Commit 84bedb3f authored by Mathieu Courcelles's avatar Mathieu Courcelles

Rename to CLMSVault

parent 8507813d
......@@ -292,15 +292,13 @@ def read_PDB_sequences(pdb_file):
for residue in chain:
if residue.get_resname() == 'HOH':
print '-'
#sequence += '-'
elif residue.get_resname() == 'SEP':
print 'S'
if residue.get_resname() == 'SEP':
sequence += 'S'
else:
print three_to_one(residue.get_resname())
sequence += three_to_one(residue.get_resname())
try:
sequence += three_to_one(residue.get_resname())
except KeyError:
pass
pdb_sequences[chain] = sequence
......@@ -325,6 +323,10 @@ def sequences_alignment(fasta_sequences, pdb_sequences, protein_identity):
for (chain, pdb_seq) in pdb_sequences.items():
# Skip empty pdb_sequence
if pdb_seq == '':
continue
# Do protein sequence aligment with FASTA sequence
alignment = pairwise2.align.localms(fasta_seq, pdb_seq, 2, -1, -1, -0.5)
fasta_seq_aligned = str(alignment[0][0])
......
......@@ -128,10 +128,10 @@ MIDDLEWARE_CLASSES = (
# 'django.middleware.clickjacking.XFrameOptionsMiddleware',
)
ROOT_URLCONF = 'CLMSpipeline.urls'
ROOT_URLCONF = 'CLMSVault.urls'
# Python dotted path to the WSGI application used by Django's runserver.
WSGI_APPLICATION = 'CLMSpipeline.wsgi.application'
WSGI_APPLICATION = 'CLMSVault.wsgi.application'
TEMPLATE_DIRS = (
# Put strings here, like "/home/html/django_templates" or "C:/www/django/templates".
......@@ -169,8 +169,8 @@ INSTALLED_APPS = (
# Schema migration
#'south',
# CLMSpipeline app
'CLMSpipeline.CLMSpipeline_app',
# CLMSVault app
'CLMSVault.CLMSVault_app',
)
# A sample logging configuration. The only tangible logging
......@@ -207,6 +207,6 @@ TEST_RUNNER = 'django.test.runner.DiscoverRunner'
GRAPPELLI_ADMIN_TITLE = 'CLMSVault - Protein cross-linking mass spectrometry repository'
GRAPPELLI_INDEX_DASHBOARD = 'CLMSpipeline.dashboard.CustomIndexDashboard'
GRAPPELLI_INDEX_DASHBOARD = 'CLMSVault.dashboard.CustomIndexDashboard'
# # Copyright 2013 Mathieu Courcelles
# # Mike Tyers's lab / IRIC / Universite de Montreal
# Import standard librariesdjang
# Import Django related libraries
# Import project libraries
from .base import *
########## IN-MEMORY TEST DATABASE
DATABASES = {
"default": {
"ENGINE": "django.db.backends.sqlite3",
"NAME": ":memory:",
"USER": "",
"PASSWORD": "",
"HOST": "",
"PORT": "",
},
}
os.environ['REUSE_DB'] = "1"
SOUTH_TESTS_MIGRATE = False
\ No newline at end of file
......@@ -19,7 +19,7 @@ import os
# if running multiple sites in the same mod_wsgi process. To fix this, use
# mod_wsgi daemon mode with each site in its own daemon process, or use
# os.environ["DJANGO_SETTINGS_MODULE"] = "CLMSpipeline.settings"
os.environ.setdefault("DJANGO_SETTINGS_MODULE", "CLMSpipeline.settings")
os.environ.setdefault("DJANGO_SETTINGS_MODULE", "CLMSVault.settings")
# This application object is used by any WSGI server configured to use this
# file. This includes Django's development server, if the WSGI_APPLICATION
......
python manage.py runserver 0.0.0.0:8000
\ No newline at end of file
source ~/.profile
python manage.py runserver 0.0.0.0:8000
\ No newline at end of file
# -*- coding: utf-8 -*-
import datetime
from south.db import db
from south.v2 import SchemaMigration
from django.db import models
class Migration(SchemaMigration):
def forwards(self, orm):
# Changing field 'Dataset.cross_linker'
db.alter_column(u'CLMSpipeline_app_dataset', 'cross_linker_id', self.gf('django.db.models.fields.related.ForeignKey')(to=orm['CLMSpipeline_app.CrossLinker'], null=True))
# Changing field 'Dataset.fasta_db'
db.alter_column(u'CLMSpipeline_app_dataset', 'fasta_db_id', self.gf('django.db.models.fields.related.ForeignKey')(to=orm['CLMSpipeline_app.FastaDB'], null=True))
# Changing field 'Dataset.instrument_name'
db.alter_column(u'CLMSpipeline_app_dataset', 'instrument_name_id', self.gf('django.db.models.fields.related.ForeignKey')(to=orm['CLMSpipeline_app.Instrument'], null=True))
# Changing field 'Dataset.search_algorithm'
db.alter_column(u'CLMSpipeline_app_dataset', 'search_algorithm_id', self.gf('django.db.models.fields.related.ForeignKey')(to=orm['CLMSpipeline_app.searchAlgorithm'], null=True))
def backwards(self, orm):
# Changing field 'Dataset.cross_linker'
db.alter_column(u'CLMSpipeline_app_dataset', 'cross_linker_id', self.gf('django.db.models.fields.related.ForeignKey')(default='', to=orm['CLMSpipeline_app.CrossLinker']))
# Changing field 'Dataset.fasta_db'
db.alter_column(u'CLMSpipeline_app_dataset', 'fasta_db_id', self.gf('django.db.models.fields.related.ForeignKey')(default='', to=orm['CLMSpipeline_app.FastaDB']))
# Changing field 'Dataset.instrument_name'
db.alter_column(u'CLMSpipeline_app_dataset', 'instrument_name_id', self.gf('django.db.models.fields.related.ForeignKey')(default='', to=orm['CLMSpipeline_app.Instrument']))
# Changing field 'Dataset.search_algorithm'
db.alter_column(u'CLMSpipeline_app_dataset', 'search_algorithm_id', self.gf('django.db.models.fields.related.ForeignKey')(default='', to=orm['CLMSpipeline_app.searchAlgorithm']))
models = {
u'CLMSpipeline_app.clpeptide': {
'Meta': {'ordering': "['-match_score']", 'object_name': 'CLPeptide'},
'autovalidated': ('django.db.models.fields.BooleanField', [], {'default': 'False'}),
'cross_link': ('django.db.models.fields.BooleanField', [], {'default': 'False'}),
'dataset': ('django.db.models.fields.related.ManyToManyField', [], {'to': u"orm['CLMSpipeline_app.Dataset']", 'symmetrical': 'False'}),
'delta': ('django.db.models.fields.FloatField', [], {}),
'display_protein1': ('django.db.models.fields.CharField', [], {'max_length': '250'}),
'display_protein2': ('django.db.models.fields.CharField', [], {'max_length': '250'}),
'error': ('django.db.models.fields.FloatField', [], {}),
u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}),
'link_type': ('django.db.models.fields.IntegerField', [], {}),
'match_score': ('django.db.models.fields.FloatField', [], {}),
'not_decoy': ('django.db.models.fields.BooleanField', [], {'default': 'False'}),
'notes': ('django.db.models.fields.CharField', [], {'max_length': '100'}),
'pep1_link_pos': ('django.db.models.fields.IntegerField', [], {}),
'pep2_link_pos': ('django.db.models.fields.IntegerField', [], {}),
'peptide1': ('django.db.models.fields.CharField', [], {'max_length': '100'}),
'peptide2': ('django.db.models.fields.CharField', [], {'max_length': '100'}),
'peptide_position1': ('django.db.models.fields.IntegerField', [], {}),
'peptide_position2': ('django.db.models.fields.IntegerField', [], {}),
'peptide_wo_mod1': ('django.db.models.fields.CharField', [], {'max_length': '150'}),
'peptide_wo_mod2': ('django.db.models.fields.CharField', [], {'max_length': '150'}),
'precursor_charge': ('django.db.models.fields.CharField', [], {'max_length': '5'}),
'precursor_intensity': ('django.db.models.fields.FloatField', [], {}),
'precursor_mz': ('django.db.models.fields.FloatField', [], {}),
'rank': ('django.db.models.fields.IntegerField', [], {}),
'rejected': ('django.db.models.fields.BooleanField', [], {'default': 'False'}),
'run_name': ('django.db.models.fields.CharField', [], {'max_length': '1000'}),
'scan_number': ('django.db.models.fields.IntegerField', [], {}),
'spectrum_intensity_coverage': ('django.db.models.fields.FloatField', [], {}),
'total_fragment_matches': ('django.db.models.fields.IntegerField', [], {}),
'validated': ('django.db.models.fields.CharField', [], {'max_length': '50'})
},
u'CLMSpipeline_app.clpeptidefilter': {
'Meta': {'object_name': 'CLPeptideFilter'},
'creation_date': ('django.db.models.fields.DateTimeField', [], {'auto_now_add': 'True', 'blank': 'True'}),
'description': ('django.db.models.fields.TextField', [], {'blank': 'True'}),
u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}),
'name': ('django.db.models.fields.CharField', [], {'max_length': '100'})
},
u'CLMSpipeline_app.clpeptidefilterparam': {
'Meta': {'object_name': 'CLPeptideFilterParam'},
'clpeptidefilter': ('django.db.models.fields.related.ForeignKey', [], {'to': u"orm['CLMSpipeline_app.CLPeptideFilter']"}),
'field': ('django.db.models.fields.CharField', [], {'max_length': '100'}),
'field_lookup': ('django.db.models.fields.CharField', [], {'max_length': '50'}),
u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}),
'method': ('django.db.models.fields.CharField', [], {'max_length': '20'}),
'value': ('django.db.models.fields.CharField', [], {'max_length': '50'})
},
u'CLMSpipeline_app.crosslinker': {
'Meta': {'ordering': "['name']", 'object_name': 'CrossLinker'},
u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}),
'name': ('django.db.models.fields.CharField', [], {'unique': 'True', 'max_length': '100'})
},
u'CLMSpipeline_app.dataset': {
'Meta': {'ordering': "['-creation_date']", 'object_name': 'Dataset'},
'creation_date': ('django.db.models.fields.DateTimeField', [], {'auto_now_add': 'True', 'blank': 'True'}),
'cross_linker': ('django.db.models.fields.related.ForeignKey', [], {'to': u"orm['CLMSpipeline_app.CrossLinker']", 'null': 'True'}),
'description': ('django.db.models.fields.TextField', [], {'blank': 'True'}),
'fasta_db': ('django.db.models.fields.related.ForeignKey', [], {'to': u"orm['CLMSpipeline_app.FastaDB']", 'null': 'True'}),
u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}),
'instrument_name': ('django.db.models.fields.related.ForeignKey', [], {'to': u"orm['CLMSpipeline_app.Instrument']", 'null': 'True'}),
'name': ('django.db.models.fields.CharField', [], {'max_length': '100'}),
'prefix': ('django.db.models.fields.CharField', [], {'max_length': '25'}),
'search_algorithm': ('django.db.models.fields.related.ForeignKey', [], {'to': u"orm['CLMSpipeline_app.searchAlgorithm']", 'null': 'True'})
},
u'CLMSpipeline_app.fastadb': {
'Meta': {'ordering': "['name']", 'object_name': 'FastaDB'},
u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}),
'name': ('django.db.models.fields.CharField', [], {'unique': 'True', 'max_length': '200'})
},
u'CLMSpipeline_app.instrument': {
'Meta': {'ordering': "['name']", 'object_name': 'Instrument'},
u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}),
'name': ('django.db.models.fields.CharField', [], {'unique': 'True', 'max_length': '100'})
},
u'CLMSpipeline_app.processeddataset': {
'Meta': {'ordering': "['-creation_date']", 'object_name': 'ProcessedDataset', '_ormbases': [u'CLMSpipeline_app.Dataset']},
'clpeptidefilter': ('django.db.models.fields.related.ForeignKey', [], {'to': u"orm['CLMSpipeline_app.CLPeptideFilter']"}),
u'dataset_ptr': ('django.db.models.fields.related.OneToOneField', [], {'to': u"orm['CLMSpipeline_app.Dataset']", 'unique': 'True', 'primary_key': 'True'}),
'datasets': ('django.db.models.fields.related.ManyToManyField', [], {'related_name': "'processed_datasets'", 'symmetrical': 'False', 'to': u"orm['CLMSpipeline_app.Dataset']"})
},
u'CLMSpipeline_app.rawdataset': {
'Meta': {'ordering': "['-creation_date']", 'object_name': 'RawDataset', '_ormbases': [u'CLMSpipeline_app.Dataset']},
u'dataset_ptr': ('django.db.models.fields.related.OneToOneField', [], {'to': u"orm['CLMSpipeline_app.Dataset']", 'unique': 'True', 'primary_key': 'True'}),
'extra_file': ('django.db.models.fields.files.FileField', [], {'max_length': '100', 'blank': 'True'}),
'file': ('django.db.models.fields.files.FileField', [], {'max_length': '100'}),
'parsing_log': ('django.db.models.fields.CharField', [], {'max_length': '1000', 'null': 'True', 'blank': 'True'}),
'parsing_status': ('django.db.models.fields.BooleanField', [], {'default': 'False'})
},
u'CLMSpipeline_app.searchalgorithm': {
'Meta': {'ordering': "['name']", 'object_name': 'searchAlgorithm'},
u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}),
'name': ('django.db.models.fields.CharField', [], {'unique': 'True', 'max_length': '100'})
}
}
complete_apps = ['CLMSpipeline_app']
\ No newline at end of file
# -*- coding: utf-8 -*-
import datetime
from south.db import db
from south.v2 import SchemaMigration
from django.db import models
class Migration(SchemaMigration):
def forwards(self, orm):
# Changing field 'ProcessedDataset.clpeptidefilter'
db.alter_column(u'CLMSpipeline_app_processeddataset', 'clpeptidefilter_id', self.gf('django.db.models.fields.related.ForeignKey')(to=orm['CLMSpipeline_app.CLPeptideFilter'], null=True))
def backwards(self, orm):
# Changing field 'ProcessedDataset.clpeptidefilter'
db.alter_column(u'CLMSpipeline_app_processeddataset', 'clpeptidefilter_id', self.gf('django.db.models.fields.related.ForeignKey')(default='', to=orm['CLMSpipeline_app.CLPeptideFilter']))
models = {
u'CLMSpipeline_app.clpeptide': {
'Meta': {'ordering': "['-match_score']", 'object_name': 'CLPeptide'},
'autovalidated': ('django.db.models.fields.BooleanField', [], {'default': 'False'}),
'cross_link': ('django.db.models.fields.BooleanField', [], {'default': 'False'}),
'dataset': ('django.db.models.fields.related.ManyToManyField', [], {'to': u"orm['CLMSpipeline_app.Dataset']", 'symmetrical': 'False'}),
'delta': ('django.db.models.fields.FloatField', [], {}),
'display_protein1': ('django.db.models.fields.CharField', [], {'max_length': '250'}),
'display_protein2': ('django.db.models.fields.CharField', [], {'max_length': '250'}),
'error': ('django.db.models.fields.FloatField', [], {}),
u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}),
'link_type': ('django.db.models.fields.IntegerField', [], {}),
'match_score': ('django.db.models.fields.FloatField', [], {}),
'not_decoy': ('django.db.models.fields.BooleanField', [], {'default': 'False'}),
'notes': ('django.db.models.fields.CharField', [], {'max_length': '100'}),
'pep1_link_pos': ('django.db.models.fields.IntegerField', [], {}),
'pep2_link_pos': ('django.db.models.fields.IntegerField', [], {}),
'peptide1': ('django.db.models.fields.CharField', [], {'max_length': '100'}),
'peptide2': ('django.db.models.fields.CharField', [], {'max_length': '100'}),
'peptide_position1': ('django.db.models.fields.IntegerField', [], {}),
'peptide_position2': ('django.db.models.fields.IntegerField', [], {}),
'peptide_wo_mod1': ('django.db.models.fields.CharField', [], {'max_length': '150'}),
'peptide_wo_mod2': ('django.db.models.fields.CharField', [], {'max_length': '150'}),
'precursor_charge': ('django.db.models.fields.CharField', [], {'max_length': '5'}),
'precursor_intensity': ('django.db.models.fields.FloatField', [], {}),
'precursor_mz': ('django.db.models.fields.FloatField', [], {}),
'rank': ('django.db.models.fields.IntegerField', [], {}),
'rejected': ('django.db.models.fields.BooleanField', [], {'default': 'False'}),
'run_name': ('django.db.models.fields.CharField', [], {'max_length': '1000'}),
'scan_number': ('django.db.models.fields.IntegerField', [], {}),
'spectrum_intensity_coverage': ('django.db.models.fields.FloatField', [], {}),
'total_fragment_matches': ('django.db.models.fields.IntegerField', [], {}),
'validated': ('django.db.models.fields.CharField', [], {'max_length': '50'})
},
u'CLMSpipeline_app.clpeptidefilter': {
'Meta': {'object_name': 'CLPeptideFilter'},
'creation_date': ('django.db.models.fields.DateTimeField', [], {'auto_now_add': 'True', 'blank': 'True'}),
'description': ('django.db.models.fields.TextField', [], {'blank': 'True'}),
u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}),
'name': ('django.db.models.fields.CharField', [], {'max_length': '100'})
},
u'CLMSpipeline_app.clpeptidefilterparam': {
'Meta': {'object_name': 'CLPeptideFilterParam'},
'clpeptidefilter': ('django.db.models.fields.related.ForeignKey', [], {'to': u"orm['CLMSpipeline_app.CLPeptideFilter']"}),
'field': ('django.db.models.fields.CharField', [], {'max_length': '100'}),
'field_lookup': ('django.db.models.fields.CharField', [], {'max_length': '50'}),
u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}),
'method': ('django.db.models.fields.CharField', [], {'max_length': '20'}),
'value': ('django.db.models.fields.CharField', [], {'max_length': '50'})
},
u'CLMSpipeline_app.crosslinker': {
'Meta': {'ordering': "['name']", 'object_name': 'CrossLinker'},
u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}),
'name': ('django.db.models.fields.CharField', [], {'unique': 'True', 'max_length': '100'})
},
u'CLMSpipeline_app.dataset': {
'Meta': {'ordering': "['-creation_date']", 'object_name': 'Dataset'},
'creation_date': ('django.db.models.fields.DateTimeField', [], {'auto_now_add': 'True', 'blank': 'True'}),
'cross_linker': ('django.db.models.fields.related.ForeignKey', [], {'to': u"orm['CLMSpipeline_app.CrossLinker']", 'null': 'True'}),
'description': ('django.db.models.fields.TextField', [], {'blank': 'True'}),
'fasta_db': ('django.db.models.fields.related.ForeignKey', [], {'to': u"orm['CLMSpipeline_app.FastaDB']", 'null': 'True'}),
u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}),
'instrument_name': ('django.db.models.fields.related.ForeignKey', [], {'to': u"orm['CLMSpipeline_app.Instrument']", 'null': 'True'}),
'name': ('django.db.models.fields.CharField', [], {'max_length': '100'}),
'prefix': ('django.db.models.fields.CharField', [], {'max_length': '25'}),
'search_algorithm': ('django.db.models.fields.related.ForeignKey', [], {'to': u"orm['CLMSpipeline_app.searchAlgorithm']", 'null': 'True'})
},
u'CLMSpipeline_app.fastadb': {
'Meta': {'ordering': "['name']", 'object_name': 'FastaDB'},
u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}),
'name': ('django.db.models.fields.CharField', [], {'unique': 'True', 'max_length': '200'})
},
u'CLMSpipeline_app.instrument': {
'Meta': {'ordering': "['name']", 'object_name': 'Instrument'},
u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}),
'name': ('django.db.models.fields.CharField', [], {'unique': 'True', 'max_length': '100'})
},
u'CLMSpipeline_app.processeddataset': {
'Meta': {'ordering': "['-creation_date']", 'object_name': 'ProcessedDataset', '_ormbases': [u'CLMSpipeline_app.Dataset']},
'clpeptidefilter': ('django.db.models.fields.related.ForeignKey', [], {'to': u"orm['CLMSpipeline_app.CLPeptideFilter']", 'null': 'True', 'blank': 'True'}),
u'dataset_ptr': ('django.db.models.fields.related.OneToOneField', [], {'to': u"orm['CLMSpipeline_app.Dataset']", 'unique': 'True', 'primary_key': 'True'}),
'datasets': ('django.db.models.fields.related.ManyToManyField', [], {'related_name': "'processed_datasets'", 'symmetrical': 'False', 'to': u"orm['CLMSpipeline_app.Dataset']"})
},
u'CLMSpipeline_app.rawdataset': {
'Meta': {'ordering': "['-creation_date']", 'object_name': 'RawDataset', '_ormbases': [u'CLMSpipeline_app.Dataset']},
u'dataset_ptr': ('django.db.models.fields.related.OneToOneField', [], {'to': u"orm['CLMSpipeline_app.Dataset']", 'unique': 'True', 'primary_key': 'True'}),
'extra_file': ('django.db.models.fields.files.FileField', [], {'max_length': '100', 'blank': 'True'}),
'file': ('django.db.models.fields.files.FileField', [], {'max_length': '100'}),
'parsing_log': ('django.db.models.fields.CharField', [], {'max_length': '1000', 'null': 'True', 'blank': 'True'}),
'parsing_status': ('django.db.models.fields.BooleanField', [], {'default': 'False'})
},
u'CLMSpipeline_app.searchalgorithm': {
'Meta': {'ordering': "['name']", 'object_name': 'searchAlgorithm'},
u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}),
'name': ('django.db.models.fields.CharField', [], {'unique': 'True', 'max_length': '100'})
}
}
complete_apps = ['CLMSpipeline_app']
\ No newline at end of file
# -*- coding: utf-8 -*-
import datetime
from south.db import db
from south.v2 import SchemaMigration
from django.db import models
class Migration(SchemaMigration):
def forwards(self, orm):
# Changing field 'CLPeptide.link_type'
db.alter_column(u'CLMSpipeline_app_clpeptide', 'link_type', self.gf('django.db.models.fields.CharField')(max_length=50))
def backwards(self, orm):
# Changing field 'CLPeptide.link_type'
db.alter_column(u'CLMSpipeline_app_clpeptide', 'link_type', self.gf('django.db.models.fields.IntegerField')())
models = {
u'CLMSpipeline_app.clpeptide': {
'Meta': {'ordering': "['-match_score']", 'object_name': 'CLPeptide'},
'autovalidated': ('django.db.models.fields.BooleanField', [], {'default': 'False'}),
'cross_link': ('django.db.models.fields.BooleanField', [], {'default': 'False'}),
'dataset': ('django.db.models.fields.related.ManyToManyField', [], {'to': u"orm['CLMSpipeline_app.Dataset']", 'symmetrical': 'False'}),
'delta': ('django.db.models.fields.FloatField', [], {}),
'display_protein1': ('django.db.models.fields.CharField', [], {'max_length': '250'}),
'display_protein2': ('django.db.models.fields.CharField', [], {'max_length': '250'}),
'error': ('django.db.models.fields.FloatField', [], {}),
u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}),
'link_type': ('django.db.models.fields.CharField', [], {'max_length': '50'}),
'match_score': ('django.db.models.fields.FloatField', [], {}),
'not_decoy': ('django.db.models.fields.BooleanField', [], {'default': 'False'}),
'notes': ('django.db.models.fields.CharField', [], {'max_length': '100'}),
'pep1_link_pos': ('django.db.models.fields.IntegerField', [], {}),
'pep2_link_pos': ('django.db.models.fields.IntegerField', [], {}),
'peptide1': ('django.db.models.fields.CharField', [], {'max_length': '100'}),
'peptide2': ('django.db.models.fields.CharField', [], {'max_length': '100'}),
'peptide_position1': ('django.db.models.fields.IntegerField', [], {}),
'peptide_position2': ('django.db.models.fields.IntegerField', [], {}),
'peptide_wo_mod1': ('django.db.models.fields.CharField', [], {'max_length': '150'}),
'peptide_wo_mod2': ('django.db.models.fields.CharField', [], {'max_length': '150'}),
'precursor_charge': ('django.db.models.fields.CharField', [], {'max_length': '5'}),
'precursor_intensity': ('django.db.models.fields.FloatField', [], {}),
'precursor_mz': ('django.db.models.fields.FloatField', [], {}),
'rank': ('django.db.models.fields.IntegerField', [], {}),
'rejected': ('django.db.models.fields.BooleanField', [], {'default': 'False'}),
'run_name': ('django.db.models.fields.CharField', [], {'max_length': '1000'}),
'scan_number': ('django.db.models.fields.IntegerField', [], {}),
'spectrum_intensity_coverage': ('django.db.models.fields.FloatField', [], {}),
'total_fragment_matches': ('django.db.models.fields.IntegerField', [], {}),
'validated': ('django.db.models.fields.CharField', [], {'max_length': '50'})
},
u'CLMSpipeline_app.clpeptidefilter': {
'Meta': {'object_name': 'CLPeptideFilter'},
'creation_date': ('django.db.models.fields.DateTimeField', [], {'auto_now_add': 'True', 'blank': 'True'}),
'description': ('django.db.models.fields.TextField', [], {'blank': 'True'}),
u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}),
'name': ('django.db.models.fields.CharField', [], {'max_length': '100'})
},
u'CLMSpipeline_app.clpeptidefilterparam': {
'Meta': {'object_name': 'CLPeptideFilterParam'},
'clpeptidefilter': ('django.db.models.fields.related.ForeignKey', [], {'to': u"orm['CLMSpipeline_app.CLPeptideFilter']"}),
'field': ('django.db.models.fields.CharField', [], {'max_length': '100'}),
'field_lookup': ('django.db.models.fields.CharField', [], {'max_length': '50'}),
u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}),
'method': ('django.db.models.fields.CharField', [], {'max_length': '20'}),
'value': ('django.db.models.fields.CharField', [], {'max_length': '50'})
},
u'CLMSpipeline_app.crosslinker': {
'Meta': {'ordering': "['name']", 'object_name': 'CrossLinker'},
u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}),
'name': ('django.db.models.fields.CharField', [], {'unique': 'True', 'max_length': '100'})
},
u'CLMSpipeline_app.dataset': {
'Meta': {'ordering': "['-creation_date']", 'object_name': 'Dataset'},
'creation_date': ('django.db.models.fields.DateTimeField', [], {'auto_now_add': 'True', 'blank': 'True'}),
'cross_linker': ('django.db.models.fields.related.ForeignKey', [], {'to': u"orm['CLMSpipeline_app.CrossLinker']", 'null': 'True'}),
'description': ('django.db.models.fields.TextField', [], {'blank': 'True'}),
'fasta_db': ('django.db.models.fields.related.ForeignKey', [], {'to': u"orm['CLMSpipeline_app.FastaDB']", 'null': 'True'}),
u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}),
'instrument_name': ('django.db.models.fields.related.ForeignKey', [], {'to': u"orm['CLMSpipeline_app.Instrument']", 'null': 'True'}),
'name': ('django.db.models.fields.CharField', [], {'max_length': '100'}),
'prefix': ('django.db.models.fields.CharField', [], {'max_length': '25'}),
'search_algorithm': ('django.db.models.fields.related.ForeignKey', [], {'to': u"orm['CLMSpipeline_app.searchAlgorithm']", 'null': 'True'})
},
u'CLMSpipeline_app.fastadb': {
'Meta': {'ordering': "['name']", 'object_name': 'FastaDB'},
u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}),
'name': ('django.db.models.fields.CharField', [], {'unique': 'True', 'max_length': '200'})
},
u'CLMSpipeline_app.instrument': {
'Meta': {'ordering': "['name']", 'object_name': 'Instrument'},
u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}),
'name': ('django.db.models.fields.CharField', [], {'unique': 'True', 'max_length': '100'})
},
u'CLMSpipeline_app.processeddataset': {
'Meta': {'ordering': "['-creation_date']", 'object_name': 'ProcessedDataset', '_ormbases': [u'CLMSpipeline_app.Dataset']},
'clpeptidefilter': ('django.db.models.fields.related.ForeignKey', [], {'to': u"orm['CLMSpipeline_app.CLPeptideFilter']", 'null': 'True', 'blank': 'True'}),
u'dataset_ptr': ('django.db.models.fields.related.OneToOneField', [], {'to': u"orm['CLMSpipeline_app.Dataset']", 'unique': 'True', 'primary_key': 'True'}),
'datasets': ('django.db.models.fields.related.ManyToManyField', [], {'related_name': "'processed_datasets'", 'symmetrical': 'False', 'to': u"orm['CLMSpipeline_app.Dataset']"})
},
u'CLMSpipeline_app.rawdataset': {
'Meta': {'ordering': "['-creation_date']", 'object_name': 'RawDataset', '_ormbases': [u'CLMSpipeline_app.Dataset']},
u'dataset_ptr': ('django.db.models.fields.related.OneToOneField', [], {'to': u"orm['CLMSpipeline_app.Dataset']", 'unique': 'True', 'primary_key': 'True'}),
'extra_file': ('django.db.models.fields.files.FileField', [], {'max_length': '100', 'blank': 'True'}),
'file': ('django.db.models.fields.files.FileField', [], {'max_length': '100'}),
'parsing_log': ('django.db.models.fields.CharField', [], {'max_length': '1000', 'null': 'True', 'blank': 'True'}),
'parsing_status': ('django.db.models.fields.BooleanField', [], {'default': 'False'})
},
u'CLMSpipeline_app.searchalgorithm': {
'Meta': {'ordering': "['name']", 'object_name': 'searchAlgorithm'},
u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}),
'name': ('django.db.models.fields.CharField', [], {'unique': 'True', 'max_length': '100'})
}
}
complete_apps = ['CLMSpipeline_app']
\ No newline at end of file
# -*- coding: utf-8 -*-
import datetime
from south.db import db
from south.v2 import SchemaMigration
from django.db import models
class Migration(SchemaMigration):
def forwards(self, orm):
# Adding field 'CLPeptideFilter.fp_cutoff'
db.add_column(u'CLMSpipeline_app_clpeptidefilter', 'fp_cutoff',
self.gf('django.db.models.fields.FloatField')(default=1),
keep_default=False)
def backwards(self, orm):
# Deleting field 'CLPeptideFilter.fp_cutoff'
db.delete_column(u'CLMSpipeline_app_clpeptidefilter', 'fp_cutoff')