# Open Source Database Monitor With the rise of cheminformatics, so comes the rise of open source databases. Unfortunately, open source databases are spread amongst a variety of URLS and can be hard to keep track in an efficient fashion. We create the `Uptime` bot {% embed url="" %} ``` Zinc 15 OpenFDA Zinc 20 Metabolites Biological Role PubChem MetaboAnalyst NIST Chemistry Webhook Adverse Drug Reaction Classification System Chem Exper Metabolism and Transport Database NMR Shift Database Ecology Toxicity Drug Bank Human and Environment Risk Assessment Binding Database International Toxicity Information for Risk Assesments Spectral Database for Organic Compounds Japan Exisiting Database Sider National Pesticide Center ChemSpider Pesticide Info Stitch Kyoto Encyclopedia of Genes and Genomes CardPred Hetereocycles Comparative Toxicogenomics Database Chemical Resolver AMED Cardiotoxicity Database LookChem Tox21 Lipid Maps Drug Safety Analysis System ``` **Imports** ``` from global_chem_extensions import GlobalChemExtensions do = GlobalChemExtensions().development_operations() ``` **Check Cheminformatic Databases** {% tabs %} {% tab title="Code" %} ``` successes, failures = do.check_status_on_open_source_cheminformatic_databases() print (successes) print (failures) ``` {% endtab %} {% tab title="Output" %} ``` {' Zinc 15': 'Up', ' Zinc 20': 'Up', ' PubChem': 'Up', ' NIST Chemistry Webhook': 'Up', ' Chem Exper': 'Up', ' NMR Shift Database': 'Up', ' Binding Database': 'Up', ' Spectral Database for Organic Compounds': 'Up', ' Sider': 'Up', ' ChemSpider': 'Up', ' Stitch': 'Up', ' CardPred': 'Up', ' Comparative Toxicogenomics Database': 'Up', ' AMED Cardiotoxicity Database': 'Up', ' Tox21': 'Up', ' Drug Safety Analysis System': 'Up', ' OpenFDA': 'Up', ' Metabolites Biological Role': 'Up', ' MetaboAnalyst': 'Up', ' Adverse Drug Reaction Classification System': 'Up', ' Metabolism and Transport Database': 'Up', ' Ecology Toxicity ': 'Up', ' Japan Exisiting Database': 'Up', ' National Pesticide Center': 'Up', ' Pesticide Info': 'Up', ' Kyoto Encyclopedia of Genes and Genomes': 'Up', ' Hetereocycles': 'Up', ' Chemical Resolver': 'Up', ' LookChem': 'Up', ' Lipid Maps': 'Up'} {' Drug Bank': 'Down', ' Human and Environment Risk Assessment ': 'Down', ' International Toxicity Information for Risk Assesments': 'Down'} ``` {% endtab %} {% endtabs %} **Check Bacteria Databases** {% tabs %} {% tab title="Code" %} ``` successes, failures = do.check_status_on_open_source_bacteria_databases() print (successes) print (failures) ``` {% endtab %} {% tab title="Output" %} ``` {' European Molecular Biology Laboratory': 'Up', ' DDBJ bioinformatics': 'Up', ' BROAD Institute': 'Up', ' Biocyc Genome Database': 'Up', ' National Center for Bioinformatics Microbial Genome Database': 'Up', ' Ensembl Bacteria': 'Up', ' NIH Human Microbiome Project': 'Up', ' Microbial Genome Database': 'Up', ' JGI Genomes ': 'Up', ' Pseudomonas Genome Database': 'Up', ' Ecocyc': 'Up', ' ECMDB': 'Up', ' Staphylococcus regulator RNA Database': 'Up', ' Vibrio Cholera Genome Database': 'Up'} {' ATCC': 'Down', ' EzBioCloud Public Genome': 'Down'} ``` {% endtab %} {% endtabs %} **Github Repository** ![](https://538359177-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FUSbA3Zf4EXyGn0UpfW5b%2Fuploads%2F7i8jzU9DAnWlPqpZgESS%2FScreen%20Shot%202022-02-24%20at%2010.26.09%20AM.png?alt=media\&token=fa320059-26a9-4c9c-8936-44248714b8ca) The bot serves as a heart beat checker pinging URLS for databases that are most often used by cheminformaticians. ![](https://538359177-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FUSbA3Zf4EXyGn0UpfW5b%2Fuploads%2F8IrSXQ32vvV57BHlioq8%2FScreen%20Shot%202022-02-24%20at%2010.28.37%20AM.png?alt=media\&token=dca01c81-eb74-4602-98c9-340b4c2ccd32) Within the GlobalChemExtensions component we would like a persistent monitoring system tied to the same URLS the bot is also pinging. ``` for i in contents: if 'name' in i and \ '#' not in i and 'chemistrydb.com' not in i \ and 'Cheminformatic Database Statuses' not in i: i = i.strip('\n').split('name:')[1] names.append(i) if 'url' in i: i = i.strip('\n').split('url:')[1] urls.append(i) return urls, names ``` The code then checks the status code to see if it still alive. If not it gets reported as a failure. This is useful for folk relying on these databases for whatever processing they are doing. ``` response = urllib.request.urlopen(url) status_code = response.getcode() if '200' == status_code: successes[name] = 'Up' except: failures[name] = 'Down' ``` --- # Agent Instructions: Querying This Documentation If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question. Perform an HTTP GET request on the current page URL with the `ask` query parameter: ``` GET https://globalchem.gitbook.io/globalchem-your-chemical-graph-network/development-operations/open-source-database-monitor.md?ask= ``` The question should be specific, self-contained, and written in natural language. The response will contain a direct answer to the question and relevant excerpts and sources from the documentation. Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.