Json neo4j

[qle2]

This PR contains all the files I created to import data, either directly from our core pipeline or from files in zip folders located in output, to Neo4j based on our current ontology (which is subject to change later on). While there are a few things from the ontology that I haven't included, please let me know if you find anything major missing. I also slightly modified some of our core files for my own needs so if I had broken anything, please let me know. Above is the picture of our current ontology.

Steps for test runs:

• Open Neo4j Desktop and start up a local graph database.
• Set your password to 1234 . This is just how I set up my password for quick testing. We can come up with a universal password for all of our graphs later on. I think there's a way to disable passwords but I don't know how.
• For test runs:
  • If you want to create graphs directly from the pipeline, run main.py. It can be run from main and from example_model. I suggest you create a small csv file for a quick run and review instead of waiting for 1000+ SMILES and even larger number of features. Once this PR is done, you can run it on the whole file and I'll address the problems that occurred when running in large CSVs.
  • If you want to create graphs from your zip files, go to output_to_neo4j.py, uncomment the last line and run it. Again I suggest you have a small working example for reasons mentioned above.

In the files I created, I included documentation that explains: the objective of the script, the objective of the function and intent behind the function for each file.

Also @dickeygh, while I was designing this script, I only tested it on regression models. Please run classification models on CSVs that don't have any irregular SMILES and let me know if anything breaks

If you have any questions or concerns, I'll be happy to answer them

[pep8speaks]

Hello @qle2! Thanks for opening this PR. We checked the lines you've touched for PEP 8 issues, and found:

• In the file core/features.py:

Line 202:80: E501 line too long (83 > 79 characters) Line 202:80: E501 line too long (83 > 79 characters) Line 202:84: W292 no newline at end of file Line 202:84: W292 no newline at end of file Line 202:84: W292 no newline at end of file

• In the file core/fragments.py:

Line 2:80: E501 line too long (92 > 79 characters) Line 19:80: E501 line too long (109 > 79 characters) Line 30:80: E501 line too long (116 > 79 characters) Line 31:80: E501 line too long (114 > 79 characters) Line 32:80: E501 line too long (118 > 79 characters) Line 36:80: E501 line too long (117 > 79 characters) Line 42:80: E501 line too long (94 > 79 characters) Line 43:80: E501 line too long (118 > 79 characters) Line 44:80: E501 line too long (98 > 79 characters) Line 45:80: E501 line too long (84 > 79 characters) Line 50:80: E501 line too long (100 > 79 characters) Line 51:80: E501 line too long (95 > 79 characters) Line 58:80: E501 line too long (80 > 79 characters) Line 59:80: E501 line too long (112 > 79 characters) Line 60:80: E501 line too long (118 > 79 characters) Line 61:80: E501 line too long (108 > 79 characters) Line 62:80: E501 line too long (117 > 79 characters) Line 68:80: E501 line too long (89 > 79 characters) Line 70:80: E501 line too long (107 > 79 characters) Line 71:80: E501 line too long (90 > 79 characters) Line 79:80: E501 line too long (91 > 79 characters)

• In the file core/models.py:

Line 120:33: W292 no newline at end of file

• In the file core/name.py:

Line 84:80: E501 line too long (86 > 79 characters) Line 85:80: E501 line too long (90 > 79 characters) Line 89:80: E501 line too long (83 > 79 characters) Line 90:80: E501 line too long (84 > 79 characters) Line 93:80: E501 line too long (122 > 79 characters) Line 96:80: E501 line too long (88 > 79 characters) Line 98:80: E501 line too long (95 > 79 characters) Line 111:20: W292 no newline at end of file

• In the file core/nodes_to_neo4j.py:

Line 2:80: E501 line too long (111 > 79 characters) Line 17:80: E501 line too long (84 > 79 characters) Line 18:80: E501 line too long (111 > 79 characters) Line 19:80: E501 line too long (112 > 79 characters) Line 24:80: E501 line too long (83 > 79 characters) Line 28:80: E501 line too long (85 > 79 characters) Line 35:80: E501 line too long (83 > 79 characters) Line 36:80: E501 line too long (88 > 79 characters) Line 38:80: E501 line too long (113 > 79 characters) Line 39:80: E501 line too long (116 > 79 characters) Line 40:80: E501 line too long (120 > 79 characters) Line 41:80: E501 line too long (117 > 79 characters) Line 43:80: E501 line too long (103 > 79 characters) Line 44:80: E501 line too long (114 > 79 characters) Line 47:80: E501 line too long (85 > 79 characters) Line 51:80: E501 line too long (88 > 79 characters) Line 54:80: E501 line too long (90 > 79 characters) Line 64:80: E501 line too long (115 > 79 characters) Line 65:80: E501 line too long (100 > 79 characters) Line 73:80: E501 line too long (116 > 79 characters) Line 78:80: E501 line too long (88 > 79 characters) Line 86:80: E501 line too long (116 > 79 characters) Line 89:80: E501 line too long (96 > 79 characters) Line 90:80: E501 line too long (89 > 79 characters) Line 91:80: E501 line too long (86 > 79 characters) Line 96:80: E501 line too long (94 > 79 characters) Line 110:80: E501 line too long (101 > 79 characters) Line 111:80: E501 line too long (111 > 79 characters) Line 113:80: E501 line too long (96 > 79 characters) Line 117:80: E501 line too long (94 > 79 characters) Line 119:80: E501 line too long (96 > 79 characters) Line 125:80: E501 line too long (81 > 79 characters) Line 126:80: E501 line too long (113 > 79 characters) Line 131:80: E501 line too long (82 > 79 characters) Line 131:83: W291 trailing whitespace Line 135:80: E501 line too long (84 > 79 characters)

• In the file core/output_nodes_to_neo4j.py:

Line 2:80: E501 line too long (111 > 79 characters) Line 16:80: E501 line too long (84 > 79 characters) Line 17:80: E501 line too long (113 > 79 characters) Line 18:80: E501 line too long (86 > 79 characters) Line 19:80: E501 line too long (120 > 79 characters) Line 24:80: E501 line too long (87 > 79 characters) Line 29:80: E501 line too long (88 > 79 characters) Line 32:80: E501 line too long (90 > 79 characters) Line 42:80: E501 line too long (115 > 79 characters) Line 49:80: E501 line too long (116 > 79 characters) Line 54:80: E501 line too long (85 > 79 characters) Line 62:80: E501 line too long (120 > 79 characters) Line 65:80: E501 line too long (96 > 79 characters) Line 66:80: E501 line too long (89 > 79 characters) Line 67:80: E501 line too long (86 > 79 characters) Line 73:80: E501 line too long (109 > 79 characters) Line 85:80: E501 line too long (88 > 79 characters) Line 87:80: E501 line too long (119 > 79 characters) Line 88:80: E501 line too long (111 > 79 characters) Line 90:80: E501 line too long (100 > 79 characters) Line 94:80: E501 line too long (94 > 79 characters) Line 96:80: E501 line too long (100 > 79 characters) Line 99:80: E501 line too long (81 > 79 characters) Line 102:80: E501 line too long (117 > 79 characters) Line 107:80: E501 line too long (86 > 79 characters) Line 109:80: E501 line too long (94 > 79 characters) Line 111:80: E501 line too long (88 > 79 characters) Line 117:54: W292 no newline at end of file

• In the file core/output_rel_to_neo4j.py:

Line 2:80: E501 line too long (119 > 79 characters) Line 23:80: E501 line too long (95 > 79 characters) Line 25:80: E501 line too long (80 > 79 characters) Line 32:80: E501 line too long (106 > 79 characters) Line 33:80: E501 line too long (98 > 79 characters) Line 34:80: E501 line too long (94 > 79 characters) Line 35:36: E128 continuation line under-indented for visual indent Line 35:80: E501 line too long (82 > 79 characters) Line 37:80: E501 line too long (106 > 79 characters) Line 38:80: E501 line too long (98 > 79 characters) Line 39:80: E501 line too long (94 > 79 characters) Line 40:80: E501 line too long (88 > 79 characters) Line 42:80: E501 line too long (98 > 79 characters) Line 44:80: E501 line too long (87 > 79 characters) Line 48:80: E501 line too long (110 > 79 characters) Line 50:80: E501 line too long (89 > 79 characters) Line 54:80: E501 line too long (92 > 79 characters) Line 56:80: E501 line too long (83 > 79 characters) Line 59:80: E501 line too long (103 > 79 characters) Line 61:80: E501 line too long (92 > 79 characters) Line 64:80: E501 line too long (103 > 79 characters) Line 68:80: E501 line too long (98 > 79 characters) Line 69:80: E501 line too long (87 > 79 characters) Line 72:80: E501 line too long (105 > 79 characters) Line 74:80: E501 line too long (85 > 79 characters) Line 77:80: E501 line too long (111 > 79 characters) Line 79:80: E501 line too long (99 > 79 characters) Line 82:80: E501 line too long (101 > 79 characters) Line 88:80: E501 line too long (102 > 79 characters) Line 91:80: E501 line too long (114 > 79 characters) Line 93:80: E501 line too long (83 > 79 characters) Line 96:80: E501 line too long (104 > 79 characters) Line 99:80: E501 line too long (84 > 79 characters) Line 100:80: E501 line too long (98 > 79 characters) Line 101:80: E501 line too long (103 > 79 characters) Line 103:80: E501 line too long (103 > 79 characters) Line 105:80: E501 line too long (102 > 79 characters) Line 106:80: E501 line too long (98 > 79 characters) Line 107:80: E501 line too long (84 > 79 characters) Line 112:80: E501 line too long (104 > 79 characters) Line 114:80: E501 line too long (83 > 79 characters) Line 119:80: E501 line too long (111 > 79 characters) Line 120:80: E501 line too long (99 > 79 characters) Line 121:80: E501 line too long (118 > 79 characters) Line 128:80: E501 line too long (104 > 79 characters) Line 135:80: E501 line too long (81 > 79 characters) Line 140:1: W391 blank line at end of file

• In the file core/output_to_neo4j.py:

Line 2:80: E501 line too long (115 > 79 characters) Line 20:80: E501 line too long (117 > 79 characters) Line 21:80: E501 line too long (119 > 79 characters) Line 22:80: E501 line too long (88 > 79 characters) Line 42:80: E501 line too long (115 > 79 characters) Line 43:80: E501 line too long (118 > 79 characters) Line 44:80: E501 line too long (120 > 79 characters) Line 45:80: E501 line too long (107 > 79 characters) Line 56:80: E501 line too long (89 > 79 characters) Line 57:80: E501 line too long (85 > 79 characters) Line 58:80: E501 line too long (89 > 79 characters) Line 59:80: E501 line too long (110 > 79 characters) Line 60:80: E501 line too long (120 > 79 characters) Line 62:80: E501 line too long (82 > 79 characters) Line 63:80: E501 line too long (99 > 79 characters) Line 65:80: E501 line too long (89 > 79 characters) Line 66:80: E501 line too long (106 > 79 characters) Line 73:80: E501 line too long (118 > 79 characters) Line 79:80: E501 line too long (87 > 79 characters) Line 86:80: E501 line too long (92 > 79 characters) Line 92:80: E501 line too long (112 > 79 characters)

• In the file core/prep_from_outputs.py:

Line 2:80: E501 line too long (104 > 79 characters) Line 13:80: E501 line too long (110 > 79 characters) Line 14:80: E501 line too long (117 > 79 characters) Line 15:80: E501 line too long (119 > 79 characters) Line 16:80: E501 line too long (114 > 79 characters) Line 26:80: E501 line too long (106 > 79 characters) Line 27:80: E501 line too long (117 > 79 characters) Line 28:80: E501 line too long (109 > 79 characters) Line 30:80: E501 line too long (101 > 79 characters) Line 31:80: E501 line too long (116 > 79 characters) Line 32:80: E501 line too long (115 > 79 characters) Line 33:80: E501 line too long (120 > 79 characters) Line 34:80: E501 line too long (117 > 79 characters) Line 40:80: E501 line too long (96 > 79 characters) Line 41:80: E501 line too long (98 > 79 characters) Line 43:80: E501 line too long (90 > 79 characters) Line 51:80: E501 line too long (107 > 79 characters) Line 53:80: E501 line too long (80 > 79 characters) Line 54:80: E501 line too long (112 > 79 characters) Line 56:80: E501 line too long (117 > 79 characters) Line 57:80: E501 line too long (121 > 79 characters) Line 63:80: E501 line too long (88 > 79 characters) Line 70:80: E501 line too long (83 > 79 characters) Line 71:80: E501 line too long (94 > 79 characters) Line 72:80: E501 line too long (92 > 79 characters)

• In the file core/rel_to_neo4j.py:

Line 2:80: E501 line too long (119 > 79 characters) Line 15:80: E501 line too long (94 > 79 characters) Line 16:80: E501 line too long (116 > 79 characters) Line 17:80: E501 line too long (119 > 79 characters) Line 21:80: E501 line too long (100 > 79 characters) Line 24:80: E501 line too long (117 > 79 characters) Line 26:80: E501 line too long (80 > 79 characters) Line 32:80: E501 line too long (102 > 79 characters) Line 33:80: E501 line too long (92 > 79 characters) Line 34:80: E501 line too long (118 > 79 characters) Line 36:80: E501 line too long (98 > 79 characters) Line 38:80: E501 line too long (87 > 79 characters) Line 42:80: E501 line too long (110 > 79 characters) Line 44:80: E501 line too long (89 > 79 characters) Line 48:80: E501 line too long (92 > 79 characters) Line 53:80: E501 line too long (103 > 79 characters) Line 55:80: E501 line too long (85 > 79 characters) Line 58:80: E501 line too long (103 > 79 characters) Line 62:80: E501 line too long (98 > 79 characters) Line 63:80: E501 line too long (87 > 79 characters) Line 66:80: E501 line too long (105 > 79 characters) Line 68:80: E501 line too long (85 > 79 characters) Line 71:80: E501 line too long (111 > 79 characters) Line 73:80: E501 line too long (94 > 79 characters) Line 76:80: E501 line too long (101 > 79 characters) Line 82:80: E501 line too long (102 > 79 characters) Line 85:80: E501 line too long (114 > 79 characters) Line 90:80: E501 line too long (104 > 79 characters) Line 93:80: E501 line too long (84 > 79 characters) Line 94:80: E501 line too long (98 > 79 characters) Line 95:80: E501 line too long (98 > 79 characters) Line 97:80: E501 line too long (103 > 79 characters) Line 99:80: E501 line too long (102 > 79 characters) Line 100:80: E501 line too long (98 > 79 characters) Line 101:80: E501 line too long (84 > 79 characters) Line 105:80: E501 line too long (104 > 79 characters) Line 107:80: E501 line too long (83 > 79 characters) Line 111:80: E501 line too long (111 > 79 characters) Line 112:80: E501 line too long (99 > 79 characters) Line 113:80: E501 line too long (113 > 79 characters) Line 118:80: E501 line too long (104 > 79 characters) Line 125:80: E501 line too long (81 > 79 characters) Line 129:46: W292 no newline at end of file

• In the file core/train.py:

Line 31:80: E501 line too long (80 > 79 characters)

• In the file main.py:

Line 80:80: E501 line too long (80 > 79 characters) Line 93:80: E501 line too long (85 > 79 characters) Line 153:80: E501 line too long (102 > 79 characters) Line 199:6: E114 indentation is not a multiple of four (comment) Line 199:6: E117 over-indented (comment)