Juni Kim
2 years ago
9 changed files with 291 additions and 5 deletions
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1.gitignore
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0__init__.py
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95app.py
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10templates/admin.html
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0templates/batch.html
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21templates/batchadd.html
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47templates/batchquery.html
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118validate.py
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{% extends "base.html" %} |
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{% block content %} |
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<h2>Batch Upload Chemicals</h2> |
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<a href="https://git.junickim.me/junikimm717/walker-database/raw/master/validate.py"> Source Code with required type definitions </a> |
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<form method="post" enctype="multipart/form-data"> |
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<label for="csv">CSV: </label> |
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<input type="file" name="csv"> |
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<input type="submit" value="Submit"> |
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</form> |
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{% if invalid %} |
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<p style="color: red;">Data Points are Incorrectly added: {{invalid}}</p> |
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{% endif %} |
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{% if success %} |
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<p style="color: green;">Success!</p> |
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{% endif %} |
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{% endblock %} |
@ -0,0 +1,47 @@ |
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{% extends "base.html" %} |
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{% block content %} |
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<h2>Batch Query Chemicals</h2> |
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<a href="https://git.junickim.me/junikimm717/walker-database/raw/master/validate.py"> Source Code with required type definitions </a> |
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<form method="post" enctype="multipart/form-data"> |
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<label for="csv">CSV: </label> |
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<input type="file" name="csv"> |
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<input type="submit" value="Submit"> |
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</form> |
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{% if invalid %} |
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<p style="color: red;">Data Points are Incorrectly added: {{invalid}}</p> |
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{% endif %} |
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{% if success %} |
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<p style="color: green;">Success!</p> |
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{% for result in data %} |
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<hr> |
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<h2>Query {{loop.index}}</h2> |
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<p> |
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{{result.query.mz_min}} < M/Z Ratio < {{result.query.mz_max}}, |
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{{result.query.rt_min}} < Retention Time < {{result.query.rt_max}} |
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</p> |
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{% for hit in result.hits %} |
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<div> |
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<a href="{{hit.url}}"> |
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<h3>{{hit.name}}</h3> |
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</a> |
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<table> |
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<tr> |
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<td>Retention Time</td> |
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<td>{{hit.rt}}</td> |
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</tr> |
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<tr> |
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<td>M/Z Ratio</td> |
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<td>{{hit.mz}}</td> |
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</tr> |
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</table> |
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</div> |
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{% endfor %} |
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{% endfor %} |
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{% endif %} |
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{% endblock %} |
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import csv |
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from datetime import date |
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_required_fields = [ |
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("name", "str"), |
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("formula", "str"), |
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("mass", "float"), |
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("final_mz", "float"), |
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("final_rt", "float"), |
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] |
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_optional_fields = [ |
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("chemical_db_id", "str"), |
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("library", "str"), |
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("pubchem_cid", "int"), |
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("pubmed_refcount", "int"), |
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("standard_class", "str"), |
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("inchikey", "str"), |
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("inchikey14", "str"), |
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("final_adduct", "str"), |
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("adduct", "str"), |
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("detected_adducts", "str"), |
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("adduct_calc_mz", "str"), |
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("msms_detected", "yesno"), |
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("msms_purity", "float"), |
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] |
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_query_fields = [ |
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("rt_min", "float"), |
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("rt_max", "float"), |
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("mz_min", "float"), |
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("mz_max", "float"), |
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# ("year_max", "int"), |
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# ("day_max", "int"), |
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# ("month_max", "int"), |
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] |
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def _validate_type(field: str, value: str, t): |
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if t == "yesno": |
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l = value.strip().lower() |
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if l == "yes": |
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return True |
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elif l == "no": |
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return False |
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else: |
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raise ValueError( |
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f"Yes/No field {field} does not have a valid value {value}") |
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elif t == "int": |
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try: |
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return int(value) |
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except ValueError: |
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raise ValueError( |
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f"Integer field {field} does not have a valid value {value}") |
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elif t == "float": |
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try: |
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return float(value) |
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except ValueError: |
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raise ValueError( |
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f"Float field {field} does not have a valid value {value}") |
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elif t == "str": |
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return value |
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else: |
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raise ValueError("Impossible") |
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def validate_insertion_csv_fields(reader: csv.DictReader) -> tuple[list[dict], str]: |
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chemicals: list[dict] = [] |
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for row in reader: |
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chemical = {} |
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for field, t in _required_fields: |
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if field not in row: |
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return [], f"Required field \"{field}\" not present in csv" |
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try: |
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value = _validate_type(field, row[field], t) |
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chemical[field] = value |
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except ValueError as e: |
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return [], str(e) |
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for field, t in _optional_fields: |
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if field not in row: |
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continue |
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try: |
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value = _validate_type(field, row[field], t) |
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chemical[field] = value |
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except ValueError as e: |
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return [], str(e) |
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chemicals.append(chemical) |
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return chemicals, "" |
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def validate_query_csv_fields(reader: csv.DictReader) -> tuple[list[dict], str]: |
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queries: list[dict] = [] |
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for row in reader: |
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query = {} |
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for field, t in _query_fields: |
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if field not in row: |
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return [], f"Required field \"{field}\" not present in csv" |
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try: |
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value = _validate_type(field, row[field], t) |
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query[field] = value |
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except ValueError as e: |
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return [], str(e) |
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# year_max, month_max, day_max = query.get( |
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# 'year_max'), query.get('month_max'), query.get('day_max') |
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# try: |
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# d = date(year_max, month_max, day_max) |
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# query["date"] = d |
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# except ValueError as e: |
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# return [], f"Invalid Date Value Provided for {month_max}/{day_max}/{year_max}" |
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queries.append(query) |
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return queries, "" |
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