Bacquerya_api

Backend API for the BacQuerya website.

Routes

/geneQuery

• Uses a POST method to search for a gene query in the elastic gene index and returns a JSON containing a list of search results. If searchType = gene the first 100 results for the query are returned. If searchType = consistentNameList, a list of genes are iteratively queried in the index and the first exact match for each gene is returned. The pageNumber parameter tells elastic which chunk of the search results should be returned: pageNumber == 1 returns the first 100 results, pageNumber == 2 returns the second 100 results etc.

/isolateQuery

• Uses a POST method to search for an isolate query in the elastic isolate index. If searchType = isolate the route returns a JSON containing a list of search results. If searchType = species returns all S. pneumoniae isolate results, If searchType = biosampleList, searches for each biosample in the index and returns the metadata for the highest ranked result for each BioSample. The pageNumber parameter tells elastic which chunk of the search results should be returned: pageNumber == 1 returns the first 100 results, pageNumber == 2 returns the second 100 results etc.

/sequence

• Searches for a query sequence in a static COBS index available through the BacQuerya storage instance. Returns a list of key value pairs where the key is the gene name and the value is the proportion of matching k-mers between the query sequence and the gene sequence in the result.

/study

• Searches for a query term in the PubMed database using the Biopython entrez API.

/bulkdownloads

• Accepts a list of sequence URLs for isolates. If there are 100 or fewer sequences, the sequences are downloaded and tarred. If there are more than 100 sequences, a list of sequence download links for all relevant isolates is returned instead. If an email is specified, an email is sent containing a download link for the created file or directory.

/downloads/<token>

• Uses an encoded token to check if the sequence download tarfile or txt file has successfully been created and serves a HTML page indicating success or failure.

/download_link/<path:token>

• Sends the requested sequence file specified by the token for download.

/alignment/<consistentName>

• Sends a static multiple sequence alignment for the gene of interest.

/alignmentView/<consistentName>

• REST route to return a JSON of the relevant multiple sequence alignment file by gene name.

/upload_template

• Sends the upload template for submitting the accession IDs of isolates used in studies.

/upload_accessions

• Recieves and saves a CSV file containing the accession IDs of isolates used in a particular study. The accession IDs are then extracted and indexed with the study DOI using a SQLite database.

/retrieve_accessions/<DOI>

• Queries a SQLite database to return a list of isolate accession IDs associated with a particular study DOI.

/population_assembly_stats

• Returns a JSON of population-wide isolate assembly statistics.

Testing

To run the flask server locally at http://localhost:5000 install the dependencies with:

conda env create -f environment.yml
conda activate BQ_api

To connect to and retrieve entries from the Azure SQL database, you will also need to install the ODBC driver.

Contributors

The BacQuerya-api was developed by Daniel Anderson and John Lees.