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-rw-r--r--etc/default_settings.py10
-rwxr-xr-xscripts/run_debug.sh20
-rw-r--r--wqflask/wqflask/static/new/javascript/dataset_menu_structure.json443
-rw-r--r--wqflask/wqflask/templates/base.html2
-rw-r--r--wqflask/wqflask/user_manager.py3
-rw-r--r--wqflask/wqflask/user_session.py21
-rw-r--r--wqflask/wqflask/views.py1
7 files changed, 473 insertions, 27 deletions
diff --git a/etc/default_settings.py b/etc/default_settings.py
index 64a78686..f368237b 100644
--- a/etc/default_settings.py
+++ b/etc/default_settings.py
@@ -32,7 +32,7 @@ GN_SERVER_URL = "http://localhost:8880/" # REST API server
SQL_URI = "mysql://gn2:mysql_password@localhost/db_webqtl_s"
SQL_ALCHEMY_POOL_RECYCLE = 3600
GN_SERVER_URL = "http://localhost:8880/" # REST API server
-GN2_BASE_URL = "http://genenetwork.org/"
+GN2_BASE_URL = "http://genenetwork.org/" # to pick up REST API
GN2_BRANCH_URL = GN2_BASE_URL
# ---- Flask configuration (see website)
@@ -44,7 +44,13 @@ SECURITY_RECOVERABLE = True
SECURITY_EMAIL_SENDER = "no-reply@genenetwork.org"
SECURITY_POST_LOGIN_VIEW = "/thank_you"
-SERVER_PORT = 5003 # running on localhost
+# ---- SERVER_PORT needs an override before firing up the server
+SERVER_PORT = os.environ['SERVER_PORT']
+if isinstance(SERVER_PORT, str):
+ SERVER_PORT = int(SERVER_PORT) # don't do this for other settings!
+else:
+ SERVER_PORT = 5003
+
SECRET_HMAC_CODE = '\x08\xdf\xfa\x93N\x80\xd9\\H@\\\x9f`\x98d^\xb4a;\xc6OM\x946a\xbc\xfc\x80:*\xebc'
GITHUB_CLIENT_ID = "UNKNOWN"
diff --git a/scripts/run_debug.sh b/scripts/run_debug.sh
new file mode 100755
index 00000000..be7ecdb8
--- /dev/null
+++ b/scripts/run_debug.sh
@@ -0,0 +1,20 @@
+#! /bin/bash
+#
+# PLEASE DO NOT CHANGE THIS FILE - copy it elsewhere to run
+#
+# Run with GN2_PROFILE and SERVER_PORT overrides, e.g.
+#
+# env GN2_PROFILE=/usr/local/guix-profiles/gn-latest SERVER_PORT=5010 scripts/run_debug.sh
+
+[ -z $GN2_PROFILE ] && export GN2_PROFILE=/usr/local/guix-profiles/gn-latest
+[ -z $SERVER_PORT ] && export SERVER_PORT=5010
+
+echo Running on port $SERVER_PORT from $GN2_PROFILE
+
+cwd=`pwd`
+echo Running source from $cwd
+
+mkdir -p ~/tmp
+
+env TMPDIR=~/tmp WEBSERVER_MODE=DEBUG LOG_LEVEL=DEBUG GENENETWORK_FILES=/export/data/genenetwork/genotype_files/ SQL_URI=mysql://webqtlout:webqtlout@localhost/db_webqtl ./bin/genenetwork2 etc/default_settings.py -gunicorn-dev
+
diff --git a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json
index 679e38b0..2699afdc 100644
--- a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json
+++ b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json
@@ -1930,6 +1930,7 @@
]
},
"HCP": {
+<<<<<<< HEAD
"Phenotypes": [
[
"None",
@@ -2116,20 +2117,42 @@
]
},
"TIGEM-Retina-RNA-Seq": {
+=======
+>>>>>>> penguin2
"Phenotypes": [
[
"None",
- "TIGEM-Retina-RNA-SeqPublish",
- "TIGEM-Retina-RNA-Seq Phenotypes"
+ "HCPPublish",
+ "HCP Private Phenotypes"
+ ]
+ ]
+ },
+ "HLC": {
+ "Liver mRNA": [
+ [
+ "320",
+ "HLC_0311",
+ "GSE9588 Human Liver Normal (Mar11) Both Sexes"
+ ],
+ [
+ "384",
+ "HLCF_0311",
+ "GSE9588 Human Liver Normal (Mar11) Females"
+ ],
+ [
+ "383",
+ "HLCM_0311",
+ "GSE9588 Human Liver Normal (Mar11) Males"
]
],
- "Retina mRNA": [
+ "Phenotypes": [
[
- "802",
- "TIGEM_hg38_ret_rna-seq_0916",
- "TIGEM Human Retina RNA-Seq (Sep16) RPKM log2"
+ "635",
+ "HLCPublish",
+ "HLC Published Phenotypes"
]
]
+<<<<<<< HEAD
}
},
"macaque monkey": {
@@ -2167,6 +2190,173 @@
"252",
"INIA_MacFas_Pf_RMA_0110",
"INIA Macaca fasicularis Prefrontal Cortex (Jan10) RMA"
+=======
+ },
+ "HLT": {
+ "Lung mRNA": [
+ [
+ "455",
+ "GSE23546HLT0613",
+ "Super Series GSE23546 Whole-Genome GXD Non-Tumorous Human Lung Tissues Affy HuRSTA array (Jun11) RMA"
+ ],
+ [
+ "454",
+ "GRNG-GSE23545HLT0613",
+ "GRNG/GSE23545 Whole-Genome GXD Non-Tumorous Human Lung Tissues Affy HuRSTA array (Jun11) RMA"
+ ]
+ ]
+ },
+ "HSB": {
+ "Amygdala mRNA": [
+ [
+ "330",
+ "KIN_YSM_AMY_0711",
+ "GN330 Human Amygdala Affy Hu-Exon 1.0 ST (Jul11) Quantile"
+ ]
+ ],
+ "Cerebellar Cortex mRNA": [
+ [
+ "331",
+ "KIN_YSM_CBC_0711",
+ "Human Cerebellar Cortex Affy Hu-Exon 1.0 ST (Jul11) Quantile"
+ ]
+ ],
+ "Dorsolateral Prefrontal Cortex mRNA": [
+ [
+ "333",
+ "KIN_YSM_DFC_0711",
+ "Human Dorsolateral Prefrontal Cortex Affy Hu-Exon 1.0 ST (Jul11) Quantile"
+ ]
+ ],
+ "Hippocampus mRNA": [
+ [
+ "337",
+ "KIN_YSM_HIP_0711",
+ "Human Hippocampus Affy Hu-Exon 1.0 ST (Jul11) Quantile"
+ ]
+ ],
+ "Inferior Temporal Cortex mRNA": [
+ [
+ "339",
+ "KIN_YSM_ITC_0711",
+ "Human Inferior Temporal Cortex Affy Hu-Exon 1.0 ST (Jul11) Quantile"
+ ]
+ ],
+ "Medial Prefrontal Cortex mRNA": [
+ [
+ "343",
+ "KIN_YSM_MFC_0711",
+ "Human Medial Prefrontal Cortex Affy Hu-Exon 1.0 ST (Jul11) Quantile"
+ ]
+ ],
+ "Mediodorsal Nucleus of Thalamus mRNA": [
+ [
+ "342",
+ "KIN_YSM_MD_0711",
+ "Human Mediodorsal Nucleus of Thalamus Affy Hu-Exon 1.0 ST (Jul11) Quantile"
+ ]
+ ],
+ "Orbital Prefrontal Cortex mRNA": [
+ [
+ "347",
+ "KIN_YSM_OFC_0711",
+ "Human Orbital Prefrontal Cortex Affy Hu-Exon 1.0 ST (Jul11) Quantile"
+ ]
+ ],
+ "Phenotypes": [
+ [
+ "None",
+ "HSBPublish",
+ "HSB Published Phenotypes"
+ ]
+ ],
+ "Posterior Inferior Parietal Cortex mRNA": [
+ [
+ "338",
+ "KIN_YSM_IPC_0711",
+ "Human Posterior Inferior Parietal Cortex Affy Hu-Exon 1.0 ST (Jul11) Quantile"
+ ]
+ ],
+ "Posterior Superior Temporal Cortex mRNA": [
+ [
+ "350",
+ "KIN_YSM_STC_0711",
+ "Human Posterior Superior Temporal Cortex Affy Hu-Exon 1.0 ST (Jul11) Quantile"
+ ]
+ ],
+ "Primary Auditory (A1) Cortex mRNA": [
+ [
+ "329",
+ "KIN_YSM_A1C_0711",
+ "Human Primary Auditory (A1) Cortex Affy Hu-Exon 1.0 ST (Jul11) Quantile"
+ ]
+ ],
+ "Primary Motor (M1) Cortex mRNA": [
+ [
+ "341",
+ "KIN_YSM_M1C_0711",
+ "Human Primary Motor (M1) Cortex Affy Hu-Exon 1.0 ST (Jul11) Quantile"
+ ]
+ ],
+ "Primary Somatosensory (S1) Cortex mRNA": [
+ [
+ "349",
+ "KIN_YSM_S1C_0711",
+ "Human Primary Somatosensory (S1) Cortex Affy Hu-Exon 1.0 ST (Jul11) Quantile"
+ ]
+ ],
+ "Primary Visual Cortex mRNA": [
+ [
+ "354",
+ "KIN_YSM_V1C_0711",
+ "Human Primary Visual Cortex Affy Hu-Exon 1.0 ST (Jul11) Quantile"
+ ]
+ ],
+ "Striatum mRNA": [
+ [
+ "351",
+ "KIN_YSM_STR_0711",
+ "Human Striatum Affy Hu-Exon 1.0 ST (Jul11) Quantile"
+ ]
+ ],
+ "Ventrolateral Prefrontal Cortex mRNA": [
+ [
+ "356",
+ "KIN_YSM_VFC_0711",
+ "Human Ventrolateral Prefrontal Cortex Affy Hu-Exon 1.0 ST (Jul11) Quantile"
+ ]
+ ]
+ },
+ "Islets-Gerling": {
+ "Islets mRNA": [
+ [
+ "824",
+ "UTHSC_HuIslets_Mar17",
+ "UTHSC Human Islets Affy Human Gene 2.0 ST (Mar17) RMA"
+ ]
+ ],
+ "Phenotypes": [
+ [
+ "None",
+ "Islets-GerlingPublish",
+ "Islets-Gerling Phenotypes"
+ ]
+ ]
+ },
+ "TIGEM-Retina-RNA-Seq": {
+ "Phenotypes": [
+ [
+ "None",
+ "TIGEM-Retina-RNA-SeqPublish",
+ "TIGEM-Retina-RNA-Seq Phenotypes"
+ ]
+ ],
+ "Retina mRNA": [
+ [
+ "802",
+ "TIGEM_hg38_ret_rna-seq_0916",
+ "TIGEM Human Retina RNA-Seq (Sep16) RPKM log2"
+>>>>>>> penguin2
]
]
}
@@ -3516,6 +3706,11 @@
"EPFL/LISP BXD HFD Liver Affy Mouse Gene 1.0 ST (Apr13) RMA"
],
[
+ "849",
+ "EPFLMouseLiverCDEx0413",
+ "EPFL/LISP BXD CD Liver Affy Mouse Gene 1.0 ST (Apr13) RMA Exon Level"
+ ],
+ [
"848",
"EPFLMouseLiverHFCEx0413",
"EPFL/LISP BXD HFC Liver Affy Mouse Gene 1.0 ST (Apr13) RMA Exon Level"
@@ -3526,11 +3721,6 @@
"EPFL/LISP BXD CD Liver Affy Mouse Gene 1.0 ST (Apr13) RMA"
],
[
- "849",
- "EPFLMouseLiverCDEx0413",
- "EPFL/LISP BXD CD Liver Affy Mouse Gene 1.0 ST (Apr13) RMA Exon Level"
- ],
- [
"433",
"EPFLMouseLiverBothExRMA0413",
"EPFL/LISP BXD CD+HFD Liver Affy Mouse Gene 1.0 ST (Apr13) RMA Exon Level"
@@ -3871,6 +4061,7 @@
"135",
"VCUSal_1206_R",
"VCU BXD PFC Sal M430 2.0 (Dec06) RMA"
+<<<<<<< HEAD
],
[
"136",
@@ -3913,6 +4104,50 @@
"VCU BXD PFC CIE EtOH M430 2.0 (Jan11) RMA"
],
[
+=======
+ ],
+ [
+ "136",
+ "VCUEtOH_1206_R",
+ "VCU BXD PFC EtOH M430 2.0 (Dec06) RMA"
+ ],
+ [
+ "137",
+ "VCUSal_1006_R",
+ "VCU BXD PFC Et vs Sal M430 2.0 (Dec06) Sscore"
+ ],
+ [
+ "788",
+ "VCU_BXD_PFC_CIE_Air_0416",
+ "VCU BXD PFC CIE Air Masked ComBat M430 2.0 (Apr16) RMA"
+ ],
+ [
+ "789",
+ "VCU_BXD_PFC_CIE_AirZ_0416",
+ "VCU BXD PFC CIE Air Masked ComBat M430 2.0 (Apr16) RMA Z-score"
+ ],
+ [
+ "790",
+ "VCU_BXD_PFC_CIE_Et_0416",
+ "VCU BXD PFC CIE EtOH Masked ComBat M430 2.0 (Apr16) RMA"
+ ],
+ [
+ "791",
+ "VCU_BXD_PFC_CIE_EtZ_0416",
+ "VCU BXD PFC CIE EtOH Masked ComBat M430 2.0 (Apr16) RMA Z-score"
+ ],
+ [
+ "299",
+ "VCU_PF_AvE_0111_Ss",
+ "VCU BXD PFC EtOH vs CIE Air M430 2.0 (Jan11) Sscore*"
+ ],
+ [
+ "300",
+ "VCU_PF_Et_0111_R",
+ "VCU BXD PFC CIE EtOH M430 2.0 (Jan11) RMA"
+ ],
+ [
+>>>>>>> penguin2
"301",
"VCU_PF_Air_0111_R",
"VCU BXD PFC CIE Air M430 2.0 (Jan11) RMA"
@@ -4854,6 +5089,11 @@
],
"Hippocampus mRNA": [
[
+ "214",
+ "Illum_LXS_Hipp_NOE_1008",
+ "Hippocampus Illumina NOE (Oct08) RankInv beta"
+ ],
+ [
"211",
"Illum_LXS_Hipp_RSS_1008",
"Hippocampus Illumina RSS (Oct08) RankInv beta"
@@ -4874,11 +5114,6 @@
"Hippocampus Illumina RSE (Oct08) RankInv beta"
],
[
- "214",
- "Illum_LXS_Hipp_NOE_1008",
- "Hippocampus Illumina NOE (Oct08) RankInv beta"
- ],
- [
"143",
"Illum_LXS_Hipp_loess0807",
"Hippocampus Illumina (Aug07) LOESS"
@@ -5451,6 +5686,7 @@
"TIGEM-Retina-RNA-Seq",
"Retina: Normal Adult Gene Expression, RNA-Seq (TIGEM)",
"Family:None"
+<<<<<<< HEAD
]
],
"macaque monkey": [
@@ -5458,6 +5694,8 @@
"Macaca-fasicularis",
"Macaca fasicularis (Cynomolgus monkey)",
"Family:None"
+=======
+>>>>>>> penguin2
]
],
"mouse": [
@@ -5495,6 +5733,175 @@
"LXS",
"ILSXISS (LXS) Family",
"Family:Reference Populations"
+<<<<<<< HEAD
+ ],
+ [
+ "MDP",
+ "Mouse Diversity Panel",
+ "Family:Reference Populations"
+ ],
+ [
+ "B6D2RI",
+ "BXD Aged Hippocampus",
+ "Family:BXD Individual Data"
+ ],
+ [
+ "BXD-Bone",
+ "BXD Bone Individual Data",
+ "Family:BXD Individual Data"
+ ],
+ [
+ "DOD-BXD-GWI",
+ "BXD DOD Gulf War Illness",
+ "Family:BXD Individual Data"
+ ],
+ [
+ "BXD-Harvested",
+ "BXD NIA Longevity Study",
+ "Family:BXD Individual Data"
+ ],
+ [
+ "UTHSC-Cannabinoid",
+ "BXD UTHSC Cannabinoid Pilot",
+ "Family:BXD Individual Data"
+ ],
+ [
+ "B6BTBRF2",
+ "B6BTBRF2",
+ "Family:Crosses, AIL, HS"
+ ],
+ [
+ "BHHBF2",
+ "B6C3HF2 UCLA Metabolism",
+ "Family:Crosses, AIL, HS"
+ ],
+ [
+ "BHF2",
+ "B6C3HF2(APOE-) UCLA Metabolism",
+ "Family:Crosses, AIL, HS"
+ ],
+ [
+ "Linsenbardt-Boehm",
+ "B6D2 EtOH Selected Advanced Intercross",
+ "Family:Crosses, AIL, HS"
+ ],
+ [
+ "B6D2F2",
+ "B6D2F2 OHSU Brain",
+ "Family:Crosses, AIL, HS"
+ ],
+ [
+ "BDF2-2005",
+ "B6D2F2 OHSU Striatum",
+ "Family:Crosses, AIL, HS"
+ ],
+ [
+ "B6D2F2-PSU",
+ "B6D2F2 PSU Muscle",
+ "Family:Crosses, AIL, HS"
+ ],
+ [
+ "BDF2-1999",
+ "B6D2F2 UCLA Liver",
+ "Family:Crosses, AIL, HS"
+ ],
+ [
+ "CTB6F2",
+ "CastB6/B6Cast F2 UCLA",
+ "Family:Crosses, AIL, HS"
+ ],
+ [
+ "CFW",
+ "CFW Outbred GWAS",
+ "Family:Crosses, AIL, HS"
+ ],
+ [
+ "HET3-ITP",
+ "HET3 ITP Longevity",
+ "Family:Crosses, AIL, HS"
+ ],
+ [
+ "HS",
+ "Heterogeneous Stock",
+ "Family:Crosses, AIL, HS"
+ ],
+ [
+ "HS-CC",
+ "Heterogeneous Stock Collaborative Cross",
+ "Family:Crosses, AIL, HS"
+ ],
+ [
+ "LGSM-AI-G34_39-43-GBS",
+ "LGSM AI G34 G39-43 Palmer (GBS)",
+ "Family:Crosses, AIL, HS"
+ ],
+ [
+ "LGSM-AI-G34-A",
+ "LGSM AI G34 Palmer (Array)",
+ "Family:Crosses, AIL, HS"
+ ],
+ [
+ "LGSM-AI-G34-GBS",
+ "LGSM AI G34 Palmer (GBS)",
+ "Family:Crosses, AIL, HS"
+ ],
+ [
+ "LGSM-AIG34_50-56-GBS",
+ "LGSM AI G34/50-56 Lionikas (GBS)",
+ "Family:Crosses, AIL, HS"
+ ],
+ [
+ "LGSM-AI-G39-43-GBS",
+ "LGSM AI G39-43 Palmer (GBS)",
+ "Family:Crosses, AIL, HS"
+ ],
+ [
+ "LGSM-AI",
+ "LGSM AI Palmer",
+ "Family:Crosses, AIL, HS"
+ ],
+ [
+ "SOTNOT-OHSU",
+ "SOTNOT-OHSU",
+ "Family:Crosses, AIL, HS"
+ ],
+ [
+ "B6-Lens",
+ "B6 Lens",
+ "Family:Non-genetic Cohort"
+ ],
+ [
+ "CIE-INIA",
+ "Chronic Intermittent Ethanol Phase 1",
+ "Family:Non-genetic Cohort"
+ ],
+ [
+ "CIE-RMA",
+ "Chronic Intermittent Ethanol Phase 2",
+ "Family:Non-genetic Cohort"
+ ],
+ [
+ "CMS",
+ "Chronic Mild Stress",
+ "Family:Non-genetic Cohort"
+ ],
+ [
+ "D2GM",
+ "D2 Glaucoma Model",
+ "Family:Non-genetic Cohort"
+ ],
+ [
+ "JAX-D2-Mono-RNA-Seq",
+ "D2 Glaucoma Monocyte JAX",
+ "Family:Non-genetic Cohort"
+ ],
+ [
+ "EMSR",
+ "Ethanol-Medicated Stress Reduction",
+ "Family:Non-genetic Cohort"
+ ],
+ [
+=======
],
[
"MDP",
@@ -5662,6 +6069,7 @@
"Family:Non-genetic Cohort"
],
[
+>>>>>>> penguin2
"B6D2",
"Glaucoma and Aged Retina UTHSC",
"Family:Non-genetic Cohort"
@@ -6674,6 +7082,7 @@
]
]
},
+<<<<<<< HEAD
"macaque monkey": {
"Macaca-fasicularis": [
[
@@ -6698,6 +7107,8 @@
]
]
},
+=======
+>>>>>>> penguin2
"mouse": {
"AKXD": [
[
diff --git a/wqflask/wqflask/templates/base.html b/wqflask/wqflask/templates/base.html
index f9d4e859..07c1b48e 100644
--- a/wqflask/wqflask/templates/base.html
+++ b/wqflask/wqflask/templates/base.html
@@ -72,6 +72,7 @@
<li><a href="httP://datafiles.genenetwork.org">Interplanetary File System</a></li>
</ul>
</li>
+ {% if g.user_session %}
<li class="">
<a href="/collections/list">Collections
<span class="badge badge-info">{{ g.user_session.num_collections }}</span>
@@ -93,6 +94,7 @@
<a id="login_in" href="/n/login">Sign in</a>
{% endif %}
</li>
+ {% endif %}
<!--
<li style="margin-left: 20px;">
<a href="http://gn2-staging.genenetwork.org" style="font-weight: bold;" >Use Staging Branch</a>
diff --git a/wqflask/wqflask/user_manager.py b/wqflask/wqflask/user_manager.py
index 1b27d7cb..ce76e0e8 100644
--- a/wqflask/wqflask/user_manager.py
+++ b/wqflask/wqflask/user_manager.py
@@ -351,7 +351,8 @@ class UserSession(object):
logger.debug("At end of delete_session")
@app.before_request
-def before_request():
+def get_cookie():
+ logger.info("@app.before_request get cookie")
g.user_session = UserSession()
g.cookie_session = AnonUser()
diff --git a/wqflask/wqflask/user_session.py b/wqflask/wqflask/user_session.py
index fd1779fb..4c2305ba 100644
--- a/wqflask/wqflask/user_session.py
+++ b/wqflask/wqflask/user_session.py
@@ -25,6 +25,19 @@ logger = getLogger(__name__)
THREE_DAYS = 60 * 60 * 24 * 3
THIRTY_DAYS = 60 * 60 * 24 * 30
+@app.before_request
+def get_user_session():
+ logger.info("@app.before_request get_session")
+ g.user_session = UserSession()
+
+@app.after_request
+def set_user_session(response):
+ if hasattr(g, 'user_session'):
+ if not request.cookies.get(g.user_session.cookie_name):
+ response.set_cookie(g.user_session.cookie_name, g.user_session.cookie)
+ return response
+
+
def verify_cookie(cookie):
the_uuid, separator, the_signature = cookie.partition(':')
assert len(the_uuid) == 36, "Is session_id a uuid?"
@@ -280,12 +293,4 @@ class UserSession(object):
Redis.delete(self.redis_key)
self.logged_in = False
-@app.before_request
-def before_request():
- g.user_session = UserSession()
-@app.after_request
-def set_cookie(response):
- if not request.cookies.get(g.user_session.cookie_name):
- response.set_cookie(g.user_session.cookie_name, g.user_session.cookie)
- return response \ No newline at end of file
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 7d3dfa48..44752246 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -80,6 +80,7 @@ logger = utility.logger.getLogger(__name__ )
@app.before_request
def connect_db():
+ logger.info("@app.before_request connect_db")
db = getattr(g, '_database', None)
if db is None:
logger.debug("Get new database connector")