From 82bcb31455d658a462bfde711c862480fc9acd05 Mon Sep 17 00:00:00 2001 From: Zachary Sloan Date: Thu, 25 Oct 2012 18:09:11 -0500 Subject: Worked on search page code; got to the part that actually does the search Renamed RISet and cross to "group" throughout webqtlDataset.py and search_results.py --- wqflask/base/webqtlDataset.py | 28 +- wqflask/wqflask/search_results.py | 215 ++++----- wqflask/wqflask/templates/index_page.html | 669 +++++++++++++++----------- wqflask/wqflask/templates/new_index_page.html | 423 ---------------- wqflask/wqflask/templates/old_index_page.html | 320 ++++++++++++ wqflask/wqflask/views.py | 7 - 6 files changed, 821 insertions(+), 841 deletions(-) delete mode 100644 wqflask/wqflask/templates/new_index_page.html create mode 100644 wqflask/wqflask/templates/old_index_page.html (limited to 'wqflask') diff --git a/wqflask/base/webqtlDataset.py b/wqflask/base/webqtlDataset.py index 4f98e90c..933077fd 100755 --- a/wqflask/base/webqtlDataset.py +++ b/wqflask/base/webqtlDataset.py @@ -34,6 +34,7 @@ class webqtlDataset: """ Dataset class defines a dataset in webqtl, can be either Microarray, Published phenotype, genotype, or user input dataset(temp) + """ def __init__(self, dbName, cursor=None): @@ -42,7 +43,7 @@ class webqtlDataset: self.id = 0 self.name = '' self.type = '' - self.riset = '' + self.group = '' self.cursor = cursor #temporary storage @@ -81,14 +82,15 @@ class webqtlDataset: self.name = dbName if self.cursor and self.id == 0: self.retrieveName() - - def __str__(self): - return self.name - - __repr__ = __str__ + + + # Delete this eventually + @property + def riset(): + Weve_Renamed_This_As_Group - def getRISet(self): + def get_group(self): assert self.cursor if self.type == 'Publish': query = ''' @@ -124,12 +126,12 @@ class webqtlDataset: else: return "" self.cursor.execute(query) - RISet, RIID = self.cursor.fetchone() - if RISet == 'BXD300': - RISet = "BXD" - self.riset = RISet - self.risetid = RIID - return RISet + group, RIID = self.cursor.fetchone() + if group == 'BXD300': + group = "BXD" + self.group = group + self.group_id = RIID + return group def retrieveName(self): diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py index 1b846771..2269b9e7 100644 --- a/wqflask/wqflask/search_results.py +++ b/wqflask/wqflask/search_results.py @@ -36,17 +36,9 @@ from wqflask import parser from utility import webqtlUtil from dbFunction import webqtlDatabaseFunction -#import logging -#logging.basicConfig(filename=app.config['LOGFILE'], level=logging.INFO) -# -#_log = logging.getLogger("search") -#_ch = logging.StreamHandler() -#_log.addHandler(_ch) - from utility import formatting import sys -#_log.info("sys.path is: %s" % (sys.path)) #from base.JinjaPage import JinjaEnv, JinjaPage @@ -64,116 +56,112 @@ class SearchResultPage(templatePage): import logging_tree logging_tree.printout() self.fd = fd - if not self.openMysql(): - print("ge0") - #return - - print("Start...") - print("Type of fd:", type(fd)) - print("Value of fd:", pf(fd)) - database = [fd['database']] - print("End...") - - # change back to self.database - if not self.database or self.database == 'spacer': - #Error, No database selected + templatePage.__init__(self, fd) + assert self.openMysql(), "Couldn't open MySQL" + + print("fd is:", pf(fd)) + self.dataset = fd['dataset'] + + # change back to self.dataset + if not self.dataset or self.dataset == 'spacer': + #Error, No dataset selected heading = "Search Result" - detail = ['''No database was selected for this search, please - go back and SELECT at least one database.'''] - print("ge0.6") - self.error(heading=heading,detail=detail,error="No Database Selected") - #return + detail = ['''No dataset was selected for this search, please + go back and SELECT at least one dataset.'''] + self.error(heading=heading,detail=detail,error="No dataset Selected") + return - print("ge1") ########################################### # Names and IDs of RISet / F2 set ########################################### - if self.database == ['_allPublish']: + if self.dataset == "All Phenotypes": self.cursor.execute(""" select PublishFreeze.Name, InbredSet.Name, InbredSet.Id from PublishFreeze, InbredSet where PublishFreeze.Name not like 'BXD300%' and InbredSet.Id = PublishFreeze.InbredSetId""") results = self.cursor.fetchall() - self.database = map(lambda x: webqtlDataset(x[0], self.cursor), results) - self.databaseCrosses = map(lambda x: x[1], results) - self.databaseCrossIds = map(lambda x: x[2], results) - self.singleCross = False + self.dataset = map(lambda x: webqtlDataset(x[0], self.cursor), results) + self.datasetGroups = map(lambda x: x[1], results) + self.datasetGroupIds = map(lambda x: x[2], results) + self.single_group = False else: - self.database = map(lambda x: webqtlDataset(x, self.cursor), self.database) + print("self.dataset is:", pf(self.dataset)) + self.dataset = webqtlDataset(self.dataset, self.cursor) + print("self.dataset is now:", pf(self.dataset)) + #self.dataset = map(lambda x: webqtlDataset(x, self.cursor), self.dataset) #currently, webqtl won't allow multiple crosses #for other than multiple publish db search - #so we can use the first database as example - if self.database[0].type=="Publish": - pass - elif self.database[0].type in ("Geno", "ProbeSet"): + #so we can use the first dataset as example + #if self.dataset.type=="Publish": + # pass + if self.dataset.type in ("Geno", "ProbeSet"): #userExist = None - - for individualDB in self.database: - # Can't use paramater substitution for table names apparently - db_type = self.database[0].type + "Freeze" - print("db_type [%s]: %s" % (type(db_type), db_type)) - - query = '''SELECT Id, Name, FullName, confidentiality, - AuthorisedUsers FROM %s WHERE Name = %%s''' % (db_type) - - self.cursor.execute(query, (individualDB,)) - - (indId, - indName, - indFullName, - confidential, - AuthorisedUsers) = self.cursor.fetchall()[0] - - if confidential: - access_to_confidential_dataset = 0 - - #for the dataset that confidentiality is 1 - #1. 'admin' and 'root' can see all of the dataset - #2. 'user' can see the dataset that AuthorisedUsers contains his id(stored in the Id field of User table) - if webqtlConfig.USERDICT[self.privilege] > webqtlConfig.USERDICT['user']: - access_to_confidential_dataset = 1 - else: - AuthorisedUsersList=AuthorisedUsers.split(',') - if AuthorisedUsersList.__contains__(self.userName): - access_to_confidential_dataset = 1 - - if not access_to_confidential_dataset: - #Error, No database selected - heading = "Search Result" - detail = ["The %s database you selected is not open to the public at this time, please go back and SELECT other database." % indFullName] - self.error(heading=heading,detail=detail,error="Confidential Database") - return - else: - heading = "Search Result" - detail = ['''The database has not been established yet, please - go back and SELECT at least one database.'''] - self.error(heading=heading,detail=detail,error="No Database Selected") - return - - print("ge2") - self.database[0].getRISet() - self.databaseCrosses = [self.database[0].riset] - self.databaseCrossIds = [self.database[0].risetid] - self.singleCross = True - #XZ, August 24,2010: Since self.singleCross = True, it's safe to assign one species Id. - self.speciesId = webqtlDatabaseFunction.retrieveSpeciesId(self.cursor, self.database[0].riset) + # Can't use paramater substitution for table names apparently + db_type = self.dataset.type + "Freeze" + print("db_type [%s]: %s" % (type(db_type), db_type)) + + query = '''SELECT Id, Name, FullName, confidentiality, + AuthorisedUsers FROM %s WHERE Name = %%s''' % (db_type) + + self.cursor.execute(query, self.dataset.name) + + (indId, + indName, + indFullName, + confidential, + AuthorisedUsers) = self.cursor.fetchall()[0] + + if confidential: + # Allow confidential data later + NoConfindetialDataForYouTodaySorry + #access_to_confidential_dataset = 0 + # + ##for the dataset that confidentiality is 1 + ##1. 'admin' and 'root' can see all of the dataset + ##2. 'user' can see the dataset that AuthorisedUsers contains his id(stored in the Id field of User table) + #if webqtlConfig.USERDICT[self.privilege] > webqtlConfig.USERDICT['user']: + # access_to_confidential_dataset = 1 + #else: + # AuthorisedUsersList=AuthorisedUsers.split(',') + # if AuthorisedUsersList.__contains__(self.userName): + # access_to_confidential_dataset = 1 + # + #if not access_to_confidential_dataset: + # #Error, No dataset selected + # heading = "Search Result" + # detail = ["The %s dataset you selected is not open to the public at this time, please go back and SELECT other dataset." % indFullName] + # self.error(heading=heading,detail=detail,error="Confidential dataset") + # return + #else: + # heading = "Search Result" + # detail = ['''The dataset has not been established yet, please + # go back and SELECT at least one dataset.'''] + # self.error(heading=heading,detail=detail,error="No dataset Selected") + # return + + self.dataset.get_group() + self.single_group = True + #XZ, August 24,2010: Since self.single_group = True, it's safe to assign one species Id. + self.species_id = webqtlDatabaseFunction.retrieveSpeciesId(self.cursor, + self.dataset.group) ########################################### - # make sure search from same type of databases + # make sure search from same type of datasets ########################################### - #dbTypes = map(lambda X: X.type, self.database) - dbTypes = [table.type for table in self.database] - self.dbType = dbTypes[0] - for item in dbTypes: - if item != self.dbType: - heading = "Search Result" - detail = ["Search can only be performed among the same type of databases"] - self.error(heading=heading,detail=detail,error="Error") - return - - print("ge3") - if self.dbType == "Publish": + #dbTypes = map(lambda X: X.type, self.dataset) + #db_types = [table.type for table in self.dataset] + #self.db_type = db_types[0] + #for item in dbTypes: + # if item != self.dbType: + # heading = "Search Result" + # detail = ["Search can only be performed among the same type of datasets"] + # self.error(heading=heading,detail=detail,error="Error") + # return + + + #self.db_type = self.dataset.type + if self.dataset.type == "Publish": self.searchField = ['Phenotype.Post_publication_description', 'Phenotype.Pre_publication_description', 'Phenotype.Pre_publication_abbreviation', @@ -185,7 +173,7 @@ class SearchResultPage(templatePage): 'Publication.Authors', 'PublishXRef.Id'] - elif self.dbType == "ProbeSet": + elif self.dataset.type == "ProbeSet": self.searchField = ['Name', 'Description', 'Probe_Target_Description', @@ -194,11 +182,12 @@ class SearchResultPage(templatePage): 'GenbankId', 'UniGeneId', 'RefSeq_TranscriptId'] - elif self.dbType == "Geno": + elif self.dataset.type == "Geno": self.searchField = ['Name','Chr'] - print("ge4") + self.do_search() + self.gen_search_result() ########################################### # Search Options @@ -272,11 +261,11 @@ class SearchResultPage(templatePage): # return #self.nresults = self.executeQuery() # - #if len(self.database) > 1: - # dbUrl = "Multiple phenotype databases" + #if len(self.dataset) > 1: + # dbUrl = "Multiple phenotype datasets" # dbUrlLink = " were" #else: - # dbUrl = self.database[0].genHTML() + # dbUrl = self.dataset[0].genHTML() # dbUrlLink = " was" #SearchText = HT.Blockquote('GeneNetwork searched the ', dbUrl, ' for all records ') @@ -355,17 +344,13 @@ class SearchResultPage(templatePage): #TD_LR.append(HT.Paragraph('Search Results', Class="title"), SearchText) - self.start_search() - self.genSearchResultTable() #self.dict['body'] = str(TD_LR) #self.dict['js1'] = '' #self.dict['js2'] = 'onLoad="pageOffset()"' #self.dict['layer'] = self.generateWarningLayer() - def start_search(self): - pass - def genSearchResultTable(self): + def gen_search_result(self): #pageTable = HT.TableLite(cellSpacing=2,cellPadding=0,width="100%",border=0) @@ -399,8 +384,8 @@ class SearchResultPage(templatePage): #tbl = HT.TableLite(cellSpacing=2,cellPadding=0,width="90%",border=0) #seq = self.pageNumber*self.NPerPage+1 //Edited out because we show all results in one page now - Zach 2/22/11 seq = 1 - RISet = self.databaseCrosses[i] - self.thisFormName = thisFormName = 'showDatabase'+RISet + group = self.databaseCrosses[i] + self.thisFormName = thisFormName = 'showDatabase'+group #selectall = HT.Href(url="#", onClick="checkAll(document.getElementsByName('%s')[0]);" % thisFormName) #selectall_img = HT.Image("/images/select_all2_final.jpg", name="selectall", alt="Select All", title="Select All", style="border:none;") #selectall.append(selectall_img) @@ -423,7 +408,7 @@ class SearchResultPage(templatePage): tblobj = {} mainfmName = thisFormName - species = webqtlDatabaseFunction.retrieveSpecies(cursor=self.cursor, RISet=RISet) + species = webqtlDatabaseFunction.retrieveSpecies(cursor=self.cursor, RISet=group) if thisTrait.db.type=="Geno": tblobj['header'] = self.getTableHeaderForGeno(worksheet=worksheet, newrow=newrow, headingStyle=headingStyle) @@ -480,7 +465,7 @@ class SearchResultPage(templatePage): #traitForm = HT.Form(cgi= os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), enctype='multipart/form-data', name=thisFormName, submit=HT.Input(type='hidden')) - hddn = {'FormID':'showDatabase','ProbeSetID':'_','database':'_','CellID':'_','RISet':RISet} + hddn = {'FormID':'showDatabase','ProbeSetID':'_','database':'_','CellID':'_','group':group} hddn['incparentsf1']='ON' # for key in hddn.keys(): # traitForm.append(HT.Input(name=key, value=hddn[key], type='hidden')) diff --git a/wqflask/wqflask/templates/index_page.html b/wqflask/wqflask/templates/index_page.html index db0b2d9e..695129a9 100644 --- a/wqflask/wqflask/templates/index_page.html +++ b/wqflask/wqflask/templates/index_page.html @@ -1,320 +1,423 @@ -{% extends "base.html" %} -{% block title %}GeneNetwork{% endblock %} -{% block content %} - - - - - - - + - - -
-

Select and - Search

- -
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
- Species: - -
Group: - -
Type: - -
Database: - -
-

    Databases marked with ** - suffix are not public yet.
-     Access requires user login.

-
- Search:
-

    Enter terms, genes, ID numbers in the - Search field.
-     Use * or ? wildcards (Cyp*a?, - synap*).
-     Use quotes for terms such as "tyrosine - kinase".

-
         
-
- -

 ______________________________________________________

- -

  Quick HELP - Examples and User's Guide

  You can also use advanced - commands. Copy these simple examples
-   into the Get Any or Combined search fields: - -
    -
  • POSITION=(chr1 25 30) finds genes, markers, or transcripts on - chromosome 1 between 25 and 30 Mb.
    • - -
  • MEAN=(15 16) LRS=(23 46) in the Combined field finds - highly expressed genes (15 to 16 log2 units) AND with peak LRS linkage between 23 and 46.
    • - -
  • RIF=mitochondrial searches RNA databases for GeneRIF links.
    • - -
  • WIKI=nicotine searches GeneWiki for genes that you or other users have annotated - with the word nicotine.
    • - -
  • GO:0045202 searches for synapse-associated genes listed in the - Gene Ontology.
    • - -
  • GO:0045202 LRS=(9 99 Chr4 122 155) cisLRS=(9 999 10)
    - in Combined finds synapse-associated genes with cis eQTL on Chr 4 from 122 and 155 Mb with LRS scores - between 9 and 999.
    • - -
  • RIF=diabetes LRS=(9 999 Chr2 100 105) transLRS=(9 999 10)
    - in Combined finds diabetes-associated transcripts with peak trans eQTLs on Chr 2 between 100 and 105 Mb with LRS - scores between 9 and 999.
    • + + + + + GeneNetwork + + + + + + + + + + + + + + + +
    +
    +
    + + GeneNetwork +
    + +
    +
    +
    +
    + +
    +
    +

    GeneNetwork

    +

    Open source bioinformatics for systems genetics
    + Brought to you by the University of Tennessee

    +
    +
    + + +
    +
    +
    + -
-

Websites Affiliated with - GeneNetwork

+
+ -
  • Optional: Use the Make Default button to save your preferences
    • - +
    +
    +

    Getting started

    +
    -

    ____________________________

    +
      +
    1. Select Species (or All)
      2. -

      How to Use - GeneNetwork

      +
    2. Select Group (a specific sample)
      3. -
      -

      Take a 20-40 minute - GeneNetwork Tour that includes screen shots and - typical steps in the analysis.

      -
      +
    3. Select Type of data: -
      -

      For information about - resources and methods, select the INFO buttons.

      +
        +
      • Phenotype (traits)
        • -

        Try the Workstation site to explore data and features that are - being implemented.

        +
      • Genotype (markers)
        • -

        Review the Conditions - and Contacts pages for information on the status of data sets - and advice on their use and citation.

        -
      +
    4. Expression (mRNAs)
      5. + + -

      Mirror and Development - Sites

      +
    5. Select a Database
      6. -
    -
  • Germany at the HZI
    • +

    User Guide

    +
    Read the + + user guide.
    -
  • Netherlands at the Hubrecht - (Development)
    • +
    -
  • Memphis at the U of M
    • -
  • Singapore at the NUS
    • +
    +
    +

    Advanced commands

    +
    -
  • Switzerland at the EPFL
    • - +

    GeneNetwork supports a variety of advanced searches.

    -

    History and - Archive

    - -
    -

    GeneNetwork's Time - Machine links to earlier versions that correspond to specific - publication dates.

    -
    -
    - - - - - -{% endblock %} +

    To try them out copy these examples into the search field:

    + + + + +
    +
    +

    Tour and more info

    +
    + +

    Thirty minute tour

    +

    + Take the 30 minute + GeneNetwork tour that includes screen shots and + typical steps in the analysis. +

    + +

    Even more info

    +

    + For information about + resources and methods, select the Info buttons next to the Group + and Database fields above. +

    + +

    The conditions + and contact + pages have information on the status of data sets + and advice on their use and citation.

    + +
    + +
    +
    +

    Affiliates and mirrors

    +
    +

    Websites affiliated with GeneNetwork

    + +

    Mirror and development sites

    + +

    History and archive

    + +

    The + + time machine + has earlier versions that correspond to specific publication dates. +

    + +

    The next generation

    +

    Try the + development site to explore experimental data and features.

    +
    + + + + + + + + + + + + + + + + + + diff --git a/wqflask/wqflask/templates/new_index_page.html b/wqflask/wqflask/templates/new_index_page.html deleted file mode 100644 index 695129a9..00000000 --- a/wqflask/wqflask/templates/new_index_page.html +++ /dev/null @@ -1,423 +0,0 @@ - - - - - GeneNetwork - - - - - - - - - - - - - - - -
    -
    -
    - - GeneNetwork -
    - -
    -
    -
    -
    - -
    -
    -

    GeneNetwork

    -

    Open source bioinformatics for systems genetics
    - Brought to you by the University of Tennessee

    -
    -
    - - -
    -
    -
    - -
    - -
    - - -
    -
    -

    Getting started

    -
    - -
      -
    1. Select Species (or All)
      2. - -
    2. Select Group (a specific sample)
      3. - -
    3. Select Type of data: - -
        -
      • Phenotype (traits)
        • - -
      • Genotype (markers)
        • - -
      • Expression (mRNAs)
        • -
      -
      4. - -
    4. Select a Database
      5. - -
    5. Enter terms in the search field: words, - genes, ID numbers, probes, advanced search commands
      6. - -
    6. Click the Search button
      7. - -
    7. Optional: Use the Make Default button to save your preferences
      8. -
    - -

    User Guide

    -
    Read the - - user guide.
    - -
    - - -
    -
    -

    Advanced commands

    -
    - -

    GeneNetwork supports a variety of advanced searches.

    - -

    To try them out copy these examples into the search field:

    - -
      -
    • POSITION=(chr1 25 30) finds genes, markers, or transcripts on - chromosome 1 between 25 and 30 Mb.
      • - -
    • MEAN=(15 16) LRS=(23 46) in the Combined field finds - highly expressed genes (15 to 16 log2 units) AND with peak LRS - linkage between 23 and 46.
      • - -
    • RIF=mitochondrial searches RNA databases for - GeneRIF links.
      • - -
    • WIKI=nicotine searches - GeneWiki for genes that you or other users have annotated - with the word nicotine.
      • - -
    • GO:0045202 searches for synapse-associated genes listed in the - - Gene Ontology.
      • - -
    • GO:0045202 LRS=(9 99 Chr4 122 155) cisLRS=(9 999 10) - finds synapse-associated genes with - cis eQTL on Chr 4 from 122 and 155 Mb with LRS scores - between 9 and 999.
      • - -
    • RIF=diabetes LRS=(9 999 Chr2 100 105) transLRS=(9 999 10) - finds diabetes-associated transcripts with peak - trans eQTLs on Chr 2 between 100 and 105 Mb with LRS - scores between 9 and 999.
      • -
    -
    - -
    -
    -

    Tour and more info

    -
    - -

    Thirty minute tour

    -

    - Take the 30 minute - GeneNetwork tour that includes screen shots and - typical steps in the analysis. -

    - -

    Even more info

    -

    - For information about - resources and methods, select the Info buttons next to the Group - and Database fields above. -

    - -

    The conditions - and contact - pages have information on the status of data sets - and advice on their use and citation.

    - -
    - -
    -
    -

    Affiliates and mirrors

    -
    -

    Websites affiliated with GeneNetwork

    - -

    Mirror and development sites

    - -

    History and archive

    - -

    The - - time machine - has earlier versions that correspond to specific publication dates. -

    - -

    The next generation

    -

    Try the - development site to explore experimental data and features.

    -
    -
    -
    -
    - - - - - - - - - - - - - - - diff --git a/wqflask/wqflask/templates/old_index_page.html b/wqflask/wqflask/templates/old_index_page.html new file mode 100644 index 00000000..db0b2d9e --- /dev/null +++ b/wqflask/wqflask/templates/old_index_page.html @@ -0,0 +1,320 @@ +{% extends "base.html" %} +{% block title %}GeneNetwork{% endblock %} +{% block content %} + + + + + + + + + + +
    +

    Select and + Search

    + +
    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    + Species: + +
    Group: + +
    Type: + +
    Database: + +
    +

        Databases marked with ** + suffix are not public yet.
    +     Access requires user login.

    +
    + Search:
    +

        Enter terms, genes, ID numbers in the + Search field.
    +     Use * or ? wildcards (Cyp*a?, + synap*).
    +     Use quotes for terms such as "tyrosine + kinase".

    +
             
    +
    + +

     ______________________________________________________

    + +

      Quick HELP + Examples and User's Guide

      You can also use advanced + commands. Copy these simple examples
    +   into the Get Any or Combined search fields: + +
      +
    • POSITION=(chr1 25 30) finds genes, markers, or transcripts on + chromosome 1 between 25 and 30 Mb.
      • + +
    • MEAN=(15 16) LRS=(23 46) in the Combined field finds + highly expressed genes (15 to 16 log2 units) AND with peak LRS linkage between 23 and 46.
      • + +
    • RIF=mitochondrial searches RNA databases for GeneRIF links.
      • + +
    • WIKI=nicotine searches GeneWiki for genes that you or other users have annotated + with the word nicotine.
      • + +
    • GO:0045202 searches for synapse-associated genes listed in the + Gene Ontology.
      • + +
    • GO:0045202 LRS=(9 99 Chr4 122 155) cisLRS=(9 999 10)
      + in Combined finds synapse-associated genes with cis eQTL on Chr 4 from 122 and 155 Mb with LRS scores + between 9 and 999.
      • + +
    • RIF=diabetes LRS=(9 999 Chr2 100 105) transLRS=(9 999 10)
      + in Combined finds diabetes-associated transcripts with peak trans eQTLs on Chr 2 between 100 and 105 Mb with LRS + scores between 9 and 999.
      • +
    +     		+

    Websites Affiliated with + GeneNetwork

    + +

    + + + +

    ____________________________

    + +

    Getting Started +   

    + +
      +
    1. Select Species (or select All)
      2. + +
    2. Select Group (a specific sample)
      3. + +
    3. Select Type of data: + +
        +
      • Phenotype (traits)
        • + +
      • Genotype (markers)
        • + +
      • Expression (mRNAs)
        • +
      +
      4. + +
    4. Select a Database
      5. + +
    5. Enter search terms in the Get Any or Combined field: words, + genes, ID numbers, probes, advanced search commands
      6. + +
    6. Click on the Search button
      7. + +
    7. Optional: Use the Make Default button to save your preferences
      8. +
    + +

    ____________________________

    + +

    How to Use + GeneNetwork

    + +
    +

    Take a 20-40 minute + GeneNetwork Tour that includes screen shots and + typical steps in the analysis.

    +
    + +
    +

    For information about + resources and methods, select the INFO buttons.

    + +

    Try the Workstation site to explore data and features that are + being implemented.

    + +

    Review the Conditions + and Contacts pages for information on the status of data sets + and advice on their use and citation.

    +
    + +

    Mirror and Development + Sites

    + + + +

    History and + Archive

    + +
    +

    GeneNetwork's Time + Machine links to earlier versions that correspond to specific + publication dates.

    +
    +
    + + + + + +{% endblock %} + diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index d639ed07..629a5b15 100644 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -33,13 +33,6 @@ def index_page(): print("Sending index_page") return render_template("index_page.html") - -@app.route("/new") -def new_index_page(): - print("Sending index_page") - - return render_template("new_index_page.html") - @app.route("/data_sharing") def data_sharing_page(): print("In data_sharing") -- cgit 1.4.1