grnsight 6.0.4 → 6.0.7
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/database/README.md +40 -16
- package/database/expression-database/README.md +2 -2
- package/database/expression-database/schema.sql +14 -14
- package/database/expression-database/scripts/loader.py +6 -6
- package/database/network-database/README.md +36 -4
- package/database/network-database/schema.sql +7 -7
- package/database/network-database/scripts/filter_genes.py +1 -1
- package/database/network-database/scripts/generate_network.py +1 -1
- package/database/network-database/scripts/generate_new_network_version.py +223 -0
- package/database/network-database/scripts/loader.py +3 -3
- package/database/network-database/scripts/loader_updates.py +99 -0
- package/package.json +2 -2
- package/server/controllers/custom-workbook-controller.js +4 -3
- package/server/dals/expression-dal.js +8 -7
- package/server/dals/network-dal.js +3 -3
- package/web-client/public/js/api/grnsight-api.js +56 -55
- package/web-client/public/js/generateNetwork.js +15 -7
- package/web-client/public/js/setup-load-and-import-handlers.js +171 -170
- package/web-client/public/js/upload.js +74 -95
- package/.bundle/config +0 -3
- package/GRNsight - Beta.html +0 -194
- package/Gemfile.lock +0 -259
- package/_gh_pages/about.html +0 -807
- package/_gh_pages/assets/css/bootstrap.min.css +0 -10
- package/_gh_pages/assets/css/footer.css +0 -3
- package/_gh_pages/assets/css/main.css +0 -363
- package/_gh_pages/assets/images/21-genes_31-edges_Schade-data_estimation_output_binary-no-targetless-genes_sif.png +0 -0
- package/_gh_pages/assets/images/21-genes_31-edges_Schade-data_estimation_output_binary_sif.png +0 -0
- package/_gh_pages/assets/images/21-genes_31-edges_Schade-data_graphml_3-edges-and-footer.png +0 -0
- package/_gh_pages/assets/images/21-genes_31-edges_Schade-data_graphml_header-and-3-nodes.png +0 -0
- package/_gh_pages/assets/images/21-genes_31-edges_Schade-data_graphml_output_3-edges-and-footer.png +0 -0
- package/_gh_pages/assets/images/21-genes_31-edges_Schade-data_graphml_output_header-and-3-nodes.png +0 -0
- package/_gh_pages/assets/images/21-genes_31-edges_Schade-data_input_binary-no-targetless-genes_sif.png +0 -0
- package/_gh_pages/assets/images/21-genes_31-edges_Schade-data_input_binary_sif.png +0 -0
- package/_gh_pages/assets/images/21-genes_31-edges_Schade-data_input_concatenated-no-targetless-genes_sif.png +0 -0
- package/_gh_pages/assets/images/21-genes_31-edges_Schade-data_input_concatenated_sif.png +0 -0
- package/_gh_pages/assets/images/Carrillo_Roque_LMU_Symposium_2015.pptx +0 -0
- package/_gh_pages/assets/images/Choe-Shin_CMSI402-poster-session_20180430.jpg +0 -0
- package/_gh_pages/assets/images/Choe_SCCUR_2017.jpg +0 -0
- package/_gh_pages/assets/images/Dahlquist-BMB-2015-Fig1.jpg +0 -0
- package/_gh_pages/assets/images/Dahlquist-BMB-2015-Fig8.jpg +0 -0
- package/_gh_pages/assets/images/Dahlquist-Choe-Shin_CMSI402-poster-session_20180430.jpg +0 -0
- package/_gh_pages/assets/images/Demo-3-auto-layout.jpg +0 -0
- package/_gh_pages/assets/images/Demo-3-paper-layout.jpg +0 -0
- package/_gh_pages/assets/images/Demo-4-auto-layout.jpg +0 -0
- package/_gh_pages/assets/images/Demo-4-paper-layout.jpg +0 -0
- package/_gh_pages/assets/images/Dionisio-Dahlquist_GRNsight-shades_20170506.jpg +0 -0
- package/_gh_pages/assets/images/GRNsight_logo_20140710_main.jpg +0 -0
- package/_gh_pages/assets/images/GRNsight_logo_20140710_main_resized.jpg +0 -0
- package/_gh_pages/assets/images/GRNsight_logo_20140710_rollover.jpg +0 -0
- package/_gh_pages/assets/images/GRNsight_logo_20140710_rollover_resized.jpg +0 -0
- package/_gh_pages/assets/images/Johnson_Williams_LMU_Symposium_2015.pptx +0 -0
- package/_gh_pages/assets/images/Klein_Samdarshi_TriBeta_2018_20180317.jpg +0 -0
- package/_gh_pages/assets/images/LMULogoHQ2.png +0 -0
- package/_gh_pages/assets/images/LMUSymposium_Group_20150321-2.jpg +0 -0
- package/_gh_pages/assets/images/LMUSymposium_Group_20150321-2_resized.jpg +0 -0
- package/_gh_pages/assets/images/Sample_network_optimized_weights_worksheet.jpg +0 -0
- package/_gh_pages/assets/images/Sample_network_worksheet.jpg +0 -0
- package/_gh_pages/assets/images/Shin_SCCUR_2017.jpg +0 -0
- package/_gh_pages/assets/images/demo-3_network-sheet.png +0 -0
- package/_gh_pages/assets/images/demo-4_network-optimized-weights-sheet.png +0 -0
- package/_gh_pages/assets/images/gene-pages-0.png +0 -0
- package/_gh_pages/assets/images/gene-pages-1.png +0 -0
- package/_gh_pages/assets/images/gene-pages-2.png +0 -0
- package/_gh_pages/assets/images/gene-pages-3.png +0 -0
- package/_gh_pages/assets/images/grnsight2020.png +0 -0
- package/_gh_pages/assets/images/lmu logo.gif +0 -0
- package/_gh_pages/assets/images/v3demo2-grid+nodecoloring.png +0 -0
- package/_gh_pages/assets/images/v3demo2-nodecoloring.png +0 -0
- package/_gh_pages/assets/images/v3demo2.png +0 -0
- package/_gh_pages/assets/js/ga-report.js +0 -35
- package/_gh_pages/assets/js/iframeResizer.min.js +0 -9
- package/_gh_pages/assets/js/main.js +0 -132
- package/_gh_pages/beta.html +0 -144
- package/_gh_pages/contact.html +0 -178
- package/_gh_pages/coverage/coverage.json +0 -1
- package/_gh_pages/coverage/coverage.raw.json +0 -1
- package/_gh_pages/coverage/lcov-report/base.css +0 -223
- package/_gh_pages/coverage/lcov-report/block-navigation.js +0 -63
- package/_gh_pages/coverage/lcov-report/controllers/additional-sheet-parser.js.html +0 -330
- package/_gh_pages/coverage/lcov-report/controllers/constants.js.html +0 -243
- package/_gh_pages/coverage/lcov-report/controllers/export-controller.js.html +0 -285
- package/_gh_pages/coverage/lcov-report/controllers/exporters/graphml.js.html +0 -405
- package/_gh_pages/coverage/lcov-report/controllers/exporters/index.html +0 -110
- package/_gh_pages/coverage/lcov-report/controllers/exporters/sif.js.html +0 -150
- package/_gh_pages/coverage/lcov-report/controllers/helpers.js.html +0 -114
- package/_gh_pages/coverage/lcov-report/controllers/import-controller.js.html +0 -233
- package/_gh_pages/coverage/lcov-report/controllers/importers/graphml.js.html +0 -716
- package/_gh_pages/coverage/lcov-report/controllers/importers/index.html +0 -106
- package/_gh_pages/coverage/lcov-report/controllers/importers/sif.js.html +0 -488
- package/_gh_pages/coverage/lcov-report/controllers/index.html +0 -162
- package/_gh_pages/coverage/lcov-report/controllers/semantic-checker.js.html +0 -810
- package/_gh_pages/coverage/lcov-report/controllers/spreadsheet-controller.js.html +0 -1779
- package/_gh_pages/coverage/lcov-report/index.html +0 -136
- package/_gh_pages/coverage/lcov-report/prettify.css +0 -1
- package/_gh_pages/coverage/lcov-report/prettify.js +0 -1
- package/_gh_pages/coverage/lcov-report/server/controllers/additional-sheet-parser.js.html +0 -330
- package/_gh_pages/coverage/lcov-report/server/controllers/constants.js.html +0 -243
- package/_gh_pages/coverage/lcov-report/server/controllers/export-controller.js.html +0 -285
- package/_gh_pages/coverage/lcov-report/server/controllers/exporters/graphml.js.html +0 -405
- package/_gh_pages/coverage/lcov-report/server/controllers/exporters/index.html +0 -110
- package/_gh_pages/coverage/lcov-report/server/controllers/exporters/sif.js.html +0 -150
- package/_gh_pages/coverage/lcov-report/server/controllers/graphml-constants.js.html +0 -585
- package/_gh_pages/coverage/lcov-report/server/controllers/helpers.js.html +0 -114
- package/_gh_pages/coverage/lcov-report/server/controllers/import-controller.js.html +0 -237
- package/_gh_pages/coverage/lcov-report/server/controllers/importers/graphml.js.html +0 -585
- package/_gh_pages/coverage/lcov-report/server/controllers/importers/index.html +0 -110
- package/_gh_pages/coverage/lcov-report/server/controllers/importers/sif.js.html +0 -492
- package/_gh_pages/coverage/lcov-report/server/controllers/index.html +0 -188
- package/_gh_pages/coverage/lcov-report/server/controllers/semantic-checker.js.html +0 -810
- package/_gh_pages/coverage/lcov-report/server/controllers/spreadsheet-controller.js.html +0 -1779
- package/_gh_pages/coverage/lcov-report/sort-arrow-sprite.png +0 -0
- package/_gh_pages/coverage/lcov-report/sorter.js +0 -158
- package/_gh_pages/coverage/lcov-report/web-client/public/js/grnstate.js.html +0 -225
- package/_gh_pages/coverage/lcov-report/web-client/public/js/index.html +0 -97
- package/_gh_pages/coverage/lcov.info +0 -49
- package/_gh_pages/documentation.html +0 -1132
- package/_gh_pages/documents/abstracts/SIGGRAPH 2017 Abstract/siggraph-abstract-review.aux +0 -47
- package/_gh_pages/documents/abstracts/SIGGRAPH 2017 Abstract/siggraph-abstract-review.bbl +0 -73
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- package/_gh_pages/documents/abstracts/SIGGRAPH 2017 Abstract/siggraph-abstract-review.synctex.gz +0 -0
- package/_gh_pages/documents/manuscripts/peerj-computerscience-2016/revisions/GRNsight_PeerJ-CS_manuscript_2016_text-only_revised-Dondi.docx +0 -0
- package/_gh_pages/encryption/server.cert +0 -21
- package/_gh_pages/encryption/server.key +0 -28
- package/_gh_pages/favicon.ico +0 -0
- package/_gh_pages/googlea1a858c5bc91c87e.html +0 -1
- package/_gh_pages/index.html +0 -163
- package/_gh_pages/links.html +0 -177
- package/_gh_pages/news.html +0 -367
- package/_gh_pages/onlyfooter.html +0 -78
- package/_gh_pages/onlyheader.html +0 -64
- package/_gh_pages/onlysidebar.html +0 -73
- package/_gh_pages/package-lock.json +0 -14048
- package/_gh_pages/params.json +0 -1
- package/_gh_pages/people.html +0 -260
- package/_gh_pages/privacy.html +0 -147
- package/_gh_pages/publications.html +0 -378
- package/_gh_pages/robots.txt +0 -1
- package/_gh_pages/server/API Project-7d45e9f24a96.p12 +0 -0
- package/_gh_pages/server/grnmap.pem +0 -31
- package/_gh_pages/server/grnsight.pem +0 -19
- package/_gh_pages/sitemap.xml +0 -174
- package/_gh_pages/test-files/import-samples/attributes.graphml +0 -40
- package/_gh_pages/test-files/import-samples/port.graphml +0 -32
- package/_gh_pages/test-files/import-samples/simple.graphml +0 -31
- package/_gh_pages/web-client/public/js/grnsight.min.js +0 -2347
- package/_gh_pages/web-client/public/stylesheets/grnsight.css +0 -443
- package/coverage/coverage.json +0 -1
- package/coverage/coverage.raw.json +0 -1
- package/coverage/lcov-report/base.css +0 -223
- package/coverage/lcov-report/block-navigation.js +0 -63
- package/coverage/lcov-report/controllers/additional-sheet-parser.js.html +0 -330
- package/coverage/lcov-report/controllers/constants.js.html +0 -243
- package/coverage/lcov-report/controllers/export-controller.js.html +0 -285
- package/coverage/lcov-report/controllers/exporters/graphml.js.html +0 -405
- package/coverage/lcov-report/controllers/exporters/index.html +0 -110
- package/coverage/lcov-report/controllers/exporters/sif.js.html +0 -150
- package/coverage/lcov-report/controllers/helpers.js.html +0 -114
- package/coverage/lcov-report/controllers/import-controller.js.html +0 -233
- package/coverage/lcov-report/controllers/importers/graphml.js.html +0 -716
- package/coverage/lcov-report/controllers/importers/index.html +0 -106
- package/coverage/lcov-report/controllers/importers/sif.js.html +0 -488
- package/coverage/lcov-report/controllers/index.html +0 -162
- package/coverage/lcov-report/controllers/semantic-checker.js.html +0 -810
- package/coverage/lcov-report/controllers/spreadsheet-controller.js.html +0 -1779
- package/coverage/lcov-report/index.html +0 -136
- package/coverage/lcov-report/prettify.css +0 -1
- package/coverage/lcov-report/prettify.js +0 -1
- package/coverage/lcov-report/server/controllers/additional-sheet-parser.js.html +0 -330
- package/coverage/lcov-report/server/controllers/constants.js.html +0 -243
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- package/encryption/server.cert +0 -21
- package/encryption/server.key +0 -28
- package/gdb/PG_VERSION +0 -1
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# PostgreSQL Client Authentication Configuration File
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# ===================================================
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#
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# Refer to the "Client Authentication" section in the PostgreSQL
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# documentation for a complete description of this file. A short
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# synopsis follows.
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#
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# This file controls: which hosts are allowed to connect, how clients
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# are authenticated, which PostgreSQL user names they can use, which
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# databases they can access. Records take one of these forms:
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#
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# local DATABASE USER METHOD [OPTIONS]
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# host DATABASE USER ADDRESS METHOD [OPTIONS]
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# hostssl DATABASE USER ADDRESS METHOD [OPTIONS]
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# hostnossl DATABASE USER ADDRESS METHOD [OPTIONS]
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# hostgssenc DATABASE USER ADDRESS METHOD [OPTIONS]
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# hostnogssenc DATABASE USER ADDRESS METHOD [OPTIONS]
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# (The uppercase items must be replaced by actual values.)
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# - "host" is a TCP/IP socket (encrypted or not)
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# - "hostssl" is a TCP/IP socket that is SSL-encrypted
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#
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# DATABASE can be "all", "sameuser", "samerole", "replication", a
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# database name, or a comma-separated list thereof. The "all"
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# keyword does not match "replication". Access to replication
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# must be enabled in a separate record (see example below).
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#
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# USER can be "all", a user name, a group name prefixed with "+", or a
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# comma-separated list thereof. In both the DATABASE and USER fields
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# you can also write a file name prefixed with "@" to include names
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# from a separate file.
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#
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# ADDRESS specifies the set of hosts the record matches. It can be a
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# host name, or it is made up of an IP address and a CIDR mask that is
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# an integer (between 0 and 32 (IPv4) or 128 (IPv6) inclusive) that
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# specifies the number of significant bits in the mask. A host name
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# that starts with a dot (.) matches a suffix of the actual host name.
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# Alternatively, you can write an IP address and netmask in separate
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# columns to specify the set of hosts. Instead of a CIDR-address, you
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# can write "samehost" to match any of the server's own IP addresses,
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# or "samenet" to match any address in any subnet that the server is
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# directly connected to.
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#
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# METHOD can be "trust", "reject", "md5", "password", "scram-sha-256",
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# "gss", "sspi", "ident", "peer", "pam", "ldap", "radius" or "cert".
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# Note that "password" sends passwords in clear text; "md5" or
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# "scram-sha-256" are preferred since they send encrypted passwords.
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#
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# OPTIONS are a set of options for the authentication in the format
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# NAME=VALUE. The available options depend on the different
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# authentication methods -- refer to the "Client Authentication"
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# section in the documentation for a list of which options are
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# available for which authentication methods.
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#
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# Database and user names containing spaces, commas, quotes and other
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# special characters must be quoted. Quoting one of the keywords
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# "all", "sameuser", "samerole" or "replication" makes the name lose
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# its special character, and just match a database or username with
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# that name.
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#
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# This file is read on server startup and when the server receives a
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# SIGHUP signal. If you edit the file on a running system, you have to
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# SIGHUP the server for the changes to take effect, run "pg_ctl reload",
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# or execute "SELECT pg_reload_conf()".
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#
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# Put your actual configuration here
|
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# ----------------------------------
|
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#
|
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# If you want to allow non-local connections, you need to add more
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# "host" records. In that case you will also need to make PostgreSQL
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# listen on a non-local interface via the listen_addresses
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# configuration parameter, or via the -i or -h command line switches.
|
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-
|
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# CAUTION: Configuring the system for local "trust" authentication
|
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# allows any local user to connect as any PostgreSQL user, including
|
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# the database superuser. If you do not trust all your local users,
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# use another authentication method.
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|
-
|
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-
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# TYPE DATABASE USER ADDRESS METHOD
|
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-
|
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# "local" is for Unix domain socket connections only
|
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local all all trust
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|
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# IPv4 local connections:
|
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|
-
host all all 127.0.0.1/32 trust
|
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# IPv6 local connections:
|
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|
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host all all ::1/128 trust
|
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|
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# Allow replication connections from localhost, by a user with the
|
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# replication privilege.
|
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local replication all trust
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host replication all 127.0.0.1/32 trust
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host replication all ::1/128 trust
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# PostgreSQL User Name Maps
|
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# =========================
|
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#
|
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# Refer to the PostgreSQL documentation, chapter "Client
|
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# Authentication" for a complete description. A short synopsis
|
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# follows.
|
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#
|
|
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|
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# This file controls PostgreSQL user name mapping. It maps external
|
|
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# user names to their corresponding PostgreSQL user names. Records
|
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# are of the form:
|
|
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#
|
|
12
|
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# MAPNAME SYSTEM-USERNAME PG-USERNAME
|
|
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#
|
|
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|
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# (The uppercase quantities must be replaced by actual values.)
|
|
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-
#
|
|
16
|
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# MAPNAME is the (otherwise freely chosen) map name that was used in
|
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# pg_hba.conf. SYSTEM-USERNAME is the detected user name of the
|
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|
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# client. PG-USERNAME is the requested PostgreSQL user name. The
|
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# existence of a record specifies that SYSTEM-USERNAME may connect as
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# PG-USERNAME.
|
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#
|
|
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|
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# If SYSTEM-USERNAME starts with a slash (/), it will be treated as a
|
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# regular expression. Optionally this can contain a capture (a
|
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# parenthesized subexpression). The substring matching the capture
|
|
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|
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# will be substituted for \1 (backslash-one) if present in
|
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# PG-USERNAME.
|
|
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#
|
|
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|
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# Multiple maps may be specified in this file and used by pg_hba.conf.
|
|
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#
|
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|
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# No map names are defined in the default configuration. If all
|
|
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|
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# system user names and PostgreSQL user names are the same, you don't
|
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# need anything in this file.
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#
|
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|
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# This file is read on server startup and when the postmaster receives
|
|
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# a SIGHUP signal. If you edit the file on a running system, you have
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# to SIGHUP the postmaster for the changes to take effect. You can
|
|
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# use "pg_ctl reload" to do that.
|
|
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|
-
|
|
39
|
-
# Put your actual configuration here
|
|
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|
-
# ----------------------------------
|
|
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|
-
|
|
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|
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# MAPNAME SYSTEM-USERNAME PG-USERNAME
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