From 1afae8c3ee402ce6cddcbc43276fd88b8072b366 Mon Sep 17 00:00:00 2001 From: nh916 Date: Wed, 26 Apr 2023 14:20:11 -0700 Subject: [PATCH] Fixed Cao Protein and is passing db schema (#15) * changed node field to array added UID * changed node field to array instead of string * added UID to inventory and project materials * added python `venv` to .gitignore * added IDE settings to .gitignore * fixed uid field * got reference for citation working * Process WPI Centrifugation issue * formatted the JSON * matching UID to field name * ['collection'][0]['experiment'][0]['process'][0] working * ['collection'][0]['experiment'][0]['process'][1] working * mass replaced `ingredients`, `products`, and `quantities` * db schema has them as singular instead of plural * converted a couple of strings to material nodes * made some material nodes from string to nodes * ['collection'][0]['experiment'][1]['process'][3] successful * ['collection'][0]['experiment'][1]['process'][3] successful * ['collection'][0]['experiment'][1]['process'][6] successful * ['collection'][0]['experiment'][1]['process'][7] successful * formatted cao_protein.json * ['collection'][0]['experiment'][2]['process'][1] fixed * ['collection'][0]['experiment'][3]['process'][1] successful * ['collection'][0]['experiment'][4]['process'][1] successful * ['collection'][0]['experiment'][5]['process'][1] successful * ['collection'][0]['experiment'][6]['process'][1] successful * ['collection'][0]['experiment'][7]['process'][1] successful * made all process types as `"type": "multistep"` * all process types are `"type": "multistep"` * all data types are `"type": "rxn_conv"` * all data types are `"type": "multistep"` for process 2 * all data types are `"type": "multistep"` for process 3 * all data types are `"type": "multistep"` for process 4 * all data types are `"type": "multistep"` for process 5 * all data types are `"type": "multistep"` for process 6 * all data types are `"type": "multistep"` for process 7 * all data types are `"type": "multistep"` for process 8 * all data types are `"type": "rxn_conv"` ['collection'][0]['experiment'][8]['data'] * changed all process types and data types * process types are `"type": "multistep"` * data types are `"type": "rxn_conv"` * changed process and data types. experiment 10 * process types are `"type": "multistep"` * data types are `"type": "rxn_conv"` * changed process and data types. experiment 11 * process types are `"type": "multistep"` * fixed product to be material node * data types are `"type": "rxn_conv"` * changed process and data types. experiment 12 * process types are `"type": "multistep"` * data types are `"type": "rxn_conv"` * changed process and data types. experiment 13 * process types are `"type": "multistep"` * data types are `"type": "rxn_conv"` * changed process and data types. experiment 14 * process types are `"type": "multistep"` * data types are `"type": "rxn_conv"` * formatted JSON * changed process and data types. experiment 15 * process types are `"type": "multistep"` * data types are `"type": "rxn_conv"` * changed process and data types. experiment 16 * process types are `"type": "multistep"` * data types are `"type": "rxn_conv"` * changed process and data types. experiment 17 * process types are `"type": "multistep"` * data types are `"type": "rxn_conv"` * changed process and data types. experiment 18 * process types are `"type": "multistep"` * data types are `"type": "rxn_conv"` * changed process and data types. experiment 18 * process types are `"type": "multistep"` * data types are `"type": "rxn_conv"` * changed process and data types. experiment 19 * process types are `"type": "multistep"` * data types are `"type": "rxn_conv"` * changed process and data types. experiment 21 * process types are `"type": "multistep"` * data types are `"type": "rxn_conv"` * changed process and data types. experiment 22 * process types are `"type": "multistep"` * data types are `"type": "rxn_conv"` * fixed uid regex * made process product into material node * made process product into material node * formatted JSON * made material string into JSON object material node * made material string into JSON object material node * made material string into JSON object material node * fixed prerequisit process * fixed prerequisit process * fixed prerequisit process * fixed prerequisit process * fixed prerequisit process * fixed prerequisit process * fixed prerequisit process * fixed prerequisit process * fixed prerequisit process * ingredient to material node * ingredient to material node * ingredient to material node * ingredient to material node * ingredient to material node * ingredient to material node * ingredient to material node * formatted * converting ingredient to material * converting ingredient to material * formatted JSON * converting ingredient to material * converting ingredient to material * converting ingredient to material * converting ingredient to material * converting ingredient to material * converting ingredient to material * converting ingredient to material * converting ingredient to material * converting ingredient to material * converting ingredient to material * converting ingredient to material * converting ingredient to material * converting ingredient to material * converting product to material * converting product to material * converting product to material * converting product to material * converting product to material * converting product to material * converting product to material * update * update * update * update * update * update * update * update * update * update * update * update * update * update * update * update * update * update * update * passing db schema! * changed quantity from `"null"` to `null` --- .gitignore | 9 + cript_graph_json/JSON/cao_protein.json | 8031 ++++++++++++++++-------- 2 files changed, 5569 insertions(+), 2471 deletions(-) diff --git a/.gitignore b/.gitignore index f40fbd8..28fba9a 100644 --- a/.gitignore +++ b/.gitignore @@ -3,3 +3,12 @@ _site .jekyll-cache .jekyll-metadata vendor + +# ignore python venv +venv/ + +# ignore jetbrains IDE settings +.idea/ + +# ignore vscode settings +.vscode/ \ No newline at end of file diff --git a/cript_graph_json/JSON/cao_protein.json b/cript_graph_json/JSON/cao_protein.json index f8be62d..29c3240 100644 --- a/cript_graph_json/JSON/cao_protein.json +++ b/cript_graph_json/JSON/cao_protein.json @@ -1,2483 +1,5572 @@ { - "Project": { - "node": "Project", - "group": { - "node": "Group", - "name": "CRIPT_E2E" - }, - "Collection": [ - { - "node": "Collection", - "name": "Cao et al. Protein Elastomers", - "experiment": [ - { - "node": "Experiment", - "name": "Methacrylation", - "process": [ - { - "node": "Process", - "name": "WPI Centrifugation", - "type": "null", - "ingredients": [ - { - "node": "Ingredient", - "material": "Whey protein isolate", - "quantities": [ - "null" - ] - }, - { - "node": "Ingredient", - "material": "water", - "quantities": [ - "null" - ] - } - ], - "products": [ - "WPI supernatant" - ] - }, - { - "node": "Process", - "name": "WPP Centrifugation", - "type": "null", - "ingredients": [ - { - "node": "Ingredient", - "material": "Whey protein concentrate", - "quantities": [ - "null" - ] - }, - { - "node": "Ingredient", - "material": "water", - "quantities": [ - "null" - ] - } - ], - "products": [ - "WPC supernatant" - ] - }, - { - "node": "Process", - "name": "WPC Centrifugation", - "type": "null", - "ingredients": [ - { - "node": "Ingredient", - "material": "Whey protein powder", - "quantities": [ - "null" - ] - }, - { - "node": "Ingredient", - "material": "water", - "quantities": [ - "null" - ] - } - ], - "products": [ - "WPP supernatant" - ] - }, - { - "node": "Process", - "name": "BSA Centrifugation", - "type": "null", - "ingredients": [ - { - "node": "Ingredient", - "material": "Bovine serum albumin", - "quantities": [ - "null" - ] - }, - { - "node": "Ingredient", - "material": "water", - "quantities": [ - "null" - ] - } - ], - "products": [ - "BSA supernatant" - ] - }, - { - "node": "Process", - "name": "SPI Centrifugation", - "type": "null", - "ingredients": [ - { - "node": "Ingredient", - "material": "Soy protein isolate", - "quantities": [ - "null" - ] - }, - { - "node": "Ingredient", - "material": "water", - "quantities": [ - "null" - ] - } - ], - "products": [ - "SPI supernatant" - ] - }, - { - "node": "Process", - "name": "PPI Centrifugation", - "type": "null", - "ingredients": [ - { - "node": "Ingredient", - "material": "Pea protein isolate", - "quantities": [ - "null" - ] - }, - { - "node": "Ingredient", - "material": "water", - "quantities": [ - "null" - ] - } - ], - "products": [ - "PPI supernatant" - ] - }, - { - "node": "Process", - "name": "WPI Methacrylation", - "type": "null", - "prerequisite_process": [ - { - "node": "Process", - "name": "WPI Centrifugation", - "type": "null", - "ingredients": [ - { - "node": "Ingredient", - "material": "Whey protein isolate", - "quantities": [ - "null" - ] + "node": [ + "Project" + ], + "name": "CRIPT End-to-End Test Papers", + "collection": [ + { + "node": [ + "Collection" + ], + "name": "Cao et al. Protein Elastomers", + "experiment": [ + { + "node": [ + "Experiment" + ], + "name": "Methacrylation", + "process": [ + { + "node": [ + "Process" + ], + "name": "WPI Centrifugation", + "type": "multistep", + "ingredient": [ + { + "node": [ + "Ingredient" + ], + "material": { + "node": [ + "Material" + ], + "name": "Whey protein isolate", + "uid": "_:Whey protein isolate" + }, + "quantity": [ + null + ] + }, + { + "node": [ + "Ingredient" + ], + "material": { + "node": [ + "Material" + ], + "name": "water", + "uid": "_:water" + }, + "quantity": [ + null + ] + } + ], + "product": [ + { + "node": [ + "Material" + ], + "name": "Pea protein isolate", + "uid": "_:Pea protein isolate" + } + ] + }, + { + "node": [ + "Process" + ], + "name": "WPP Centrifugation", + "type": "multistep", + "ingredient": [ + { + "node": [ + "Ingredient" + ], + "material": { + "node": [ + "Material" + ], + "name": "Whey protein concentrate", + "uid": "_:Whey protein concentrate" + }, + "quantity": [ + null + ] + }, + { + "node": [ + "Ingredient" + ], + "material": { + "node": [ + "Material" + ], + "name": "water", + "uid": "_:water" + }, + "quantity": [ + null + ] + } + ], + "product": [ + { + "node": [ + "Material" + ], + "name": "WPC supernatant", + "uid": "_:WPC supernatant" + } + ] + }, + { + "node": [ + "Process" + ], + "name": "WPC Centrifugation", + "type": "multistep", + "ingredient": [ + { + "node": [ + "Ingredient" + ], + "material": { + "node": [ + "Material" + ], + "name": "Whey protein powder", + "uid": "_:Whey protein powder" + }, + "quantity": [ + null + ] + }, + { + "node": [ + "Ingredient" + ], + "material": { + "node": [ + "Material" + ], + "name": "water", + "uid": "_:water" + }, + "quantity": [ + null + ] + } + ], + "product": [ + { + "node": [ + "Material" + ], + "name": "WPP supernatant", + "uid": "_:WPP supernatant" + } + ] + }, + { + "node": [ + "Process" + ], + "name": "BSA Centrifugation", + "type": "multistep", + "ingredient": [ + { + "node": [ + "Ingredient" + ], + "material": { + "node": [ + "Material" + ], + "name": "Bovine serum albumin", + "uid": "_:Bovine serum albumin" + }, + "quantity": [ + null + ] + }, + { + "node": [ + "Ingredient" + ], + "material": { + "node": [ + "Material" + ], + "name": "water", + "uid": "_:water" + }, + "quantity": [ + null + ] + } + ], + "product": [ + { + "node": [ + "Material" + ], + "name": "BSA supernatant", + "uid": "_:BSA supernatant" + } + ] + }, + { + "node": [ + "Process" + ], + "name": "SPI Centrifugation", + "type": "multistep", + "ingredient": [ + { + "node": [ + "Ingredient" + ], + "material": { + "node": [ + "Material" + ], + "name": "Soy protein isolate", + "uid": "_:Soy protein isolate" + }, + "quantity": [ + null + ] + }, + { + "node": [ + "Ingredient" + ], + "material": { + "node": [ + "Material" + ], + "name": "water", + "uid": "_:water" + }, + "quantity": [ + null + ] + } + ], + "product": [ + { + "node": [ + "Material" + ], + "name": "SPI supernatant", + "uid": "_:SPI supernatant" + } + ] + }, + { + "node": [ + "Process" + ], + "name": "PPI Centrifugation", + "type": "multistep", + "ingredient": [ + { + "node": [ + "Ingredient" + ], + "material": { + "node": [ + "Material" + ], + "name": "Pea protein isolate", + "uid": "_:Pea protein isolate" + }, + "quantity": [ + null + ] + }, + { + "node": [ + "Ingredient" + ], + "material": { + "node": [ + "Material" + ], + "name": "water", + "uid": "_:water" + }, + "quantity": [ + null + ] + } + ], + "product": [ + { + "node": [ + "Material" + ], + "name": "PPI supernatant", + "uid": "_:PPI supernatant" + } + ] + }, + { + "node": [ + "Process" + ], + "name": "WPI Methacrylation", + "type": "multistep", + "prerequisite_process": [ + { + "node": [ + "Process" + ], + "name": "WPI Centrifugation", + "type": "multistep", + "ingredient": [ + { + "node": [ + "Ingredient" + ], + "material": { + "node": [ + "Material" + ], + "name": "Whey protein isolate", + "uid": "_:Whey protein isolate" + }, + "quantity": [ + null + ] + }, + { + "node": [ 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"uid": "_:WPP supernatant" + } + ] + } + ], + "ingredient": [ + { + "node": [ + "Ingredient" + ], + "material": { + "node": [ + "Material" + ], + "name": "WPP supernatant", + "uid": "_:WPP supernatant" + }, + "quantity": [ + null + ] + }, + { + "node": [ + "Ingredient" + ], + "material": { + "node": [ + "Material" + ], + "name": "Sodium hydroxide", + "uid": "_:Sodium hydroxide" + }, + "quantity": [ + null + ] + }, + { + "node": [ + "Ingredient" + ], + "material": { + "node": [ + "Material" + ], + "name": "Methacrylic anhydride", + "uid": "_:Methacrylic anhydride" + }, + "quantity": [ + null + ] + } + ], + "product": [ + { + "node": [ + "Material" + ], + "name": "WPC methacrylate", + "uid": "_:WPC methacrylate" + } + ] + }, + { + "node": [ + "Process" + ], + "name": "BSA Methacrylation", + "type": "multistep", + "prerequisite_process": [ + { + "node": [ + "Process" + ], + "name": "BSA Centrifugation", + "type": "multistep", + "ingredient": [ + { + "node": [ + "Ingredient" + ], + "material": { + "node": [ + "Material" + ], + "name": "Bovine serum albumin", + "uid": "_:Bovine serum albumin" + }, + "quantity": [ + null + ] + }, + { + "node": [ + "Ingredient" + ], + "material": { + "node": [ + "Material" + ], + "name": "water", + "uid": "_:water" + }, + "quantity": [ + null + ] + } + ], + "product": [ + { + "node": [ + "Material" + ], + "name": "BSA supernatant", + "uid": "_:BSA supernatant" + } + ] + } + ], + "ingredient": [ + { + "node": [ + "Ingredient" + ], + "material": { + "node": [ + "Material" + ], + "name": "BSA supernatant", + "uid": "_:BSA supernatant" + }, + "quantity": [ + null + ] + }, + { + "node": [ + "Ingredient" + ], + "material": { + "node": [ + "Material" + ], + "name": "Sodium hydroxide", + "uid": "_:Sodium hydroxide" + }, + "quantity": [ + null + ] + }, + { + "node": [ + "Ingredient" + ], + "material": { + "node": [ + "Material" + ], + "name": "Methacrylic anhydride", + "uid": "_:Methacrylic anhydride" + }, + "quantity": [ + null + ] + } + ], 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