parse

package
v0.0.0-...-bc5e03d Latest Latest
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Published: Apr 29, 2023 License: AFL-3.0, CC-BY-3.0 Imports: 7 Imported by: 1

Documentation

Index

Constants

This section is empty.

Variables

This section is empty.

Functions

func PubmedXML

func PubmedXML(xmlPaths *[]string, stdin *[]byte, outfn string, keywords *[]string, thread int)

PubmedXML convert Pubmed XML to json

func SraXML

func SraXML(xmlPaths *[]string, stdin *[]byte, outfn string, keywords *[]string, thread int)

SraXML convert Sra XML to json

Types

type ArticleId

type ArticleId struct {
	Text   string `xml:",chardata"`
	IdType string `xml:"IdType,attr"`
}

type BigdArticle

type BigdArticle struct {
	ID                    int                 `json:"id"`
	Title                 string              `json:"title"`
	Author                string              `json:"author"`
	Abst                  string              `json:"abst"`
	Journal               string              `json:"journal"`
	JournalAbbr           string              `json:"journalAbbr"`
	Volume                interface{}         `json:"volume"`
	Issue                 interface{}         `json:"issue"`
	PubYear               int                 `json:"pubYear"`
	PubMonth              interface{}         `json:"pubMonth"`
	PubDay                int                 `json:"pubDay"`
	Pmid                  interface{}         `json:"pmid"`
	Doi                   string              `json:"doi"`
	Citation              int                 `json:"citation"`
	Type                  interface{}         `json:"type"`
	CreateTime            string              `json:"createTime"`
	LastModified          string              `json:"lastModified"`
	PubDate               string              `json:"pubDate"`
	Keyword               interface{}         `json:"keyword"`
	Source                string              `json:"source"`
	Pprid                 interface{}         `json:"pprid"`
	Affiliation           interface{}         `json:"affiliation"`
	Exclude               int                 `json:"exclude"`
	PublicationReviewList []interface{}       `json:"publicationReviewList"`
	URLs                  []string            `json:"urls"`
	Correlation           map[string][]string `json:"correlation"`
	Keywords              []string            `json:"keywords"`
}

type BigdArticleList

type BigdArticleList struct {
	Draw            int           `json:"draw"`
	RecordsTotal    int           `json:"recordsTotal"`
	RecordsFiltered int           `json:"recordsFiltered"`
	Data            []BigdArticle `json:"data"`
	Error           interface{}   `json:"error"`
}

type ExperimentPkg

type ExperimentPkg struct {
	EXPERIMENT struct {
		Accession   string `xml:"accession,attr"`
		Alias       string `xml:"alias,attr"`
		IDENTIFIERS struct {
			PRIMARYID string `xml:"PRIMARY_ID"`
		} `xml:"IDENTIFIERS"`
		TITLE    string `xml:"TITLE"`
		STUDYREF struct {
			Accession   string `xml:"accession,attr"`
			IDENTIFIERS struct {
				PRIMARYID  string `xml:"PRIMARY_ID"`
				EXTERNALID struct {
					Namespace string `xml:"namespace,attr"`
				} `xml:"EXTERNAL_ID"`
			} `xml:"IDENTIFIERS"`
		} `xml:"STUDY_REF"`
		DESIGN struct {
			DESIGNDESCRIPTION string `xml:"DESIGN_DESCRIPTION"`
			SAMPLEDESCRIPTOR  struct {
				Accession   string `xml:"accession,attr"`
				IDENTIFIERS struct {
					PRIMARYID  string `xml:"PRIMARY_ID"`
					EXTERNALID struct {
						Namespace string `xml:"namespace,attr"`
					} `xml:"EXTERNAL_ID"`
				} `xml:"IDENTIFIERS"`
			} `xml:"SAMPLE_DESCRIPTOR"`
			LIBRARYDESCRIPTOR struct {
				LIBRARYNAME      string `xml:"LIBRARY_NAME"`
				LIBRARYSTRATEGY  string `xml:"LIBRARY_STRATEGY"`
				LIBRARYSOURCE    string `xml:"LIBRARY_SOURCE"`
				LIBRARYSELECTION string `xml:"LIBRARY_SELECTION"`
				LIBRARYLAYOUT    struct {
					PAIRED string `xml:"PAIRED"`
				} `xml:"LIBRARY_LAYOUT"`
			} `xml:"LIBRARY_DESCRIPTOR"`
		} `xml:"DESIGN"`
		PLATFORM struct {
			ILLUMINA struct {
				INSTRUMENTMODEL string `xml:"INSTRUMENT_MODEL"`
			} `xml:"ILLUMINA"`
		} `xml:"PLATFORM"`
	} `xml:"EXPERIMENT"`
	SUBMISSION struct {
		LabName     string `xml:"lab_name,attr"`
		CenterName  string `xml:"center_name,attr"`
		Accession   string `xml:"accession,attr"`
		Alias       string `xml:"alias,attr"`
		IDENTIFIERS struct {
			PRIMARYID string `xml:"PRIMARY_ID"`
		} `xml:"IDENTIFIERS"`
	} `xml:"SUBMISSION"`
	Organization struct {
		Type    string `xml:"type,attr"`
		Name    string `xml:"Name"`
		Address struct {
			PostalCode  string `xml:"postal_code,attr"`
			Department  string `xml:"Department"`
			Institution string `xml:"Institution"`
			Street      string `xml:"Street"`
			City        string `xml:"City"`
			Country     string `xml:"Country"`
		} `xml:"Address"`
		Contact struct {
			Email    string `xml:"email,attr"`
			SecEmail string `xml:"sec_email,attr"`
			Address  struct {
				PostalCode  string `xml:"postal_code,attr"`
				Department  string `xml:"Department"`
				Institution string `xml:"Institution"`
				Street      string `xml:"Street"`
				City        string `xml:"City"`
				Country     string `xml:"Country"`
			} `xml:"Address"`
			Name struct {
				First string `xml:"First"`
				Last  string `xml:"Last"`
			} `xml:"Name"`
		} `xml:"Contact"`
	} `xml:"Organization"`
	STUDY struct {
		CenterName  string `xml:"center_name,attr"`
		Alias       string `xml:"alias,attr"`
		Accession   string `xml:"accession,attr"`
		IDENTIFIERS struct {
			PRIMARYID  string `xml:"PRIMARY_ID"`
			EXTERNALID struct {
				Namespace string `xml:"namespace,attr"`
				Label     string `xml:"label,attr"`
			} `xml:"EXTERNAL_ID"`
		} `xml:"IDENTIFIERS"`
		DESCRIPTOR struct {
			STUDYTITLE string `xml:"STUDY_TITLE"`
			STUDYTYPE  struct {
				ExistingStudyType string `xml:"existing_study_type,attr"`
			} `xml:"STUDY_TYPE"`
			STUDYABSTRACT     string `xml:"STUDY_ABSTRACT"`
			CENTERPROJECTNAME string `xml:"CENTER_PROJECT_NAME"`
		} `xml:"DESCRIPTOR"`
	} `xml:"STUDY"`
	SAMPLE struct {
		Alias       string `xml:"alias,attr"`
		Accession   string `xml:"accession,attr"`
		IDENTIFIERS struct {
			PRIMARYID  string `xml:"PRIMARY_ID"`
			EXTERNALID struct {
				Namespace string `xml:"namespace,attr"`
			} `xml:"EXTERNAL_ID"`
		} `xml:"IDENTIFIERS"`
		TITLE      string `xml:"TITLE"`
		SAMPLENAME struct {
			TAXONID        string `xml:"TAXON_ID"`
			SCIENTIFICNAME string `xml:"SCIENTIFIC_NAME"`
		} `xml:"SAMPLE_NAME"`
		SAMPLELINKS struct {
			SAMPLELINK struct {
				XREFLINK struct {
					DB    string `xml:"DB"`
					ID    string `xml:"ID"`
					LABEL string `xml:"LABEL"`
				} `xml:"XREF_LINK"`
			} `xml:"SAMPLE_LINK"`
		} `xml:"SAMPLE_LINKS"`
		SAMPLEATTRIBUTES struct {
			SAMPLEATTRIBUTE []struct {
				TAG   string `xml:"TAG"`
				VALUE string `xml:"VALUE"`
			} `xml:"SAMPLE_ATTRIBUTE"`
		} `xml:"SAMPLE_ATTRIBUTES"`
	} `xml:"SAMPLE"`
	Pool struct {
		Member struct {
			MemberName  string `xml:"member_name,attr"`
			Accession   string `xml:"accession,attr"`
			SampleName  string `xml:"sample_name,attr"`
			SampleTitle string `xml:"sample_title,attr"`
			Spots       string `xml:"spots,attr"`
			Bases       string `xml:"bases,attr"`
			TaxID       string `xml:"tax_id,attr"`
			Organism    string `xml:"organism,attr"`
			IDENTIFIERS struct {
				PRIMARYID  string `xml:"PRIMARY_ID"`
				EXTERNALID struct {
					Namespace string `xml:"namespace,attr"`
				} `xml:"EXTERNAL_ID"`
			} `xml:"IDENTIFIERS"`
		} `xml:"Member"`
	} `xml:"Pool"`
	RUNSET struct {
		RUN struct {
			Accession           string `xml:"accession,attr"`
			Alias               string `xml:"alias,attr"`
			TotalSpots          string `xml:"total_spots,attr"`
			TotalBases          string `xml:"total_bases,attr"`
			Size                string `xml:"size,attr"`
			LoadDone            string `xml:"load_done,attr"`
			Published           string `xml:"published,attr"`
			IsPublic            string `xml:"is_public,attr"`
			ClusterName         string `xml:"cluster_name,attr"`
			StaticDataAvailable string `xml:"static_data_available,attr"`
			IDENTIFIERS         struct {
				PRIMARYID string `xml:"PRIMARY_ID"`
			} `xml:"IDENTIFIERS"`
			EXPERIMENTREF struct {
				Accession   string `xml:"accession,attr"`
				IDENTIFIERS string `xml:"IDENTIFIERS"`
			} `xml:"EXPERIMENT_REF"`
			Pool struct {
				Member struct {
					MemberName  string `xml:"member_name,attr"`
					Accession   string `xml:"accession,attr"`
					SampleName  string `xml:"sample_name,attr"`
					SampleTitle string `xml:"sample_title,attr"`
					Spots       string `xml:"spots,attr"`
					Bases       string `xml:"bases,attr"`
					TaxID       string `xml:"tax_id,attr"`
					Organism    string `xml:"organism,attr"`
					IDENTIFIERS struct {
						PRIMARYID  string `xml:"PRIMARY_ID"`
						EXTERNALID struct {
							Namespace string `xml:"namespace,attr"`
						} `xml:"EXTERNAL_ID"`
					} `xml:"IDENTIFIERS"`
				} `xml:"Member"`
			} `xml:"Pool"`
			SRAFiles   SraFns `xml:"SRAFiles"`
			CloudFiles struct {
				CloudFile []struct {
					Filetype string `xml:"filetype,attr"`
					Provider string `xml:"provider,attr"`
					Location string `xml:"location,attr"`
				} `xml:"CloudFile"`
			} `xml:"CloudFiles"`
			Statistics struct {
				Nreads string `xml:"nreads,attr"`
				Nspots string `xml:"nspots,attr"`
				Read   []struct {
					Index   string `xml:"index,attr"`
					Count   string `xml:"count,attr"`
					Average string `xml:"average,attr"`
					Stdev   string `xml:"stdev,attr"`
				} `xml:"Read"`
			} `xml:"Statistics"`
			Databases struct {
				Database struct {
					Table struct {
						Name       string `xml:"name,attr"`
						Statistics struct {
							Source string `xml:"source,attr"`
							Rows   struct {
								Count string `xml:"count,attr"`
							} `xml:"Rows"`
							Elements struct {
								Count string `xml:"count,attr"`
							} `xml:"Elements"`
						} `xml:"Statistics"`
					} `xml:"Table"`
				} `xml:"Database"`
			} `xml:"Databases"`
			Bases struct {
				CsNative string `xml:"cs_native,attr"`
				Count    string `xml:"count,attr"`
				Base     []struct {
					Value string `xml:"value,attr"`
					Count string `xml:"count,attr"`
				} `xml:"Base"`
			} `xml:"Bases"`
		} `xml:"RUN"`
	} `xml:"RUN_SET"`
}

type ExperimentPkgJSON

type ExperimentPkgJSON struct {
	EXPERIMENT struct {
		Accession   string `json:"Accession"`
		Alias       string `json:"Alias"`
		IDENTIFIERS struct {
			PRIMARYID string `json:"PRIMARYID"`
		} `json:"IDENTIFIERS"`
		TITLE    string `json:"TITLE"`
		STUDYREF struct {
			Accession   string `json:"Accession"`
			IDENTIFIERS struct {
				PRIMARYID  string `json:"PRIMARYID"`
				EXTERNALID struct {
					Namespace string `json:"Namespace"`
				} `json:"EXTERNALID"`
			} `json:"IDENTIFIERS"`
		} `json:"STUDYREF"`
		DESIGN struct {
			DESIGNDESCRIPTION string `json:"DESIGNDESCRIPTION"`
			SAMPLEDESCRIPTOR  struct {
				Accession   string `json:"Accession"`
				IDENTIFIERS struct {
					PRIMARYID  string `json:"PRIMARYID"`
					EXTERNALID struct {
						Namespace string `json:"Namespace"`
					} `json:"EXTERNALID"`
				} `json:"IDENTIFIERS"`
			} `json:"SAMPLEDESCRIPTOR"`
			LIBRARYDESCRIPTOR struct {
				LIBRARYNAME      string `json:"LIBRARYNAME"`
				LIBRARYSTRATEGY  string `json:"LIBRARYSTRATEGY"`
				LIBRARYSOURCE    string `json:"LIBRARYSOURCE"`
				LIBRARYSELECTION string `json:"LIBRARYSELECTION"`
				LIBRARYLAYOUT    struct {
					PAIRED string `json:"PAIRED"`
				} `json:"LIBRARYLAYOUT"`
			} `json:"LIBRARYDESCRIPTOR"`
		} `json:"DESIGN"`
		PLATFORM struct {
			ILLUMINA struct {
				INSTRUMENTMODEL string `json:"INSTRUMENTMODEL"`
			} `json:"ILLUMINA"`
		} `json:"PLATFORM"`
	} `json:"EXPERIMENT"`
	SUBMISSION struct {
		LabName     string `json:"LabName"`
		CenterName  string `json:"CenterName"`
		Accession   string `json:"Accession"`
		Alias       string `json:"Alias"`
		IDENTIFIERS struct {
			PRIMARYID string `json:"PRIMARYID"`
		} `json:"IDENTIFIERS"`
	} `json:"SUBMISSION"`
	Organization struct {
		Type    string `json:"Type"`
		Name    string `json:"Name"`
		Address struct {
			PostalCode  string `json:"PostalCode"`
			Department  string `json:"Department"`
			Institution string `json:"Institution"`
			Street      string `json:"Street"`
			City        string `json:"City"`
			Country     string `json:"Country"`
		} `json:"Address"`
		Contact struct {
			Email    string `json:"Email"`
			SecEmail string `json:"SecEmail"`
			Address  struct {
				PostalCode  string `json:"PostalCode"`
				Department  string `json:"Department"`
				Institution string `json:"Institution"`
				Street      string `json:"Street"`
				City        string `json:"City"`
				Country     string `json:"Country"`
			} `json:"Address"`
			Name struct {
				First string `json:"First"`
				Last  string `json:"Last"`
			} `json:"Name"`
		} `json:"Contact"`
	} `json:"Organization"`
	STUDY struct {
		CenterName  string `json:"CenterName"`
		Alias       string `json:"Alias"`
		Accession   string `json:"Accession"`
		IDENTIFIERS struct {
			PRIMARYID  string `json:"PRIMARYID"`
			EXTERNALID struct {
				Namespace string `json:"Namespace"`
				Label     string `json:"Label"`
			} `json:"EXTERNALID"`
		} `json:"IDENTIFIERS"`
		DESCRIPTOR struct {
			STUDYTITLE string `json:"STUDYTITLE"`
			STUDYTYPE  struct {
				ExistingStudyType string `json:"ExistingStudyType"`
			} `json:"STUDYTYPE"`
			STUDYABSTRACT     string `json:"STUDYABSTRACT"`
			CENTERPROJECTNAME string `json:"CENTERPROJECTNAME"`
		} `json:"DESCRIPTOR"`
	} `json:"STUDY"`
	SAMPLE struct {
		Alias       string `json:"Alias"`
		Accession   string `json:"Accession"`
		IDENTIFIERS struct {
			PRIMARYID  string `json:"PRIMARYID"`
			EXTERNALID struct {
				Namespace string `json:"Namespace"`
			} `json:"EXTERNALID"`
		} `json:"IDENTIFIERS"`
		TITLE      string `json:"TITLE"`
		SAMPLENAME struct {
			TAXONID        string `json:"TAXONID"`
			SCIENTIFICNAME string `json:"SCIENTIFICNAME"`
		} `json:"SAMPLENAME"`
		SAMPLELINKS struct {
			SAMPLELINK struct {
				XREFLINK struct {
					DB    string `json:"DB"`
					ID    string `json:"ID"`
					LABEL string `json:"LABEL"`
				} `json:"XREFLINK"`
			} `json:"SAMPLELINK"`
		} `json:"SAMPLELINKS"`
		SAMPLEATTRIBUTES struct {
			SAMPLEATTRIBUTE []struct {
				TAG   string `json:"TAG"`
				VALUE string `json:"VALUE"`
			} `json:"SAMPLEATTRIBUTE"`
		} `json:"SAMPLEATTRIBUTES"`
	} `json:"SAMPLE"`
	Pool struct {
		Member struct {
			MemberName  string `json:"MemberName"`
			Accession   string `json:"Accession"`
			SampleName  string `json:"SampleName"`
			SampleTitle string `json:"SampleTitle"`
			Spots       string `json:"Spots"`
			Bases       string `json:"Bases"`
			TaxID       string `json:"TaxID"`
			Organism    string `json:"Organism"`
			IDENTIFIERS struct {
				PRIMARYID  string `json:"PRIMARYID"`
				EXTERNALID struct {
					Namespace string `json:"Namespace"`
				} `json:"EXTERNALID"`
			} `json:"IDENTIFIERS"`
		} `json:"Member"`
	} `json:"Pool"`
	RUNSET struct {
		RUN struct {
			Accession           string `json:"Accession"`
			Alias               string `json:"Alias"`
			TotalSpots          string `json:"TotalSpots"`
			TotalBases          string `json:"TotalBases"`
			Size                string `json:"Size"`
			LoadDone            string `json:"LoadDone"`
			Published           string `json:"Published"`
			IsPublic            string `json:"IsPublic"`
			ClusterName         string `json:"ClusterName"`
			StaticDataAvailable string `json:"StaticDataAvailable"`
			IDENTIFIERS         struct {
				PRIMARYID string `json:"PRIMARYID"`
			} `json:"IDENTIFIERS"`
			EXPERIMENTREF struct {
				Accession   string `json:"Accession"`
				IDENTIFIERS string `json:"IDENTIFIERS"`
			} `json:"EXPERIMENTREF"`
			Pool struct {
				Member struct {
					MemberName  string `json:"MemberName"`
					Accession   string `json:"Accession"`
					SampleName  string `json:"SampleName"`
					SampleTitle string `json:"SampleTitle"`
					Spots       string `json:"Spots"`
					Bases       string `json:"Bases"`
					TaxID       string `json:"TaxID"`
					Organism    string `json:"Organism"`
					IDENTIFIERS struct {
						PRIMARYID  string `json:"PRIMARYID"`
						EXTERNALID struct {
							Namespace string `json:"Namespace"`
						} `json:"EXTERNALID"`
					} `json:"IDENTIFIERS"`
				} `json:"Member"`
			} `json:"Pool"`
			SRAFiles struct {
				SRAFile SRAFileJSON `json:"SRAFile"`
			} `json:"SRAFiles"`
			CloudFiles struct {
				CloudFile []struct {
					Filetype string `json:"Filetype"`
					Provider string `json:"Provider"`
					Location string `json:"Location"`
				} `json:"CloudFile"`
			} `json:"CloudFiles"`
			Statistics struct {
				Nreads string `json:"Nreads"`
				Nspots string `json:"Nspots"`
				Read   []struct {
					Index   string `json:"Index"`
					Count   string `json:"Count"`
					Average string `json:"Average"`
					Stdev   string `json:"Stdev"`
				} `json:"Read"`
			} `json:"Statistics"`
			Databases struct {
				Database struct {
					Table struct {
						Name       string `json:"Name"`
						Statistics struct {
							Source string `json:"Source"`
							Rows   struct {
								Count string `json:"Count"`
							} `json:"Rows"`
							Elements struct {
								Count string `json:"Count"`
							} `json:"Elements"`
						} `json:"Statistics"`
					} `json:"Table"`
				} `json:"Database"`
			} `json:"Databases"`
			Bases struct {
				CsNative string `json:"CsNative"`
				Count    string `json:"Count"`
				Base     []struct {
					Value string `json:"Value"`
					Count string `json:"Count"`
				} `json:"Base"`
			} `json:"Bases"`
		} `json:"RUN"`
	} `json:"RUNSET"`
}

type MedlineCitationJson

type MedlineCitationJson struct {
	Status string `json:"Status"`
	Owner  string `json:"Owner"`
	PMID   struct {
		Text    string `json:"Text"`
		Version string `json:"Version"`
	} `json:"PMID"`
	DateRevised struct {
		Year  string `json:"Year"`
		Month string `json:"Month"`
		Day   string `json:"Day"`
	} `json:"DateRevised"`
	Article struct {
		PubModel string `json:"PubModel"`
		Journal  struct {
			ISSN struct {
				Text     string `json:"Text"`
				IssnType string `json:"IssnType"`
			} `json:"ISSN"`
			JournalIssue struct {
				CitedMedium string `json:"CitedMedium"`
				Volume      string `json:"Volume"`
				Issue       string `json:"Issue"`
				PubDate     struct {
					Year  string `json:"Year"`
					Month string `json:"Month"`
				} `json:"PubDate"`
			} `json:"JournalIssue"`
			Title           string `json:"Title"`
			ISOAbbreviation string `json:"ISOAbbreviation"`
		} `json:"Journal"`
		ArticleTitle struct {
			Text string   `json:"Text"`
			I    []string `json:"I"`
			Sup  string   `json:"Sup"`
		} `json:"ArticleTitle"`
		Pagination struct {
			MedlinePgn string `json:"MedlinePgn"`
		} `json:"Pagination"`
		ELocationID struct {
			Text    string `json:"Text"`
			EIDType string `json:"EIdType"`
			ValidYN string `json:"ValidYN"`
		} `json:"ELocationID"`
		Abstract struct {
			AbstractText struct {
				Text string      `json:"Text"`
				I    []string    `json:"I"`
				B    string      `json:"B"`
				Sub  string      `json:"Sub"`
				Sup  interface{} `json:"Sup"`
			} `json:"AbstractText"`
		} `json:"Abstract"`
		AuthorList struct {
			CompleteYN string `json:"CompleteYN"`
			Author     []struct {
				ValidYN         string `json:"ValidYN"`
				LastName        string `json:"LastName"`
				ForeName        string `json:"ForeName"`
				Initials        string `json:"Initials"`
				AffiliationInfo []struct {
					Affiliation string `json:"Affiliation"`
				} `json:"AffiliationInfo"`
				Identifier struct {
					Text   string `json:"Text"`
					Source string `json:"Source"`
				} `json:"Identifier"`
			} `json:"Author"`
		} `json:"AuthorList"`
		Language  string `json:"Language"`
		GrantList struct {
			CompleteYN string `json:"CompleteYN"`
			Grant      []struct {
				GrantID string `json:"GrantID"`
				Acronym string `json:"Acronym"`
				Agency  string `json:"Agency"`
				Country string `json:"Country"`
			} `json:"Grant"`
		} `json:"GrantList"`
		PublicationTypeList struct {
			PublicationType []struct {
				Text string `json:"Text"`
				UI   string `json:"UI"`
			} `json:"PublicationType"`
		} `json:"PublicationTypeList"`
		ArticleDate struct {
			DateType string `json:"DateType"`
			Year     string `json:"Year"`
			Month    string `json:"Month"`
			Day      string `json:"Day"`
		} `json:"ArticleDate"`
	} `json:"Article"`
	MedlineJournalInfo struct {
		Country     string `json:"Country"`
		MedlineTA   string `json:"MedlineTA"`
		NlmUniqueID string `json:"NlmUniqueID"`
		ISSNLinking string `json:"ISSNLinking"`
	} `json:"MedlineJournalInfo"`
	CitationSubset string `json:"CitationSubset"`
	KeywordList    struct {
		Owner   string `json:"Owner"`
		Keyword []struct {
			Text         string `json:"Text"`
			MajorTopicYN string `json:"MajorTopicYN"`
		} `json:"Keyword"`
	} `json:"KeywordList"`
}

type PubmedArticle

type PubmedArticle struct {
	MedlineCitation struct {
		Status string `xml:"Status,attr"`
		Owner  string `xml:"Owner,attr"`
		PMID   struct {
			Text    string `xml:",chardata"`
			Version string `xml:"Version,attr"`
		} `xml:"PMID"`
		DateRevised struct {
			Year  string `xml:"Year"`
			Month string `xml:"Month"`
			Day   string `xml:"Day"`
		} `xml:"DateRevised"`
		Article struct {
			PubModel string `xml:"PubModel,attr"`
			Journal  struct {
				ISSN struct {
					Text     string `xml:",chardata"`
					IssnType string `xml:"IssnType,attr"`
				} `xml:"ISSN"`
				JournalIssue struct {
					CitedMedium string `xml:"CitedMedium,attr"`
					Volume      string `xml:"Volume"`
					Issue       string `xml:"Issue"`
					PubDate     struct {
						Year  string `xml:"Year"`
						Month string `xml:"Month"`
					} `xml:"PubDate"`
				} `xml:"JournalIssue"`
				Title           string `xml:"Title"`
				ISOAbbreviation string `xml:"ISOAbbreviation"`
			} `xml:"Journal"`
			ArticleTitle struct {
				Text string   `xml:",chardata"`
				I    []string `xml:"i"`
				Sup  string   `xml:"sup"`
			} `xml:"ArticleTitle"`
			Pagination struct {
				MedlinePgn string `xml:"MedlinePgn"`
			} `xml:"Pagination"`
			ELocationID struct {
				Text    string `xml:",chardata"`
				EIdType string `xml:"EIdType,attr"`
				ValidYN string `xml:"ValidYN,attr"`
			} `xml:"ELocationID"`
			Abstract struct {
				AbstractText struct {
					Text string   `xml:",chardata"`
					I    []string `xml:"i"`
					B    string   `xml:"b"`
					Sub  string   `xml:"sub"`
					Sup  []string `xml:"sup"`
				} `xml:"AbstractText"`
			} `xml:"Abstract"`
			AuthorList struct {
				CompleteYN string `xml:"CompleteYN,attr"`
				Author     []struct {
					ValidYN         string `xml:"ValidYN,attr"`
					LastName        string `xml:"LastName"`
					ForeName        string `xml:"ForeName"`
					Initials        string `xml:"Initials"`
					AffiliationInfo []struct {
						Affiliation string `xml:"Affiliation"`
					} `xml:"AffiliationInfo"`
					Identifier struct {
						Text   string `xml:",chardata"`
						Source string `xml:"Source,attr"`
					} `xml:"Identifier"`
				} `xml:"Author"`
			} `xml:"AuthorList"`
			Language  string `xml:"Language"`
			GrantList struct {
				CompleteYN string `xml:"CompleteYN,attr"`
				Grant      []struct {
					GrantID string `xml:"GrantID"`
					Acronym string `xml:"Acronym"`
					Agency  string `xml:"Agency"`
					Country string `xml:"Country"`
				} `xml:"Grant"`
			} `xml:"GrantList"`
			PublicationTypeList struct {
				PublicationType []struct {
					Text string `xml:",chardata"`
					UI   string `xml:"UI,attr"`
				} `xml:"PublicationType"`
			} `xml:"PublicationTypeList"`
			ArticleDate struct {
				DateType string `xml:"DateType,attr"`
				Year     string `xml:"Year"`
				Month    string `xml:"Month"`
				Day      string `xml:"Day"`
			} `xml:"ArticleDate"`
		} `xml:"Article"`
		MedlineJournalInfo struct {
			Country     string `xml:"Country"`
			MedlineTA   string `xml:"MedlineTA"`
			NlmUniqueID string `xml:"NlmUniqueID"`
			ISSNLinking string `xml:"ISSNLinking"`
		} `xml:"MedlineJournalInfo"`
		CitationSubset string `xml:"CitationSubset"`
		KeywordList    struct {
			Owner   string `xml:"Owner,attr"`
			Keyword []struct {
				Text         string `xml:",chardata"`
				MajorTopicYN string `xml:"MajorTopicYN,attr"`
			} `xml:"Keyword"`
		} `xml:"KeywordList"`
	} `xml:"MedlineCitation"`
	PubmedData struct {
		History struct {
			PubMedPubDate []struct {
				PubStatus string `xml:"PubStatus,attr"`
				Year      string `xml:"Year"`
				Month     string `xml:"Month"`
				Day       string `xml:"Day"`
				Hour      string `xml:"Hour"`
				Minute    string `xml:"Minute"`
			} `xml:"PubMedPubDate"`
		} `xml:"History"`
		PublicationStatus string `xml:"PublicationStatus"`
		ArticleIdList     struct {
			ArticleId []ArticleId `xml:"ArticleId"`
		} `xml:"ArticleIdList"`
		ReferenceList struct {
			Reference struct {
				Citation      string `xml:"Citation"`
				ArticleIdList struct {
					ArticleId struct {
						Text   string `xml:",chardata"`
						IdType string `xml:"IdType,attr"`
					} `xml:"ArticleId"`
				} `xml:"ArticleIdList"`
			} `xml:"Reference"`
		} `xml:"ReferenceList"`
	} `xml:"PubmedData"`
}

type PubmedArticleJSON

type PubmedArticleJSON struct {
	MedlineCitation MedlineCitationJson `json:"MedlineCitation"`
	PubmedData      PubmedDataJSON      `json:"PubmedData"`
}

type PubmedArticleSet

type PubmedArticleSet struct {
	XMLName       xml.Name        `xml:"PubmedArticleSet"`
	PubmedArticle []PubmedArticle `xml:"PubmedArticle"`
}

type PubmedDataJSON

type PubmedDataJSON struct {
	History struct {
		PubMedPubDate []struct {
			PubStatus string `json:"PubStatus"`
			Year      string `json:"Year"`
			Month     string `json:"Month"`
			Day       string `json:"Day"`
			Hour      string `json:"Hour"`
			Minute    string `json:"Minute"`
		} `json:"PubMedPubDate"`
	} `json:"History"`
	PublicationStatus string `json:"PublicationStatus"`
	ArticleIDList     struct {
		ArticleID []struct {
			Text   string `json:"Text"`
			IDType string `json:"IdType"`
		} `json:"ArticleId"`
	} `json:"ArticleIdList"`
	ReferenceList struct {
		Reference struct {
			Citation      string `json:"Citation"`
			ArticleIDList struct {
				ArticleID struct {
					Text   string `json:"Text"`
					IDType string `json:"IdType"`
				} `json:"ArticleId"`
			} `json:"ArticleIdList"`
		} `json:"Reference"`
	} `json:"ReferenceList"`
}

type SRAFile

type SRAFile struct {
	Cluster      string `xml:"cluster,attr"`
	Filename     string `xml:"filename,attr"`
	URL          string `xml:"url,attr"`
	Size         string `xml:"size,attr"`
	Date         string `xml:"date,attr"`
	Md5          string `xml:"md5,attr"`
	SemanticName string `xml:"semantic_name,attr"`
	Supertype    string `xml:"supertype,attr"`
	Sratoolkit   string `xml:"sratoolkit,attr"`
	Alternatives []struct {
		URL        string `xml:"url,attr"`
		FreeEgress string `xml:"free_egress,attr"`
		AccessType string `xml:"access_type,attr"`
		Org        string `xml:"org,attr"`
	} `xml:"Alternatives"`
}

type SRAFileJSON

type SRAFileJSON struct {
	Cluster      string `json:"Cluster"`
	Filename     string `json:"Filename"`
	URL          string `json:"URL"`
	Size         string `json:"Size"`
	Date         string `json:"Date"`
	Md5          string `json:"Md5"`
	SemanticName string `json:"SemanticName"`
	Supertype    string `json:"Supertype"`
	Sratoolkit   string `json:"Sratoolkit"`
	Alternatives []struct {
		URL        string `json:"URL"`
		FreeEgress string `json:"FreeEgress"`
		AccessType string `json:"AccessType"`
		Org        string `json:"Org"`
	} `json:"Alternatives"`
}

type SraFns

type SraFns struct {
	SRAFile SRAFile `xml:"SRAFile"`
}

type SraSets

type SraSets struct {
	XMLName           xml.Name        `xml:"EXPERIMENT_PACKAGE_SET"`
	EXPERIMENTPACKAGE []ExperimentPkg `xml:"EXPERIMENT_PACKAGE"`
}

SraSets defines extracted Sra fields

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