diff options
Diffstat (limited to 'wqflask/base')
| -rw-r--r-- | wqflask/base/data_set.py | 3 | ||||
| -rw-r--r-- | wqflask/base/mrna_assay_tissue_data.py | 6 | ||||
| -rw-r--r-- | wqflask/base/trait.py | 18 | ||||
| -rw-r--r-- | wqflask/base/webqtlCaseData.py | 6 | ||||
| -rw-r--r-- | wqflask/base/webqtlConfig.py | 24 |
5 files changed, 36 insertions, 21 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index 1b4e1195..fddfce58 100644 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -107,7 +107,8 @@ Publish or ProbeSet. E.g. else: new_type = "ProbeSet" self.datasets[short_dataset_name] = new_type - logger.info("datasets",self.datasets) + # Set LOG_LEVEL_DEBUG=5 to see the following: + logger.debugf(5,"datasets",self.datasets) def __call__(self, name): return self.datasets[name] diff --git a/wqflask/base/mrna_assay_tissue_data.py b/wqflask/base/mrna_assay_tissue_data.py index e99ef7b5..eb836e6c 100644 --- a/wqflask/base/mrna_assay_tissue_data.py +++ b/wqflask/base/mrna_assay_tissue_data.py @@ -57,7 +57,7 @@ class MrnaAssayTissueData(object): as x inner join TissueProbeSetXRef as t on t.Symbol = x.Symbol and t.Mean = x.maxmean; '''.format(in_clause) - logger.sql(query) + results = g.db.execute(query).fetchall() lower_symbols = [] @@ -91,7 +91,7 @@ class MrnaAssayTissueData(object): def get_symbol_values_pairs(self): id_list = [self.data[symbol].data_id for symbol in self.data] - + symbol_values_dict = {} if len(id_list) > 0: @@ -100,8 +100,6 @@ class MrnaAssayTissueData(object): WHERE TissueProbeSetData.Id IN {} and TissueProbeSetXRef.DataId = TissueProbeSetData.Id""".format(db_tools.create_in_clause(id_list)) - logger.sql('tissue query',query) - results = g.db.execute(query).fetchall() for result in results: if result.Symbol.lower() not in symbol_values_dict: diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py index 9566c192..32032ba7 100644 --- a/wqflask/base/trait.py +++ b/wqflask/base/trait.py @@ -116,7 +116,6 @@ class GeneralTrait(object): return stringy - def display_name(self): stringy = "" if self.dataset and self.name: @@ -323,7 +322,7 @@ class GeneralTrait(object): #phenotype traits, then display the pre-publication description instead #of the post-publication description if self.confidential: - self.description_display = "" + self.description_display = self.pre_publication_description #if not webqtlUtil.hasAccessToConfidentialPhenotypeTrait( # privilege=self.dataset.privilege, @@ -331,11 +330,11 @@ class GeneralTrait(object): # authorized_users=self.authorized_users): # # description = self.pre_publication_description - - if description: - self.description_display = description.strip() else: - self.description_display = "" + if description: + self.description_display = description.strip() + else: + self.description_display = "" if not self.year.isdigit(): self.pubmed_text = "N/A" @@ -364,7 +363,7 @@ class GeneralTrait(object): FROM Homologene, Species, InbredSet WHERE - Homologene.GeneId =%s AND + Homologene.GeneId ='%s' AND InbredSet.Name = '%s' AND InbredSet.SpeciesId = Species.Id AND Species.TaxonomyId = Homologene.TaxonomyId @@ -613,7 +612,10 @@ class GeneralTrait(object): if self.probe_target_description: formatted += "; " + self.probe_target_description elif self.dataset.type == 'Publish': - formatted = self.post_publication_description + if self.confidential: + formatted = self.pre_publication_description + else: + formatted = self.post_publication_description else: formatted = "Not available" return formatted.capitalize() diff --git a/wqflask/base/webqtlCaseData.py b/wqflask/base/webqtlCaseData.py index c80fcb65..2f88f778 100644 --- a/wqflask/base/webqtlCaseData.py +++ b/wqflask/base/webqtlCaseData.py @@ -16,8 +16,6 @@ # Contact Drs. Robert W. Williams and Xiaodong Zhou (2010) # at rwilliams@uthsc.edu and xzhou15@uthsc.edu # -# -# # This module is used by GeneNetwork project (www.genenetwork.org) # # Created by GeneNetwork Core Team 2010/08/10 @@ -52,6 +50,10 @@ class webqtlCaseData(object): str += " variance=%2.3f" % self.variance if self.num_cases != None: str += " ndata=%d" % self.num_cases + if self.name != None: + str += " name=%s" % self.name + if self.name2 != None: + str += " name2=%s" % self.name2 return str @property diff --git a/wqflask/base/webqtlConfig.py b/wqflask/base/webqtlConfig.py index f76d8140..e5f10edf 100644 --- a/wqflask/base/webqtlConfig.py +++ b/wqflask/base/webqtlConfig.py @@ -8,7 +8,7 @@ # ######################################### -from utility.tools import valid_path, mk_dir, assert_dir, flat_files, TEMPDIR +from utility.tools import valid_path, mk_dir, assert_dir, assert_writable_dir, flat_files, TEMPDIR #Debug Level #1 for debug, mod python will reload import each time @@ -60,24 +60,36 @@ ENSEMBLETRANSCRIPT_URL="http://useast.ensembl.org/Mus_musculus/Lucene/Details?sp # HTMLPATH is replaced by GENODIR # IMGDIR is replaced by GENERATED_IMAGE_DIR -# Temporary storage: +# Temporary storage (note that this TMPDIR can be set as an +# environment variable - use utility.tools.TEMPDIR when you +# want to reach this base dir +assert_writable_dir(TEMPDIR) + TMPDIR = mk_dir(TEMPDIR+'/gn2/') -CACHEDIR = mk_dir(TEMPDIR+'/cache/') +assert_writable_dir(TMPDIR) + +CACHEDIR = mk_dir(TMPDIR+'/cache/') # We can no longer write into the git tree: GENERATED_IMAGE_DIR = mk_dir(TMPDIR+'/generated/') GENERATED_TEXT_DIR = mk_dir(TMPDIR+'/generated_text/') +# Make sure we have permissions to access these +assert_writable_dir(CACHEDIR) +assert_writable_dir(GENERATED_IMAGE_DIR) +assert_writable_dir(GENERATED_TEXT_DIR) + # Flat file directories GENODIR = flat_files('genotype')+'/' +assert_dir(GENODIR) + +# JSON genotypes are OBSOLETE JSON_GENODIR = flat_files('genotype/json')+'/' if not valid_path(JSON_GENODIR): # fall back on old location (move the dir, FIXME) JSON_GENODIR = flat_files('json') -assert_dir(GENODIR) +# Are we using the following...? PORTADDR = "http://50.16.251.170" - INFOPAGEHREF = '/dbdoc/%s.html' CGIDIR = '/webqtl/' #XZ: The variable name 'CGIDIR' should be changed to 'PYTHONDIR' SCRIPTFILE = 'main.py' - |