Code for NMDC to NCBI export #518
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| import datetime | ||
| import xml.etree.ElementTree as ET | ||
| import xml.dom.minidom | ||
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| from nmdc_runtime.site.export.ncbi_xml_utils import ( | ||
| handle_controlled_identified_term_value, | ||
| handle_controlled_term_value, | ||
| handle_geolocation_value, | ||
| handle_quantity_value, | ||
| handle_text_value, | ||
| handle_timestamp_value, | ||
| handle_float_value, | ||
| handle_string_value, | ||
| load_mappings, | ||
| validate_xml, | ||
| ) | ||
| from nmdc_runtime.site.export.nmdc_api_client import NMDCApiClient | ||
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| class NCBISubmissionXML: | ||
| def __init__(self, ncbi_submission_fields: dict): | ||
| self.root = ET.Element("Submission") | ||
| self.nmdc_study_id = ncbi_submission_fields.get("nmdc_study_id") | ||
| self.nmdc_ncbi_attribute_mapping_file_url = ncbi_submission_fields.get( | ||
| "nmdc_ncbi_attribute_mapping_file_url" | ||
| ) | ||
| self.ncbi_submission_metadata = ncbi_submission_fields.get( | ||
| "ncbi_submission_metadata", {} | ||
| ) | ||
| self.ncbi_bioproject_metadata = ncbi_submission_fields.get( | ||
| "ncbi_bioproject_metadata", {} | ||
| ) | ||
| self.ncbi_biosample_metadata = ncbi_submission_fields.get( | ||
| "ncbi_biosample_metadata", {} | ||
| ) | ||
| self.nmdc_api_client = NMDCApiClient() | ||
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| # dispatcher dictionary capturing handlers for NMDC object to NCBI flat Attribute | ||
| # type handlers | ||
| self.type_handlers = { | ||
| "QuantityValue": handle_quantity_value, | ||
| "TextValue": handle_text_value, | ||
| "TimestampValue": handle_timestamp_value, | ||
| "ControlledTermValue": handle_controlled_term_value, | ||
| "ControlledIdentifiedTermValue": handle_controlled_identified_term_value, | ||
| "GeolocationValue": handle_geolocation_value, | ||
| "float": handle_float_value, | ||
| "string": handle_string_value, | ||
| } | ||
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| def set_element(self, tag, text="", attrib=None, children=None): | ||
| attrib = attrib or {} | ||
| children = children or [] | ||
| element = ET.Element(tag, attrib=attrib) | ||
| element.text = text | ||
| for child in children: | ||
| element.append(child) | ||
| return element | ||
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| def set_description(self, email, user, first, last, org, date=None): | ||
| date = date or datetime.datetime.now().strftime("%Y-%m-%d") | ||
| description = self.set_element( | ||
| "Description", | ||
| children=[ | ||
| self.set_element( | ||
| "Comment", f"NMDC Submission for {self.nmdc_study_id}" | ||
| ), | ||
| self.set_element("Submitter", attrib={"user_name": user}), | ||
| self.set_element( | ||
| "Organization", | ||
| attrib={"role": "owner", "type": "center"}, | ||
| children=[ | ||
| self.set_element("Name", org), | ||
| self.set_element( | ||
| "Contact", | ||
| attrib={"email": email}, | ||
| children=[ | ||
| self.set_element( | ||
| "Name", | ||
| children=[ | ||
| self.set_element("First", first), | ||
| self.set_element("Last", last), | ||
| ], | ||
| ) | ||
| ], | ||
| ), | ||
| ], | ||
| ), | ||
| self.set_element("Hold", attrib={"release_date": date}), | ||
| ], | ||
| ) | ||
| self.root.append(description) | ||
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| def set_descriptor(self, title, description): | ||
| descriptor_elements = [] | ||
| descriptor_elements.append(self.set_element("Title", title)) | ||
| descriptor_elements.append( | ||
| self.set_element( | ||
| "Description", children=[self.set_element("p", description)] | ||
| ) | ||
| ) | ||
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| return descriptor_elements | ||
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| def set_bioproject(self, title, project_id, description, data_type, org): | ||
| action = self.set_element("Action") | ||
| add_data = self.set_element("AddData", attrib={"target_db": "BioProject"}) | ||
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| data_element = self.set_element("Data", attrib={"content_type": "XML"}) | ||
| xml_content = self.set_element("XmlContent") | ||
| project = self.set_element("Project", attrib={"schema_version": "2.0"}) | ||
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| project_id_element = self.set_element("ProjectID") | ||
| spuid = self.set_element("SPUID", project_id, {"spuid_namespace": org}) | ||
| project_id_element.append(spuid) | ||
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| descriptor = self.set_descriptor(title, description) | ||
| project_type = self.set_element("ProjectType") | ||
| project_type_submission = self.set_element( | ||
| "ProjectTypeSubmission", attrib={"sample_scope": "eEnvironment"} | ||
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| ) | ||
| intended_data_type_set = self.set_element("IntendedDataTypeSet") | ||
| data_type_element = self.set_element("DataType", data_type) | ||
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| intended_data_type_set.append(data_type_element) | ||
| project_type_submission.append(intended_data_type_set) | ||
| project_type.append(project_type_submission) | ||
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| project.extend([project_id_element] + descriptor + [project_type]) | ||
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| xml_content.append(project) | ||
| data_element.append(xml_content) | ||
| add_data.append(data_element) | ||
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| identifier = self.set_element("Identifier") | ||
| spuid_identifier = self.set_element( | ||
| "SPUID", project_id, {"spuid_namespace": org} | ||
| ) | ||
| identifier.append(spuid_identifier) | ||
| add_data.append(identifier) | ||
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| action.append(add_data) | ||
| self.root.append(action) | ||
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| def set_biosample( | ||
| self, | ||
| organism_name, | ||
| package, | ||
| org, | ||
| nmdc_biosamples, | ||
| ): | ||
| attribute_mappings, slot_range_mappings = load_mappings( | ||
| self.nmdc_ncbi_attribute_mapping_file_url | ||
| ) | ||
|
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There was a problem hiding this comment. I would try to not tie the process of obtaining the mapping directly into this class. Let this class be just about transformation. Let the client of the class worry about how to get the mapping and pass it (the mapping itself, not a URL) to this class. |
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| for biosample in nmdc_biosamples: | ||
| attributes = {} | ||
| sample_id_value = None | ||
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| for json_key, value in biosample.items(): | ||
| if isinstance(value, list): | ||
| continue # Skip processing for list values | ||
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| # Special handling for NMDC Biosample "id" | ||
| if json_key == "id": | ||
| sample_id_value = value | ||
| continue | ||
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| if json_key not in attribute_mappings: | ||
| continue | ||
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| xml_key = attribute_mappings[json_key] | ||
| value_type = slot_range_mappings.get(json_key, "string") | ||
| handler = self.type_handlers.get(value_type, handle_string_value) | ||
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| formatted_value = handler(value) | ||
| attributes[xml_key] = formatted_value | ||
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| # Create the BioSample XML block with these attributes for each biosample | ||
| biosample_elements = [ | ||
| self.set_element( | ||
| "SampleId", | ||
| children=[ | ||
| self.set_element( | ||
| "SPUID", sample_id_value, {"spuid_namespace": org} | ||
| ) | ||
| ], | ||
| ), | ||
| self.set_element( | ||
| "Descriptor", | ||
| children=[ | ||
| self.set_element( | ||
| "Title", | ||
| f"NMDC Biosample {sample_id_value} from {organism_name} part of {self.nmdc_study_id} study", | ||
| ), | ||
| ], | ||
| ), | ||
| self.set_element( | ||
| "Organism", | ||
| children=[self.set_element("OrganismName", organism_name)], | ||
| ), | ||
| self.set_element("Package", package), | ||
| self.set_element( | ||
| "Attributes", | ||
| children=[ | ||
| self.set_element( | ||
| "Attribute", attributes[key], {"attribute_name": key} | ||
| ) | ||
| for key in sorted(attributes) | ||
| ], | ||
| ), | ||
| ] | ||
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| action = self.set_element( | ||
| "Action", | ||
| children=[ | ||
| self.set_element( | ||
| "AddData", | ||
| attrib={"target_db": "BioSample"}, | ||
| children=[ | ||
| self.set_element( | ||
| "Data", | ||
| attrib={"content_type": "XML"}, | ||
| children=[ | ||
| self.set_element( | ||
| "XmlContent", | ||
| children=[ | ||
| self.set_element( | ||
| "BioSample", | ||
| attrib={"schema_version": "2.0"}, | ||
| children=biosample_elements, | ||
| ), | ||
| ], | ||
| ), | ||
| ], | ||
| ), | ||
| self.set_element( | ||
| "Identifier", | ||
| children=[ | ||
| self.set_element( | ||
| "SPUID", | ||
| sample_id_value, | ||
| {"spuid_namespace": org}, | ||
| ), | ||
| ], | ||
| ), | ||
| ], | ||
| ), | ||
| ], | ||
| ) | ||
| self.root.append(action) | ||
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| def get_submission_xml(self): | ||
| self.set_description( | ||
| email=self.ncbi_submission_metadata.get("email", ""), | ||
| user=self.ncbi_submission_metadata.get("user", ""), | ||
| first=self.ncbi_submission_metadata.get("first", ""), | ||
| last=self.ncbi_submission_metadata.get("last", ""), | ||
| org=self.ncbi_submission_metadata.get("organization", ""), | ||
| ) | ||
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| self.set_bioproject( | ||
| title=self.ncbi_bioproject_metadata.get("title", ""), | ||
| project_id=self.ncbi_bioproject_metadata.get("project_id", ""), | ||
| description=self.ncbi_bioproject_metadata.get("description", ""), | ||
| data_type=self.ncbi_bioproject_metadata.get("data_type", ""), | ||
| org=self.ncbi_submission_metadata.get("organization", ""), | ||
| ) | ||
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| biosamples_list = self.nmdc_api_client.get_biosamples_part_of_study( | ||
| self.nmdc_study_id | ||
| ) | ||
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| self.set_biosample( | ||
| organism_name=self.ncbi_biosample_metadata.get("organism_name", ""), | ||
| package=self.ncbi_biosample_metadata.get("package", ""), | ||
| org=self.ncbi_submission_metadata.get("organization", ""), | ||
| nmdc_biosamples=biosamples_list, | ||
| ) | ||
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| rough_string = ET.tostring(self.root, "unicode") | ||
| reparsed = xml.dom.minidom.parseString(rough_string) | ||
| submission_xml = reparsed.toprettyxml(indent=" ", newl="\n") | ||
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There was a problem hiding this comment. Is there a reason for this serialize-deserialize step? Is it just to get nicely formatted XML? If so, would the |
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| # ============= Uncomment the following code to validate the XML against NCBI XSDs ============ # | ||
| # submission_xsd_url = "https://www.ncbi.nlm.nih.gov/viewvc/v1/trunk/submit/public-docs/common/submission.xsd?view=co" | ||
| # submission_xsd_validation = validate_xml(submission_xml, submission_xsd_url) | ||
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| # bioproject_xsd_url = "https://www.ncbi.nlm.nih.gov/viewvc/v1/trunk/submit/public-docs/common/bioproject.xsd?view=co" | ||
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| # bioproject_xsd_validation = validate_xml(submission_xml, bioproject_xsd_url) | ||
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| # biosample_xsd_url = "https://www.ncbi.nlm.nih.gov/viewvc/v1/trunk/submit/public-docs/common/biosample.xsd?view=co" | ||
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| # biosample_xsd_validation = validate_xml(submission_xml, biosample_xsd_url) | ||
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There was a problem hiding this comment. I wouldn't leave commented-out code like this in. But I would turn these into unit tests. |
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| return submission_xml | ||
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Some quibbles about naming.
NCBISubmissionXMLfeels more representative of what this class produces. So what is the class itself? Something likeNCBISubmissionGeneratororNCBISubmissionTranslator?Also this class has a lot of methods named
set_*. When I see a method with such a name I expect it to set some piece of internal class state and return nothing. Instead, some of these methods (set_element,set_descriptor) produce XML elements and return them. Other (set_description,set_bioproject,set_biosample) produce XML elements and append them to the XML root. I think this code might be a bit more readable if all those methods were named something likebuild_*orgenerate_*and always return what they produced. Then the caller (get_submission_xml) would be responsible for taking the return values and use them as needed (appending to the root element).