first commit

.gitattributes

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+*.csv filter=lfs diff=lfs merge=lfs -text
+*.xlsx filter=lfs diff=lfs merge=lfs -text

.gitignore

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+__pycache__
+.DS_Store
+/venv

csv/1.csv (Stored with Git LFS)

+size 2753

csv/2.csv (Stored with Git LFS)

+size 38956

data1.py

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+#!/usr/bin/env python3
+
+from pandas import read_csv
+from pprint import pprint
+
+df = read_csv("./csv/1.csv")
+pprint(list(enumerate(df.columns)))
+cols = [
+    ('chemical_db_id', 1),
+    ('library', 2),
+    ('name', 4),
+    ('formula', 5),
+    ('mass', 6),
+    ('pubchem_cid', 7),
+    ('pubmed_refcount', 8),
+    ('standard_class', 9),
+    ('inchikey', 11),
+    ('inchikey14', 12),
+    ('final_mz', 15),
+    ('final_rt', 16),
+    ('final_adduct', 17),
+    ('adduct', 18),
+    ('detected_adducts', 20),
+    ('adduct_calc_mz', 21),
+    ('msms_detected', 24),
+    ('msms_purity', 26)
+]
+idxs = [x[1] for x in cols]
+
+data = [{x[0]: row[x[1]] for x in cols} for row in df.to_dict('tight')['data']]
+for x in data:
+    if x['msms_detected'] == 'No':
+        del x['msms_detected']

data2.py

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+#!/usr/bin/env python3
+
+from pandas import read_csv
+from pprint import pprint
+
+df = read_csv("./csv/2.csv")
+pprint(list(enumerate(df.columns)))
+
+cols = [
+    ('chemical_db_id', 1),
+    ('library', 2),
+    ('name', 4),
+    ('formula', 6),
+    ('mass', 7),
+    ('pubchem_cid', 10),
+    ('pubmed_refcount', 8),
+    ('standard_class', 11),
+    ('inchikey', 13),
+    ('inchikey14', 14),
+    ('final_mz', 17),
+    ('final_rt', 18),
+    ('final_adduct', 19),
+    ('adduct', 20),
+    ('detected_adducts', 22),
+    ('adduct_calc_mz', 23),
+    ('msms_detected', 26),
+    ('msms_purity', 28)
+]
+
+data = [{x[0]: row[x[1]] for x in cols} for row in df.to_dict('tight')['data']]
+for x in data:
+    if x['msms_detected'] == 'No':
+        del x['msms_detected']

enter_data.py

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+#!/usr/bin/env python3
+
+import requests
+import sys
+import data2
+import data1
+
+baseurl = "http://127.0.0.1:5000"
+session = requests.session()
+
+with session.post(baseurl + "/admin/login", {'username': 'admin', 'password': 'admin'}) as req:
+    if req.status_code != 200:
+        print("Auth Failed")
+        sys.exit(1)
+
+for x in data1.data + data2.data:
+    print(f"POSTing for {x}...")
+    req = session.post(baseurl + "/chemical/create", x)
+    if req.status_code != 200:
+        print(f"Request Failed for {x}")
+    print("Complete.")

requirements.txt

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+certifi==2022.12.7
+charset-normalizer==2.1.1
+idna==3.4
+numpy==1.24.0
+pandas==1.5.2
+python-dateutil==2.8.2
+pytz==2022.7
+requests==2.28.1
+six==1.16.0
+urllib3==1.26.13
+xlsx2csv==0.8.0

xlsx/Example1.xlsx (Stored with Git LFS)

+size 11700

xlsx/Example2.xlsx (Stored with Git LFS)

+size 29000