait then hit the different mapping tool buttons (In this case pylMM and r/qtl) followed by computing the results (marker regressions).
-
class MappingTest
end
@@ -14,6 +13,8 @@ describe MappingTest do
it "pyLMM mapping tool selection" do
url = $host+'/show_trait?trait_id=1435395_s_at&dataset=HC_M2_0606_P'
page = @agent.get(url)
+ json = JSON::load(File.read('test/data/input/mapping/1435395_s_at_HC_M2_0606_P.json'))
+ p json
# get the form
# form = @agent.page.form_with(:name => "my-form")
# get the button you want from the form
--
cgit v1.2.3
From f69c43a8900ac55218ec0fc9a6c00cf654190d6d Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Sun, 25 Sep 2016 10:43:38 +0000
Subject: Logger: use output for assessing mapping parameters
---
etc/default_settings.py | 1 +
wqflask/wqflask/views.py | 5 +++--
2 files changed, 4 insertions(+), 2 deletions(-)
diff --git a/etc/default_settings.py b/etc/default_settings.py
index 9dddd0ad..fc79713c 100644
--- a/etc/default_settings.py
+++ b/etc/default_settings.py
@@ -7,6 +7,7 @@
# e.g.
#
# env LOG_SQL=True USE_REDIS=False ./bin/genenetwork2
+# env LOG_LEVEL=DEBUG ./bin/genenetwork2 ~/gn2_settings.py
#
# Note also that in the near future we will additionally fetch
# settings from a JSON file
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 41e2c7be..b747654a 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -432,11 +432,12 @@ def marker_regression_page():
'mapmethod_rqtl_geno',
'mapmodel_rqtl_geno'
)
- logger.info("Marker regression called with initial_start_vars:", initial_start_vars)
+ logger.debug("Marker regression called with initial_start_vars:", initial_start_vars)
start_vars = {}
for key, value in initial_start_vars.iteritems():
if key in wanted or key.startswith(('value:')):
start_vars[key] = value
+ logger.debug("Marker regression called with start_vars:", start_vars)
version = "v3"
key = "marker_regression:{}:".format(version) + json.dumps(start_vars, sort_keys=True)
@@ -546,7 +547,7 @@ def network_graph_page():
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 71890299c9f8aecb269d8dd2647b85f0a82e91ff Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Sun, 25 Sep 2016 10:51:43 +0000
Subject: Test: should be a Post with parameters filled in
---
test/data/input/mapping/1435395_s_at_HC_M2_0606_P.json | 2 +-
test/lib/mapping.rb | 5 +++--
2 files changed, 4 insertions(+), 3 deletions(-)
diff --git a/test/data/input/mapping/1435395_s_at_HC_M2_0606_P.json b/test/data/input/mapping/1435395_s_at_HC_M2_0606_P.json
index 2c4446ec..027e4d82 100644
--- a/test/data/input/mapping/1435395_s_at_HC_M2_0606_P.json
+++ b/test/data/input/mapping/1435395_s_at_HC_M2_0606_P.json
@@ -1,6 +1,6 @@
{ "maf" : "0.01",
"control_marker" : "mCV24506226",
- "dataset" : "HC_M2_0606_P",
+ "dataset" : "HC_M2_0606_P",
"do_control" : "false",
"maf" : "0.01",
"manhattan_plot" : "False",
diff --git a/test/lib/mapping.rb b/test/lib/mapping.rb
index bd88b88e..da580185 100644
--- a/test/lib/mapping.rb
+++ b/test/lib/mapping.rb
@@ -11,10 +11,11 @@ describe MappingTest do
describe MappingTest do
it "pyLMM mapping tool selection" do
- url = $host+'/show_trait?trait_id=1435395_s_at&dataset=HC_M2_0606_P'
- page = @agent.get(url)
+ url = $host+'/marker_regression?trait_id=1435395_s_at&dataset=HC_M2_0606_P'
+ page = @agent.post(url)
json = JSON::load(File.read('test/data/input/mapping/1435395_s_at_HC_M2_0606_P.json'))
p json
+ p page
# get the form
# form = @agent.page.form_with(:name => "my-form")
# get the button you want from the form
--
cgit v1.2.3
From 1ab5479fa48d645f5b2e3899f7d5e568e4c6fcdc Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Mon, 26 Sep 2016 07:11:42 +0000
Subject: Settings: LOCAL_PRIVATE_FILES
---
etc/default_settings.py | 1 +
1 file changed, 1 insertion(+)
diff --git a/etc/default_settings.py b/etc/default_settings.py
index fc79713c..547478df 100644
--- a/etc/default_settings.py
+++ b/etc/default_settings.py
@@ -55,6 +55,7 @@ USE_GN_SERVER = 'False' # Use GN_SERVER SQL calls
HOME=os.environ['HOME']
LOGFILE = HOME+"/genenetwork2.log"
GENENETWORK_FILES = HOME+"/gn2_data" # base dir for all static data files
+LOCAL_PRIVATE_FILES = HOME+"/gn2_private_data" # private static data files
# ---- GN2 Executables
PYLMM_COMMAND = str.strip(os.popen("which pylmm_redis").read())
--
cgit v1.2.3
From ade0969bdc784d71d67d8422c6fd1238ed3ca391 Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Mon, 26 Sep 2016 08:14:42 +0000
Subject: Test: mechanical Rob executes scanone test
---
test/data/input/mapping/1435395_s_at_HC_M2_0606_P.json | 8 +++++---
test/lib/mapping.rb | 14 +++++++++-----
wqflask/wqflask/views.py | 2 +-
3 files changed, 15 insertions(+), 9 deletions(-)
diff --git a/test/data/input/mapping/1435395_s_at_HC_M2_0606_P.json b/test/data/input/mapping/1435395_s_at_HC_M2_0606_P.json
index 027e4d82..9744e7b2 100644
--- a/test/data/input/mapping/1435395_s_at_HC_M2_0606_P.json
+++ b/test/data/input/mapping/1435395_s_at_HC_M2_0606_P.json
@@ -1,6 +1,8 @@
-{ "maf" : "0.01",
- "control_marker" : "mCV24506226",
- "dataset" : "HC_M2_0606_P",
+{
+ "temp_uuid" : "unknown",
+"maf" : "0.01",
+"control_marker" : "mCV24506226",
+"dataset" : "HC_M2_0606_P",
"do_control" : "false",
"maf" : "0.01",
"manhattan_plot" : "False",
diff --git a/test/lib/mapping.rb b/test/lib/mapping.rb
index da580185..2678b127 100644
--- a/test/lib/mapping.rb
+++ b/test/lib/mapping.rb
@@ -5,16 +5,20 @@ end
describe MappingTest do
before do
- @agent = Mechanize.new
- @agent.agent.http.ca_file = '/etc/ssl/certs/ca-certificates.crt'
end
describe MappingTest do
it "pyLMM mapping tool selection" do
- url = $host+'/marker_regression?trait_id=1435395_s_at&dataset=HC_M2_0606_P'
- page = @agent.post(url)
+ url = $host+'/marker_regression' # ?trait_id=1435395_s_at&dataset=HC_M2_0606_P'
+ @agent = Mechanize.new
+ @agent.agent.http.ca_file = '/etc/ssl/certs/ca-certificates.crt'
+ # @agent.idle_timeout = 0.01
+
json = JSON::load(File.read('test/data/input/mapping/1435395_s_at_HC_M2_0606_P.json'))
- p json
+ # p json
+ page = @agent.post(URI.encode(url),
+ json,
+ ({'Content-Type' => 'application/x-www-form-urlencoded'}))
p page
# get the form
# form = @agent.page.form_with(:name => "my-form")
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index b747654a..7061e0f1 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -395,6 +395,7 @@ def mapping_results_container_page():
@app.route("/marker_regression", methods=('POST',))
def marker_regression_page():
initial_start_vars = request.form
+ logger.debug("Marker regression called with initial_start_vars:", initial_start_vars.items())
temp_uuid = initial_start_vars['temp_uuid']
wanted = (
'trait_id',
@@ -432,7 +433,6 @@ def marker_regression_page():
'mapmethod_rqtl_geno',
'mapmodel_rqtl_geno'
)
- logger.debug("Marker regression called with initial_start_vars:", initial_start_vars)
start_vars = {}
for key, value in initial_start_vars.iteritems():
if key in wanted or key.startswith(('value:')):
--
cgit v1.2.3
From 50a571110b6557e2b7dbc536893d3928f0a93bd2 Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Mon, 26 Sep 2016 08:30:07 +0000
Subject: Mechanical Rob: make it possible to run single tests
---
bin/test-website | 6 +++++-
test/lib/gntest.rb | 5 +++++
test/lib/mapping.rb | 40 +++++-----------------------------------
3 files changed, 15 insertions(+), 36 deletions(-)
create mode 100644 test/lib/gntest.rb
diff --git a/bin/test-website b/bin/test-website
index 18994cc5..1d6481f4 100755
--- a/bin/test-website
+++ b/bin/test-website
@@ -4,7 +4,7 @@
USAGE = <<EOT
This is Mechanical-Rob - an automated web server tester for
Genenetwork.org that uses the brilliant
- mechanize gem.
+ mechanize gem with minitest.
To use this software you need to install mechanize. Run it from
the root of the genenetwork2 source tree as, for example,
@@ -15,6 +15,10 @@ If you are using the small deployment database you can use
./bin/test-website --skip -n
+To run individual tests on localhost you can do
+
+ ruby -Itest -Itest/lib test/lib/mapping.rb --name="/Mapping/"
+
For more information see http://genenetwork.org/
EOT
diff --git a/test/lib/gntest.rb b/test/lib/gntest.rb
new file mode 100644
index 00000000..865ef51d
--- /dev/null
+++ b/test/lib/gntest.rb
@@ -0,0 +1,5 @@
+require 'minitest/autorun'
+require 'mechanize'
+
+# ---- Use some default parameters if not set
+$host = "http://localhost:5003" if !$host
diff --git a/test/lib/mapping.rb b/test/lib/mapping.rb
index 2678b127..47c4875b 100644
--- a/test/lib/mapping.rb
+++ b/test/lib/mapping.rb
@@ -1,18 +1,19 @@
# In these tests we navigate from the main page to a specific trait then hit the different mapping tool buttons (In this case pylMM and r/qtl) followed by computing the results (marker regressions).
+require 'gntest'
+
class MappingTest
end
describe MappingTest do
before do
+ @agent = Mechanize.new
+ @agent.agent.http.ca_file = '/etc/ssl/certs/ca-certificates.crt'
end
describe MappingTest do
- it "pyLMM mapping tool selection" do
+ it "R/qtl mapping tool selection" do
url = $host+'/marker_regression' # ?trait_id=1435395_s_at&dataset=HC_M2_0606_P'
- @agent = Mechanize.new
- @agent.agent.http.ca_file = '/etc/ssl/certs/ca-certificates.crt'
- # @agent.idle_timeout = 0.01
json = JSON::load(File.read('test/data/input/mapping/1435395_s_at_HC_M2_0606_P.json'))
# p json
@@ -20,38 +21,7 @@ describe MappingTest do
json,
({'Content-Type' => 'application/x-www-form-urlencoded'}))
p page
- # get the form
- # form = @agent.page.form_with(:name => "my-form")
- # get the button you want from the form
- # page.forms.each do |form|
- # p form
- # end
- # button = page.button_with(:value => "pylmm_compute")
- # submit the form using that button
- # agent.submit(form, button)
- # link = page.link_with(text: 'pyLMM')
- # page = link.click
- # puts page.uri
- # link = page.link_with(text: 'Compute')
- # page = link.click
- # puts page.uri
- # probe_link.uri.to_s.must_equal "/marker_regression"
end
end
end
-
-describe MappingTest do
- it "R/qtl mapping tool selection" do
- break if $options[:skip_broken]
- page = @agent.get($host+'/show_trait?trait_id=1435395_s_at&dataset=HC_M2_0606_P')
- link = page.link_with(text: 'R/qtl')
- page = link.click
- puts page.uri
- form.field_with(:name => 'Methods').options[2].select
- link = page.link_with(text: 'Compute')
- page = link.click
- puts page.uri
- probe_link.uri.to_s.must_equal "/marker_regression"
- end
-end
--
cgit v1.2.3
From 2f9055a2b77386a7b91b9257f86b50f1432e47cd Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Mon, 26 Sep 2016 12:24:54 +0000
Subject: Doc: edits from Zwets
---
doc/Architecture.org | 42 ++++++++++++++++++++----------------------
1 file changed, 20 insertions(+), 22 deletions(-)
diff --git a/doc/Architecture.org b/doc/Architecture.org
index ec56f9a9..c5876196 100644
--- a/doc/Architecture.org
+++ b/doc/Architecture.org
@@ -26,29 +26,27 @@ Findable, Accessible, Interoperable, and Re-usable (FAIR) principles
(see the Wilkinson Nature paper on [[http://www.nature.com/articles/sdata201618][FAIR Guiding Principles for
scientific data management and stewardship]]).
-With GN2 we are solving these requirements by assigning unique
-identifiers (cryptographic HASH values calculated over immutable data
-content and including that value in the file names or directories) and
-making these identifiers available through web interfaces (e.g.,
-through a REST API). This means that at any point in the future the
-exact same data can be retrieved using a known non-changeable
-identifier (see also
+GeneNetwork (GN2) solves this by assigning unique identifiers
+(cryptographic HASH values calculated over immutable data content),
+including these values in file or directory names, and making them
+available through web interfaces (e.g., through a through a REST
+API). This means that at any point in the future the exact same data
+can be retrieved using a known non-changeable identifier (see also
https://github.com/pjotrp/genenetwork2/blob/staging/doc/submit-data.org).
Synchronisation, integrity checking and backups become trivial using
these HASH values, even for very large datasets. Since everything is
managed at the file system level we can also use Unix authorisation
-systems. HIPAA compliancy is achieved by using HASH values and
+systems. HIPAA compliancy is achieved by using HASH references and
bringing the software into the controlled HIPAA environment.
-In the context of GeneNetwork we are using git and github for version
-control of software source code
-(https://github.com/genenetwork/). Software can be treated just like
-data, i.e., git uses HASH identifiers to retrieve specific versions of
-source. I.e., versions of source code are identifiable and retrievable
-and can be matched with data into an analysis pipeline. The
-combination of software and data, again, makes a unique HASH value
-which identifies the analysis pipe-line.
+In the context of GeneNetwork we are using git for version control of
+software source code (https://github.com/genenetwork/). Software can
+be treated just like data, i.e., git uses HASH identifiers to retrieve
+specific versions of source. I.e., versions of source code are
+identifiable and retrievable and can be matched with data into an
+analysis pipeline. The combination of software and data, again, makes
+a unique HASH value which identifies the analysis pipeline.
For combining runnable software and data into an analysis pipeline we
use GNU Guix which, yet again, turns everything into a unique HASH
@@ -68,12 +66,12 @@ deployment (described in JOSS paper). We also use automated test tools
(Ruby mechanize) for integration testing of the web services and we
use unit testing of all backend services. All our software source code
is published as `free and open source software' (FOSS) which means
-that anyone can view code on github, comment on it, or even
-contribute. GeneNetwork is becoming increasingly modular and has a
-growing number of contributers who, in principle, abide by the THE
-SMALL TOOLS MANIFESTO FOR BIOINFORMATICS which we wrote up
-(https://github.com/pjotrp/bioinformatics) and was signed by 51
-bioinformaticians.
+that anyone can view code on github, comment on, or even contribute
+to. GeneNetwork is becoming increasingly modular and has a growing
+number of contributers who subscribe to the principles of THE SMALL
+TOOLS MANIFESTO FOR BIOINFORMATICS
+(https://github.com/pjotrp/bioinformatics) which we drew up and was
+signed by over fifty bioinformaticians.
* Webserver
--
cgit v1.2.3
From fb754ded72f3b2303277f86b75b9fae8d352c4cf Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Mon, 26 Sep 2016 12:29:21 +0000
Subject: Test: --all switch added
---
bin/test-website | 20 ++++++++++++--------
1 file changed, 12 insertions(+), 8 deletions(-)
diff --git a/bin/test-website b/bin/test-website
index 1d6481f4..b693bd60 100755
--- a/bin/test-website
+++ b/bin/test-website
@@ -40,6 +40,10 @@ opts = OptionParser.new do |o|
end
end
+ o.on('--all', 'Run all tests') do
+ options[:all] = true
+ end
+
o.on('-l','--link-checker', 'Check for dead links') do
options[:link_checker] = true
end
@@ -88,16 +92,16 @@ require 'minitest/autorun'
libpath = File.dirname(File.dirname(__FILE__))
$: << File.join(libpath,'test/lib')
-if options[:link_checker]
- require 'link_checker'
-else
- require 'main_web_functionality'
+require 'main_web_functionality'
+
+if options[:all] or options[:mapping_test]
+ require 'mapping'
end
-if options[:navigation_test]
- require 'navigation'
+if options[:all] or options[:link_checker]
+ require 'link_checker'
end
-if options[:mapping_test]
- require 'mapping'
+if options[:all] or options[:navigation_test]
+ require 'navigation'
end
--
cgit v1.2.3
From 2d04ad9552f5b3f0551c31797f8fa714e3af4c7a Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Mon, 26 Sep 2016 14:26:47 +0000
Subject: Test: added pylmm test
---
test/data/input/mapping/1435395_s_at_HC_M2_0606_P.json | 2 +-
test/lib/mapping.rb | 15 +++++++++++++++
2 files changed, 16 insertions(+), 1 deletion(-)
diff --git a/test/data/input/mapping/1435395_s_at_HC_M2_0606_P.json b/test/data/input/mapping/1435395_s_at_HC_M2_0606_P.json
index 9744e7b2..15428553 100644
--- a/test/data/input/mapping/1435395_s_at_HC_M2_0606_P.json
+++ b/test/data/input/mapping/1435395_s_at_HC_M2_0606_P.json
@@ -12,7 +12,7 @@
"num_bootstrap" : "2000",
"num_perm" : "",
"pair_scan" : "false",
- "suggestive" : "[object Object]",
+ "suggestive" : "0",
"trait_id" : "1433387_at",
"value:129S1/SvImJ" : "6.920",
"value:A/J" : "7.437",
diff --git a/test/lib/mapping.rb b/test/lib/mapping.rb
index 47c4875b..1b52d797 100644
--- a/test/lib/mapping.rb
+++ b/test/lib/mapping.rb
@@ -11,6 +11,21 @@ describe MappingTest do
@agent.agent.http.ca_file = '/etc/ssl/certs/ca-certificates.crt'
end
+ describe MappingTest do
+ it "pylmm mapping tool selection" do
+ url = $host+'/marker_regression'
+
+ json = JSON::load(File.read('test/data/input/mapping/1435395_s_at_HC_M2_0606_P.json'))
+ json["method"] = "pylmm"
+ # p json
+ page = @agent.post(URI.encode(url), json)
+ # Unpacking the page is slow - but the run is enough as a test
+ # form = page.forms[1]
+ # form = page.forms_with("marker_regression")[0]
+ # form.fields.select { |fld| fld.name == 'corr_dataset' }.first.value.must_equal 'HC_M2_0606_P'
+ end
+ end
+
describe MappingTest do
it "R/qtl mapping tool selection" do
url = $host+'/marker_regression' # ?trait_id=1435395_s_at&dataset=HC_M2_0606_P'
--
cgit v1.2.3
From 3fa5e9c2effdab27ba9492203a875d01ddae766c Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Mon, 26 Sep 2016 14:38:27 +0000
Subject: Test: added mechanize test for CIM (reaper)
---
test/lib/mapping.rb | 21 ++++++++++++++++++---
1 file changed, 18 insertions(+), 3 deletions(-)
diff --git a/test/lib/mapping.rb b/test/lib/mapping.rb
index 1b52d797..4c8ff632 100644
--- a/test/lib/mapping.rb
+++ b/test/lib/mapping.rb
@@ -20,9 +20,9 @@ describe MappingTest do
# p json
page = @agent.post(URI.encode(url), json)
# Unpacking the page is slow - but the run is enough as a test
- # form = page.forms[1]
# form = page.forms_with("marker_regression")[0]
- # form.fields.select { |fld| fld.name == 'corr_dataset' }.first.value.must_equal 'HC_M2_0606_P'
+ # form.fields.select { |fld| fld.name == 'dataset' }.first.value.must_equal 'HC_M2_0606_P'
+ # form.fields.select { |fld| fld.name == 'value:BXD1' }.first.value.must_equal '6.749'
end
end
@@ -35,7 +35,22 @@ describe MappingTest do
page = @agent.post(URI.encode(url),
json,
({'Content-Type' => 'application/x-www-form-urlencoded'}))
- p page
+ form = page.forms_with("marker_regression")[0]
+ form.fields.select { |fld| fld.name == 'dataset' }.first.value.must_equal 'HC_M2_0606_P'
+ form.fields.select { |fld| fld.name == 'value:BXD1' }.first.value.must_equal '6.749'
+ end
+ end
+
+ describe MappingTest do
+ it "CIM mapping tool selection (using reaper)" do
+ url = $host+'/marker_regression'
+
+ json = JSON::load(File.read('test/data/input/mapping/1435395_s_at_HC_M2_0606_P.json'))
+ json["method"] = "reaper"
+ page = @agent.post(URI.encode(url), json)
+ form = page.forms_with("marker_regression")[0]
+ form.fields.select { |fld| fld.name == 'dataset' }.first.value.must_equal 'HC_M2_0606_P'
+ form.fields.select { |fld| fld.name == 'value:BXD1' }.first.value.must_equal '6.749'
end
end
--
cgit v1.2.3
From a14887e0c548e5d6b33a2f05092f82a9d4931b13 Mon Sep 17 00:00:00 2001
From: Lei Yan
Date: Thu, 29 Sep 2016 23:39:05 +0000
Subject: Fix global search "il6" for "Internal Server Error". Add single
quotes into MySQL query.
---
wqflask/base/trait.py | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index 900e050c..32032ba7 100644
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -363,7 +363,7 @@ class GeneralTrait(object):
FROM
Homologene, Species, InbredSet
WHERE
- Homologene.GeneId =%s AND
+ Homologene.GeneId ='%s' AND
InbredSet.Name = '%s' AND
InbredSet.SpeciesId = Species.Id AND
Species.TaxonomyId = Homologene.TaxonomyId
--
cgit v1.2.3
From 8f1b5b86a843ee2d17b427e2318eb13b29093d5d Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Fri, 30 Sep 2016 08:40:42 +0000
Subject: Add logging for qtlreaper
---
.../wqflask/marker_regression/marker_regression.py | 4 ++++
.../marker_regression/marker_regression_gn1.py | 20 ++++++++++++--------
2 files changed, 16 insertions(+), 8 deletions(-)
diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py
index d2b27991..d7c78db0 100644
--- a/wqflask/wqflask/marker_regression/marker_regression.py
+++ b/wqflask/wqflask/marker_regression/marker_regression.py
@@ -41,6 +41,9 @@ from utility.tools import locate, locate_ignore_error, PYLMM_COMMAND, GEMMA_COMM
from utility.external import shell
from base.webqtlConfig import TMPDIR, GENERATED_TEXT_DIR
+import utility.logger
+logger = utility.logger.getLogger(__name__ )
+
class MarkerRegression(object):
def __init__(self, start_vars, temp_uuid):
@@ -194,6 +197,7 @@ class MarkerRegression(object):
self.control_marker = start_vars['control_marker']
self.do_control = start_vars['do_control']
+ logger.info("Running qtlreaper")
results = self.gen_reaper_results()
elif self.mapping_method == "plink":
results = self.run_plink()
diff --git a/wqflask/wqflask/marker_regression/marker_regression_gn1.py b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
index 9cef3cec..bc147f75 100644
--- a/wqflask/wqflask/marker_regression/marker_regression_gn1.py
+++ b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
@@ -44,6 +44,9 @@ from utility import Plot
from wqflask.interval_analyst import GeneUtil
from base.webqtlConfig import TMPDIR, GENERATED_TEXT_DIR, GENERATED_IMAGE_DIR
+import utility.logger
+logger = utility.logger.getLogger(__name__ )
+
#########################################
# Inteval Mapping Plot Page
#########################################
@@ -159,6 +162,7 @@ class MarkerRegression(object):
#if not self.openMysql():
# return
+ logger.info("Running qtlreaper")
#helper_functions.get_species_dataset_trait(self, start_vars)
@@ -211,7 +215,7 @@ class MarkerRegression(object):
self.plotScale = start_vars['mapping_scale']
else:
self.plotScale = "physic"
-
+
self.manhattan_plot = start_vars['manhattan_plot']
if 'permCheck' in start_vars.keys():
@@ -514,13 +518,13 @@ class MarkerRegression(object):
if self.dataset.group.species == "mouse":
if self.selectedChr == 20:
- chrName = "X"
+ chrName = "X"
else:
chrName = self.selectedChr
self.geneCol = GeneUtil.loadGenes(chrName, self.diffCol, self.startMb, self.endMb, webqtldatabase, "mouse")
elif self.dataset.group.species == "rat":
if self.selectedChr == 21:
- chrName = "X"
+ chrName = "X"
else:
chrName = self.selectedChr
self.geneCol = GeneUtil.loadGenes(chrName, self.diffCol, self.startMb, self.endMb, webqtldatabase, "rat")
@@ -860,7 +864,7 @@ 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( [])
@@ -883,8 +887,8 @@ class MarkerRegression(object):
else:
Xc = startX + (_locus.cM-_chr[0].cM)*plotXScale
BootCoord[-1].append([Xc, self.bootResult[i]])
- i += 1
-
+ i += 1
+
#reduce bootResult
if self.selectedChr > -1:
maxBootBar = 80.0
@@ -1851,7 +1855,7 @@ 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)
@@ -2963,7 +2967,7 @@ class MarkerRegression(object):
chr_as_int = 20
else:
chr_as_int = int(theGO["Chromosome"]) - 1
-
+
geneLength = (float(theGO["TxEnd"]) - float(theGO["TxStart"]))
#geneLengthURL = "javascript:centerIntervalMapOnRange2('%s', %f, %f, document.changeViewForm)" % (theGO["Chromosome"], float(theGO["TxStart"])-(geneLength*0.1), float(theGO["TxEnd"])+(geneLength*0.1))
geneLengthURL = "javascript:rangeView('%s', %f, %f)" % (theGO["Chromosome"], float(theGO["TxStart"])-(geneLength*0.1), float(theGO["TxEnd"])+(geneLength*0.1))
--
cgit v1.2.3
From 56ba5dcc2b2ba7ff2103b7b291db1aa610c24d11 Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Fri, 30 Sep 2016 04:58:15 -0500
Subject: Add missing __init__.py
---
wqflask/maintenance/__init__.py | 0
1 file changed, 0 insertions(+), 0 deletions(-)
create mode 100644 wqflask/maintenance/__init__.py
diff --git a/wqflask/maintenance/__init__.py b/wqflask/maintenance/__init__.py
new file mode 100644
index 00000000..e69de29b
--
cgit v1.2.3
From c3f3632230f40c86f422a72cd080e5eb1b56bbf1 Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Sun, 2 Oct 2016 10:34:21 +0000
Subject: Error screen improvements with animated gifs
---
.../wqflask/static/gif/error/Wild-Type-Mouse.gif | Bin 0 -> 37328 bytes
.../static/gif/error/animated-gifs-aliens-29.gif | Bin 0 -> 14088 bytes
.../static/gif/error/animated-gifs-angels-04.gif | Bin 0 -> 12155 bytes
.../static/gif/error/animated-gifs-cats-016.gif | Bin 0 -> 10388 bytes
.../static/gif/error/animated-gifs-cats-031.gif | Bin 0 -> 6937 bytes
.../gif/error/animated-gifs-cell-phones-03.gif | Bin 0 -> 14902 bytes
.../gif/error/animated-gifs-cell-phones-16.gif | Bin 0 -> 7307 bytes
.../gif/error/animated-gifs-computers-13.gif | Bin 0 -> 7616 bytes
.../gif/error/animated-gifs-computers-28.gif | Bin 0 -> 7566 bytes
.../gif/error/animated-gifs-computers-32.gif | Bin 0 -> 2970 bytes
.../gif/error/animated-gifs-computers-42.gif | Bin 0 -> 9391 bytes
.../gif/error/animated-gifs-computers-60.gif | Bin 0 -> 35873 bytes
.../gif/error/animated-gifs-computers-64.gif | Bin 0 -> 20728 bytes
.../gif/error/animated-gifs-computers-65.gif | Bin 0 -> 26358 bytes
.../gif/error/animated-gifs-computers-72.gif | Bin 0 -> 16361 bytes
.../gif/error/animated-gifs-computers-74.gif | Bin 0 -> 21087 bytes
.../gif/error/animated-gifs-computers-75.gif | Bin 0 -> 98317 bytes
.../error/animated-gifs-construction-sites-038.gif | Bin 0 -> 949 bytes
.../static/gif/error/animated-gifs-dogs-04.gif | Bin 0 -> 9450 bytes
.../static/gif/error/animated-gifs-dogs-14.gif | Bin 0 -> 2532 bytes
.../static/gif/error/animated-gifs-dogs-18.gif | Bin 0 -> 3596 bytes
.../static/gif/error/animated-gifs-dogs-47.gif | Bin 0 -> 13920 bytes
.../static/gif/error/animated-gifs-dogs-50.gif | Bin 0 -> 7297 bytes
.../gif/error/animated-gifs-lava-lamps-01.gif | Bin 0 -> 27122 bytes
.../static/gif/error/animated-gifs-mice-02.gif | Bin 0 -> 73345 bytes
.../static/gif/error/animated-gifs-mice-09.gif | Bin 0 -> 27822 bytes
.../static/gif/error/animated-gifs-mice-24.gif | Bin 0 -> 10566 bytes
.../static/gif/error/animated-gifs-smileys-063.gif | Bin 0 -> 2230 bytes
.../static/gif/error/animated-gifs-smileys-068.gif | Bin 0 -> 11751 bytes
.../static/gif/error/animated-gifs-smileys-134.gif | Bin 0 -> 21431 bytes
.../static/gif/error/animated-gifs-smileys-211.gif | Bin 0 -> 11209 bytes
.../static/gif/error/animated-gifs-smileys-234.gif | Bin 0 -> 8677 bytes
.../gif/error/animated-gifs-stickmen-001.gif | Bin 0 -> 6897 bytes
.../gif/error/animated-gifs-stickmen-002.gif | Bin 0 -> 14098 bytes
.../gif/error/animated-gifs-stickmen-005.gif | Bin 0 -> 13264 bytes
.../gif/error/animated-gifs-stickmen-012.gif | Bin 0 -> 12141 bytes
.../gif/error/animated-gifs-stickmen-056.gif | Bin 0 -> 5946 bytes
.../gif/error/animated-gifs-stickmen-059.gif | Bin 0 -> 16427 bytes
.../gif/error/animated-gifs-stickmen-060.gif | Bin 0 -> 14434 bytes
.../gif/error/animated-gifs-stickmen-069.gif | Bin 0 -> 7668 bytes
wqflask/wqflask/templates/error.html | 58 +++++++++++++++++++++
wqflask/wqflask/views.py | 26 +++++++++
42 files changed, 84 insertions(+)
create mode 100644 wqflask/wqflask/static/gif/error/Wild-Type-Mouse.gif
create mode 100644 wqflask/wqflask/static/gif/error/animated-gifs-aliens-29.gif
create mode 100644 wqflask/wqflask/static/gif/error/animated-gifs-angels-04.gif
create mode 100644 wqflask/wqflask/static/gif/error/animated-gifs-cats-016.gif
create mode 100644 wqflask/wqflask/static/gif/error/animated-gifs-cats-031.gif
create mode 100644 wqflask/wqflask/static/gif/error/animated-gifs-cell-phones-03.gif
create mode 100644 wqflask/wqflask/static/gif/error/animated-gifs-cell-phones-16.gif
create mode 100644 wqflask/wqflask/static/gif/error/animated-gifs-computers-13.gif
create mode 100644 wqflask/wqflask/static/gif/error/animated-gifs-computers-28.gif
create mode 100644 wqflask/wqflask/static/gif/error/animated-gifs-computers-32.gif
create mode 100644 wqflask/wqflask/static/gif/error/animated-gifs-computers-42.gif
create mode 100644 wqflask/wqflask/static/gif/error/animated-gifs-computers-60.gif
create mode 100644 wqflask/wqflask/static/gif/error/animated-gifs-computers-64.gif
create mode 100644 wqflask/wqflask/static/gif/error/animated-gifs-computers-65.gif
create mode 100644 wqflask/wqflask/static/gif/error/animated-gifs-computers-72.gif
create mode 100644 wqflask/wqflask/static/gif/error/animated-gifs-computers-74.gif
create mode 100644 wqflask/wqflask/static/gif/error/animated-gifs-computers-75.gif
create mode 100644 wqflask/wqflask/static/gif/error/animated-gifs-construction-sites-038.gif
create mode 100644 wqflask/wqflask/static/gif/error/animated-gifs-dogs-04.gif
create mode 100644 wqflask/wqflask/static/gif/error/animated-gifs-dogs-14.gif
create mode 100644 wqflask/wqflask/static/gif/error/animated-gifs-dogs-18.gif
create mode 100644 wqflask/wqflask/static/gif/error/animated-gifs-dogs-47.gif
create mode 100644 wqflask/wqflask/static/gif/error/animated-gifs-dogs-50.gif
create mode 100644 wqflask/wqflask/static/gif/error/animated-gifs-lava-lamps-01.gif
create mode 100644 wqflask/wqflask/static/gif/error/animated-gifs-mice-02.gif
create mode 100644 wqflask/wqflask/static/gif/error/animated-gifs-mice-09.gif
create mode 100644 wqflask/wqflask/static/gif/error/animated-gifs-mice-24.gif
create mode 100644 wqflask/wqflask/static/gif/error/animated-gifs-smileys-063.gif
create mode 100644 wqflask/wqflask/static/gif/error/animated-gifs-smileys-068.gif
create mode 100644 wqflask/wqflask/static/gif/error/animated-gifs-smileys-134.gif
create mode 100644 wqflask/wqflask/static/gif/error/animated-gifs-smileys-211.gif
create mode 100644 wqflask/wqflask/static/gif/error/animated-gifs-smileys-234.gif
create mode 100644 wqflask/wqflask/static/gif/error/animated-gifs-stickmen-001.gif
create mode 100644 wqflask/wqflask/static/gif/error/animated-gifs-stickmen-002.gif
create mode 100644 wqflask/wqflask/static/gif/error/animated-gifs-stickmen-005.gif
create mode 100644 wqflask/wqflask/static/gif/error/animated-gifs-stickmen-012.gif
create mode 100644 wqflask/wqflask/static/gif/error/animated-gifs-stickmen-056.gif
create mode 100644 wqflask/wqflask/static/gif/error/animated-gifs-stickmen-059.gif
create mode 100644 wqflask/wqflask/static/gif/error/animated-gifs-stickmen-060.gif
create mode 100644 wqflask/wqflask/static/gif/error/animated-gifs-stickmen-069.gif
create mode 100644 wqflask/wqflask/templates/error.html
diff --git a/wqflask/wqflask/static/gif/error/Wild-Type-Mouse.gif b/wqflask/wqflask/static/gif/error/Wild-Type-Mouse.gif
new file mode 100644
index 00000000..2c68b5ee
Binary files /dev/null and b/wqflask/wqflask/static/gif/error/Wild-Type-Mouse.gif differ
diff --git a/wqflask/wqflask/static/gif/error/animated-gifs-aliens-29.gif b/wqflask/wqflask/static/gif/error/animated-gifs-aliens-29.gif
new file mode 100644
index 00000000..e9d38277
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diff --git a/wqflask/wqflask/static/gif/error/animated-gifs-angels-04.gif b/wqflask/wqflask/static/gif/error/animated-gifs-angels-04.gif
new file mode 100644
index 00000000..94e11847
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diff --git a/wqflask/wqflask/static/gif/error/animated-gifs-cats-016.gif b/wqflask/wqflask/static/gif/error/animated-gifs-cats-016.gif
new file mode 100644
index 00000000..7e6ec9a3
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diff --git a/wqflask/wqflask/static/gif/error/animated-gifs-cats-031.gif b/wqflask/wqflask/static/gif/error/animated-gifs-cats-031.gif
new file mode 100644
index 00000000..af7ef655
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diff --git a/wqflask/wqflask/static/gif/error/animated-gifs-cell-phones-03.gif b/wqflask/wqflask/static/gif/error/animated-gifs-cell-phones-03.gif
new file mode 100644
index 00000000..89c79ddf
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diff --git a/wqflask/wqflask/static/gif/error/animated-gifs-cell-phones-16.gif b/wqflask/wqflask/static/gif/error/animated-gifs-cell-phones-16.gif
new file mode 100644
index 00000000..7530d180
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diff --git a/wqflask/wqflask/static/gif/error/animated-gifs-computers-13.gif b/wqflask/wqflask/static/gif/error/animated-gifs-computers-13.gif
new file mode 100644
index 00000000..afb05c62
Binary files /dev/null and b/wqflask/wqflask/static/gif/error/animated-gifs-computers-13.gif differ
diff --git a/wqflask/wqflask/static/gif/error/animated-gifs-computers-28.gif b/wqflask/wqflask/static/gif/error/animated-gifs-computers-28.gif
new file mode 100644
index 00000000..f5b4a563
Binary files /dev/null and b/wqflask/wqflask/static/gif/error/animated-gifs-computers-28.gif differ
diff --git a/wqflask/wqflask/static/gif/error/animated-gifs-computers-32.gif b/wqflask/wqflask/static/gif/error/animated-gifs-computers-32.gif
new file mode 100644
index 00000000..7258e594
Binary files /dev/null and b/wqflask/wqflask/static/gif/error/animated-gifs-computers-32.gif differ
diff --git a/wqflask/wqflask/static/gif/error/animated-gifs-computers-42.gif b/wqflask/wqflask/static/gif/error/animated-gifs-computers-42.gif
new file mode 100644
index 00000000..ed1f8722
Binary files /dev/null and b/wqflask/wqflask/static/gif/error/animated-gifs-computers-42.gif differ
diff --git a/wqflask/wqflask/static/gif/error/animated-gifs-computers-60.gif b/wqflask/wqflask/static/gif/error/animated-gifs-computers-60.gif
new file mode 100644
index 00000000..f58d69f1
Binary files /dev/null and b/wqflask/wqflask/static/gif/error/animated-gifs-computers-60.gif differ
diff --git a/wqflask/wqflask/static/gif/error/animated-gifs-computers-64.gif b/wqflask/wqflask/static/gif/error/animated-gifs-computers-64.gif
new file mode 100644
index 00000000..5d5b4fdf
Binary files /dev/null and b/wqflask/wqflask/static/gif/error/animated-gifs-computers-64.gif differ
diff --git a/wqflask/wqflask/static/gif/error/animated-gifs-computers-65.gif b/wqflask/wqflask/static/gif/error/animated-gifs-computers-65.gif
new file mode 100644
index 00000000..b4b10845
Binary files /dev/null and b/wqflask/wqflask/static/gif/error/animated-gifs-computers-65.gif differ
diff --git a/wqflask/wqflask/static/gif/error/animated-gifs-computers-72.gif b/wqflask/wqflask/static/gif/error/animated-gifs-computers-72.gif
new file mode 100644
index 00000000..e60cb4fe
Binary files /dev/null and b/wqflask/wqflask/static/gif/error/animated-gifs-computers-72.gif differ
diff --git a/wqflask/wqflask/static/gif/error/animated-gifs-computers-74.gif b/wqflask/wqflask/static/gif/error/animated-gifs-computers-74.gif
new file mode 100644
index 00000000..bd7b72f3
Binary files /dev/null and b/wqflask/wqflask/static/gif/error/animated-gifs-computers-74.gif differ
diff --git a/wqflask/wqflask/static/gif/error/animated-gifs-computers-75.gif b/wqflask/wqflask/static/gif/error/animated-gifs-computers-75.gif
new file mode 100644
index 00000000..916d6b33
Binary files /dev/null and b/wqflask/wqflask/static/gif/error/animated-gifs-computers-75.gif differ
diff --git a/wqflask/wqflask/static/gif/error/animated-gifs-construction-sites-038.gif b/wqflask/wqflask/static/gif/error/animated-gifs-construction-sites-038.gif
new file mode 100644
index 00000000..0ec782c4
Binary files /dev/null and b/wqflask/wqflask/static/gif/error/animated-gifs-construction-sites-038.gif differ
diff --git a/wqflask/wqflask/static/gif/error/animated-gifs-dogs-04.gif b/wqflask/wqflask/static/gif/error/animated-gifs-dogs-04.gif
new file mode 100644
index 00000000..9515c18a
Binary files /dev/null and b/wqflask/wqflask/static/gif/error/animated-gifs-dogs-04.gif differ
diff --git a/wqflask/wqflask/static/gif/error/animated-gifs-dogs-14.gif b/wqflask/wqflask/static/gif/error/animated-gifs-dogs-14.gif
new file mode 100644
index 00000000..f1e2e1f5
Binary files /dev/null and b/wqflask/wqflask/static/gif/error/animated-gifs-dogs-14.gif differ
diff --git a/wqflask/wqflask/static/gif/error/animated-gifs-dogs-18.gif b/wqflask/wqflask/static/gif/error/animated-gifs-dogs-18.gif
new file mode 100644
index 00000000..572849d5
Binary files /dev/null and b/wqflask/wqflask/static/gif/error/animated-gifs-dogs-18.gif differ
diff --git a/wqflask/wqflask/static/gif/error/animated-gifs-dogs-47.gif b/wqflask/wqflask/static/gif/error/animated-gifs-dogs-47.gif
new file mode 100644
index 00000000..d808c9ee
Binary files /dev/null and b/wqflask/wqflask/static/gif/error/animated-gifs-dogs-47.gif differ
diff --git a/wqflask/wqflask/static/gif/error/animated-gifs-dogs-50.gif b/wqflask/wqflask/static/gif/error/animated-gifs-dogs-50.gif
new file mode 100644
index 00000000..9865ee45
Binary files /dev/null and b/wqflask/wqflask/static/gif/error/animated-gifs-dogs-50.gif differ
diff --git a/wqflask/wqflask/static/gif/error/animated-gifs-lava-lamps-01.gif b/wqflask/wqflask/static/gif/error/animated-gifs-lava-lamps-01.gif
new file mode 100644
index 00000000..ee9c113d
Binary files /dev/null and b/wqflask/wqflask/static/gif/error/animated-gifs-lava-lamps-01.gif differ
diff --git a/wqflask/wqflask/static/gif/error/animated-gifs-mice-02.gif b/wqflask/wqflask/static/gif/error/animated-gifs-mice-02.gif
new file mode 100644
index 00000000..5ca2ee5c
Binary files /dev/null and b/wqflask/wqflask/static/gif/error/animated-gifs-mice-02.gif differ
diff --git a/wqflask/wqflask/static/gif/error/animated-gifs-mice-09.gif b/wqflask/wqflask/static/gif/error/animated-gifs-mice-09.gif
new file mode 100644
index 00000000..7cb361e4
Binary files /dev/null and b/wqflask/wqflask/static/gif/error/animated-gifs-mice-09.gif differ
diff --git a/wqflask/wqflask/static/gif/error/animated-gifs-mice-24.gif b/wqflask/wqflask/static/gif/error/animated-gifs-mice-24.gif
new file mode 100644
index 00000000..96a26450
Binary files /dev/null and b/wqflask/wqflask/static/gif/error/animated-gifs-mice-24.gif differ
diff --git a/wqflask/wqflask/static/gif/error/animated-gifs-smileys-063.gif b/wqflask/wqflask/static/gif/error/animated-gifs-smileys-063.gif
new file mode 100644
index 00000000..62de166c
Binary files /dev/null and b/wqflask/wqflask/static/gif/error/animated-gifs-smileys-063.gif differ
diff --git a/wqflask/wqflask/static/gif/error/animated-gifs-smileys-068.gif b/wqflask/wqflask/static/gif/error/animated-gifs-smileys-068.gif
new file mode 100644
index 00000000..3550e978
Binary files /dev/null and b/wqflask/wqflask/static/gif/error/animated-gifs-smileys-068.gif differ
diff --git a/wqflask/wqflask/static/gif/error/animated-gifs-smileys-134.gif b/wqflask/wqflask/static/gif/error/animated-gifs-smileys-134.gif
new file mode 100644
index 00000000..954ab614
Binary files /dev/null and b/wqflask/wqflask/static/gif/error/animated-gifs-smileys-134.gif differ
diff --git a/wqflask/wqflask/static/gif/error/animated-gifs-smileys-211.gif b/wqflask/wqflask/static/gif/error/animated-gifs-smileys-211.gif
new file mode 100644
index 00000000..596174d7
Binary files /dev/null and b/wqflask/wqflask/static/gif/error/animated-gifs-smileys-211.gif differ
diff --git a/wqflask/wqflask/static/gif/error/animated-gifs-smileys-234.gif b/wqflask/wqflask/static/gif/error/animated-gifs-smileys-234.gif
new file mode 100644
index 00000000..5aba636b
Binary files /dev/null and b/wqflask/wqflask/static/gif/error/animated-gifs-smileys-234.gif differ
diff --git a/wqflask/wqflask/static/gif/error/animated-gifs-stickmen-001.gif b/wqflask/wqflask/static/gif/error/animated-gifs-stickmen-001.gif
new file mode 100644
index 00000000..7896ff1f
Binary files /dev/null and b/wqflask/wqflask/static/gif/error/animated-gifs-stickmen-001.gif differ
diff --git a/wqflask/wqflask/static/gif/error/animated-gifs-stickmen-002.gif b/wqflask/wqflask/static/gif/error/animated-gifs-stickmen-002.gif
new file mode 100644
index 00000000..89da6441
Binary files /dev/null and b/wqflask/wqflask/static/gif/error/animated-gifs-stickmen-002.gif differ
diff --git a/wqflask/wqflask/static/gif/error/animated-gifs-stickmen-005.gif b/wqflask/wqflask/static/gif/error/animated-gifs-stickmen-005.gif
new file mode 100644
index 00000000..b7887630
Binary files /dev/null and b/wqflask/wqflask/static/gif/error/animated-gifs-stickmen-005.gif differ
diff --git a/wqflask/wqflask/static/gif/error/animated-gifs-stickmen-012.gif b/wqflask/wqflask/static/gif/error/animated-gifs-stickmen-012.gif
new file mode 100644
index 00000000..f6697d02
Binary files /dev/null and b/wqflask/wqflask/static/gif/error/animated-gifs-stickmen-012.gif differ
diff --git a/wqflask/wqflask/static/gif/error/animated-gifs-stickmen-056.gif b/wqflask/wqflask/static/gif/error/animated-gifs-stickmen-056.gif
new file mode 100644
index 00000000..2b2496a4
Binary files /dev/null and b/wqflask/wqflask/static/gif/error/animated-gifs-stickmen-056.gif differ
diff --git a/wqflask/wqflask/static/gif/error/animated-gifs-stickmen-059.gif b/wqflask/wqflask/static/gif/error/animated-gifs-stickmen-059.gif
new file mode 100644
index 00000000..f2188656
Binary files /dev/null and b/wqflask/wqflask/static/gif/error/animated-gifs-stickmen-059.gif differ
diff --git a/wqflask/wqflask/static/gif/error/animated-gifs-stickmen-060.gif b/wqflask/wqflask/static/gif/error/animated-gifs-stickmen-060.gif
new file mode 100644
index 00000000..aa8f7bd3
Binary files /dev/null and b/wqflask/wqflask/static/gif/error/animated-gifs-stickmen-060.gif differ
diff --git a/wqflask/wqflask/static/gif/error/animated-gifs-stickmen-069.gif b/wqflask/wqflask/static/gif/error/animated-gifs-stickmen-069.gif
new file mode 100644
index 00000000..473212e4
Binary files /dev/null and b/wqflask/wqflask/static/gif/error/animated-gifs-stickmen-069.gif differ
diff --git a/wqflask/wqflask/templates/error.html b/wqflask/wqflask/templates/error.html
new file mode 100644
index 00000000..a2eaad5c
--- /dev/null
+++ b/wqflask/wqflask/templates/error.html
@@ -0,0 +1,58 @@
+{% extends "base.html" %}
+{% block title %}Error: {{message}}{% endblock %}
+{% block content %}
+<!-- Start of body -->
+
+<div class="col-md-8">
+<div class="form-group has-error">
+ <div class="control-label" for="inputError1">
+
+ <img src="/static/gif/error/{{ error_image }}">
+
+ <h1>ERROR</h1>
+
+ <p>
+ This error is not what we wanted to see. Unfortunately errors
+ are part of all software systems and we need to resolve this
+ together.
+ </p>
+ <p>
+ <b>It is important to report this so we
+ can fix it</b>.
+ </p>
+
+ <p>
+ Report to the GeneNetwork team by recording the steps you take
+ to reproduce this error. Next to those steps, copy-paste below
+ stack trace, either as
+ a <a href="https://github.com/genenetwork/genenetwork2/issues/new">new
+ issue</a> (GeneNetwork error: {{message}}) or E-mail this full page to one of the developers
+ directly.
+ </p>
+ </div>
+
+ <pre>
+ {{ message }} (error)
+ {{ stack[-3] }}
+ {{ stack[-2] }}
+ </pre>
+
+ <p>
+ To check if this already a known issue, search the
+ <a href="https://github.com/genenetwork/genenetwork2/issues">issue
+ tracker</a>.
+ </p>
+
+ <a href="#Stack" class="btn btn-default" data-toggle="collapse">Toggle full stack trace</a>
+ <div id="Stack" class="collapse">
+ <pre>
+ {% for line in stack %}
+ {{ line }}
+ {% endfor %}
+ </pre>
+ </div>
+</div>
+</div>
+
+
+{% endblock %}
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 7061e0f1..c01056a8 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -4,6 +4,9 @@
from __future__ import absolute_import, division, print_function
+import traceback # for error page
+import os # for error gifs
+import random # for random error gif
import sys
import csv
import xlsxwriter
@@ -58,6 +61,8 @@ from wqflask import user_manager
from wqflask import collect
from wqflask.database import db_session
+import werkzeug
+
import utility.logger
logger = utility.logger.getLogger(__name__ )
@@ -82,6 +87,26 @@ def shutdown_session(exception=None):
# from wqflask import tracer
# tracer.turn_on()
+@app.errorhandler(Exception)
+def handle_bad_request(e):
+ logger.error(str(e))
+ exc_type, exc_value, exc_traceback = sys.exc_info()
+ # print "*** format_exc, first and last line:"
+ # logger.error(formatted_lines[0])
+ # logger.error(formatted_lines[-3])
+ # logger.error(formatted_lines[-2])
+ # logger.error(formatted_lines[-1])
+ logger.error(traceback.format_exc())
+ formatted_lines = traceback.format_exc().splitlines()
+
+ # for file in os.listdir("./wqflask/static/gif/error"):
+ # if file.endswith(".gif"):
+ # print(file)
+
+ list = [fn for fn in os.listdir("./wqflask/static/gif/error") if fn.endswith(".gif") ]
+ # print(list)
+ return render_template("error.html",message=str(e),stack=formatted_lines,error_image=random.choice(list))
+
@app.route("/")
def index_page():
logger.info("Sending index_page")
@@ -394,6 +419,7 @@ def mapping_results_container_page():
@app.route("/marker_regression", methods=('POST',))
def marker_regression_page():
+ raise Exception("Just an error")
initial_start_vars = request.form
logger.debug("Marker regression called with initial_start_vars:", initial_start_vars.items())
temp_uuid = initial_start_vars['temp_uuid']
--
cgit v1.2.3
From 9b3c087e46b6dfdc2fe686a60ac26e98c7cbe93d Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Sun, 2 Oct 2016 10:35:16 +0000
Subject: Error: remove test error
---
wqflask/wqflask/views.py | 1 -
1 file changed, 1 deletion(-)
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index c01056a8..85c2c824 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -419,7 +419,6 @@ def mapping_results_container_page():
@app.route("/marker_regression", methods=('POST',))
def marker_regression_page():
- raise Exception("Just an error")
initial_start_vars = request.form
logger.debug("Marker regression called with initial_start_vars:", initial_start_vars.items())
temp_uuid = initial_start_vars['temp_uuid']
--
cgit v1.2.3
From 3496c5eeae6d9d6064188720902b0cc1b415f610 Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Sun, 2 Oct 2016 11:06:02 +0000
Subject: Error page: use cookies to fixate the animation for one error
---
wqflask/wqflask/templates/error.html | 3 +--
wqflask/wqflask/views.py | 28 +++++++++++++++-------------
2 files changed, 16 insertions(+), 15 deletions(-)
diff --git a/wqflask/wqflask/templates/error.html b/wqflask/wqflask/templates/error.html
index a2eaad5c..9d9e66d4 100644
--- a/wqflask/wqflask/templates/error.html
+++ b/wqflask/wqflask/templates/error.html
@@ -17,8 +17,7 @@
together.
</p>
<p>
- <b>It is important to report this so we
- can fix it</b>.
+ <b>It is important to report this error so we can fix it for everyone</b>.
</p>
<p>
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 85c2c824..40a77df3 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -29,7 +29,7 @@ import base64
import array
import sqlalchemy
from wqflask import app
-from flask import g, Response, request, render_template, send_from_directory, jsonify, redirect
+from flask import g, Response, request, make_response, render_template, send_from_directory, jsonify, redirect
from wqflask import search_results
from wqflask import gsearch
from wqflask import update_search_results
@@ -89,23 +89,25 @@ def shutdown_session(exception=None):
@app.errorhandler(Exception)
def handle_bad_request(e):
- logger.error(str(e))
+ err_msg = str(e)
+ logger.error(err_msg)
+ # get the stack trace and send it to the logger
exc_type, exc_value, exc_traceback = sys.exc_info()
- # print "*** format_exc, first and last line:"
- # logger.error(formatted_lines[0])
- # logger.error(formatted_lines[-3])
- # logger.error(formatted_lines[-2])
- # logger.error(formatted_lines[-1])
logger.error(traceback.format_exc())
formatted_lines = traceback.format_exc().splitlines()
- # for file in os.listdir("./wqflask/static/gif/error"):
- # if file.endswith(".gif"):
- # print(file)
+ # Handle random animations
+ # Use a cookie to have one animation on refresh
+ animation = request.cookies.get(err_msg)
+ if not animation:
+ list = [fn for fn in os.listdir("./wqflask/static/gif/error") if fn.endswith(".gif") ]
+ animation = random.choice(list)
- list = [fn for fn in os.listdir("./wqflask/static/gif/error") if fn.endswith(".gif") ]
- # print(list)
- return render_template("error.html",message=str(e),stack=formatted_lines,error_image=random.choice(list))
+ resp = make_response(render_template("error.html",message=err_msg,stack=formatted_lines,error_image=animation))
+
+ # logger.error("Set cookie %s with %s" % (err_msg, animation))
+ resp.set_cookie(err_msg,animation)
+ return resp
@app.route("/")
def index_page():
--
cgit v1.2.3
From b4521df539a9817ecf9d70fe5dbe41a5c39d64a0 Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Sun, 2 Oct 2016 11:21:44 +0000
Subject: Error page: also display the URL
---
wqflask/wqflask/templates/error.html | 8 ++++----
wqflask/wqflask/views.py | 3 ++-
2 files changed, 6 insertions(+), 5 deletions(-)
diff --git a/wqflask/wqflask/templates/error.html b/wqflask/wqflask/templates/error.html
index 9d9e66d4..95485f1e 100644
--- a/wqflask/wqflask/templates/error.html
+++ b/wqflask/wqflask/templates/error.html
@@ -17,12 +17,12 @@
together.
</p>
<p>
- <b>It is important to report this error so we can fix it for everyone</b>.
+ <b>It is important to report this ERROR so we can fix it for everyone</b>.
</p>
<p>
Report to the GeneNetwork team by recording the steps you take
- to reproduce this error. Next to those steps, copy-paste below
+ to reproduce this ERROR. Next to those steps, copy-paste below
stack trace, either as
a <a href="https://github.com/genenetwork/genenetwork2/issues/new">new
issue</a> (GeneNetwork error: {{message}}) or E-mail this full page to one of the developers
@@ -31,6 +31,7 @@
</div>
<pre>
+ {{ stack[0] }}
{{ message }} (error)
{{ stack[-3] }}
{{ stack[-2] }}
@@ -45,8 +46,7 @@
<a href="#Stack" class="btn btn-default" data-toggle="collapse">Toggle full stack trace</a>
<div id="Stack" class="collapse">
<pre>
- {% for line in stack %}
- {{ line }}
+ {% for line in stack %} {{ line }}
{% endfor %}
</pre>
</div>
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 40a77df3..12d43052 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -91,10 +91,11 @@ def shutdown_session(exception=None):
def handle_bad_request(e):
err_msg = str(e)
logger.error(err_msg)
+ logger.error(request.url)
# get the stack trace and send it to the logger
exc_type, exc_value, exc_traceback = sys.exc_info()
logger.error(traceback.format_exc())
- formatted_lines = traceback.format_exc().splitlines()
+ formatted_lines = [request.url]+traceback.format_exc().splitlines()
# Handle random animations
# Use a cookie to have one animation on refresh
--
cgit v1.2.3
From 1107259dc258d0cfcb447519cc36e59e78facdef Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Sun, 2 Oct 2016 11:52:47 +0000
Subject: Errors: added time stamps in UTC
---
wqflask/utility/logger.py | 6 +++++-
wqflask/wqflask/views.py | 6 +++++-
2 files changed, 10 insertions(+), 2 deletions(-)
diff --git a/wqflask/utility/logger.py b/wqflask/utility/logger.py
index ddc0ea82..b873e16f 100644
--- a/wqflask/utility/logger.py
+++ b/wqflask/utility/logger.py
@@ -31,6 +31,7 @@ import string
from inspect import isfunction
from pprint import pformat as pf
from inspect import stack
+import datetime
from utility.tools import LOG_LEVEL, LOG_LEVEL_DEBUG, LOG_SQL, LOG_FORMAT
@@ -66,7 +67,10 @@ LOG_LEVEL_DEBUG (NYI).
def error(self,*args):
"""Call logging.error for multiple args"""
- self.collect(self.logger.error,*args)
+ now = datetime.datetime.utcnow()
+ time_str = now.strftime('%H:%M:%S UTC %Y%m%d')
+ l = [time_str]+list(args)
+ self.collect(self.logger.error,*l)
def infof(self,*args):
"""Call logging.info for multiple args lazily"""
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 12d43052..7abcc17d 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -7,6 +7,8 @@ from __future__ import absolute_import, division, print_function
import traceback # for error page
import os # for error gifs
import random # for random error gif
+import datetime # for errors
+import time # for errors
import sys
import csv
import xlsxwriter
@@ -95,7 +97,9 @@ def handle_bad_request(e):
# get the stack trace and send it to the logger
exc_type, exc_value, exc_traceback = sys.exc_info()
logger.error(traceback.format_exc())
- formatted_lines = [request.url]+traceback.format_exc().splitlines()
+ now = datetime.datetime.utcnow()
+ time_str = now.strftime('%l:%M%p UTC %b %d, %Y')
+ formatted_lines = [request.url + " ("+time_str+")"]+traceback.format_exc().splitlines()
# Handle random animations
# Use a cookie to have one animation on refresh
--
cgit v1.2.3
From 2115fcfde74375252f556153d48f52f4d15fb298 Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Sun, 2 Oct 2016 12:02:46 +0000
Subject: Error page: trim error messages
---
wqflask/wqflask/templates/error.html | 6 +++++-
wqflask/wqflask/views.py | 4 ++--
2 files changed, 7 insertions(+), 3 deletions(-)
diff --git a/wqflask/wqflask/templates/error.html b/wqflask/wqflask/templates/error.html
index 95485f1e..7ab2bf2f 100644
--- a/wqflask/wqflask/templates/error.html
+++ b/wqflask/wqflask/templates/error.html
@@ -25,11 +25,15 @@
to reproduce this ERROR. Next to those steps, copy-paste below
stack trace, either as
a <a href="https://github.com/genenetwork/genenetwork2/issues/new">new
- issue</a> (GeneNetwork error: {{message}}) or E-mail this full page to one of the developers
+ issue</a> or E-mail this full page to one of the developers
directly.
</p>
</div>
+ <p>
+ (GeneNetwork error: {{message[:128]}})
+ </p>
+
<pre>
{{ stack[0] }}
{{ message }} (error)
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 7abcc17d..cf316bee 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -103,7 +103,7 @@ def handle_bad_request(e):
# Handle random animations
# Use a cookie to have one animation on refresh
- animation = request.cookies.get(err_msg)
+ animation = request.cookies.get(err_msg[:64])
if not animation:
list = [fn for fn in os.listdir("./wqflask/static/gif/error") if fn.endswith(".gif") ]
animation = random.choice(list)
@@ -111,7 +111,7 @@ def handle_bad_request(e):
resp = make_response(render_template("error.html",message=err_msg,stack=formatted_lines,error_image=animation))
# logger.error("Set cookie %s with %s" % (err_msg, animation))
- resp.set_cookie(err_msg,animation)
+ resp.set_cookie(err_msg[:64],animation)
return resp
@app.route("/")
--
cgit v1.2.3