diff options
| -rwxr-xr-x | wqflask/base/data_set.py | 33 | ||||
| -rwxr-xr-x | wqflask/base/webqtlConfigLocal.py | 4 | ||||
| -rwxr-xr-x | wqflask/base/webqtlTrait.py | 69 | ||||
| -rw-r--r-- | wqflask/cfg/zach_settings.py | 3 | ||||
| -rw-r--r-- | wqflask/wqflask/do_search.py | 24 | ||||
| -rw-r--r-- | wqflask/wqflask/search_results.py | 3 | ||||
| -rwxr-xr-x | wqflask/wqflask/show_trait/show_trait.py | 25 | ||||
| -rw-r--r-- | wqflask/wqflask/views.py | 14 |
8 files changed, 106 insertions, 69 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index 633f7545..015b2623 100755 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -22,6 +22,8 @@ from __future__ import print_function, division +from flask import Flask, g + from htmlgen import HTMLgen2 as HT import webqtlConfig @@ -31,25 +33,28 @@ from pprint import pformat as pf # Used by create_database to instantiate objects DS_NAME_MAP = {} -def create_dataset(db_conn, dataset_name): - cursor = db_conn.cursor() - cursor.execute(""" +def create_dataset(dataset_name): + #cursor = db_conn.cursor() + print("dataset_name:", dataset_name) + + dataset_type = g.db.execute(""" SELECT DBType.Name FROM DBList, DBType WHERE DBList.Name = %s and DBType.Id = DBList.DBTypeId - """, (dataset_name)) - print("dataset_name:", dataset_name) - dataset_type = cursor.fetchone()[0] - print("dataset_type:", pf(dataset_type)) + """, (dataset_name)).fetchone().Name + + #dataset_type = cursor.fetchone()[0] + print("[blubber] dataset_type:", pf(dataset_type)) dataset_ob = DS_NAME_MAP[dataset_type] #dataset_class = getattr(data_set, dataset_ob) - + print("dataset_ob:", dataset_ob) print("DS_NAME_MAP:", pf(DS_NAME_MAP)) dataset_class = globals()[dataset_ob] - return dataset_class(dataset_name, db_conn) + return dataset_class(dataset_name) + class DataSet(object): """ @@ -58,12 +63,12 @@ class DataSet(object): """ - def __init__(self, name, db_conn): + def __init__(self, name): assert name self.name = name - self.db_conn = db_conn - self.cursor = self.db_conn.cursor() + #self.db_conn = db_conn + #self.cursor = self.db_conn.cursor() self.id = None self.type = None self.group = None @@ -271,7 +276,7 @@ class GenotypeDataSet(DataSet): def check_confidentiality(self): return geno_mrna_confidentiality(self) - def get_trait_info(self, trait_list): + def get_trait_info(self, trait_list, species=None): for this_trait in trait_list: if not this_trait.haveinfo: this_trait.retrieveInfo() @@ -355,7 +360,7 @@ class MrnaAssayDataSet(DataSet): ProbeFreeze.InbredSetId = InbredSet.Id AND ProbeFreeze.Id = ProbeSetFreeze.ProbeFreezeId AND ProbeSetFreeze.Name = "%s" - ''' % self.db_conn.escape_string(self.name) + ''' % g.db.escape_string(self.name) def check_confidentiality(self): diff --git a/wqflask/base/webqtlConfigLocal.py b/wqflask/base/webqtlConfigLocal.py index 5aab48ac..84686234 100755 --- a/wqflask/base/webqtlConfigLocal.py +++ b/wqflask/base/webqtlConfigLocal.py @@ -4,12 +4,12 @@ MYSQL_SERVER = 'localhost' DB_NAME = 'db_webqtl_zas1024' -DB_USER = 'webqtlupd' +DB_USER = 'webqtl' DB_PASSWD = 'webqtl' MYSQL_UPDSERVER = 'localhost' DB_UPDNAME = 'db_webqtl_zas1024' -DB_UPDUSER = 'webqtlupd' +DB_UPDUSER = 'webqtl' DB_UPDPASSWD = 'webqtl' GNROOT = '/home/zas1024/gn/' diff --git a/wqflask/base/webqtlTrait.py b/wqflask/base/webqtlTrait.py index cc0e2321..1dceba08 100755 --- a/wqflask/base/webqtlTrait.py +++ b/wqflask/base/webqtlTrait.py @@ -12,6 +12,7 @@ from utility import webqtlUtil from pprint import pformat as pf +from flask import Flask, g class webqtlTrait: """ @@ -20,38 +21,46 @@ class webqtlTrait: """ - def __init__(self, db_conn, **kw): + def __init__(self, **kw): print("in webqtlTrait") - self.db_conn = db_conn - self.cursor = self.db_conn.cursor() - self.dataset = None # database object - self.name = '' # Trait ID, ProbeSet ID, Published ID, etc. - self.cellid = '' - self.identification = 'un-named trait' - self.group = '' - self.haveinfo = 0 - self.sequence = '' # Blat sequence, available for ProbeSet - self.data = {} - print("foo") - print("kw in webqtlTrait are:", pf(kw)) - print("printed\n\n") - for name, value in kw.items(): - if self.__dict__.has_key(name): - setattr(self, name, value) - elif name == 'fullname': - name2 = value.split("::") - if len(name2) == 2: - self.dataset, self.name = name2 - elif len(name2) == 3: - self.dataset, self.name, self.cellid = name2 - else: - raise KeyError, repr(value) + ' parameter format error.' - else: - raise KeyError, repr(name) + ' not a valid parameter for this class.' + #self.db_conn = db_conn + #self.cursor = self.db_conn.cursor() + self.dataset = kw.get('dataset', None) # database object + self.name = kw.get('name', None) # Trait ID, ProbeSet ID, Published ID, etc. + self.cellid = kw.get('cellid', None) + self.identification = kw.get('identification', 'un-named trait') + self.group = kw.get('group', None) + self.haveinfo = kw.get(haveinfo, False) + self.sequence = kw.get(sequence, None) # Blat sequence, available for ProbeSet + self.data = kw.get(data, {}) + + if kw.get('fullname'): + name2 = value.split("::") + if len(name2) == 2: + self.dataset, self.name = name2 + elif len(name2) == 3: + self.dataset, self.name, self.cellid = name2 + + #print("foo") + #print("kw in webqtlTrait are:", pf(kw)) + #print("printed\n\n") + #for name, value in kw.items(): + # if self.__dict__.has_key(name): + # setattr(self, name, value) + # elif name == 'fullname': + # name2 = value.split("::") + # if len(name2) == 2: + # self.dataset, self.name = name2 + # elif len(name2) == 3: + # self.dataset, self.name, self.cellid = name2 + # else: + # raise KeyError, repr(value) + ' parameter format error.' + # else: + # raise KeyError, repr(name) + ' not a valid parameter for this class.' if self.dataset and isinstance(self.dataset, basestring): - assert self.cursor, "Don't have a cursor" - self.dataset = create_dataset(self.db_conn, self.dataset) + #assert self.cursor, "Don't have a cursor" + self.dataset = create_dataset(self.dataset) #if self.dataset == None, not from a database print("self.dataset is:", self.dataset, type(self.dataset)) @@ -432,7 +441,7 @@ class webqtlTrait: self.cursor.execute(query) traitInfo = self.cursor.fetchone() if traitInfo: - self.haveinfo = 1 + self.haveinfo = True #XZ: assign SQL query result to trait attributes. for i, field in enumerate(self.dataset.display_fields): diff --git a/wqflask/cfg/zach_settings.py b/wqflask/cfg/zach_settings.py index ed97f222..8d3bf4ab 100644 --- a/wqflask/cfg/zach_settings.py +++ b/wqflask/cfg/zach_settings.py @@ -1,2 +1,5 @@ LOGFILE = """/tmp/flask_gn_log""" + TRAP_BAD_REQUEST_ERRORS = True + +DB_URI = """mysql://webqtl:webqtl@localhost/db_webqtl_zas1024"""
\ No newline at end of file diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py index 17078802..bae3df08 100644 --- a/wqflask/wqflask/do_search.py +++ b/wqflask/wqflask/do_search.py @@ -144,14 +144,22 @@ class PhenotypeSearch(DoSearch): 'Publication.Title', 'Publication.Authors', 'PublishXRef.Id') + + header_fields = ['', + 'Record ID', + 'Description', + 'Authors', + 'Year', + 'Max LRS', + 'Max LRS Location'] def get_where_clause(self): """Generate clause for WHERE portion of query""" #Todo: Zach will figure out exactly what both these lines mean #and comment here - if "'" not in self.search_term: - search_term = "[[:<:]]" + self.search_term + "[[:>:]]" + if "'" not in self.search_term[0]: + search_term = "[[:<:]]" + self.search_term[0] + "[[:>:]]" # This adds a clause to the query that matches the search term # against each field in the search_fields tuple @@ -195,6 +203,10 @@ class GenotypeSearch(DoSearch): FROM GenoXRef, GenoFreeze, Geno """ search_fields = ('Name', 'Chr') + + header_fields = ['', + 'Record ID', + 'Location'] def get_fields_clause(self): """Generate clause for part of the WHERE portion of query""" @@ -203,13 +215,13 @@ class GenotypeSearch(DoSearch): # against each field in search_fields (above) fields_clause = [] - if "'" not in self.search_term: - self.search_term = "[[:<:]]" + self.search_term + "[[:>:]]" + if "'" not in self.search_term[0]: + self.search_term = "[[:<:]]" + self.search_term[0] + "[[:>:]]" for field in self.search_fields: fields_clause.append('''%s REGEXP "%s"''' % ("%s.%s" % self.mescape(self.dataset.type, - field, - self.search_term))) + field), + self.search_term)) print("hello ;where_clause is:", pf(fields_clause)) fields_clause = "(%s)" % ' OR '.join(fields_clause) diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py index c7bbdaf2..04b14e8f 100644 --- a/wqflask/wqflask/search_results.py +++ b/wqflask/wqflask/search_results.py @@ -83,7 +83,8 @@ class SearchResultPage(templatePage): self.dataset_group_ids = map(lambda x: x[2], results) else: print("self.dataset is:", pf(self.dataset)) - self.dataset = create_dataset(self.db_conn, self.dataset) + # Replaces a string with an object + self.dataset = create_dataset(self.dataset) print("self.dataset is now:", pf(self.dataset)) self.search() diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py index e8ad0b1d..7060f2ea 100755 --- a/wqflask/wqflask/show_trait/show_trait.py +++ b/wqflask/wqflask/show_trait/show_trait.py @@ -31,16 +31,15 @@ from pprint import pformat as pf class ShowTrait(templatePage): - def __init__(self, fd): - self.fd = fd + def __init__(self, args): + print("in ShowTrait, args are:", args) + self.group = args.group + self.trait_id = trait_id + self.dataset = dataset - print("red1 fd.group:", fd.group) - templatePage.__init__(self, fd) + #assert self.openMysql(), "No database!" - print("red2 fd.group:", fd.group) - assert self.openMysql(), "No database!" - - print("red3 fd.group:", fd.group) + #print("red3 fd.group:", fd.group) this_trait = self.get_this_trait() print("red4 fd.group:", fd.group) @@ -183,11 +182,13 @@ class ShowTrait(templatePage): #if traitInfos: # database, ProbeSetID, CellID = traitInfos #else: - dataset = self.fd['dataset'] - trait_id = self.fd['trait_id'] - cell_id = self.fd.get('CellID') + #dataset = self.fd['dataset'] + #trait_id = self.fd['trait_id'] + #cell_id = self.fd.get('CellID') - this_trait = webqtlTrait(self.db_conn, dataset=dataset, name=trait_id, cellid=cell_id) + this_trait = webqtlTrait(dataset=dataset, + name=trait_id, + cellid=cell_id) ##identification, etc. self.fd.identification = '%s : %s' % (this_trait.dataset.shortname, trait_id) diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index cdc3379f..17dc42fb 100644 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -7,10 +7,12 @@ import simplejson as json import yaml import flask +import sqlalchemy +#import config from wqflask import app -from flask import render_template, request, make_response, Response +from flask import render_template, request, make_response, Response, Flask, g, config from wqflask import search_results from wqflask.show_trait import show_trait @@ -27,6 +29,10 @@ from pprint import pformat as pf #logging.basicConfig(filename="/tmp/gn_log", level=logging.INFO) #_log = logging.getLogger("correlation") +@app.before_request +def connect_db(): + print("blue app.config:", app.config, pf(vars(app.config))) + g.db = sqlalchemy.create_engine(app.config['DB_URI']) @app.route("/") def index_page(): @@ -86,9 +92,9 @@ def whats_new_page(): @app.route("/show_trait") def show_trait_page(): # Here it's currently too complicated not to use an fd that is a webqtlFormData - fd = webqtlFormData.webqtlFormData(request.args) - print("stp y1:", pf(vars(fd))) - template_vars = show_trait.ShowTrait(fd) + #fd = webqtlFormData.webqtlFormData(request.args) + #print("stp y1:", pf(vars(fd))) + template_vars = show_trait.ShowTrait(request.args) template_vars.js_data = json.dumps(template_vars.js_data, default=json_default_handler, indent=" ", |