SYMBOL INDEX (324 symbols across 13 files)

FILE: pysradb/cli.py
  class CustomFormatterArgP (line 33) | class CustomFormatterArgP(
  class ArgParser (line 39) | class ArgParser(argparse.ArgumentParser):
    method error (line 40) | def error(self, message):
  function pretty_print_df (line 46) | def pretty_print_df(df, include_header=True):
  function _create_table (line 92) | def _create_table(df, terminal_width, include_header, format_value):
  function _print_save_df (line 149) | def _print_save_df(df, saveto=None):
  function metadata (line 189) | def metadata(
  function download (line 248) | def download(
  function search (line 299) | def search(saveto, db, verbosity, return_max, fields):
  function get_geo_search_info (line 370) | def get_geo_search_info():
  function gse_to_gsm (line 385) | def gse_to_gsm(gse_ids, saveto, detailed, desc, expand):
  function gse_to_srp (line 400) | def gse_to_srp(gse_ids, saveto, detailed, desc, expand):
  function gsm_to_gse (line 415) | def gsm_to_gse(gsm_ids, saveto, detailed, desc, expand):
  function gsm_to_srp (line 430) | def gsm_to_srp(gsm_ids, saveto, detailed, desc, expand):
  function gsm_to_srr (line 445) | def gsm_to_srr(gsm_ids, saveto, detailed, desc, expand):
  function gsm_to_srs (line 460) | def gsm_to_srs(gsm_ids, saveto, detailed, desc, expand):
  function gsm_to_srx (line 475) | def gsm_to_srx(gsm_ids, saveto, detailed, desc, expand):
  function srp_to_gse (line 490) | def srp_to_gse(srp_id, saveto, detailed, desc, expand):
  function srp_to_srr (line 505) | def srp_to_srr(srp_id, saveto, detailed, desc, expand):
  function srp_to_srs (line 520) | def srp_to_srs(srp_id, saveto, detailed, desc, expand):
  function srp_to_srx (line 535) | def srp_to_srx(srp_id, saveto, detailed, desc, expand):
  function srr_to_gsm (line 550) | def srr_to_gsm(srr_ids, saveto, detailed, desc, expand):
  function srr_to_srp (line 565) | def srr_to_srp(srr_ids, saveto, detailed, desc, expand):
  function srr_to_srs (line 580) | def srr_to_srs(srr_ids, saveto, detailed, desc, expand):
  function srr_to_srx (line 595) | def srr_to_srx(srr_ids, saveto, detailed, desc, expand):
  function srs_to_gsm (line 610) | def srs_to_gsm(srs_ids, saveto, detailed, desc, expand):
  function srs_to_srx (line 625) | def srs_to_srx(srs_ids, saveto, detailed, desc, expand):
  function srx_to_srp (line 640) | def srx_to_srp(srx_ids, saveto, detailed, desc, expand):
  function srx_to_srr (line 655) | def srx_to_srr(srx_ids, saveto, detailed, desc, expand):
  function srx_to_srs (line 670) | def srx_to_srs(srx_ids, saveto, detailed, desc, expand):
  function srp_to_pmid (line 681) | def srp_to_pmid(srp_ids, saveto):
  function sra_to_pmid (line 687) | def sra_to_pmid(sra_ids, saveto):
  function gse_to_pmid (line 694) | def gse_to_pmid(gse_ids, saveto):
  function pmid_to_gse (line 700) | def pmid_to_gse(pmid_ids, saveto):
  function pmid_to_srp (line 706) | def pmid_to_srp(pmid_ids, saveto):
  function pmc_to_identifiers (line 712) | def pmc_to_identifiers(pmc_ids, saveto):
  function pmid_to_identifiers (line 718) | def pmid_to_identifiers(pmid_ids, saveto):
  function doi_to_gse (line 724) | def doi_to_gse(doi_ids, saveto):
  function doi_to_srp (line 730) | def doi_to_srp(doi_ids, saveto):
  function doi_to_identifiers (line 736) | def doi_to_identifiers(doi_ids, saveto):
  function geo_matrix (line 746) | def geo_matrix(accession, to_tsv, output_dir):
  function parse_args (line 765) | def parse_args(args=None):

FILE: pysradb/download.py
  function _get_ftp_file_size (line 24) | def _get_ftp_file_size(url):
  function _download_ftp_file (line 48) | def _download_ftp_file(
  function millify (line 120) | def millify(n):
  function get_file_size (line 145) | def get_file_size(row, url_col):
  function md5_validate_file (line 192) | def md5_validate_file(file_path, md5_hash):
  function download_file (line 218) | def download_file(

FILE: pysradb/exceptions.py
  class MissingQueryException (line 4) | class MissingQueryException(Exception):
    method __init__ (line 13) | def __init__(self):
  class IncorrectFieldException (line 23) | class IncorrectFieldException(Exception):

FILE: pysradb/filter_attrs.py
  function _get_sample_attr_keys (line 8) | def _get_sample_attr_keys(sample_attribute):
  function expand_sample_attribute_columns (line 60) | def expand_sample_attribute_columns(metadata_df):
  function guess_cell_type (line 123) | def guess_cell_type(sample_attribute):
  function guess_tissue_type (line 163) | def guess_tissue_type(sample_attribute):
  function guess_strain_type (line 189) | def guess_strain_type(sample_attribute):

FILE: pysradb/geoweb.py
  class GEOweb (line 21) | class GEOweb(object):
    method __init__ (line 22) | def __init__(self):
    method get_download_links (line 25) | def get_download_links(self, gse):
    method download (line 62) | def download(self, links, root_url, gse, verbose=False, out_dir=None):
  function download_geo_matrix (line 111) | def download_geo_matrix(accession, output_dir="."):
  function parse_geo_matrix_to_tsv (line 141) | def parse_geo_matrix_to_tsv(input_file, output_file):

FILE: pysradb/metadata_enrichment.py
  function _prompt_install_enrichment_dependencies (line 19) | def _prompt_install_enrichment_dependencies() -> bool:
  class MetadataExtractor (line 60) | class MetadataExtractor(ABC):
    method __init__ (line 63) | def __init__(self):
    method extract_metadata (line 67) | def extract_metadata(
    method extract_batch (line 82) | def extract_batch(
    method _find_column_variant (line 97) | def _find_column_variant(self, df: pd.DataFrame, target_col: str) -> O...
    method enrich_dataframe (line 121) | def enrich_dataframe(
  class _MetadataExtraction (line 211) | class _MetadataExtraction(BaseModel):
  function load_ontology_reference (line 256) | def load_ontology_reference() -> Dict[str, List[str]]:
  class LLMMetadataExtractor (line 279) | class LLMMetadataExtractor(MetadataExtractor):
    method __init__ (line 282) | def __init__(
    method _provider_env_key (line 305) | def _provider_env_key(self) -> Optional[str]:
    method _check_ollama_available (line 319) | def _check_ollama_available(self) -> bool:
    method _initialize_client (line 346) | def _initialize_client(self):
    method _create_extraction_prompt (line 381) | def _create_extraction_prompt(
    method _call_llm (line 486) | def _call_llm(self, prompt: str) -> Dict[str, Any]:
    method extract_metadata (line 507) | def extract_metadata(
  class EmbeddingMetadataExtractor (line 542) | class EmbeddingMetadataExtractor(MetadataExtractor):
    method __init__ (line 545) | def __init__(
    method _load_model (line 578) | def _load_model(self):
    method _get_cache_path (line 611) | def _get_cache_path(self) -> str:
    method _compute_reference_embeddings (line 625) | def _compute_reference_embeddings(self) -> Dict[str, Any]:
    method _find_best_match (line 660) | def _find_best_match(
    method _parse_structured_fields (line 682) | def _parse_structured_fields(self, text: str) -> Dict[str, str]:
    method _match_value_or_text (line 704) | def _match_value_or_text(
    method extract_metadata (line 751) | def extract_metadata(
  function create_metadata_extractor (line 826) | def create_metadata_extractor(
  function apply_dataframe_enrichment (line 865) | def apply_dataframe_enrichment(

FILE: pysradb/search.py
  class QuerySearch (line 22) | class QuerySearch:
    method __init__ (line 94) | def __init__(
    method _input_multi_regex_checker (line 171) | def _input_multi_regex_checker(self, regex_matcher, input_query, error...
    method _validate_fields (line 218) | def _validate_fields(self):
    method _list_stat (line 451) | def _list_stat(self, stat_header):
    method show_result_statistics (line 461) | def show_result_statistics(self):
    method visualise_results (line 494) | def visualise_results(
    method search (line 576) | def search(self):
    method get_df (line 579) | def get_df(self):
    method get_plot_objects (line 583) | def get_plot_objects(self):
    method _plot_graph (line 587) | def _plot_graph(self, plt, axes, show, savedir, too_many_organisms):
  class SraSearch (line 681) | class SraSearch(QuerySearch):
    method __init__ (line 718) | def __init__(
    method search (line 755) | def search(self):
    method get_uids (line 803) | def get_uids(self):
    method _format_query_string (line 811) | def _format_query_string(self):
    method _format_request (line 840) | def _format_request(self):
    method _format_response (line 849) | def _format_response(self, content):
    method _format_result (line 870) | def _format_result(self):
    method _parse_entry (line 931) | def _parse_entry(self, entry_root):
    method _update_entry (line 1096) | def _update_entry(self, field_name, field_content):
    method _update_stats (line 1122) | def _update_stats(self):
    method _merge_selected_columns (line 1204) | def _merge_selected_columns(self, regex):
  class EnaSearch (line 1217) | class EnaSearch(QuerySearch):
    method search (line 1252) | def search(self):
    method _format_query_string (line 1277) | def _format_query_string(self):
    method _format_request (line 1342) | def _format_request(self):
    method _format_result (line 1381) | def _format_result(self, content):
    method _update_stats (line 1421) | def _update_stats(self):
  class GeoSearch (line 1499) | class GeoSearch(SraSearch):
    method __init__ (line 1537) | def __init__(
    method _format_geo_query_string (line 1620) | def _format_geo_query_string(self):
    method _format_geo_request (line 1637) | def _format_geo_request(self):
    method _format_request (line 1647) | def _format_request(self):
    method search (line 1660) | def search(self):
    method _combine_uids (line 1749) | def _combine_uids(self, uids_from_sra, uids_from_geo):
    method info (line 1769) | def info(cls):

FILE: pysradb/sraweb.py
  function xmlescape (line 23) | def xmlescape(data):
  function _make_hashable (line 27) | def _make_hashable(obj):
  function _order_first (line 45) | def _order_first(df, column_order_list):
  function _retry_response (line 59) | def _retry_response(base_url, payload, key, max_retries=10):
  function get_retmax (line 74) | def get_retmax(n_records, retmax=500):
  class SRAweb (line 80) | class SRAweb(object):
    method __init__ (line 81) | def __init__(self, api_key=None):
    method format_xml (line 131) | def format_xml(string):
    method xml_to_json (line 147) | def xml_to_json(xml):
    method bioproject_to_srp (line 169) | def bioproject_to_srp(self, bioproject):
    method fetch_ena_fastq (line 236) | def fetch_ena_fastq(self, srp):
    method create_esummary_params (line 321) | def create_esummary_params(self, esearchresult, db="sra"):
    method get_esummary_response (line 339) | def get_esummary_response(self, db, term, usehistory="y"):
    method get_efetch_response (line 411) | def get_efetch_response(self, db, term, usehistory="y"):
    method sra_metadata (line 495) | def sra_metadata(
    method fetch_gds_results (line 936) | def fetch_gds_results(self, gse, **kwargs):
    method fetch_gsm_soft (line 972) | def fetch_gsm_soft(self, gsm_ids):
    method geo_metadata (line 1039) | def geo_metadata(
    method metadata (line 1465) | def metadata(self, accession, **kwargs):
    method gse_to_gsm (line 1506) | def gse_to_gsm(self, gse, **kwargs):
    method gse_to_srp (line 1536) | def gse_to_srp(self, gse, **kwargs):
    method gsm_to_srp (line 1604) | def gsm_to_srp(self, gsm, **kwargs):
    method gsm_to_srr (line 1612) | def gsm_to_srr(self, gsm, **kwargs):
    method gsm_to_srs (line 1627) | def gsm_to_srs(self, gsm, **kwargs):
    method gsm_to_srx (line 1641) | def gsm_to_srx(self, gsm, **kwargs):
    method gsm_to_gse (line 1652) | def gsm_to_gse(self, gsm, **kwargs):
    method srp_to_gse (line 1697) | def srp_to_gse(self, srp, **kwargs):
    method srp_to_srr (line 1722) | def srp_to_srr(self, srp, **kwargs):
    method srp_to_srs (line 1727) | def srp_to_srs(self, srp, **kwargs):
    method srp_to_srx (line 1732) | def srp_to_srx(self, srp, **kwargs):
    method srr_to_gsm (line 1738) | def srr_to_gsm(self, srr, **kwargs):
    method srr_to_srp (line 1758) | def srr_to_srp(self, srr, **kwargs):
    method srr_to_srs (line 1768) | def srr_to_srs(self, srr, **kwargs):
    method srr_to_srx (line 1776) | def srr_to_srx(self, srr, **kwargs):
    method srs_to_gsm (line 1784) | def srs_to_gsm(self, srs, **kwargs):
    method srx_to_gsm (line 1795) | def srx_to_gsm(self, srx, **kwargs):
    method srs_to_srx (line 1805) | def srs_to_srx(self, srs, **kwargs):
    method srx_to_srp (line 1810) | def srx_to_srp(self, srx, **kwargs):
    method srx_to_srr (line 1815) | def srx_to_srr(self, srx, **kwargs):
    method srx_to_srs (line 1820) | def srx_to_srs(self, srx, **kwargs):
    method search (line 1825) | def search(self, *args, **kwargs):
    method fetch_bioproject_pmids (line 1828) | def fetch_bioproject_pmids(self, bioprojects):
    method srp_to_pmid (line 1912) | def srp_to_pmid(self, srp_accessions):
    method _search_fallback_pmids (line 1965) | def _search_fallback_pmids(self, srp_accessions):
    method _extract_sra_accession (line 2000) | def _extract_sra_accession(self, row):
    method _get_smallest_pmid (line 2010) | def _get_smallest_pmid(self, pmids):
    method extract_external_sources (line 2025) | def extract_external_sources(self, metadata_df):
    method _search_gse_gsm_pmids (line 2064) | def _search_gse_gsm_pmids(self, metadata_df, sra_accessions):
    method _bioproject_to_gse (line 2128) | def _bioproject_to_gse(self, bioproject):
    method _srp_to_gse_via_elink (line 2187) | def _srp_to_gse_via_elink(self, srp_id):
    method _search_pmc_by_bioproject (line 2270) | def _search_pmc_by_bioproject(self, bioproject_id):
    method search_pmc_for_external_sources (line 2337) | def search_pmc_for_external_sources(self, external_sources):
    method sra_to_pmid (line 2411) | def sra_to_pmid(self, sra_accessions):
    method srr_to_pmid (line 2437) | def srr_to_pmid(self, srr):
    method srx_to_pmid (line 2441) | def srx_to_pmid(self, srx):
    method srs_to_pmid (line 2445) | def srs_to_pmid(self, srs):
    method gse_to_pmid (line 2449) | def gse_to_pmid(self, gse_accessions):
    method doi_to_pmid (line 2479) | def doi_to_pmid(self, dois):
    method pmid_to_pmc (line 2529) | def pmid_to_pmc(self, pmids):
    method fetch_pmc_fulltext (line 2579) | def fetch_pmc_fulltext(self, pmc_id):
    method extract_identifiers_from_text (line 2610) | def extract_identifiers_from_text(self, text):
    method pmc_to_identifiers (line 2651) | def pmc_to_identifiers(self, pmc_ids, convert_missing=True):
    method pmid_to_identifiers (line 2802) | def pmid_to_identifiers(self, pmids):
    method pmid_to_gse (line 2873) | def pmid_to_gse(self, pmids):
    method pmid_to_srp (line 2889) | def pmid_to_srp(self, pmids):
    method doi_to_identifiers (line 2905) | def doi_to_identifiers(self, dois):
    method doi_to_gse (line 2976) | def doi_to_gse(self, dois):
    method doi_to_srp (line 2992) | def doi_to_srp(self, dois):

FILE: pysradb/utils.py
  function path_leaf (line 26) | def path_leaf(path):
  function requests_3_retries (line 43) | def requests_3_retries():
  function scientific_name_to_taxid (line 64) | def scientific_name_to_taxid(name):
  function unique (line 110) | def unique(sequence):
  class TqdmUpTo (line 126) | class TqdmUpTo(tqdm):
    method update_to (line 136) | def update_to(self, b=1, bsize=1, tsize=None):
  function _extract_first_field (line 150) | def _extract_first_field(data):
  function _find_aspera_keypath (line 155) | def _find_aspera_keypath(aspera_dir=None):
  function mkdir_p (line 177) | def mkdir_p(path):
  function order_dataframe (line 195) | def order_dataframe(df, columns):
  function _get_url (line 212) | def _get_url(url, download_to, show_progress=True):
  function run_command (line 237) | def run_command(command, verbose=False):
  function get_gzip_uncompressed_size (line 255) | def get_gzip_uncompressed_size(filepath):
  function confirm (line 272) | def confirm(preceeding_text):
  function copyfileobj (line 295) | def copyfileobj(fsrc, fdst, bufsize=16384, filesize=None, desc=""):

FILE: tests/test_geoweb.py
  function geoweb_connection (line 13) | def geoweb_connection():
  function test_valid_download_links (line 19) | def test_valid_download_links(geoweb_connection):
  function test_invalid_download_links (line 25) | def test_invalid_download_links(geoweb_connection):
  function test_file_download (line 31) | def test_file_download(geoweb_connection):

FILE: tests/test_search.py
  function valid_search_inputs_1 (line 25) | def valid_search_inputs_1():
  function valid_search_inputs_2 (line 224) | def valid_search_inputs_2():
  function valid_search_inputs_geo (line 343) | def valid_search_inputs_geo():
  function empty_search_inputs (line 499) | def empty_search_inputs():
  function empty_search_inputs_geo (line 523) | def empty_search_inputs_geo():
  function invalid_search_inputs (line 550) | def invalid_search_inputs():
  function sra_response_xml_1 (line 781) | def sra_response_xml_1():
  function sra_formatted_responses_1 (line 786) | def sra_formatted_responses_1():
  function sra_response_xml_2 (line 812) | def sra_response_xml_2():
  function sra_formatted_responses_2 (line 817) | def sra_formatted_responses_2():
  function sra_uids (line 843) | def sra_uids():
  function ena_responses_json (line 850) | def ena_responses_json():
  function ena_formatted_responses (line 859) | def ena_formatted_responses():
  function missing_query_test (line 887) | def missing_query_test(empty_search_inputs):
  function test_invalid_search_query (line 893) | def test_invalid_search_query(invalid_search_inputs):
  function test_sra_search_1 (line 919) | def test_sra_search_1():
  function test_sra_uids (line 930) | def test_sra_uids(sra_uids):
  function test_valid_search_query_1_sra (line 938) | def test_valid_search_query_1_sra(valid_search_inputs_1):
  function test_valid_search_query_2_sra (line 960) | def test_valid_search_query_2_sra(valid_search_inputs_2):
  function test_sra_search_format_request (line 982) | def test_sra_search_format_request():
  function test_sra_search_format_result_1 (line 995) | def test_sra_search_format_result_1(sra_response_xml_1, sra_formatted_re...
  function test_sra_search_format_result_2 (line 1023) | def test_sra_search_format_result_2(sra_response_xml_2, sra_formatted_re...
  function _test_ena_search_1 (line 1049) | def _test_ena_search_1():
  function _test_ena_search_2 (line 1061) | def _test_ena_search_2(capsys):
  function _test_ena_search_3 (line 1068) | def _test_ena_search_3(capsys):
  function _test_valid_search_query_1_ena (line 1076) | def _test_valid_search_query_1_ena(valid_search_inputs_1):
  function _test_valid_search_query_2_ena (line 1104) | def _test_valid_search_query_2_ena(valid_search_inputs_2):
  function test_ena_search_format_request (line 1134) | def test_ena_search_format_request():
  function test_ena_search_format_result (line 1153) | def test_ena_search_format_result(ena_responses_json, ena_formatted_resp...
  function missing_query_test_geo (line 1171) | def missing_query_test_geo(empty_search_inputs_geo):
  function test_geo_search_1 (line 1177) | def test_geo_search_1():
  function test_valid_search_query_geo (line 1191) | def test_valid_search_query_geo(valid_search_inputs_geo):
  function test_geo_search_format_request (line 1219) | def test_geo_search_format_request():
  function test_geo_info (line 1232) | def test_geo_info():

FILE: tests/test_sraweb.py
  function sraweb_connection (line 12) | def sraweb_connection():
  function test_sra_metadata (line 18) | def test_sra_metadata(sraweb_connection):
  function test_sra_metadata_missing_orgname (line 24) | def test_sra_metadata_missing_orgname(sraweb_connection):
  function test_sra_metadata_multiple (line 31) | def test_sra_metadata_multiple(sraweb_connection):
  function test_sra_metadata_multiple_detailed (line 41) | def test_sra_metadata_multiple_detailed(sraweb_connection):
  function test_tissue_column (line 57) | def test_tissue_column(sraweb_connection):
  function test_metadata_exp_accession (line 63) | def test_metadata_exp_accession(sraweb_connection):
  function test_fetch_gds_results (line 69) | def test_fetch_gds_results(sraweb_connection):
  function test_srp_to_gse (line 75) | def test_srp_to_gse(sraweb_connection):
  function test_srp_to_srr (line 81) | def test_srp_to_srr(sraweb_connection):
  function test_srp_to_srs (line 93) | def test_srp_to_srs(sraweb_connection):
  function test_srp_to_srx (line 106) | def test_srp_to_srx(sraweb_connection):
  function test_gse_to_gsm (line 112) | def test_gse_to_gsm(sraweb_connection):
  function test_gse_to_gsm2 (line 118) | def test_gse_to_gsm2(sraweb_connection):
  function test_gse_to_gsm1 (line 124) | def test_gse_to_gsm1(sraweb_connection):
  function test_gse_to_srp (line 130) | def test_gse_to_srp(sraweb_connection):
  function test_gse_to_srp2 (line 136) | def test_gse_to_srp2(sraweb_connection):
  function test_gse_to_srp_with_nan_sra (line 143) | def test_gse_to_srp_with_nan_sra(sraweb_connection):
  function test_gsm_to_srp (line 159) | def test_gsm_to_srp(sraweb_connection):
  function test_gsm_to_gse (line 165) | def test_gsm_to_gse(sraweb_connection):
  function test_gsm_to_gse_multiple_gses (line 171) | def test_gsm_to_gse_multiple_gses(sraweb_connection):
  function test_gsm_to_srr (line 190) | def test_gsm_to_srr(sraweb_connection):
  function test_gsm_to_srs (line 196) | def test_gsm_to_srs(sraweb_connection):
  function test_gsm_to_srx (line 202) | def test_gsm_to_srx(sraweb_connection):
  function test_srr_to_gsm (line 208) | def test_srr_to_gsm(sraweb_connection):
  function test_srr_to_srp (line 213) | def test_srr_to_srp(sraweb_connection):
  function test_srr_to_srp1 (line 219) | def test_srr_to_srp1(sraweb_connection):
  function test_srr_to_srs (line 225) | def test_srr_to_srs(sraweb_connection):
  function test_srr_to_srx (line 231) | def test_srr_to_srx(sraweb_connection):
  function test_srs_to_gsm (line 237) | def test_srs_to_gsm(sraweb_connection):
  function test_srs_to_srx (line 243) | def test_srs_to_srx(sraweb_connection):
  function test_srx_to_gsm (line 249) | def test_srx_to_gsm(sraweb_connection):
  function test_srx_to_srp (line 255) | def test_srx_to_srp(sraweb_connection):
  function test_srx_to_srr (line 261) | def test_srx_to_srr(sraweb_connection):
  function test_srx_to_srr1 (line 267) | def test_srx_to_srr1(sraweb_connection):
  function test_srx_to_srs (line 273) | def test_srx_to_srs(sraweb_connection):
  function _test_xmlns_id (line 280) | def _test_xmlns_id(sraweb_connection):
  function test_GCP_url (line 287) | def test_GCP_url(sraweb_connection):
  function test_GCP_url2 (line 292) | def test_GCP_url2(sraweb_connection):
  function test_gse_to_srp3 (line 297) | def test_gse_to_srp3(sraweb_connection):
  function test_gse_to_srp_multiple_srps (line 303) | def test_gse_to_srp_multiple_srps(sraweb_connection):
  function test_geo_metadata_for_gse_without_srp (line 326) | def test_geo_metadata_for_gse_without_srp(sraweb_connection):
  function test_geo_metadata_with_sample_attributes (line 335) | def test_geo_metadata_with_sample_attributes(sraweb_connection):
  function test_geo_metadata_covid19_characteristics (line 342) | def test_geo_metadata_covid19_characteristics(sraweb_connection):
  function test_fetch_bioproject_pmids (line 417) | def test_fetch_bioproject_pmids(sraweb_connection):
  function test_fetch_bioproject_pmids_multiple (line 425) | def test_fetch_bioproject_pmids_multiple(sraweb_connection):
  function test_search_pmc_by_bioproject (line 438) | def test_search_pmc_by_bioproject(sraweb_connection):
  function test_fetch_bioproject_pmids_with_pmc_fallback (line 448) | def test_fetch_bioproject_pmids_with_pmc_fallback(sraweb_connection):
  function test_srp_to_pmid_with_pmc_fallback (line 460) | def test_srp_to_pmid_with_pmc_fallback(sraweb_connection):
  function test_sra_to_pmid (line 476) | def test_sra_to_pmid(sraweb_connection):
  function test_srp_to_pmid (line 484) | def test_srp_to_pmid(sraweb_connection):
  function test_srr_to_pmid (line 492) | def test_srr_to_pmid(sraweb_connection):
  function test_sra_to_pmid_multiple (line 500) | def test_sra_to_pmid_multiple(sraweb_connection):
  function test_srp_to_pmid_multiple (line 507) | def test_srp_to_pmid_multiple(sraweb_connection):
  function test_gse_to_pmid (line 516) | def test_gse_to_pmid(sraweb_connection):
  function test_gse_to_pmid_multiple (line 525) | def test_gse_to_pmid_multiple(sraweb_connection):
  function test_pmid_to_pmc (line 534) | def test_pmid_to_pmc(sraweb_connection):
  function test_pmid_to_pmc_multiple (line 541) | def test_pmid_to_pmc_multiple(sraweb_connection):
  function test_extract_identifiers_from_text (line 548) | def test_extract_identifiers_from_text(sraweb_connection):
  function test_pmc_to_identifiers (line 560) | def test_pmc_to_identifiers(sraweb_connection):
  function test_pmid_to_identifiers (line 571) | def test_pmid_to_identifiers(sraweb_connection):
  function test_pmid_to_gse (line 581) | def test_pmid_to_gse(sraweb_connection):
  function test_pmid_to_srp (line 591) | def test_pmid_to_srp(sraweb_connection):
  function test_doi_to_pmid (line 600) | def test_doi_to_pmid(sraweb_connection):
  function test_doi_to_pmid_multiple (line 607) | def test_doi_to_pmid_multiple(sraweb_connection):
  function test_doi_to_identifiers (line 617) | def test_doi_to_identifiers(sraweb_connection):
  function test_doi_to_gse (line 627) | def test_doi_to_gse(sraweb_connection):
  function test_doi_to_srp (line 637) | def test_doi_to_srp(sraweb_connection):
  function test_unified_metadata_with_gse (line 646) | def test_unified_metadata_with_gse(sraweb_connection):
  function test_unified_metadata_with_srp (line 654) | def test_unified_metadata_with_srp(sraweb_connection):
  function test_unified_metadata_with_multiple_gse (line 662) | def test_unified_metadata_with_multiple_gse(sraweb_connection):
  function test_unified_metadata_invalid_accession (line 671) | def test_unified_metadata_invalid_accession(sraweb_connection):

FILE: tests/test_utils.py
  function invalid_name (line 9) | def invalid_name():
  function valid_name (line 14) | def valid_name():
  function invalid_scientific_name_to_taxid (line 18) | def invalid_scientific_name_to_taxid(invalid_name):
  function valid_scientific_name_to_taxid (line 24) | def valid_scientific_name_to_taxid(valid_name):