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-rw-r--r--wqflask/wqflask/db_info.py254
1 files changed, 127 insertions, 127 deletions
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"<tr>.+?</tr>", data, re.DOTALL)
- for i, match in enumerate(matches):
- if i == 0:
- continue
- cells = re.findall(r"<td.+?>.+?</td>", match, re.DOTALL)
- full_filename = re.search(r"<a href=\"(.+?)\"", cells[1], re.DOTALL).group(1).strip()
- filename = full_filename.split("/")[-1]
- filesize = 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"<tr>.+?</tr>", data, re.DOTALL)
+ for i, match in enumerate(matches):
+ if i == 0:
+ continue
+ cells = re.findall(r"<td.+?>.+?</td>", match, re.DOTALL)
+ full_filename = re.search(r"<a href=\"(.+?)\"", cells[1], re.DOTALL).group(1).strip()
+ filename = full_filename.split("/")[-1]
+ filesize = 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
+
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-24 09:29:52 +0000