Merge pull request #4719 from solgenomics/topic/fixing_histogram
[sgn.git] / sgn_test.conf
blob769acdcd1da90e574f45dfc1f96e0d71a3aabe0b
1 # Database configs
2 dbhost breedbase_db
3 dbname db
4 dbuser postgres
5 dbpass postgres
7 # Server configuration
8 production_server 0
9 debug 1
10 main_production_site_url http://localhost
12 # Species options
13 supportedCrop   Cassava
14 preferred_species Manihot esculenta
16 # Ontology options
17 composable_cvs trait,attribute,tod,toy
18 composable_cvs_allowed_combinations Image|trait+attribute+tod+toy
19 composable_cvterm_delimiter |
20 composable_cvterm_format concise
21 composable_tod_root_cvterm "Image Pre-Process Type|ISOL:0000021"
22 composable_toy_root_cvterm "time of year|TIME:0000005"
23 trait_ontology_db_name CO
24 trait_ontology_cv_name cassava_trait
25 trait_ontology_cvterm_name CGIAR cassava trait ontology
26 onto_root_namespaces  GO (Gene Ontology), PO (Plant Ontology), SO (Sequence Ontology), PATO (Phenotype and Trait Ontology)
27 trait_variable_onto_root_namespaces CO (Cassava Ontology), COMP (Composed Variables)
28 allow_observation_variable_submission_interface 1
29 onto_root_namespaces  GO (Gene Ontology), PO (Plant Ontology), SO (Sequence Ontology), PATO (Phenotype and Trait Ontology), UO (Units), CASSTISS (Cass tissues), ISOL (Imagesol), G2F (G2F), TIME (Time), SGNSTAT (SGNSTAT)
31 project_name "breeDBase"
33 # Login options
34 disable_login 0
35 default_login_janedoe 0
36 require_login 0
38 # BrAPI options
39 brapi_require_login 1
40 brapi_GET any
41 brapi_POST any
42 brapi_PUT any
43 brapi_OPTIONS any
45 # for drone stuff
46 python_executable /usr/bin/python3
47 python_executable_maskrcnn_env /usr/bin/python3
49 # slurm config
50 backend Slurm
52 # web server user
53 www_user www-data
54 www_group www-data
56 # Directory configs
57 clear_tempfiles_on_restart  1
58 rootpath /home/production/cxgn
59 basepath /home/production/cxgn/sgn
60 homepage_files_dir        /home/production/cxgn/sgn/static/
61 static_datasets_path      /home/production/SGN_data/public
62 image_dir                 images/image_files
63 cluster_shared_tempdir  /tmp/production/SGN-site/
64 solgs_dir /home/production/tmp/solgs/__USERNAME__
65 vigs_db_path             /export/prod/blast/databases/current/vigs/
66 vigs_default_db          Nicotiana_benthamiana_v0.4.4
67 trial_download_logfile /tmp/production/trial_download_log
68 archive_path /home/production/archive
69 image_path images/image_files_test
70 tempfiles_base /home/production/tmp/breedbase-site
71 static_content_url  /static_content
72 static_content_path /home/production/public/static_content
73 cache_file_path /home/production/cache
74 r_qtl_temp_path /home/production/tmp/solqtl___USERNAME__
75 submit_dir                /home/production/public/submit-uploads
76 blast_path                ""
77 blast_db_path             /home/production/blast/databases/current
78 ftpsite_root              /home/production/public
79 jbrowse_path              /jbrowse_cassavabase/?data=data/json
81 # Genotyping server options
82 genotyping_facilities None,Cornell IGD,DArT,Intertek,BGI
83 genotyping_server_token
84 genotyping_server_host https://ordering-testing.diversityarrays.com
85 genotyping_server_username NULL
86 genotyping_server_password NULL
87 default_genotyping_protocol GBS ApeKI genotyping v4
89 <Controller::Cview>
90     cview_default_map_id 1
91 </Controller::Cview>
92 cview_db_backend Cassava
94 #Homepage controller customization
95 homepage_display_phenotype_uploads 0
98 solyc_conversion_files /home/production/solcyc_conversion_files/tomato_unigenes_solyc_conversion_annotated.txt
100 <View::Mason>
101 #   add_comp_root /home/production/cxgn/sweetpotatobase/mason
102 #   add_comp_root /home/production/cannabase/mason
103 #    add_comp_root /home/production/cxgn/cassava/mason
104 #   add_comp_root /home/production/cxgn/nelsonlab/mason
105 #   add_comp_root /home/production/cxgn/cassbase/mason
106 #   add_comp_root /home/production/cxgn/musabase/mason
107 #   add_comp_root /home/production/cxgn/yambase/mason
108 #   add_comp_root /home/production/cxgn/citrusgreening/mason
109 </View::Mason>
111 <DatabaseConnection sgn_test>
112   dsn dbi:Pg:host=localhost;dbname=cxgn
113   user web_usr
114   password postgres
115   search_path public
116   search_path sgn
117   search_path annotation
118   search_path genomic
119   search_path insitu
120   search_path metadata
121   search_path pheno_population
122   search_path phenome
123   search_path physical
124   search_path tomato_gff
125   search_path biosource
126   search_path gem
127 </DatabaseConnection>
129 order_properties Quantity,Comments
130 order_properties_dialog Quantity,Comments
132 ##ODK Services
133 ##odk_crossing_data_service_name NULL
134 ##odk_crossing_data_service_url https://ona.io
135 ##odk_crossing_data_service_username seedtracker
136 ##odk_crossing_data_service_password Seedtracking101
137 ##odk_crossing_data_form_name BTractTest
138 ##odk_crossing_data_test_form_name NULL
139 ##odk_crossing_data_separate_wishlist_by_location 1
140 ##odk_phenotyping_data_service_name NULL
141 ##odk_phenotyping_data_service_url https://bio.smap.com.au
142 ##odk_phenotyping_data_service_username SMAPUSER
143 ##odk_phenotyping_data_service_password SMAPPASS
144 ##crontab_file NULL
145 ##crontab_log_filepath NULL
148 noaa_ncdc_access_token DLPxdOEIwKyoiMSuQMRYrtMaiIUpNAwk
150 identifier_prefix BB
152 cluster_host breedbase_web