diff options
| -rw-r--r-- | etc/default_settings.py | 10 | ||||
| -rwxr-xr-x | scripts/run_debug.sh | 20 | ||||
| -rw-r--r-- | wqflask/wqflask/static/new/javascript/dataset_menu_structure.json | 443 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/base.html | 2 | ||||
| -rw-r--r-- | wqflask/wqflask/user_manager.py | 3 | ||||
| -rw-r--r-- | wqflask/wqflask/user_session.py | 21 | ||||
| -rw-r--r-- | wqflask/wqflask/views.py | 1 |
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") |