Fix inconsistent line ending in file

* wqflask/wqflask/db_info.py: Replace ^M with proper unix line
endings. See <http://ergoemacs.org/emacs/emacs_line_ending_char.html>

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
+