From e907e8426c3c6ae58b66ee34a2ff44686c1780c0 Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Wed, 15 Aug 2018 15:47:26 +0000 Subject: ES comment --- doc/elasticsearch.org | 206 ++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 206 insertions(+) (limited to 'doc') diff --git a/doc/elasticsearch.org b/doc/elasticsearch.org index 18adfc8b..864a8363 100644 --- a/doc/elasticsearch.org +++ b/doc/elasticsearch.org @@ -1,5 +1,12 @@ * Elasticsearch +** Introduction + +GeneNetwork uses elasticsearch (ES) for all things considered +'state'. One example is user collections, another is user management. + +** Example + To get the right environment, first you can get a python REPL with something like : env GN2_PROFILE=~/opt/gn-latest ./bin/genenetwork2 ../etc/default_settings.py -cli python @@ -39,3 +46,202 @@ record['hits']['hits'][0][u'_source']['email_address'] u"myname@email.com" #+END_SRC + +** Health + +ES provides support for checking its health: + +: curl -XGET http://localhost:9200/_cluster/health?pretty=true + +#+BEGIN_SRC json + + + { + "cluster_name" : "asgard", + "status" : "yellow", + "timed_out" : false, + "number_of_nodes" : 1, + "number_of_data_nodes" : 1, + "active_primary_shards" : 5, + "active_shards" : 5, + "relocating_shards" : 0, + "initializing_shards" : 0, + "unassigned_shards" : 5 + } + +#+END_SRC + +Yellow means just one instance is running (no worries). + +To get full cluster info + +: curl -XGET "localhost:9200/_cluster/stats?human&pretty" + +#+BEGIN_SRC json +{ + "_nodes" : { + "total" : 1, + "successful" : 1, + "failed" : 0 + }, + "cluster_name" : "elasticsearch", + "timestamp" : 1529050366452, + "status" : "yellow", + "indices" : { + "count" : 3, + "shards" : { + "total" : 15, + "primaries" : 15, + "replication" : 0.0, + "index" : { + "shards" : { + "min" : 5, + "max" : 5, + "avg" : 5.0 + }, + "primaries" : { + "min" : 5, + "max" : 5, + "avg" : 5.0 + }, + "replication" : { + "min" : 0.0, + "max" : 0.0, + "avg" : 0.0 + } + } + }, + "docs" : { + "count" : 14579, + "deleted" : 0 + }, + "store" : { + "size" : "44.7mb", + "size_in_bytes" : 46892794 + }, + "fielddata" : { + "memory_size" : "0b", + "memory_size_in_bytes" : 0, + "evictions" : 0 + }, + "query_cache" : { + "memory_size" : "0b", + "memory_size_in_bytes" : 0, + "total_count" : 0, + "hit_count" : 0, + "miss_count" : 0, + "cache_size" : 0, + "cache_count" : 0, + "evictions" : 0 + }, + "completion" : { + "size" : "0b", + "size_in_bytes" : 0 + }, + "segments" : { + "count" : 24, + "memory" : "157.3kb", + "memory_in_bytes" : 161112, + "terms_memory" : "122.6kb", + "terms_memory_in_bytes" : 125569, + "stored_fields_memory" : "15.3kb", + "stored_fields_memory_in_bytes" : 15728, + "term_vectors_memory" : "0b", + "term_vectors_memory_in_bytes" : 0, + "norms_memory" : "10.8kb", + "norms_memory_in_bytes" : 11136, + "points_memory" : "111b", + "points_memory_in_bytes" : 111, + "doc_values_memory" : "8.3kb", + "doc_values_memory_in_bytes" : 8568, + "index_writer_memory" : "0b", + "index_writer_memory_in_bytes" : 0, + "version_map_memory" : "0b", + "version_map_memory_in_bytes" : 0, + "fixed_bit_set" : "0b", + "fixed_bit_set_memory_in_bytes" : 0, + "max_unsafe_auto_id_timestamp" : -1, + "file_sizes" : { } + } + }, + "nodes" : { + "count" : { + "total" : 1, + "data" : 1, + "coordinating_only" : 0, + "master" : 1, + "ingest" : 1 + }, + "versions" : [ + "6.2.1" + ], + "os" : { + "available_processors" : 16, + "allocated_processors" : 16, + "names" : [ + { + "name" : "Linux", + "count" : 1 + } + ], + "mem" : { + "total" : "125.9gb", + "total_in_bytes" : 135189286912, + "free" : "48.3gb", + "free_in_bytes" : 51922628608, + "used" : "77.5gb", + "used_in_bytes" : 83266658304, + "free_percent" : 38, + "used_percent" : 62 + } + }, + "process" : { + "cpu" : { + "percent" : 0 + }, + "open_file_descriptors" : { + "min" : 415, + "max" : 415, + "avg" : 415 + } + }, + "jvm" : { + "max_uptime" : "1.9d", + "max_uptime_in_millis" : 165800616, + "versions" : [ + { + "version" : "9.0.4", + "vm_name" : "OpenJDK 64-Bit Server VM", + "vm_version" : "9.0.4+11", + "vm_vendor" : "Oracle Corporation", + "count" : 1 + } + ], + "mem" : { + "heap_used" : "1.1gb", + "heap_used_in_bytes" : 1214872032, + "heap_max" : "23.8gb", + "heap_max_in_bytes" : 25656426496 + }, + "threads" : 110 + }, + "fs" : { + "total" : "786.4gb", + "total_in_bytes" : 844400918528, + "free" : "246.5gb", + "free_in_bytes" : 264688160768, + "available" : "206.5gb", + "available_in_bytes" : 221771468800 + }, + "plugins" : [ ], + "network_types" : { + "transport_types" : { + "netty4" : 1 + }, + "http_types" : { + "netty4" : 1 + } + } + } +} +#+BEGIN_SRC json -- cgit v1.2.3 From ec45dcbd4b61d51eff27e67d437bcdfad126580f Mon Sep 17 00:00:00 2001 From: zsloan Date: Thu, 23 Aug 2018 11:06:46 -0500 Subject: Added "change user to elasticsearch" Added "change user to elasticsearch" to the description of how to start elasticsearch--- doc/README.org | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'doc') diff --git a/doc/README.org b/doc/README.org index f290480d..cc141098 100644 --- a/doc/README.org +++ b/doc/README.org @@ -259,7 +259,7 @@ if that works run genenetwork after setting SQL_URI to something like * Running ElasticSearch -In order to start up elasticsearch, use the following command: +In order to start up elasticsearch, change user to "elasticsearch" and use the following command: : env JAVA_HOME=/opt/jdk-9.0.4 /opt/elasticsearch-6.2.1/bin/elasticsearch -- cgit v1.2.3 From 6a41599b218263bbe27726d1dbd0a3f4d2cf7ee6 Mon Sep 17 00:00:00 2001 From: zsloan Date: Mon, 15 Oct 2018 12:23:29 -0500 Subject: Updated instructions for running elasticsearch Since I know I'll forget otherwise, updated instructions on starting up ES--- doc/README.org | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) (limited to 'doc') diff --git a/doc/README.org b/doc/README.org index cc141098..100a76ca 100644 --- a/doc/README.org +++ b/doc/README.org @@ -259,9 +259,10 @@ if that works run genenetwork after setting SQL_URI to something like * Running ElasticSearch -In order to start up elasticsearch, change user to "elasticsearch" and use the following command: +In order to start up elasticsearch: +Penguin - change user to "elasticsearch" and use the following command: "env JAVA_HOME=/opt/jdk-9.0.4 /opt/elasticsearch-6.2.1/bin/elasticsearch" -: env JAVA_HOME=/opt/jdk-9.0.4 /opt/elasticsearch-6.2.1/bin/elasticsearch +New server - "systemctl restart elasticsearch" * Read more -- cgit v1.2.3 From aa7540a3f0c1c1d79bc130b6008a299d01cc732f Mon Sep 17 00:00:00 2001 From: zsloan Date: Mon, 15 Oct 2018 12:24:32 -0500 Subject: Added "as root" for instructions on running ES Forgot to add to change user to root during the last commit--- doc/README.org | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'doc') diff --git a/doc/README.org b/doc/README.org index 100a76ca..5dc9e994 100644 --- a/doc/README.org +++ b/doc/README.org @@ -262,7 +262,7 @@ if that works run genenetwork after setting SQL_URI to something like In order to start up elasticsearch: Penguin - change user to "elasticsearch" and use the following command: "env JAVA_HOME=/opt/jdk-9.0.4 /opt/elasticsearch-6.2.1/bin/elasticsearch" -New server - "systemctl restart elasticsearch" +New server - as root run "systemctl restart elasticsearch" * Read more -- cgit v1.2.3 From 496759ad08efb02b4268ea7f3bbb7905974237e9 Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Mon, 18 Feb 2019 09:39:41 +0000 Subject: Updated installation instructions and SERVER_PORT for single flask server --- doc/README.org | 71 ++++++++++++++++++++++++++++++++++-------------- wqflask/runserver.py | 8 ++++-- wqflask/utility/tools.py | 1 + 3 files changed, 57 insertions(+), 23 deletions(-) (limited to 'doc') diff --git a/doc/README.org b/doc/README.org index 5dc9e994..620c946c 100644 --- a/doc/README.org +++ b/doc/README.org @@ -12,13 +12,15 @@ - [[#load-the-small-database-in-mysql][Load the small database in MySQL]] - [[#gn2-dependency-graph][GN2 Dependency Graph]] - [[#working-with-the-gn2-source-code][Working with the GN2 source code]] + - [[#running-elasticsearch][Running ElasticSearch]] + - [[#systemd][SystemD]] + - [[#read-more][Read more]] - [[#trouble-shooting][Trouble shooting]] - [[#importerror-no-module-named-jinja2][ImportError: No module named jinja2]] - - [[#error-can-not-find-directory-homegn2_data][ERROR: can not find directory $HOME/gn2_data]] + - [[#error-can-not-find-directory-homegn2_data-or-can-not-find-directory-homegenotype_filesgenotype][ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype']] - [[#cant-run-a-module][Can't run a module]] - [[#rpy2-error-show-now-found][Rpy2 error 'show' now found]] - [[#mysql-cant-connect-server-through-socket-error][Mysql can't connect server through socket ERROR]] - - [[#read-more][Read more]] - [[#irc-session][IRC session]] * Introduction @@ -100,11 +102,13 @@ mysql (which comes as part of the GNU Guix genenetwork2 install). As root configure and run -: adduser mysql && addgroup mysql -: mysqld --datadir=/var/mysql --initialize-insecure -: mkdir -p /var/run/mysqld -: chown mysql.mysql ~/mysql /var/run/mysqld -: mysqld -u mysql --datadir=/var/mysql --explicit_defaults_for_timestamp -P 12048" +#+BEGIN_SRC bash +adduser mysql && addgroup mysql +mysqld --datadir=/var/mysql --initialize-insecure +mkdir -p /var/run/mysqld +chown mysql.mysql ~/mysql /var/run/mysqld +mysqld -u mysql --datadir=/var/mysql --explicit_defaults_for_timestamp -P 12048" +#+END_SRC If you want to run as root you may have to set @@ -192,6 +196,41 @@ http://biogems.info/contrib/genenetwork/gn2.svg See [[development.org]]. +* Running ElasticSearch + +In order to start up elasticsearch: +Penguin - change user to "elasticsearch" and use the following command: "env JAVA_HOME=/opt/jdk-9.0.4 /opt/elasticsearch-6.2.1/bin/elasticsearch" + + +** SystemD + +New server - as root run "systemctl restart elasticsearch" + +#+BEGIN_SRC +tux01:/etc/systemd/system# cat elasticsearch.service +[Unit] +Description=Run Elasticsearch + +[Service] +ExecStart=/opt/elasticsearch-6.2.1/bin/elasticsearch +Environment=JAVA_HOME=/opt/jdk-9.0.4 +Environment="ES_JAVA_OPTS=-Xms1g -Xmx8g" +Environment="PATH=/usr/local/bin:/usr/bin:/bin:/usr/local/games:/usr/games:/opt/jdk-9.0.4/bin" +LimitNOFILE=65536 +StandardOutput=syslog +StandardError=syslog +User=elasticsearch + +[Install] +WantedBy=multi-user.target +#+END_SRC + +* Read more + +If you want to understand the architecture of GN2 read +[[Architecture.org]]. The rest of this document is mostly on deployment +of GN2. + * Trouble shooting ** ImportError: No module named jinja2 @@ -210,13 +249,17 @@ On one system: : export GEM_PATH="$HOME/.guix-profile/lib/ruby/gems/2.2.0" and perhaps a few more. -** ERROR: can not find directory $HOME/gn2_data +** ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype' The default settings file looks in your $HOME/gn2_data. Since these files come with a Guix installation you should take a hint from the values in the installed version of default_settings.py (see above in this document). +You can use the GENENETWORK_FILES switch to set the datadir, for example + +: env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2 + ** Can't run a module In rare cases, development modules are not brought in with Guix @@ -257,18 +300,6 @@ if that works run genenetwork after setting SQL_URI to something like : export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s -* Running ElasticSearch - -In order to start up elasticsearch: -Penguin - change user to "elasticsearch" and use the following command: "env JAVA_HOME=/opt/jdk-9.0.4 /opt/elasticsearch-6.2.1/bin/elasticsearch" - -New server - as root run "systemctl restart elasticsearch" - -* Read more - -If you want to understand the architecture of GN2 read -[[Architecture.org]]. The rest of this document is mostly on deployment -of GN2. * IRC session diff --git a/wqflask/runserver.py b/wqflask/runserver.py index 5f41d04d..7c06356b 100644 --- a/wqflask/runserver.py +++ b/wqflask/runserver.py @@ -27,9 +27,11 @@ app_config() werkzeug_logger = logging.getLogger('werkzeug') +from utility.tools import WEBSERVER_MODE, SERVER_PORT + if WEBSERVER_MODE == 'DEBUG': app.run(host='0.0.0.0', - port=port, + port=SERVER_PORT, debug=True, use_debugger=False, threaded=False, @@ -38,7 +40,7 @@ if WEBSERVER_MODE == 'DEBUG': elif WEBSERVER_MODE == 'DEV': werkzeug_logger.setLevel(logging.WARNING) app.run(host='0.0.0.0', - port=port, + port=SERVER_PORT, debug=False, use_debugger=False, threaded=False, @@ -46,7 +48,7 @@ elif WEBSERVER_MODE == 'DEV': use_reloader=True) else: # staging/production modes app.run(host='0.0.0.0', - port=port, + port=SERVER_PORT, debug=False, use_debugger=False, threaded=True, diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py index 86ef2e1e..8b2260f5 100644 --- a/wqflask/utility/tools.py +++ b/wqflask/utility/tools.py @@ -232,6 +232,7 @@ GN_VERSION = get_setting('GN_VERSION') HOME = get_setting('HOME') WEBSERVER_MODE = get_setting('WEBSERVER_MODE') GN_SERVER_URL = get_setting('GN_SERVER_URL') +SERVER_PORT = get_setting_int('SERVER_PORT') SQL_URI = get_setting('SQL_URI') LOG_LEVEL = get_setting('LOG_LEVEL') LOG_LEVEL_DEBUG = get_setting_int('LOG_LEVEL_DEBUG') -- cgit v1.2.3 From b283418b9c9318b0b6f78a48d15869e8c3f9444f Mon Sep 17 00:00:00 2001 From: zsloan Date: Fri, 24 May 2019 12:10:11 -0500 Subject: Put API readme in correct place --- doc/API_readme.md | 155 ++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 155 insertions(+) create mode 100644 doc/API_readme.md (limited to 'doc') diff --git a/doc/API_readme.md b/doc/API_readme.md new file mode 100644 index 00000000..96e8b246 --- /dev/null +++ b/doc/API_readme.md @@ -0,0 +1,155 @@ +# API Query Documentation # +--- +# Fetching Dataset/Trait info/data # +--- +## Fetch Species List ## + +To get a list of species with data available in GN (and their associated names and ids): +``` +curl http://gn2-zach.genenetwork.org/api/v_pre1/species +[ { "FullName": "Mus musculus", "Id": 1, "Name": "mouse", "TaxonomyId": 10090 }, ... { "FullName": "Populus trichocarpa", "Id": 10, "Name": "poplar", "TaxonomyId": 3689 } ] +``` + +Or to get a single species info: +``` +curl http://gn2-zach.genenetwork.org/api/v_pre1/species/mouse +``` +OR +``` +curl http://gn2-zach.genenetwork.org/api/v_pre1/species/mouse.json +``` + +*For all queries where the last field is a user-specified name/ID, there will be the option to append a file format type. Currently there is only JSON (and it will default to JSON if none is provided), but other formats will be added later* + +## Fetch Groups/RISets ## + +This query can optionally filter by species: + +``` +curl http://gn2-zach.genenetwork.org/api/v_pre1/groups (for all species) +``` +OR +``` +curl http://gn2-zach.genenetwork.org/api/v_pre1/mouse/groups (for just mouse groups/RISets) +[ { "DisplayName": "BXD", "FullName": "BXD RI Family", "GeneticType": "riset", "Id": 1, "MappingMethodId": "1", "Name": "BXD", "SpeciesId": 1, "public": 2 }, ... { "DisplayName": "AIL LGSM F34 and F39-43 (GBS)", "FullName": "AIL LGSM F34 and F39-43 (GBS)", "GeneticType": "intercross", "Id": 72, "MappingMethodId": "2", "Name": "AIL-LGSM-F34-F39-43-GBS", "SpeciesId": 1, "public": 2 } ] +``` + +## Fetch Genotypes for Group/RISet ## +``` +curl http://gn2-zach.genenetwork.org/api/v_pre1/genotypes/BXD +``` +Returns a CSV file with metadata in the first few rows, sample/strain names as columns, and markers as rows. Currently only works for genotypes we have stored in .geno files; I'll add the option to download BIMBAM files soon. + +## Fetch Datasets ## +``` +curl http://gn2-zach.genenetwork.org/api/v_pre1/datasets/bxd +``` +OR +``` +curl http://gn2-zach.genenetwork.org/api/v_pre1/datasets/mouse/bxd +[ { "AvgID": 1, "CreateTime": "Fri, 01 Aug 2003 00:00:00 GMT", "DataScale": "log2", "FullName": "UTHSC/ETHZ/EPFL BXD Liver Polar Metabolites Extraction A, CD Cohorts (Mar 2017) log2", "Id": 1, "Long_Abbreviation": "BXDMicroArray_ProbeSet_August03", "ProbeFreezeId": 3, "ShortName": "Brain U74Av2 08/03 MAS5", "Short_Abbreviation": "Br_U_0803_M", "confidentiality": 0, "public": 0 }, ... { "AvgID": 3, "CreateTime": "Tue, 14 Aug 2018 00:00:00 GMT", "DataScale": "log2", "FullName": "EPFL/LISP BXD CD Liver Affy Mouse Gene 1.0 ST (Aug18) RMA", "Id": 859, "Long_Abbreviation": "EPFLMouseLiverCDRMAApr18", "ProbeFreezeId": 181, "ShortName": "EPFL/LISP BXD CD Liver Affy Mouse Gene 1.0 ST (Aug18) RMA", "Short_Abbreviation": "EPFLMouseLiverCDRMA0818", "confidentiality": 0, "public": 1 } ] +``` +(I added the option to specify species just in case we end up with the same group name across multiple species at some point, though it's currently unnecessary) + +## Fetch Sample Data for Dataset ## +``` +curl http://gn2-zach.genenetwork.org/api/v_pre1/sample_data/HSNIH-PalmerPublish.csv +``` + +Returns a CSV file with sample/strain names as the columns and trait IDs as rows + +## Fetch Individual Dataset Info ## +### For mRNA Assay/"ProbeSet" ### + +``` +curl http://gn2-zach.genenetwork.org/api/v_pre1/dataset/HC_M2_0606_P +``` +OR +``` +curl http://gn2-zach.genenetwork.org/api/v_pre1/dataset/bxd/HC_M2_0606_P``` +{ "confidential": 0, "data_scale": "log2", "dataset_type": "mRNA expression", "full_name": "Hippocampus Consortium M430v2 (Jun06) PDNN", "id": 112, "name": "HC_M2_0606_P", "public": 2, "short_name": "Hippocampus M430v2 BXD 06/06 PDNN", "tissue": "Hippocampus mRNA", "tissue_id": 9 } +``` +(This also has the option to specify group/riset) + +### For "Phenotypes" (basically non-mRNA Expression; stuff like weight, sex, etc) ### +For these traits, the query fetches publication info and takes the group and phenotype 'ID' as input. For example: +``` +curl http://gn2-zach.genenetwork.org/api/v_pre1/dataset/bxd/10001 +{ "dataset_type": "phenotype", "description": "Central nervous system, morphology: Cerebellum weight, whole, bilateral in adults of both sexes [mg]", "id": 10001, "name": "CBLWT2", "pubmed_id": 11438585, "title": "Genetic control of the mouse cerebellum: identification of quantitative trait loci modulating size and architecture", "year": "2001" } +``` + +## Fetch Sample Data for Single Trait ## +``` +curl http://gn2-zach.genenetwork.org/api/v_pre1/sample_data/HC_M2_0606_P/1436869_at +[ { "data_id": 23415463, "sample_name": "129S1/SvImJ", "sample_name_2": "129S1/SvImJ", "se": 0.123, "value": 8.201 }, { "data_id": 23415463, "sample_name": "A/J", "sample_name_2": "A/J", "se": 0.046, "value": 8.413 }, { "data_id": 23415463, "sample_name": "AKR/J", "sample_name_2": "AKR/J", "se": 0.134, "value": 8.856 }, ... ] +``` + +## Fetch Trait Info (Name, Description, Location, etc) ## +### For mRNA Expression/"ProbeSet" ### +``` +curl http://gn2-zach.genenetwork.org/api/v_pre1/trait/HC_M2_0606_P/1436869_at +{ "additive": -0.214087568058076, "alias": "HHG1; HLP3; HPE3; SMMCI; Dsh; Hhg1", "chr": "5", "description": "sonic hedgehog (hedgehog)", "id": 99602, "locus": "rs8253327", "lrs": 12.7711275309832, "mb": 28.457155, "mean": 9.27909090909091, "name": "1436869_at", "p_value": 0.306, "se": null, "symbol": "Shh" } +``` + +### For "Phenotypes" ### +For phenotypes this just gets the max LRS, its location, and additive effect (as calculated by qtlreaper) + +Since each group/riset only has one phenotype "dataset", this query takes either the group/riset name or the group/riset name + "Publish" (for example "BXDPublish", which is the dataset name in the DB) as input +``` +curl http://gn2-zach.genenetwork.org/api/v_pre1/trait/BXD/10001 +{ "additive": 2.39444435069444, "id": 4, "locus": "rs48756159", "lrs": 13.4974911471087 } +``` + +--- + +# Analyses # +--- +## Mapping ## +Currently two mapping tools can be used - GEMMA and R/qtl. qtlreaper will be added later with Christian Fischer's RUST implementation - https://github.com/chfi/rust-qtlreaper + +Each method's query takes the following parameters respectively (more will be added): +### GEMMA ### +* trait_id (*required*) - ID for trait being mapped +* db (*required*) - DB name for trait above (Short_Abbreviation listed when you query for datasets) +* use_loco - Whether to use LOCO (leave one chromosome out) method (default = false) +* maf - minor allele frequency (default = 0.01) + +Example query: +``` +curl http://gn2-zach.genenetwork.org/api/v_pre1/mapping?trait_id=10015&db=BXDPublish&method=gemma&use_loco=true +``` + +### R/qtl ### +(See the R/qtl guide for information on some of these options - http://www.rqtl.org/manual/qtl-manual.pdf) +* trait_id (*required*) - ID for trait being mapped +* db (*required*) - DB name for trait above (Short_Abbreviation listed when you query for datasets) +* rqtl_method - hk (default) | ehk | em | imp | mr | mr-imp | mr-argmax ; Corresponds to the "method" option for the R/qtl scanone function. +* rqtl_model - normal (default) | binary | 2-part | np ; corresponds to the "model" option for the R/qtl scanone function +* num_perm - number of permutations; 0 by default +* control_marker - Name of marker to use as control; this relies on the user knowing the name of the marker they want to use as a covariate +* interval_mapping - Whether to use interval mapping; "false" by default +* pair_scan - *NYI* + +Example query: +``` +curl http://gn2-zach.genenetwork.org/api/v_pre1/mapping?trait_id=1418701_at&db=HC_M2_0606_P&method=rqtl&num_perm=100 +``` + +Some combinations of methods/models may not make sense. The R/qtl manual should be referred to for any questions on its use (specifically the scanone function in this case) + +## Calculate Correlation ## +Currently only Sample and Tissue correlations are implemented + +This query currently takes the following parameters (though more will be added): +* trait_id (*required*) - ID for trait used for correlation +* db (*required*) - DB name for the trait above (this is the Short_Abbreviation listed when you query for datasets) +* target_db (*required*) - Target DB name to be correlated against +* type - sample (default) | tissue +* method - pearson (default) | spearman +* return - Number of results to return (default = 500) + +Example query: +``` +curl http://gn2-zach.genenetwork.org/api/v_pre1/correlation?trait_id=1427571_at&db=HC_M2_0606_P&target_db=BXDPublish&type=sample&return_count=100 +[ { "#_strains": 6, "p_value": 0.004804664723032055, "sample_r": -0.942857142857143, "trait": 20511 }, { "#_strains": 6, "p_value": 0.004804664723032055, "sample_r": -0.942857142857143, "trait": 20724 }, { "#_strains": 12, "p_value": 1.8288943424888848e-05, "sample_r": -0.9233615170820528, "trait": 13536 }, { "#_strains": 7, "p_value": 0.006807187408935392, "sample_r": 0.8928571428571429, "trait": 10157 }, { "#_strains": 7, "p_value": 0.006807187408935392, "sample_r": -0.8928571428571429, "trait": 20392 }, ... ] +``` -- cgit v1.2.3 From 0e502113445741ecc6fcddde5d6b03b851146c02 Mon Sep 17 00:00:00 2001 From: zsloan Date: Wed, 29 May 2019 12:35:37 -0500 Subject: Added info for fetching trait list --- doc/API_readme.md | 22 +++++++++++++++------- 1 file changed, 15 insertions(+), 7 deletions(-) (limited to 'doc') diff --git a/doc/API_readme.md b/doc/API_readme.md index 96e8b246..64fc61f9 100644 --- a/doc/API_readme.md +++ b/doc/API_readme.md @@ -51,13 +51,6 @@ curl http://gn2-zach.genenetwork.org/api/v_pre1/datasets/mouse/bxd ``` (I added the option to specify species just in case we end up with the same group name across multiple species at some point, though it's currently unnecessary) -## Fetch Sample Data for Dataset ## -``` -curl http://gn2-zach.genenetwork.org/api/v_pre1/sample_data/HSNIH-PalmerPublish.csv -``` - -Returns a CSV file with sample/strain names as the columns and trait IDs as rows - ## Fetch Individual Dataset Info ## ### For mRNA Assay/"ProbeSet" ### @@ -78,12 +71,27 @@ curl http://gn2-zach.genenetwork.org/api/v_pre1/dataset/bxd/10001 { "dataset_type": "phenotype", "description": "Central nervous system, morphology: Cerebellum weight, whole, bilateral in adults of both sexes [mg]", "id": 10001, "name": "CBLWT2", "pubmed_id": 11438585, "title": "Genetic control of the mouse cerebellum: identification of quantitative trait loci modulating size and architecture", "year": "2001" } ``` +## Fetch Sample Data for Dataset ## +``` +curl http://gn2-zach.genenetwork.org/api/v_pre1/sample_data/HSNIH-PalmerPublish.csv +``` + +Returns a CSV file with sample/strain names as the columns and trait IDs as rows + ## Fetch Sample Data for Single Trait ## ``` curl http://gn2-zach.genenetwork.org/api/v_pre1/sample_data/HC_M2_0606_P/1436869_at [ { "data_id": 23415463, "sample_name": "129S1/SvImJ", "sample_name_2": "129S1/SvImJ", "se": 0.123, "value": 8.201 }, { "data_id": 23415463, "sample_name": "A/J", "sample_name_2": "A/J", "se": 0.046, "value": 8.413 }, { "data_id": 23415463, "sample_name": "AKR/J", "sample_name_2": "AKR/J", "se": 0.134, "value": 8.856 }, ... ] ``` +## Fetch Trait List for Dataset ## +``` +curl http://gn2-zach.genenetwork.org/api/v_pre1/traits/HXBBXHPublish.json +[ { "Additive": 0.0499967532467532, "Id": 10001, "LRS": 16.2831307029479, "Locus": "rs106114574", "PhenotypeId": 1449, "PublicationId": 319, "Sequence": 1 }, ... ] +``` + +Both JSON and CSV formats can be specified, with CSV as default. There is also an optional "ids_only" parameter that will only return a list of trait IDs. + ## Fetch Trait Info (Name, Description, Location, etc) ## ### For mRNA Expression/"ProbeSet" ### ``` -- cgit v1.2.3 From 4241730a9e304ea272381456555d843d85f4cb04 Mon Sep 17 00:00:00 2001 From: zsloan Date: Fri, 31 May 2019 12:55:28 -0500 Subject: Minor changes --- doc/API_readme.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'doc') diff --git a/doc/API_readme.md b/doc/API_readme.md index 64fc61f9..6c88d413 100644 --- a/doc/API_readme.md +++ b/doc/API_readme.md @@ -90,7 +90,7 @@ curl http://gn2-zach.genenetwork.org/api/v_pre1/traits/HXBBXHPublish.json [ { "Additive": 0.0499967532467532, "Id": 10001, "LRS": 16.2831307029479, "Locus": "rs106114574", "PhenotypeId": 1449, "PublicationId": 319, "Sequence": 1 }, ... ] ``` -Both JSON and CSV formats can be specified, with CSV as default. There is also an optional "ids_only" parameter that will only return a list of trait IDs. +Both JSON and CSV formats can be specified, with JSON as default. There is also an optional "ids_only" and "names_only" parameter that will only return a list of trait IDs or names, respectively. ## Fetch Trait Info (Name, Description, Location, etc) ## ### For mRNA Expression/"ProbeSet" ### -- cgit v1.2.3 From 498086d79cce435f59f72880915f8e77a44b79f6 Mon Sep 17 00:00:00 2001 From: zsloan Date: Tue, 14 Jan 2020 16:15:08 -0600 Subject: Updated Readme to reflect a couple changes --- doc/API_readme.md | 46 ++++++++++++++++++++++++++-------------------- 1 file changed, 26 insertions(+), 20 deletions(-) (limited to 'doc') diff --git a/doc/API_readme.md b/doc/API_readme.md index 6c88d413..652376a0 100644 --- a/doc/API_readme.md +++ b/doc/API_readme.md @@ -6,17 +6,17 @@ To get a list of species with data available in GN (and their associated names and ids): ``` -curl http://gn2-zach.genenetwork.org/api/v_pre1/species +curl http://gn2.genenetwork.org/api/v_pre1/species [ { "FullName": "Mus musculus", "Id": 1, "Name": "mouse", "TaxonomyId": 10090 }, ... { "FullName": "Populus trichocarpa", "Id": 10, "Name": "poplar", "TaxonomyId": 3689 } ] ``` Or to get a single species info: ``` -curl http://gn2-zach.genenetwork.org/api/v_pre1/species/mouse +curl http://gn2.genenetwork.org/api/v_pre1/species/mouse ``` OR ``` -curl http://gn2-zach.genenetwork.org/api/v_pre1/species/mouse.json +curl http://gn2.genenetwork.org/api/v_pre1/species/mouse.json ``` *For all queries where the last field is a user-specified name/ID, there will be the option to append a file format type. Currently there is only JSON (and it will default to JSON if none is provided), but other formats will be added later* @@ -26,27 +26,33 @@ curl http://gn2-zach.genenetwork.org/api/v_pre1/species/mouse.json This query can optionally filter by species: ``` -curl http://gn2-zach.genenetwork.org/api/v_pre1/groups (for all species) +curl http://gn2.genenetwork.org/api/v_pre1/groups (for all species) ``` OR ``` -curl http://gn2-zach.genenetwork.org/api/v_pre1/mouse/groups (for just mouse groups/RISets) +curl http://gn2.genenetwork.org/api/v_pre1/groups/mouse (for just mouse groups/RISets) [ { "DisplayName": "BXD", "FullName": "BXD RI Family", "GeneticType": "riset", "Id": 1, "MappingMethodId": "1", "Name": "BXD", "SpeciesId": 1, "public": 2 }, ... { "DisplayName": "AIL LGSM F34 and F39-43 (GBS)", "FullName": "AIL LGSM F34 and F39-43 (GBS)", "GeneticType": "intercross", "Id": 72, "MappingMethodId": "2", "Name": "AIL-LGSM-F34-F39-43-GBS", "SpeciesId": 1, "public": 2 } ] ``` ## Fetch Genotypes for Group/RISet ## ``` -curl http://gn2-zach.genenetwork.org/api/v_pre1/genotypes/BXD +curl http://gn2.genenetwork.org/api/v_pre1/genotypes/bimbam/BXD +curl http://gn2.genenetwork.org/api/v_pre1/genotypes/BXD.bimbam +``` +Returns a group's genotypes in one of several formats - bimbam, rqtl2, or geno (a format used by qtlreaper which is just a CSV file consisting of marker positions and genotypes) + +Rqtl2 genotype queries can also include the dataset name and will return a zip of the genotypes, phenotypes, and gene map (marker names/positions). For example: +``` +curl http://gn2.genenetwork.org/api/v_pre1/genotypes/rqtl2/BXD/HC_M2_0606_P.zip ``` -Returns a CSV file with metadata in the first few rows, sample/strain names as columns, and markers as rows. Currently only works for genotypes we have stored in .geno files; I'll add the option to download BIMBAM files soon. ## Fetch Datasets ## ``` -curl http://gn2-zach.genenetwork.org/api/v_pre1/datasets/bxd +curl http://gn2.genenetwork.org/api/v_pre1/datasets/bxd ``` OR ``` -curl http://gn2-zach.genenetwork.org/api/v_pre1/datasets/mouse/bxd +curl http://gn2.genenetwork.org/api/v_pre1/datasets/mouse/bxd [ { "AvgID": 1, "CreateTime": "Fri, 01 Aug 2003 00:00:00 GMT", "DataScale": "log2", "FullName": "UTHSC/ETHZ/EPFL BXD Liver Polar Metabolites Extraction A, CD Cohorts (Mar 2017) log2", "Id": 1, "Long_Abbreviation": "BXDMicroArray_ProbeSet_August03", "ProbeFreezeId": 3, "ShortName": "Brain U74Av2 08/03 MAS5", "Short_Abbreviation": "Br_U_0803_M", "confidentiality": 0, "public": 0 }, ... { "AvgID": 3, "CreateTime": "Tue, 14 Aug 2018 00:00:00 GMT", "DataScale": "log2", "FullName": "EPFL/LISP BXD CD Liver Affy Mouse Gene 1.0 ST (Aug18) RMA", "Id": 859, "Long_Abbreviation": "EPFLMouseLiverCDRMAApr18", "ProbeFreezeId": 181, "ShortName": "EPFL/LISP BXD CD Liver Affy Mouse Gene 1.0 ST (Aug18) RMA", "Short_Abbreviation": "EPFLMouseLiverCDRMA0818", "confidentiality": 0, "public": 1 } ] ``` (I added the option to specify species just in case we end up with the same group name across multiple species at some point, though it's currently unnecessary) @@ -55,11 +61,11 @@ curl http://gn2-zach.genenetwork.org/api/v_pre1/datasets/mouse/bxd ### For mRNA Assay/"ProbeSet" ### ``` -curl http://gn2-zach.genenetwork.org/api/v_pre1/dataset/HC_M2_0606_P +curl http://gn2.genenetwork.org/api/v_pre1/dataset/HC_M2_0606_P ``` OR ``` -curl http://gn2-zach.genenetwork.org/api/v_pre1/dataset/bxd/HC_M2_0606_P``` +curl http://gn2.genenetwork.org/api/v_pre1/dataset/bxd/HC_M2_0606_P``` { "confidential": 0, "data_scale": "log2", "dataset_type": "mRNA expression", "full_name": "Hippocampus Consortium M430v2 (Jun06) PDNN", "id": 112, "name": "HC_M2_0606_P", "public": 2, "short_name": "Hippocampus M430v2 BXD 06/06 PDNN", "tissue": "Hippocampus mRNA", "tissue_id": 9 } ``` (This also has the option to specify group/riset) @@ -67,26 +73,26 @@ curl http://gn2-zach.genenetwork.org/api/v_pre1/dataset/bxd/HC_M2_0606_P``` ### For "Phenotypes" (basically non-mRNA Expression; stuff like weight, sex, etc) ### For these traits, the query fetches publication info and takes the group and phenotype 'ID' as input. For example: ``` -curl http://gn2-zach.genenetwork.org/api/v_pre1/dataset/bxd/10001 +curl http://gn2.genenetwork.org/api/v_pre1/dataset/bxd/10001 { "dataset_type": "phenotype", "description": "Central nervous system, morphology: Cerebellum weight, whole, bilateral in adults of both sexes [mg]", "id": 10001, "name": "CBLWT2", "pubmed_id": 11438585, "title": "Genetic control of the mouse cerebellum: identification of quantitative trait loci modulating size and architecture", "year": "2001" } ``` ## Fetch Sample Data for Dataset ## ``` -curl http://gn2-zach.genenetwork.org/api/v_pre1/sample_data/HSNIH-PalmerPublish.csv +curl http://gn2.genenetwork.org/api/v_pre1/sample_data/HSNIH-PalmerPublish.csv ``` Returns a CSV file with sample/strain names as the columns and trait IDs as rows ## Fetch Sample Data for Single Trait ## ``` -curl http://gn2-zach.genenetwork.org/api/v_pre1/sample_data/HC_M2_0606_P/1436869_at +curl http://gn2.genenetwork.org/api/v_pre1/sample_data/HC_M2_0606_P/1436869_at [ { "data_id": 23415463, "sample_name": "129S1/SvImJ", "sample_name_2": "129S1/SvImJ", "se": 0.123, "value": 8.201 }, { "data_id": 23415463, "sample_name": "A/J", "sample_name_2": "A/J", "se": 0.046, "value": 8.413 }, { "data_id": 23415463, "sample_name": "AKR/J", "sample_name_2": "AKR/J", "se": 0.134, "value": 8.856 }, ... ] ``` ## Fetch Trait List for Dataset ## ``` -curl http://gn2-zach.genenetwork.org/api/v_pre1/traits/HXBBXHPublish.json +curl http://gn2.genenetwork.org/api/v_pre1/traits/HXBBXHPublish.json [ { "Additive": 0.0499967532467532, "Id": 10001, "LRS": 16.2831307029479, "Locus": "rs106114574", "PhenotypeId": 1449, "PublicationId": 319, "Sequence": 1 }, ... ] ``` @@ -95,7 +101,7 @@ Both JSON and CSV formats can be specified, with JSON as default. There is also ## Fetch Trait Info (Name, Description, Location, etc) ## ### For mRNA Expression/"ProbeSet" ### ``` -curl http://gn2-zach.genenetwork.org/api/v_pre1/trait/HC_M2_0606_P/1436869_at +curl http://gn2.genenetwork.org/api/v_pre1/trait/HC_M2_0606_P/1436869_at { "additive": -0.214087568058076, "alias": "HHG1; HLP3; HPE3; SMMCI; Dsh; Hhg1", "chr": "5", "description": "sonic hedgehog (hedgehog)", "id": 99602, "locus": "rs8253327", "lrs": 12.7711275309832, "mb": 28.457155, "mean": 9.27909090909091, "name": "1436869_at", "p_value": 0.306, "se": null, "symbol": "Shh" } ``` @@ -104,7 +110,7 @@ For phenotypes this just gets the max LRS, its location, and additive effect (a Since each group/riset only has one phenotype "dataset", this query takes either the group/riset name or the group/riset name + "Publish" (for example "BXDPublish", which is the dataset name in the DB) as input ``` -curl http://gn2-zach.genenetwork.org/api/v_pre1/trait/BXD/10001 +curl http://gn2.genenetwork.org/api/v_pre1/trait/BXD/10001 { "additive": 2.39444435069444, "id": 4, "locus": "rs48756159", "lrs": 13.4974911471087 } ``` @@ -124,7 +130,7 @@ Each method's query takes the following parameters respectively (more will be ad Example query: ``` -curl http://gn2-zach.genenetwork.org/api/v_pre1/mapping?trait_id=10015&db=BXDPublish&method=gemma&use_loco=true +curl http://gn2.genenetwork.org/api/v_pre1/mapping?trait_id=10015&db=BXDPublish&method=gemma&use_loco=true ``` ### R/qtl ### @@ -140,7 +146,7 @@ curl http://gn2-zach.genenetwork.org/api/v_pre1/mapping?trait_id=10015&db=BXDPub Example query: ``` -curl http://gn2-zach.genenetwork.org/api/v_pre1/mapping?trait_id=1418701_at&db=HC_M2_0606_P&method=rqtl&num_perm=100 +curl http://gn2.genenetwork.org/api/v_pre1/mapping?trait_id=1418701_at&db=HC_M2_0606_P&method=rqtl&num_perm=100 ``` Some combinations of methods/models may not make sense. The R/qtl manual should be referred to for any questions on its use (specifically the scanone function in this case) @@ -158,6 +164,6 @@ This query currently takes the following parameters (though more will be added): Example query: ``` -curl http://gn2-zach.genenetwork.org/api/v_pre1/correlation?trait_id=1427571_at&db=HC_M2_0606_P&target_db=BXDPublish&type=sample&return_count=100 +curl http://gn2.genenetwork.org/api/v_pre1/correlation?trait_id=1427571_at&db=HC_M2_0606_P&target_db=BXDPublish&type=sample&return_count=100 [ { "#_strains": 6, "p_value": 0.004804664723032055, "sample_r": -0.942857142857143, "trait": 20511 }, { "#_strains": 6, "p_value": 0.004804664723032055, "sample_r": -0.942857142857143, "trait": 20724 }, { "#_strains": 12, "p_value": 1.8288943424888848e-05, "sample_r": -0.9233615170820528, "trait": 13536 }, { "#_strains": 7, "p_value": 0.006807187408935392, "sample_r": 0.8928571428571429, "trait": 10157 }, { "#_strains": 7, "p_value": 0.006807187408935392, "sample_r": -0.8928571428571429, "trait": 20392 }, ... ] ``` -- cgit v1.2.3 From 3fed8e9bdb24ee0b9276794494df689d7a877421 Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Mon, 8 Jul 2019 17:14:18 +0000 Subject: Mariadb --- doc/README.org | 30 ++++++++++++++++-------------- 1 file changed, 16 insertions(+), 14 deletions(-) (limited to 'doc') diff --git a/doc/README.org b/doc/README.org index 620c946c..b15bc33f 100644 --- a/doc/README.org +++ b/doc/README.org @@ -7,8 +7,8 @@ - [[#docker][Docker]] - [[#with-source][With source]] - [[#running-gn2][Running GN2]] - - [[#run-mysql-server][Run MySQL server]] - - [[#install-mysql-with-gnu-guix][Install MySQL with GNU GUIx]] + - [[#run-mariadb-server][Run MariaDB server]] + - [[#install-mariadb-with-gnu-guix][Install MariaDB with GNU GUIx]] - [[#load-the-small-database-in-mysql][Load the small database in MySQL]] - [[#gn2-dependency-graph][GN2 Dependency Graph]] - [[#working-with-the-gn2-source-code][Working with the GN2 source code]] @@ -94,8 +94,10 @@ or you can set environment variables to override individual parameters, e.g. the debug and logging switches can be particularly useful when developing GN2. -* Run MySQL server -** Install MySQL with GNU GUIx +* Run MariaDB server +** Install MariaDB with GNU GUIx + +/Note we are moving to MariaDB/ These are the steps you can take to install a fresh installation of mysql (which comes as part of the GNU Guix genenetwork2 install). @@ -103,30 +105,30 @@ mysql (which comes as part of the GNU Guix genenetwork2 install). As root configure and run #+BEGIN_SRC bash -adduser mysql && addgroup mysql -mysqld --datadir=/var/mysql --initialize-insecure -mkdir -p /var/run/mysqld -chown mysql.mysql ~/mysql /var/run/mysqld -mysqld -u mysql --datadir=/var/mysql --explicit_defaults_for_timestamp -P 12048" +adduser mariadb && addgroup mariadb +mysqld --datadir=/home/mariadb/database --initialize-insecure +mkdir -p /var/run/mariadbd +chown mariadb.mariadb /var/run/mariadbd +mysqld -u mariadb --datadir=/home/mariadb/database/mariadb --explicit_defaults_for_timestamp -P 12048" #+END_SRC If you want to run as root you may have to set : /etc/my.cnf -: [mysqld] +: [mariadbd] : user=root To check error output in a file on start-up run with something like -: mysqld -u mysql --console --explicit_defaults_for_timestamp --datadir=/gnu/mysql --log-error=~/test.log +: mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log -Other tips are that Guix installs mysqld in your profile, so this may work +Other tips are that Guix installs mariadbd in your profile, so this may work -: /home/user/.guix-profile/bin/mysqld -u mysql --explicit_defaults_for_timestamp --datadir=/gnu/mysql +: /home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb When you get errors like: -: qlalchemy.exc.IntegrityError: (_mysql_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint') +: qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint') you may need to set -- cgit v1.2.3 From 6bdae3220dd52f136f9aeb7fe95bb40e5b0884bc Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Thu, 5 Sep 2019 05:22:52 +0000 Subject: Text search comment --- doc/README.org | 7 +++++++ 1 file changed, 7 insertions(+) (limited to 'doc') diff --git a/doc/README.org b/doc/README.org index b15bc33f..03cba62a 100644 --- a/doc/README.org +++ b/doc/README.org @@ -118,6 +118,13 @@ If you want to run as root you may have to set : [mariadbd] : user=root +You also need to set + +: ft_min_word_len = 3 + +To make sure word text searches (shh) work and rebuild the tables if +required. + To check error output in a file on start-up run with something like : mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log -- cgit v1.2.3 From e72862bdb307b016cb1c2269818edae5c9ddc150 Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Mon, 20 Apr 2020 09:46:16 -0500 Subject: Remove Elastic --- doc/README.org | 30 ------------------------------ 1 file changed, 30 deletions(-) (limited to 'doc') diff --git a/doc/README.org b/doc/README.org index 03cba62a..4057cb79 100644 --- a/doc/README.org +++ b/doc/README.org @@ -12,8 +12,6 @@ - [[#load-the-small-database-in-mysql][Load the small database in MySQL]] - [[#gn2-dependency-graph][GN2 Dependency Graph]] - [[#working-with-the-gn2-source-code][Working with the GN2 source code]] - - [[#running-elasticsearch][Running ElasticSearch]] - - [[#systemd][SystemD]] - [[#read-more][Read more]] - [[#trouble-shooting][Trouble shooting]] - [[#importerror-no-module-named-jinja2][ImportError: No module named jinja2]] @@ -205,34 +203,6 @@ http://biogems.info/contrib/genenetwork/gn2.svg See [[development.org]]. -* Running ElasticSearch - -In order to start up elasticsearch: -Penguin - change user to "elasticsearch" and use the following command: "env JAVA_HOME=/opt/jdk-9.0.4 /opt/elasticsearch-6.2.1/bin/elasticsearch" - - -** SystemD - -New server - as root run "systemctl restart elasticsearch" - -#+BEGIN_SRC -tux01:/etc/systemd/system# cat elasticsearch.service -[Unit] -Description=Run Elasticsearch - -[Service] -ExecStart=/opt/elasticsearch-6.2.1/bin/elasticsearch -Environment=JAVA_HOME=/opt/jdk-9.0.4 -Environment="ES_JAVA_OPTS=-Xms1g -Xmx8g" -Environment="PATH=/usr/local/bin:/usr/bin:/bin:/usr/local/games:/usr/games:/opt/jdk-9.0.4/bin" -LimitNOFILE=65536 -StandardOutput=syslog -StandardError=syslog -User=elasticsearch - -[Install] -WantedBy=multi-user.target -#+END_SRC * Read more -- cgit v1.2.3 From 960f42184da639a4e352ba7517cf0eece06d58f9 Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Thu, 23 Apr 2020 10:44:46 -0500 Subject: Docs --- doc/GUIX-Reproducible-from-source.org | 1 - doc/README.org | 80 ++++++++++++++++------------------- 2 files changed, 36 insertions(+), 45 deletions(-) (limited to 'doc') diff --git a/doc/GUIX-Reproducible-from-source.org b/doc/GUIX-Reproducible-from-source.org index 83adce99..19e4d14f 100644 --- a/doc/GUIX-Reproducible-from-source.org +++ b/doc/GUIX-Reproducible-from-source.org @@ -33,7 +33,6 @@ GNU Guix has to be installed as root. I tested this recipe on a fresh install of Debian 8.3.0 (in KVM) though it should work on any modern Linux distribution (including CentOS). - Note that GN2 consists of an approx. 5 GB installation including database. If you use a virtual machine we recommend to use at least double. diff --git a/doc/README.org b/doc/README.org index 4057cb79..828ed2cd 100644 --- a/doc/README.org +++ b/doc/README.org @@ -3,9 +3,6 @@ * Table of Contents :TOC: - [[#introduction][Introduction]] - [[#install][Install]] - - [[#tarball][Tarball]] - - [[#docker][Docker]] - - [[#with-source][With source]] - [[#running-gn2][Running GN2]] - [[#run-mariadb-server][Run MariaDB server]] - [[#install-mariadb-with-gnu-guix][Install MariaDB with GNU GUIx]] @@ -20,6 +17,8 @@ - [[#rpy2-error-show-now-found][Rpy2 error 'show' now found]] - [[#mysql-cant-connect-server-through-socket-error][Mysql can't connect server through socket ERROR]] - [[#irc-session][IRC session]] + - [[#notes][NOTES]] + - [[#deploying-gn2-official][Deploying GN2 official]] * Introduction @@ -38,44 +37,10 @@ an example of the [[#gn2-dependency-graph][GN2 Dependency Graph]]. * Install -The quickest way to install GN2 is by using a binary installation -(tarball or Docker image). These installations are bundled by GNU -Guix and include all dependencies. You can install GeneNetwork on most -Linux distributions, including Debian, Ubuntu, Fedora and CentOS, -provided you have administrator privileges (root). The alternative is -a Docker installation. - -** Tarball - -Download the ~800Mb tarball from -[[http://files.genenetwork.org/software/binary_tarball/]]. Validate the checksum and -unpack to root, for example - -: tar xvzf genenetwork2-2.10rc3-1538ffd-tarball-pack.tar.gz -: mv /gnu / -: mv /opt/genenetwork2 /opt/ - -Now you shoud be able to start the server with - -: /opt/genenetwork2/bin/genenetwork2 - -When the server stops with a MySQL error [[#run-mysql-server][Run MySQL server]] -and set SQL_URI to point at it. For example: - -: export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s - -See also [[#mysql-cant-connect-server-through-socket-error][Mysql can't connect server through socket ERROR]]. - -** Docker - -Docker images are also available through -[[http://files.genenetwork.org/software/]]. Validate the checksum and run -with [[https://docs.docker.com/engine/reference/commandline/load/][Docker load]]. - -** With source - -For more elaborate installation instructions on deploying GeneNetwork from -source see [[#source-deployment][Source deployment]]. +Make sure to install GNU Guix using the binary download instructions +on the main website. Follow the instructions on +[[GUIX-Reproducible-from-source.org]] to download pre-built binaries. Note +the download amounts to several GBs of data. * Running GN2 @@ -95,10 +60,10 @@ developing GN2. * Run MariaDB server ** Install MariaDB with GNU GUIx -/Note we are moving to MariaDB/ +/Note: we moved to MariaDB/ These are the steps you can take to install a fresh installation of -mysql (which comes as part of the GNU Guix genenetwork2 install). +mariadb (which comes as part of the GNU Guix genenetwork2 install). As root configure and run @@ -203,7 +168,6 @@ http://biogems.info/contrib/genenetwork/gn2.svg See [[development.org]]. - * Read more If you want to understand the architecture of GN2 read @@ -687,3 +651,31 @@ The following derivations would be built: I am building it on guix.genenetwork.org right now [10:09] nice [10:10] #+end_src + +* NOTES + +** Deploying GN2 official + +Let's see how fast we can deploy a second copy of GN2. + +- [-] Base install + + [X] First install a Debian server with GNU Guix on board + + [X] Get Guix build going + - [X] Build the correct version of Guix + - [X] Check out the correct gn-stable version of guix-bioinformatics http://git.genenetwork.org/pjotrp/guix-bioinformatics + - [X] guix package -i genenetwork2 -p /usr/local/guix-profiles/gn2-stable + + [X] Create a gn2 user and home with space + + [X] Install redis (currently debian) + - [X] add to systemd + - [X] update redis.cnf + - [X] update database + + [X] Install mariadb (currently debian mariadb-server) + - [X] add to systemd + - [X] system stop mysql + - [X] update mysql.cnf + - [X] update database (see gn-services/services/mariadb.md) + - [X] check tables + + [ ] run gn2 (rust-qtlreaper not working) + + [X] update nginx + + [ ] install genenetwork3 + - [ ] add to systemd -- cgit v1.2.3 From be09d207ee4e2705e358102f8bdbcd1da7f70ca2 Mon Sep 17 00:00:00 2001 From: zsloan Date: Fri, 24 Apr 2020 16:06:36 -0500 Subject: Replaced hard-coded instances of GN2 urls with ones pulled from settings file --- doc/API_readme.md | 42 +++++++++++----------- wqflask/base/data_set.py | 4 +-- wqflask/base/trait.py | 7 ++-- wqflask/utility/tools.py | 2 ++ wqflask/wqflask/ctl/ctl_analysis.py | 4 ++- wqflask/wqflask/do_search.py | 3 +- wqflask/wqflask/network_graph/network_graph.py | 2 ++ wqflask/wqflask/search_results.py | 3 +- wqflask/wqflask/static/new/javascript/ctl_graph.js | 8 +---- .../new/javascript/dataset_select_menu_orig.js | 1 - .../wqflask/static/new/javascript/network_graph.js | 4 +-- wqflask/wqflask/templates/ctl_results.html | 1 + wqflask/wqflask/templates/index_page.html | 4 +-- wqflask/wqflask/templates/index_page_orig.html | 4 +-- wqflask/wqflask/templates/network_graph.html | 1 + 15 files changed, 47 insertions(+), 43 deletions(-) (limited to 'doc') diff --git a/doc/API_readme.md b/doc/API_readme.md index 652376a0..be6668dc 100644 --- a/doc/API_readme.md +++ b/doc/API_readme.md @@ -6,17 +6,17 @@ To get a list of species with data available in GN (and their associated names and ids): ``` -curl http://gn2.genenetwork.org/api/v_pre1/species +curl http://genenetwork.org/api/v_pre1/species [ { "FullName": "Mus musculus", "Id": 1, "Name": "mouse", "TaxonomyId": 10090 }, ... { "FullName": "Populus trichocarpa", "Id": 10, "Name": "poplar", "TaxonomyId": 3689 } ] ``` Or to get a single species info: ``` -curl http://gn2.genenetwork.org/api/v_pre1/species/mouse +curl http://genenetwork.org/api/v_pre1/species/mouse ``` OR ``` -curl http://gn2.genenetwork.org/api/v_pre1/species/mouse.json +curl http://genenetwork.org/api/v_pre1/species/mouse.json ``` *For all queries where the last field is a user-specified name/ID, there will be the option to append a file format type. Currently there is only JSON (and it will default to JSON if none is provided), but other formats will be added later* @@ -26,33 +26,33 @@ curl http://gn2.genenetwork.org/api/v_pre1/species/mouse.json This query can optionally filter by species: ``` -curl http://gn2.genenetwork.org/api/v_pre1/groups (for all species) +curl http://genenetwork.org/api/v_pre1/groups (for all species) ``` OR ``` -curl http://gn2.genenetwork.org/api/v_pre1/groups/mouse (for just mouse groups/RISets) +curl http://genenetwork.org/api/v_pre1/groups/mouse (for just mouse groups/RISets) [ { "DisplayName": "BXD", "FullName": "BXD RI Family", "GeneticType": "riset", "Id": 1, "MappingMethodId": "1", "Name": "BXD", "SpeciesId": 1, "public": 2 }, ... { "DisplayName": "AIL LGSM F34 and F39-43 (GBS)", "FullName": "AIL LGSM F34 and F39-43 (GBS)", "GeneticType": "intercross", "Id": 72, "MappingMethodId": "2", "Name": "AIL-LGSM-F34-F39-43-GBS", "SpeciesId": 1, "public": 2 } ] ``` ## Fetch Genotypes for Group/RISet ## ``` -curl http://gn2.genenetwork.org/api/v_pre1/genotypes/bimbam/BXD -curl http://gn2.genenetwork.org/api/v_pre1/genotypes/BXD.bimbam +curl http://genenetwork.org/api/v_pre1/genotypes/bimbam/BXD +curl http://genenetwork.org/api/v_pre1/genotypes/BXD.bimbam ``` Returns a group's genotypes in one of several formats - bimbam, rqtl2, or geno (a format used by qtlreaper which is just a CSV file consisting of marker positions and genotypes) Rqtl2 genotype queries can also include the dataset name and will return a zip of the genotypes, phenotypes, and gene map (marker names/positions). For example: ``` -curl http://gn2.genenetwork.org/api/v_pre1/genotypes/rqtl2/BXD/HC_M2_0606_P.zip +curl http://genenetwork.org/api/v_pre1/genotypes/rqtl2/BXD/HC_M2_0606_P.zip ``` ## Fetch Datasets ## ``` -curl http://gn2.genenetwork.org/api/v_pre1/datasets/bxd +curl http://genenetwork.org/api/v_pre1/datasets/bxd ``` OR ``` -curl http://gn2.genenetwork.org/api/v_pre1/datasets/mouse/bxd +curl http://genenetwork.org/api/v_pre1/datasets/mouse/bxd [ { "AvgID": 1, "CreateTime": "Fri, 01 Aug 2003 00:00:00 GMT", "DataScale": "log2", "FullName": "UTHSC/ETHZ/EPFL BXD Liver Polar Metabolites Extraction A, CD Cohorts (Mar 2017) log2", "Id": 1, "Long_Abbreviation": "BXDMicroArray_ProbeSet_August03", "ProbeFreezeId": 3, "ShortName": "Brain U74Av2 08/03 MAS5", "Short_Abbreviation": "Br_U_0803_M", "confidentiality": 0, "public": 0 }, ... { "AvgID": 3, "CreateTime": "Tue, 14 Aug 2018 00:00:00 GMT", "DataScale": "log2", "FullName": "EPFL/LISP BXD CD Liver Affy Mouse Gene 1.0 ST (Aug18) RMA", "Id": 859, "Long_Abbreviation": "EPFLMouseLiverCDRMAApr18", "ProbeFreezeId": 181, "ShortName": "EPFL/LISP BXD CD Liver Affy Mouse Gene 1.0 ST (Aug18) RMA", "Short_Abbreviation": "EPFLMouseLiverCDRMA0818", "confidentiality": 0, "public": 1 } ] ``` (I added the option to specify species just in case we end up with the same group name across multiple species at some point, though it's currently unnecessary) @@ -61,11 +61,11 @@ curl http://gn2.genenetwork.org/api/v_pre1/datasets/mouse/bxd ### For mRNA Assay/"ProbeSet" ### ``` -curl http://gn2.genenetwork.org/api/v_pre1/dataset/HC_M2_0606_P +curl http://genenetwork.org/api/v_pre1/dataset/HC_M2_0606_P ``` OR ``` -curl http://gn2.genenetwork.org/api/v_pre1/dataset/bxd/HC_M2_0606_P``` +curl http://genenetwork.org/api/v_pre1/dataset/bxd/HC_M2_0606_P``` { "confidential": 0, "data_scale": "log2", "dataset_type": "mRNA expression", "full_name": "Hippocampus Consortium M430v2 (Jun06) PDNN", "id": 112, "name": "HC_M2_0606_P", "public": 2, "short_name": "Hippocampus M430v2 BXD 06/06 PDNN", "tissue": "Hippocampus mRNA", "tissue_id": 9 } ``` (This also has the option to specify group/riset) @@ -73,26 +73,26 @@ curl http://gn2.genenetwork.org/api/v_pre1/dataset/bxd/HC_M2_0606_P``` ### For "Phenotypes" (basically non-mRNA Expression; stuff like weight, sex, etc) ### For these traits, the query fetches publication info and takes the group and phenotype 'ID' as input. For example: ``` -curl http://gn2.genenetwork.org/api/v_pre1/dataset/bxd/10001 +curl http://genenetwork.org/api/v_pre1/dataset/bxd/10001 { "dataset_type": "phenotype", "description": "Central nervous system, morphology: Cerebellum weight, whole, bilateral in adults of both sexes [mg]", "id": 10001, "name": "CBLWT2", "pubmed_id": 11438585, "title": "Genetic control of the mouse cerebellum: identification of quantitative trait loci modulating size and architecture", "year": "2001" } ``` ## Fetch Sample Data for Dataset ## ``` -curl http://gn2.genenetwork.org/api/v_pre1/sample_data/HSNIH-PalmerPublish.csv +curl http://genenetwork.org/api/v_pre1/sample_data/HSNIH-PalmerPublish.csv ``` Returns a CSV file with sample/strain names as the columns and trait IDs as rows ## Fetch Sample Data for Single Trait ## ``` -curl http://gn2.genenetwork.org/api/v_pre1/sample_data/HC_M2_0606_P/1436869_at +curl http://genenetwork.org/api/v_pre1/sample_data/HC_M2_0606_P/1436869_at [ { "data_id": 23415463, "sample_name": "129S1/SvImJ", "sample_name_2": "129S1/SvImJ", "se": 0.123, "value": 8.201 }, { "data_id": 23415463, "sample_name": "A/J", "sample_name_2": "A/J", "se": 0.046, "value": 8.413 }, { "data_id": 23415463, "sample_name": "AKR/J", "sample_name_2": "AKR/J", "se": 0.134, "value": 8.856 }, ... ] ``` ## Fetch Trait List for Dataset ## ``` -curl http://gn2.genenetwork.org/api/v_pre1/traits/HXBBXHPublish.json +curl http://genenetwork.org/api/v_pre1/traits/HXBBXHPublish.json [ { "Additive": 0.0499967532467532, "Id": 10001, "LRS": 16.2831307029479, "Locus": "rs106114574", "PhenotypeId": 1449, "PublicationId": 319, "Sequence": 1 }, ... ] ``` @@ -101,7 +101,7 @@ Both JSON and CSV formats can be specified, with JSON as default. There is also ## Fetch Trait Info (Name, Description, Location, etc) ## ### For mRNA Expression/"ProbeSet" ### ``` -curl http://gn2.genenetwork.org/api/v_pre1/trait/HC_M2_0606_P/1436869_at +curl http://genenetwork.org/api/v_pre1/trait/HC_M2_0606_P/1436869_at { "additive": -0.214087568058076, "alias": "HHG1; HLP3; HPE3; SMMCI; Dsh; Hhg1", "chr": "5", "description": "sonic hedgehog (hedgehog)", "id": 99602, "locus": "rs8253327", "lrs": 12.7711275309832, "mb": 28.457155, "mean": 9.27909090909091, "name": "1436869_at", "p_value": 0.306, "se": null, "symbol": "Shh" } ``` @@ -110,7 +110,7 @@ For phenotypes this just gets the max LRS, its location, and additive effect (a Since each group/riset only has one phenotype "dataset", this query takes either the group/riset name or the group/riset name + "Publish" (for example "BXDPublish", which is the dataset name in the DB) as input ``` -curl http://gn2.genenetwork.org/api/v_pre1/trait/BXD/10001 +curl http://genenetwork.org/api/v_pre1/trait/BXD/10001 { "additive": 2.39444435069444, "id": 4, "locus": "rs48756159", "lrs": 13.4974911471087 } ``` @@ -130,7 +130,7 @@ Each method's query takes the following parameters respectively (more will be ad Example query: ``` -curl http://gn2.genenetwork.org/api/v_pre1/mapping?trait_id=10015&db=BXDPublish&method=gemma&use_loco=true +curl http://genenetwork.org/api/v_pre1/mapping?trait_id=10015&db=BXDPublish&method=gemma&use_loco=true ``` ### R/qtl ### @@ -146,7 +146,7 @@ curl http://gn2.genenetwork.org/api/v_pre1/mapping?trait_id=10015&db=BXDPublish& Example query: ``` -curl http://gn2.genenetwork.org/api/v_pre1/mapping?trait_id=1418701_at&db=HC_M2_0606_P&method=rqtl&num_perm=100 +curl http://genenetwork.org/api/v_pre1/mapping?trait_id=1418701_at&db=HC_M2_0606_P&method=rqtl&num_perm=100 ``` Some combinations of methods/models may not make sense. The R/qtl manual should be referred to for any questions on its use (specifically the scanone function in this case) @@ -164,6 +164,6 @@ This query currently takes the following parameters (though more will be added): Example query: ``` -curl http://gn2.genenetwork.org/api/v_pre1/correlation?trait_id=1427571_at&db=HC_M2_0606_P&target_db=BXDPublish&type=sample&return_count=100 +curl http://genenetwork.org/api/v_pre1/correlation?trait_id=1427571_at&db=HC_M2_0606_P&target_db=BXDPublish&type=sample&return_count=100 [ { "#_strains": 6, "p_value": 0.004804664723032055, "sample_r": -0.942857142857143, "trait": 20511 }, { "#_strains": 6, "p_value": 0.004804664723032055, "sample_r": -0.942857142857143, "trait": 20724 }, { "#_strains": 12, "p_value": 1.8288943424888848e-05, "sample_r": -0.9233615170820528, "trait": 13536 }, { "#_strains": 7, "p_value": 0.006807187408935392, "sample_r": 0.8928571428571429, "trait": 10157 }, { "#_strains": 7, "p_value": 0.006807187408935392, "sample_r": -0.8928571428571429, "trait": 20392 }, ... ] ``` diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index fae62875..8652e6b7 100644 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -56,7 +56,7 @@ from pprint import pformat as pf from db.gn_server import menu_main from db.call import fetchall,fetchone,fetch1 -from utility.tools import USE_GN_SERVER, USE_REDIS, flat_files, flat_file_exists +from utility.tools import USE_GN_SERVER, USE_REDIS, flat_files, flat_file_exists, GN2_BASE_URL from utility.logger import getLogger logger = getLogger(__name__ ) @@ -94,7 +94,7 @@ Publish or ProbeSet. E.g. """ self.datasets = {} if rebuild: #ZS: May make this the only option - data = json.loads(requests.get("http://gn2.genenetwork.org/api/v_pre1/gen_dropdown").content) + data = json.loads(requests.get(GN2_BASE_URL + "/api/v_pre1/gen_dropdown").content) #data = gen_menu.gen_dropdown_json() else: file_name = "wqflask/static/new/javascript/dataset_menu_structure.json" diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py index 5525472e..e454c593 100644 --- a/wqflask/base/trait.py +++ b/wqflask/base/trait.py @@ -14,6 +14,7 @@ from base.data_set import create_dataset from db import webqtlDatabaseFunction from utility import webqtlUtil from utility import hmac +from utility.tools import GN2_BASE_URL from wqflask import app @@ -135,9 +136,9 @@ class GeneralTrait(object): alias = 'Not available' if self.symbol: - human_response = requests.get("http://gn2.genenetwork.org/gn3/gene/aliases/" + self.symbol.upper()) - mouse_response = requests.get("http://gn2.genenetwork.org/gn3/gene/aliases/" + self.symbol.capitalize()) - other_response = requests.get("http://gn2.genenetwork.org/gn3/gene/aliases/" + self.symbol.lower()) + human_response = requests.get(GN2_BASE_URL + "gn3/gene/aliases/" + self.symbol.upper()) + mouse_response = requests.get(GN2_BASE_URL + "gn3/gene/aliases/" + self.symbol.capitalize()) + other_response = requests.get(GN2_BASE_URL + "gn3/gene/aliases/" + self.symbol.lower()) if human_response and mouse_response and other_response: alias_list = json.loads(human_response.content) + json.loads(mouse_response.content) + json.loads(other_response.content) diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py index 0fbedccb..9354ece6 100644 --- a/wqflask/utility/tools.py +++ b/wqflask/utility/tools.py @@ -234,6 +234,8 @@ def show_settings(): GN_VERSION = get_setting('GN_VERSION') HOME = get_setting('HOME') WEBSERVER_MODE = get_setting('WEBSERVER_MODE') +GN2_BASE_URL = get_setting('GN2_BASE_URL') +GN2_BRANCH_URL = get_setting('GN2_BRANCH_URL') GN_SERVER_URL = get_setting('GN_SERVER_URL') SERVER_PORT = get_setting_int('SERVER_PORT') SQL_URI = get_setting('SQL_URI') diff --git a/wqflask/wqflask/ctl/ctl_analysis.py b/wqflask/wqflask/ctl/ctl_analysis.py index 6fda02fd..4415b86a 100644 --- a/wqflask/wqflask/ctl/ctl_analysis.py +++ b/wqflask/wqflask/ctl/ctl_analysis.py @@ -20,7 +20,7 @@ from base import data_set from base import trait as TRAIT from utility import helper_functions -from utility.tools import locate +from utility.tools import locate, GN2_BRANCH_URL from rpy2.robjects.packages import importr @@ -56,6 +56,8 @@ class CTL(object): self.edges_list = [] logger.info("Obtained pointers to CTL functions") + self.gn2_url = GN2_BRANCH_URL + def addNode(self, gt): node_dict = { 'data' : {'id' : str(gt.name) + ":" + str(gt.dataset.name), 'sid' : str(gt.name), diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py index 05caa100..b0ca5ced 100644 --- a/wqflask/wqflask/do_search.py +++ b/wqflask/wqflask/do_search.py @@ -13,6 +13,7 @@ import sys # sys.path.append("..") Never in a running webserver from db import webqtlDatabaseFunction +from utility.tools import GN2_BASE_URL import logging from utility.logger import getLogger @@ -919,7 +920,7 @@ def get_aliases(symbol, species): return [] filtered_aliases = [] - response = requests.get("http://gn2.genenetwork.org/gn3/gene/aliases/" + symbol_string) + response = requests.get(GN2_BASE_URL + "/gn3/gene/aliases/" + symbol_string) if response: alias_list = json.loads(response.content) diff --git a/wqflask/wqflask/network_graph/network_graph.py b/wqflask/wqflask/network_graph/network_graph.py index a332db46..152e4168 100644 --- a/wqflask/wqflask/network_graph/network_graph.py +++ b/wqflask/wqflask/network_graph/network_graph.py @@ -47,6 +47,7 @@ from utility.TDCell import TDCell from base.trait import GeneralTrait from base import data_set from utility import webqtlUtil, helper_functions, corr_result_helpers +from utility.tools import GN2_BRANCH_URL from db import webqtlDatabaseFunction import utility.webqtlUtil #this is for parallel computing only. from wqflask.correlation import correlation_functions @@ -195,6 +196,7 @@ class NetworkGraph(object): self.nodes_list.append(node_dict) self.elements = json.dumps(self.nodes_list + self.edges_list) + self.gn2_url = GN2_BRANCH_URL groups = [] for sample in self.all_sample_list: diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py index 698389ab..8f702d58 100644 --- a/wqflask/wqflask/search_results.py +++ b/wqflask/wqflask/search_results.py @@ -28,6 +28,7 @@ from flask import render_template, Flask, g from utility import formatting from utility import hmac +from utility.tools import GN2_BASE_URL from utility.type_checking import is_float, is_int, is_str, get_float, get_int, get_string from utility.logger import getLogger @@ -295,7 +296,7 @@ def get_aliases(symbol_list, species): symbols_string = ",".join(updated_symbols) filtered_aliases = [] - response = requests.get("http://gn2.genenetwork.org/gn3/gene/aliases2/" + symbols_string) + response = requests.get(GN2_BASE_URL + "/gn3/gene/aliases2/" + symbols_string) if response: alias_lists = json.loads(response.content) seen = set() diff --git a/wqflask/wqflask/static/new/javascript/ctl_graph.js b/wqflask/wqflask/static/new/javascript/ctl_graph.js index 94bd7e9d..bd950592 100644 --- a/wqflask/wqflask/static/new/javascript/ctl_graph.js +++ b/wqflask/wqflask/static/new/javascript/ctl_graph.js @@ -82,18 +82,12 @@ window.onload=function() { function create_qtips(cy){ cy.nodes().qtip({ content: function(){ - gn_link = ''+''+this.data().id +''+'
' + gn_link = ''+''+this.data().id +''+'
' ncbi_link = 'NCBI'+'
' omim_link = 'OMIM'+'
' qtip_content = gn_link + ncbi_link + omim_link return qtip_content - //return ''+''+this.data().id +''+'' }, - // content: { - // title: ''+''+this.target() +''+'', - // text: this.target, - // button: true - // }, position: { my: 'top center', at: 'bottom center' diff --git a/wqflask/wqflask/static/new/javascript/dataset_select_menu_orig.js b/wqflask/wqflask/static/new/javascript/dataset_select_menu_orig.js index fad600d2..794804f4 100644 --- a/wqflask/wqflask/static/new/javascript/dataset_select_menu_orig.js +++ b/wqflask/wqflask/static/new/javascript/dataset_select_menu_orig.js @@ -74,7 +74,6 @@ redo_dropdown = function(dropdown, items) { this_opt_group = null for (_i = 0, _len = group_family_list.length; _i < _len; _i++) { item = group_family_list[_i]; - console.log("THE ITEM:", item) if (item[2] != "None" && current_family == ""){ current_family = item[2] this_opt_group = $("") diff --git a/wqflask/wqflask/static/new/javascript/network_graph.js b/wqflask/wqflask/static/new/javascript/network_graph.js index 4d507a18..02c3b817 100644 --- a/wqflask/wqflask/static/new/javascript/network_graph.js +++ b/wqflask/wqflask/static/new/javascript/network_graph.js @@ -85,7 +85,7 @@ window.onload=function() { cy.nodes().qtip({ content: function(){ qtip_content = '' - gn_link = ''+''+this.data().id +''+'
' + gn_link = ''+''+this.data().id +''+'
' qtip_content += gn_link if (typeof(this.data().geneid) !== 'undefined'){ ncbi_link = 'NCBI'+'
' @@ -115,7 +115,7 @@ window.onload=function() { correlation_line = 'Sample r: ' + this.data().correlation + '
' p_value_line = 'Sample p(r): ' + this.data().p_value + '
' overlap_line = 'Overlap: ' + this.data().overlap + '
' - scatter_plot = 'View Scatterplot' + scatter_plot = 'View Scatterplot' return correlation_line + p_value_line + overlap_line + scatter_plot }, position: { diff --git a/wqflask/wqflask/templates/ctl_results.html b/wqflask/wqflask/templates/ctl_results.html index d85075a9..0108d93a 100644 --- a/wqflask/wqflask/templates/ctl_results.html +++ b/wqflask/wqflask/templates/ctl_results.html @@ -61,6 +61,7 @@ diff --git a/wqflask/wqflask/templates/index_page.html b/wqflask/wqflask/templates/index_page.html index 0116245d..f8720d39 100644 --- a/wqflask/wqflask/templates/index_page.html +++ b/wqflask/wqflask/templates/index_page.html @@ -219,9 +219,9 @@

GN1 Mirror and development sites

diff --git a/wqflask/wqflask/templates/index_page_orig.html b/wqflask/wqflask/templates/index_page_orig.html index 963531cb..06b71f53 100755 --- a/wqflask/wqflask/templates/index_page_orig.html +++ b/wqflask/wqflask/templates/index_page_orig.html @@ -254,8 +254,8 @@

GeneNetwork v2:

GeneNetwork v1: