grnsight 6.0.4 → 7.1.1

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.
Files changed (1245) hide show
  1. package/.eslintrc.yml +4 -4
  2. package/database/README.md +224 -79
  3. package/database/constants.py +42 -0
  4. package/database/expression-database/README.md +2 -2
  5. package/database/expression-database/schema.sql +14 -14
  6. package/database/expression-database/scripts/loader.py +6 -6
  7. package/database/filter_update.py +168 -0
  8. package/database/grnsettings-database/README.md +52 -0
  9. package/database/grnsettings-database/schema.sql +4 -0
  10. package/database/loader.py +30 -0
  11. package/database/loader_update.py +36 -0
  12. package/database/network-database/README.md +36 -4
  13. package/database/network-database/schema.sql +7 -7
  14. package/database/network-database/scripts/generate_network.py +16 -24
  15. package/database/network-database/scripts/generate_new_network_version.py +216 -0
  16. package/database/protein-protein-database/README.md +71 -0
  17. package/database/protein-protein-database/schema.sql +37 -0
  18. package/database/protein-protein-database/scripts/generate_protein_network.py +227 -0
  19. package/database/protein-protein-database/scripts/remove_duplicates.sh +4 -0
  20. package/database/utils.py +418 -0
  21. package/package.json +2 -2
  22. package/server/app.js +2 -0
  23. package/server/config/config.js +4 -4
  24. package/server/controllers/additional-sheet-parser.js +2 -1
  25. package/server/controllers/constants.js +5 -0
  26. package/server/controllers/custom-workbook-controller.js +8 -6
  27. package/server/controllers/demo-workbooks.js +1460 -4
  28. package/server/controllers/export-constants.js +3 -2
  29. package/server/controllers/exporters/sif.js +6 -1
  30. package/server/controllers/exporters/xlsx.js +8 -3
  31. package/server/controllers/expression-sheet-parser.js +0 -6
  32. package/server/controllers/grnsettings-database-controller.js +17 -0
  33. package/server/controllers/importers/sif.js +29 -11
  34. package/server/controllers/network-database-controller.js +2 -2
  35. package/server/controllers/network-sheet-parser.js +54 -12
  36. package/server/controllers/protein-database-controller.js +18 -0
  37. package/server/controllers/sif-constants.js +4 -4
  38. package/server/controllers/spreadsheet-controller.js +44 -1
  39. package/server/controllers/workbook-constants.js +21 -4
  40. package/server/dals/expression-dal.js +8 -7
  41. package/server/dals/grnsetting-dal.js +49 -0
  42. package/server/dals/network-dal.js +13 -12
  43. package/server/dals/protein-dal.js +106 -0
  44. package/test/export-tests.js +136 -9
  45. package/test/import-sif-tests.js +54 -13
  46. package/test/test.js +1 -1
  47. package/test-files/additional-sheet-test-files/optimization-parameters-default.xlsx +0 -0
  48. package/test-files/demo-files/18_proteins_81_edges_PPI.xlsx +0 -0
  49. package/test-files/expression-data-test-sheets/expression_sheet_missing_data_ok_export_exact.xlsx +0 -0
  50. package/web-client/config/config.js +4 -4
  51. package/web-client/public/js/api/grnsight-api.js +72 -56
  52. package/web-client/public/js/constants.js +26 -12
  53. package/web-client/public/js/generateNetwork.js +173 -67
  54. package/web-client/public/js/graph.js +420 -150
  55. package/web-client/public/js/grnsight.js +25 -4
  56. package/web-client/public/js/grnstate.js +3 -1
  57. package/web-client/public/js/iframe-coordination.js +3 -3
  58. package/web-client/public/js/setup-handlers.js +28 -32
  59. package/web-client/public/js/setup-load-and-import-handlers.js +196 -170
  60. package/web-client/public/js/update-app.js +84 -17
  61. package/web-client/public/js/upload.js +193 -157
  62. package/web-client/public/lib/bootstrap.file-input/bootstrap.file-input.js +0 -1
  63. package/web-client/public/stylesheets/grnsight.styl +40 -16
  64. package/web-client/views/components/demo.pug +7 -5
  65. package/web-client/views/upload.pug +63 -49
  66. package/.bundle/config +0 -3
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  68. package/Gemfile.lock +0 -259
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- # PostgreSQL Client Authentication Configuration File
2
- # ===================================================
3
- #
4
- # Refer to the "Client Authentication" section in the PostgreSQL
5
- # documentation for a complete description of this file. A short
6
- # synopsis follows.
7
- #
8
- # This file controls: which hosts are allowed to connect, how clients
9
- # are authenticated, which PostgreSQL user names they can use, which
10
- # databases they can access. Records take one of these forms:
11
- #
12
- # local DATABASE USER METHOD [OPTIONS]
13
- # host DATABASE USER ADDRESS METHOD [OPTIONS]
14
- # hostssl DATABASE USER ADDRESS METHOD [OPTIONS]
15
- # hostnossl DATABASE USER ADDRESS METHOD [OPTIONS]
16
- # hostgssenc DATABASE USER ADDRESS METHOD [OPTIONS]
17
- # hostnogssenc DATABASE USER ADDRESS METHOD [OPTIONS]
18
- #
19
- # (The uppercase items must be replaced by actual values.)
20
- #
21
- # The first field is the connection type:
22
- # - "local" is a Unix-domain socket
23
- # - "host" is a TCP/IP socket (encrypted or not)
24
- # - "hostssl" is a TCP/IP socket that is SSL-encrypted
25
- # - "hostnossl" is a TCP/IP socket that is not SSL-encrypted
26
- # - "hostgssenc" is a TCP/IP socket that is GSSAPI-encrypted
27
- # - "hostnogssenc" is a TCP/IP socket that is not GSSAPI-encrypted
28
- #
29
- # DATABASE can be "all", "sameuser", "samerole", "replication", a
30
- # database name, or a comma-separated list thereof. The "all"
31
- # keyword does not match "replication". Access to replication
32
- # must be enabled in a separate record (see example below).
33
- #
34
- # USER can be "all", a user name, a group name prefixed with "+", or a
35
- # comma-separated list thereof. In both the DATABASE and USER fields
36
- # you can also write a file name prefixed with "@" to include names
37
- # from a separate file.
38
- #
39
- # ADDRESS specifies the set of hosts the record matches. It can be a
40
- # host name, or it is made up of an IP address and a CIDR mask that is
41
- # an integer (between 0 and 32 (IPv4) or 128 (IPv6) inclusive) that
42
- # specifies the number of significant bits in the mask. A host name
43
- # that starts with a dot (.) matches a suffix of the actual host name.
44
- # Alternatively, you can write an IP address and netmask in separate
45
- # columns to specify the set of hosts. Instead of a CIDR-address, you
46
- # can write "samehost" to match any of the server's own IP addresses,
47
- # or "samenet" to match any address in any subnet that the server is
48
- # directly connected to.
49
- #
50
- # METHOD can be "trust", "reject", "md5", "password", "scram-sha-256",
51
- # "gss", "sspi", "ident", "peer", "pam", "ldap", "radius" or "cert".
52
- # Note that "password" sends passwords in clear text; "md5" or
53
- # "scram-sha-256" are preferred since they send encrypted passwords.
54
- #
55
- # OPTIONS are a set of options for the authentication in the format
56
- # NAME=VALUE. The available options depend on the different
57
- # authentication methods -- refer to the "Client Authentication"
58
- # section in the documentation for a list of which options are
59
- # available for which authentication methods.
60
- #
61
- # Database and user names containing spaces, commas, quotes and other
62
- # special characters must be quoted. Quoting one of the keywords
63
- # "all", "sameuser", "samerole" or "replication" makes the name lose
64
- # its special character, and just match a database or username with
65
- # that name.
66
- #
67
- # This file is read on server startup and when the server receives a
68
- # SIGHUP signal. If you edit the file on a running system, you have to
69
- # SIGHUP the server for the changes to take effect, run "pg_ctl reload",
70
- # or execute "SELECT pg_reload_conf()".
71
- #
72
- # Put your actual configuration here
73
- # ----------------------------------
74
- #
75
- # If you want to allow non-local connections, you need to add more
76
- # "host" records. In that case you will also need to make PostgreSQL
77
- # listen on a non-local interface via the listen_addresses
78
- # configuration parameter, or via the -i or -h command line switches.
79
-
80
- # CAUTION: Configuring the system for local "trust" authentication
81
- # allows any local user to connect as any PostgreSQL user, including
82
- # the database superuser. If you do not trust all your local users,
83
- # use another authentication method.
84
-
85
-
86
- # TYPE DATABASE USER ADDRESS METHOD
87
-
88
- # "local" is for Unix domain socket connections only
89
- local all all trust
90
- # IPv4 local connections:
91
- host all all 127.0.0.1/32 trust
92
- # IPv6 local connections:
93
- host all all ::1/128 trust
94
- # Allow replication connections from localhost, by a user with the
95
- # replication privilege.
96
- local replication all trust
97
- host replication all 127.0.0.1/32 trust
98
- host replication all ::1/128 trust
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1
- # PostgreSQL User Name Maps
2
- # =========================
3
- #
4
- # Refer to the PostgreSQL documentation, chapter "Client
5
- # Authentication" for a complete description. A short synopsis
6
- # follows.
7
- #
8
- # This file controls PostgreSQL user name mapping. It maps external
9
- # user names to their corresponding PostgreSQL user names. Records
10
- # are of the form:
11
- #
12
- # MAPNAME SYSTEM-USERNAME PG-USERNAME
13
- #
14
- # (The uppercase quantities must be replaced by actual values.)
15
- #
16
- # MAPNAME is the (otherwise freely chosen) map name that was used in
17
- # pg_hba.conf. SYSTEM-USERNAME is the detected user name of the
18
- # client. PG-USERNAME is the requested PostgreSQL user name. The
19
- # existence of a record specifies that SYSTEM-USERNAME may connect as
20
- # PG-USERNAME.
21
- #
22
- # If SYSTEM-USERNAME starts with a slash (/), it will be treated as a
23
- # regular expression. Optionally this can contain a capture (a
24
- # parenthesized subexpression). The substring matching the capture
25
- # will be substituted for \1 (backslash-one) if present in
26
- # PG-USERNAME.
27
- #
28
- # Multiple maps may be specified in this file and used by pg_hba.conf.
29
- #
30
- # No map names are defined in the default configuration. If all
31
- # system user names and PostgreSQL user names are the same, you don't
32
- # need anything in this file.
33
- #
34
- # This file is read on server startup and when the postmaster receives
35
- # a SIGHUP signal. If you edit the file on a running system, you have
36
- # to SIGHUP the postmaster for the changes to take effect. You can
37
- # use "pg_ctl reload" to do that.
38
-
39
- # Put your actual configuration here
40
- # ----------------------------------
41
-
42
- # MAPNAME SYSTEM-USERNAME PG-USERNAME
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1
- # Do not edit this file manually!
2
- # It will be overwritten by the ALTER SYSTEM command.