From 7f94f657e51bbf9a7a1064b12a7d67b53a14eb11 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Sat, 26 Sep 2020 01:15:09 +0300 Subject: Fix inconsistent line ending in file * wqflask/wqflask/db_info.py: Replace ^M with proper unix line endings. See --- wqflask/wqflask/db_info.py | 254 ++++++++++++++++++++++----------------------- 1 file changed, 127 insertions(+), 127 deletions(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/db_info.py b/wqflask/wqflask/db_info.py index f04e38bf..5f3f5e3f 100644 --- a/wqflask/wqflask/db_info.py +++ b/wqflask/wqflask/db_info.py @@ -1,127 +1,127 @@ -import httplib, urllib2 -import re - -from flask import Flask, g - -from utility.logger import getLogger -logger = getLogger(__name__ ) - -class InfoPage(object): - def __init__(self, start_vars): - self.info = None - self.gn_accession_id = None - if 'gn_accession_id' in start_vars: - self.gn_accession_id = start_vars['gn_accession_id'] - self.info_page_name = start_vars['info_page_name'] - - self.get_info() - self.get_datasets_list() - - def get_info(self, create=False): - query_base = ("SELECT InfoPageName, GN_AccesionId, Species.MenuName, Species.TaxonomyId, Tissue.Name, InbredSet.Name, " + - "GeneChip.GeneChipName, GeneChip.GeoPlatform, AvgMethod.Name, Datasets.DatasetName, Datasets.GeoSeries, " + - "Datasets.PublicationTitle, DatasetStatus.DatasetStatusName, Datasets.Summary, Datasets.AboutCases, " + - "Datasets.AboutTissue, Datasets.AboutDataProcessing, Datasets.Acknowledgment, Datasets.ExperimentDesign, " + - "Datasets.Contributors, Datasets.Citation, Datasets.Notes, Investigators.FirstName, Investigators.LastName, " + - "Investigators.Address, Investigators.City, Investigators.State, Investigators.ZipCode, Investigators.Country, " + - "Investigators.Phone, Investigators.Email, Investigators.Url, Organizations.OrganizationName, " + - "InvestigatorId, DatasetId, DatasetStatusId, Datasets.AboutPlatform, InfoFileTitle, Specifics " + - "FROM InfoFiles " + - "LEFT JOIN Species USING (SpeciesId) " + - "LEFT JOIN Tissue USING (TissueId) " + - "LEFT JOIN InbredSet USING (InbredSetId) " + - "LEFT JOIN GeneChip USING (GeneChipId) " + - "LEFT JOIN AvgMethod USING (AvgMethodId) " + - "LEFT JOIN Datasets USING (DatasetId) " + - "LEFT JOIN Investigators USING (InvestigatorId) " + - "LEFT JOIN Organizations USING (OrganizationId) " + - "LEFT JOIN DatasetStatus USING (DatasetStatusId) WHERE ") - - if self.gn_accession_id: - final_query = query_base + "GN_AccesionId = {}".format(self.gn_accession_id) - results = g.db.execute(final_query).fetchone() - if self.info_page_name and not results: - final_query = query_base + "InfoPageName={}".format(self.info_page_name) - elif self.info_page_name: - final_query = query_base + "InfoPageName={}".format(self.info_page_name) - results = g.db.execute(final_query).fetchone() - else: - raise 'No correct parameter found' - - if results: - self.info = process_query_results(results) - - if (not results or len(results) < 1) and self.info_page_name and create: - insert_sql = "INSERT INTO InfoFiles SET InfoFiles.InfoPageName={}".format(self.info_page_name) - return self.get_info() - - if not self.gn_accession_id and self.info: - self.gn_accession_id = self.info['accession_id'] - if not self.info_page_name and self.info: - self.info_page_name = self.info['info_page_name'] - - def get_datasets_list(self): - self.filelist = [] - try: - response = urllib2.urlopen("http://datafiles.genenetwork.org/download/GN%s" % self.gn_accession_id) - data = response.read() - - matches = re.findall(r".+?", data, re.DOTALL) - for i, match in enumerate(matches): - if i == 0: - continue - cells = re.findall(r".+?", match, re.DOTALL) - full_filename = re.search(r"(.+?)<", cells[2]).group(1).strip() - filedate = "N/A" #ZS: Since we can't get it for now - - self.filelist.append([filename, filedate, filesize]) - except Exception, e: - pass - -def process_query_results(results): - info_ob = { - 'info_page_name': results[0], - 'accession_id': results[1], - 'menu_name': results[2], - 'taxonomy_id': results[3], - 'tissue_name': results[4], - 'group_name': results[5], - 'gene_chip_name': results[6], - 'geo_platform': results[7], - 'avg_method_name': results[8], - 'dataset_name': results[9], - 'geo_series': results[10], - 'publication_title': results[11], - 'dataset_status_name': results[12], - 'dataset_summary': results[13], - 'about_cases': results[14], - 'about_tissue': results[15], - 'about_data_processing': results[16], - 'acknowledgement': results[17], - 'experiment_design': results[18], - 'contributors': results[19], - 'citation': results[20], - 'notes': results[21], - 'investigator_firstname': results[22], - 'investigator_lastname': results[23], - 'investigator_address': results[24], - 'investigator_city': results[25], - 'investigator_state': results[26], - 'investigator_zipcode': results[27], - 'investigator_country': results[28], - 'investigator_phone': results[29], - 'investigator_email': results[30], - 'investigator_url': results[31], - 'organization_name': results[32], - 'investigator_id': results[33], - 'dataset_id': results[34], - 'dataset_status_is': results[35], - 'about_platform': results[36], - 'info_file_title': results[37], - 'specifics': results[38] - } - - return info_ob - \ No newline at end of file +import httplib, urllib2 +import re + +from flask import Flask, g + +from utility.logger import getLogger +logger = getLogger(__name__ ) + +class InfoPage(object): + def __init__(self, start_vars): + self.info = None + self.gn_accession_id = None + if 'gn_accession_id' in start_vars: + self.gn_accession_id = start_vars['gn_accession_id'] + self.info_page_name = start_vars['info_page_name'] + + self.get_info() + self.get_datasets_list() + + def get_info(self, create=False): + query_base = ("SELECT InfoPageName, GN_AccesionId, Species.MenuName, Species.TaxonomyId, Tissue.Name, InbredSet.Name, " + + "GeneChip.GeneChipName, GeneChip.GeoPlatform, AvgMethod.Name, Datasets.DatasetName, Datasets.GeoSeries, " + + "Datasets.PublicationTitle, DatasetStatus.DatasetStatusName, Datasets.Summary, Datasets.AboutCases, " + + "Datasets.AboutTissue, Datasets.AboutDataProcessing, Datasets.Acknowledgment, Datasets.ExperimentDesign, " + + "Datasets.Contributors, Datasets.Citation, Datasets.Notes, Investigators.FirstName, Investigators.LastName, " + + "Investigators.Address, Investigators.City, Investigators.State, Investigators.ZipCode, Investigators.Country, " + + "Investigators.Phone, Investigators.Email, Investigators.Url, Organizations.OrganizationName, " + + "InvestigatorId, DatasetId, DatasetStatusId, Datasets.AboutPlatform, InfoFileTitle, Specifics " + + "FROM InfoFiles " + + "LEFT JOIN Species USING (SpeciesId) " + + "LEFT JOIN Tissue USING (TissueId) " + + "LEFT JOIN InbredSet USING (InbredSetId) " + + "LEFT JOIN GeneChip USING (GeneChipId) " + + "LEFT JOIN AvgMethod USING (AvgMethodId) " + + "LEFT JOIN Datasets USING (DatasetId) " + + "LEFT JOIN Investigators USING (InvestigatorId) " + + "LEFT JOIN Organizations USING (OrganizationId) " + + "LEFT JOIN DatasetStatus USING (DatasetStatusId) WHERE ") + + if self.gn_accession_id: + final_query = query_base + "GN_AccesionId = {}".format(self.gn_accession_id) + results = g.db.execute(final_query).fetchone() + if self.info_page_name and not results: + final_query = query_base + "InfoPageName={}".format(self.info_page_name) + elif self.info_page_name: + final_query = query_base + "InfoPageName={}".format(self.info_page_name) + results = g.db.execute(final_query).fetchone() + else: + raise 'No correct parameter found' + + if results: + self.info = process_query_results(results) + + if (not results or len(results) < 1) and self.info_page_name and create: + insert_sql = "INSERT INTO InfoFiles SET InfoFiles.InfoPageName={}".format(self.info_page_name) + return self.get_info() + + if not self.gn_accession_id and self.info: + self.gn_accession_id = self.info['accession_id'] + if not self.info_page_name and self.info: + self.info_page_name = self.info['info_page_name'] + + def get_datasets_list(self): + self.filelist = [] + try: + response = urllib2.urlopen("http://datafiles.genenetwork.org/download/GN%s" % self.gn_accession_id) + data = response.read() + + matches = re.findall(r".+?", data, re.DOTALL) + for i, match in enumerate(matches): + if i == 0: + continue + cells = re.findall(r".+?", match, re.DOTALL) + full_filename = re.search(r"(.+?)<", cells[2]).group(1).strip() + filedate = "N/A" #ZS: Since we can't get it for now + + self.filelist.append([filename, filedate, filesize]) + except Exception, e: + pass + +def process_query_results(results): + info_ob = { + 'info_page_name': results[0], + 'accession_id': results[1], + 'menu_name': results[2], + 'taxonomy_id': results[3], + 'tissue_name': results[4], + 'group_name': results[5], + 'gene_chip_name': results[6], + 'geo_platform': results[7], + 'avg_method_name': results[8], + 'dataset_name': results[9], + 'geo_series': results[10], + 'publication_title': results[11], + 'dataset_status_name': results[12], + 'dataset_summary': results[13], + 'about_cases': results[14], + 'about_tissue': results[15], + 'about_data_processing': results[16], + 'acknowledgement': results[17], + 'experiment_design': results[18], + 'contributors': results[19], + 'citation': results[20], + 'notes': results[21], + 'investigator_firstname': results[22], + 'investigator_lastname': results[23], + 'investigator_address': results[24], + 'investigator_city': results[25], + 'investigator_state': results[26], + 'investigator_zipcode': results[27], + 'investigator_country': results[28], + 'investigator_phone': results[29], + 'investigator_email': results[30], + 'investigator_url': results[31], + 'organization_name': results[32], + 'investigator_id': results[33], + 'dataset_id': results[34], + 'dataset_status_is': results[35], + 'about_platform': results[36], + 'info_file_title': results[37], + 'specifics': results[38] + } + + return info_ob + -- cgit v1.2.3