From 5ca8a322e423986bdbfb840e2becc5221965698e Mon Sep 17 00:00:00 2001 From: Diane Trout Date: Wed, 22 Jan 2014 15:54:12 -0800 Subject: [PATCH] Change experiments.FileType.regex to a text field so it can be arbitrarily long. Also add a "regex_is_valid" computed value to the list view to help make it easier to find broken regex's. Also configure the admin edit form for FileType. --- htsworkflow/frontend/experiments/admin.py | 8 +- .../0003_auto__chg_field_filetype_regex.py | 236 ++++++++++++++++++ htsworkflow/frontend/experiments/models.py | 7 + 3 files changed, 250 insertions(+), 1 deletion(-) create mode 100644 htsworkflow/frontend/experiments/migrations/0003_auto__chg_field_filetype_regex.py diff --git a/htsworkflow/frontend/experiments/admin.py b/htsworkflow/frontend/experiments/admin.py index e9419dc..1a27a17 100644 --- a/htsworkflow/frontend/experiments/admin.py +++ b/htsworkflow/frontend/experiments/admin.py @@ -49,7 +49,13 @@ admin.site.register(DataRun, DataRunOptions) class FileTypeAdmin(admin.ModelAdmin): - list_display = ('name', 'mimetype', 'regex') + list_display = ('name', 'mimetype', 'regex', 'regex_is_valid') + fieldsets = ( + (None, { + 'fields': (('name', 'mimetype'), + ('regex')) + } + )), admin.site.register(FileType, FileTypeAdmin) # lane form setup needs to come before Flowcell form config diff --git a/htsworkflow/frontend/experiments/migrations/0003_auto__chg_field_filetype_regex.py b/htsworkflow/frontend/experiments/migrations/0003_auto__chg_field_filetype_regex.py new file mode 100644 index 0000000..8c6e746 --- /dev/null +++ b/htsworkflow/frontend/experiments/migrations/0003_auto__chg_field_filetype_regex.py @@ -0,0 +1,236 @@ +# -*- coding: utf-8 -*- +from south.utils import datetime_utils as 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 'FileType.regex' + db.alter_column(u'experiments_filetype', 'regex', self.gf('django.db.models.fields.TextField')(null=True)) + + def backwards(self, orm): + + # Changing field 'FileType.regex' + db.alter_column(u'experiments_filetype', 'regex', self.gf('django.db.models.fields.CharField')(max_length=50, null=True)) + + models = { + u'auth.group': { + 'Meta': {'object_name': 'Group'}, + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'name': ('django.db.models.fields.CharField', [], {'unique': 'True', 'max_length': '80'}), + 'permissions': ('django.db.models.fields.related.ManyToManyField', [], {'to': u"orm['auth.Permission']", 'symmetrical': 'False', 'blank': 'True'}) + }, + u'auth.permission': { + 'Meta': {'ordering': "(u'content_type__app_label', u'content_type__model', u'codename')", 'unique_together': "((u'content_type', u'codename'),)", 'object_name': 'Permission'}, + 'codename': ('django.db.models.fields.CharField', [], {'max_length': '100'}), + 'content_type': ('django.db.models.fields.related.ForeignKey', [], {'to': u"orm['contenttypes.ContentType']"}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'name': ('django.db.models.fields.CharField', [], {'max_length': '50'}) + }, + u'auth.user': { + 'Meta': {'object_name': 'User'}, + 'date_joined': ('django.db.models.fields.DateTimeField', [], {'default': 'datetime.datetime.now'}), + 'email': ('django.db.models.fields.EmailField', [], {'max_length': '75', 'blank': 'True'}), + 'first_name': ('django.db.models.fields.CharField', [], {'max_length': '30', 'blank': 'True'}), + 'groups': ('django.db.models.fields.related.ManyToManyField', [], {'symmetrical': 'False', 'related_name': "u'user_set'", 'blank': 'True', 'to': u"orm['auth.Group']"}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'is_active': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), + 'is_staff': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'is_superuser': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'last_login': ('django.db.models.fields.DateTimeField', [], {'default': 'datetime.datetime.now'}), + 'last_name': ('django.db.models.fields.CharField', [], {'max_length': '30', 'blank': 'True'}), + 'password': ('django.db.models.fields.CharField', [], {'max_length': '128'}), + 'user_permissions': ('django.db.models.fields.related.ManyToManyField', [], {'symmetrical': 'False', 'related_name': "u'user_set'", 'blank': 'True', 'to': u"orm['auth.Permission']"}), + 'username': ('django.db.models.fields.CharField', [], {'unique': 'True', 'max_length': '30'}) + }, + u'contenttypes.contenttype': { + 'Meta': {'ordering': "('name',)", 'unique_together': "(('app_label', 'model'),)", 'object_name': 'ContentType', 'db_table': "'django_content_type'"}, + 'app_label': ('django.db.models.fields.CharField', [], {'max_length': '100'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'model': ('django.db.models.fields.CharField', [], {'max_length': '100'}), + 'name': ('django.db.models.fields.CharField', [], {'max_length': '100'}) + }, + u'experiments.clusterstation': { + 'Meta': {'ordering': "['-isdefault', 'name']", 'object_name': 'ClusterStation'}, + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'isdefault': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'name': ('django.db.models.fields.CharField', [], {'unique': 'True', 'max_length': '50'}) + }, + u'experiments.datafile': { + 'Meta': {'object_name': 'DataFile'}, + 'data_run': ('django.db.models.fields.related.ForeignKey', [], {'to': u"orm['experiments.DataRun']"}), + 'file_type': ('django.db.models.fields.related.ForeignKey', [], {'to': u"orm['experiments.FileType']"}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'library': ('django.db.models.fields.related.ForeignKey', [], {'to': u"orm['samples.Library']", 'null': 'True', 'blank': 'True'}), + 'random_key': ('django.db.models.fields.CharField', [], {'default': "'8e0f4e4c-83be-11e3-bace-f0def16fbea3'", 'max_length': '64', 'db_index': 'True'}), + 'relative_pathname': ('django.db.models.fields.CharField', [], {'max_length': '255', 'db_index': 'True'}) + }, + u'experiments.datarun': { + 'Meta': {'object_name': 'DataRun'}, + 'alignment_software': ('django.db.models.fields.CharField', [], {'max_length': '50'}), + 'alignment_version': ('django.db.models.fields.CharField', [], {'max_length': '50'}), + 'basecall_software': ('django.db.models.fields.CharField', [], {'max_length': '50'}), + 'basecall_version': ('django.db.models.fields.CharField', [], {'max_length': '50'}), + 'comment': ('django.db.models.fields.TextField', [], {'blank': 'True'}), + 'cycle_start': ('django.db.models.fields.IntegerField', [], {'null': 'True', 'blank': 'True'}), + 'cycle_stop': ('django.db.models.fields.IntegerField', [], {'null': 'True', 'blank': 'True'}), + 'flowcell': ('django.db.models.fields.related.ForeignKey', [], {'to': u"orm['experiments.FlowCell']"}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'image_software': ('django.db.models.fields.CharField', [], {'max_length': '50'}), + 'image_version': ('django.db.models.fields.CharField', [], {'max_length': '50'}), + 'last_update_time': ('django.db.models.fields.DateTimeField', [], {}), + 'result_dir': ('django.db.models.fields.CharField', [], {'max_length': '255'}), + 'run_start_time': ('django.db.models.fields.DateTimeField', [], {}), + 'run_status': ('django.db.models.fields.IntegerField', [], {'null': 'True', 'blank': 'True'}), + 'runfolder_name': ('django.db.models.fields.CharField', [], {'max_length': '50'}) + }, + u'experiments.filetype': { + 'Meta': {'object_name': 'FileType'}, + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'mimetype': ('django.db.models.fields.CharField', [], {'max_length': '50', 'null': 'True', 'blank': 'True'}), + 'name': ('django.db.models.fields.CharField', [], {'max_length': '50'}), + 'regex': ('django.db.models.fields.TextField', [], {'null': 'True', 'blank': 'True'}) + }, + u'experiments.flowcell': { + 'Meta': {'ordering': "['-run_date']", 'object_name': 'FlowCell'}, + 'advanced_run': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'cluster_station': ('django.db.models.fields.related.ForeignKey', [], {'to': u"orm['experiments.ClusterStation']"}), + 'control_lane': ('django.db.models.fields.IntegerField', [], {'null': 'True', 'blank': 'True'}), + 'flowcell_id': ('django.db.models.fields.CharField', [], {'unique': 'True', 'max_length': '20', 'db_index': 'True'}), + 'flowcell_model': ('django.db.models.fields.related.ForeignKey', [], {'default': 'None', 'to': u"orm['experiments.FlowCellModel']"}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'notes': ('django.db.models.fields.TextField', [], {'blank': 'True'}), + 'paired_end': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'read_length': ('django.db.models.fields.IntegerField', [], {'default': '32'}), + 'run_date': ('django.db.models.fields.DateTimeField', [], {}), + 'sequencer': ('django.db.models.fields.related.ForeignKey', [], {'to': u"orm['experiments.Sequencer']"}) + }, + u'experiments.flowcellmodel': { + 'Meta': {'object_name': 'FlowCellModel'}, + 'fixed_time': ('django.db.models.fields.IntegerField', [], {'default': '0'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'isdefault': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'name': ('django.db.models.fields.TextField', [], {}), + 'per_cycle_time': ('django.db.models.fields.IntegerField', [], {'default': '0'}) + }, + u'experiments.lane': { + 'Meta': {'object_name': 'Lane'}, + 'cluster_estimate': ('django.db.models.fields.IntegerField', [], {'null': 'True', 'blank': 'True'}), + 'comment': ('django.db.models.fields.TextField', [], {'null': 'True', 'blank': 'True'}), + 'flowcell': ('django.db.models.fields.related.ForeignKey', [], {'to': u"orm['experiments.FlowCell']"}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'lane_number': ('django.db.models.fields.IntegerField', [], {}), + 'library': ('django.db.models.fields.related.ForeignKey', [], {'to': u"orm['samples.Library']"}), + 'pM': ('django.db.models.fields.DecimalField', [], {'default': '5', 'max_digits': '5', 'decimal_places': '2'}), + 'status': ('django.db.models.fields.IntegerField', [], {'null': 'True', 'blank': 'True'}) + }, + u'experiments.sequencer': { + 'Meta': {'ordering': "['-isdefault', '-active', 'name']", 'object_name': 'Sequencer'}, + 'active': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), + 'comment': ('django.db.models.fields.CharField', [], {'max_length': '255'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'instrument_name': ('django.db.models.fields.CharField', [], {'max_length': '50', 'db_index': 'True'}), + 'isdefault': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'model': ('django.db.models.fields.CharField', [], {'max_length': '255'}), + 'name': ('django.db.models.fields.CharField', [], {'max_length': '50', 'db_index': 'True'}), + 'serial_number': ('django.db.models.fields.CharField', [], {'max_length': '50', 'db_index': 'True'}) + }, + u'samples.affiliation': { + 'Meta': {'ordering': "['name', 'contact']", 'unique_together': "(('name', 'contact'),)", 'object_name': 'Affiliation'}, + 'contact': ('django.db.models.fields.CharField', [], {'max_length': '256', 'null': 'True', 'blank': 'True'}), + 'email': ('django.db.models.fields.EmailField', [], {'max_length': '75', 'null': 'True', 'blank': 'True'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'name': ('django.db.models.fields.CharField', [], {'max_length': '256', 'db_index': 'True'}), + 'users': ('django.db.models.fields.related.ManyToManyField', [], {'symmetrical': 'False', 'to': u"orm['samples.HTSUser']", 'null': 'True', 'blank': 'True'}) + }, + u'samples.antibody': { + 'Meta': {'ordering': "['antigene']", 'object_name': 'Antibody'}, + 'antibodies': ('django.db.models.fields.CharField', [], {'max_length': '500', 'db_index': 'True'}), + 'antigene': ('django.db.models.fields.CharField', [], {'max_length': '500', 'db_index': 'True'}), + 'biology': ('django.db.models.fields.TextField', [], {'null': 'True', 'blank': 'True'}), + 'catalog': ('django.db.models.fields.CharField', [], {'max_length': '50', 'null': 'True', 'blank': 'True'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'nickname': ('django.db.models.fields.CharField', [], {'db_index': 'True', 'max_length': '20', 'null': 'True', 'blank': 'True'}), + 'notes': ('django.db.models.fields.TextField', [], {'null': 'True', 'blank': 'True'}), + 'source': ('django.db.models.fields.CharField', [], {'db_index': 'True', 'max_length': '500', 'null': 'True', 'blank': 'True'}) + }, + u'samples.cellline': { + 'Meta': {'ordering': "['cellline_name']", 'object_name': 'Cellline'}, + 'cellline_name': ('django.db.models.fields.CharField', [], {'unique': 'True', 'max_length': '100', 'db_index': 'True'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'nickname': ('django.db.models.fields.CharField', [], {'db_index': 'True', 'max_length': '20', 'null': 'True', 'blank': 'True'}), + 'notes': ('django.db.models.fields.TextField', [], {'blank': 'True'}) + }, + u'samples.condition': { + 'Meta': {'ordering': "['condition_name']", 'object_name': 'Condition'}, + 'condition_name': ('django.db.models.fields.CharField', [], {'unique': 'True', 'max_length': '2000', 'db_index': 'True'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'nickname': ('django.db.models.fields.CharField', [], {'db_index': 'True', 'max_length': '20', 'null': 'True', 'blank': 'True'}), + 'notes': ('django.db.models.fields.TextField', [], {'blank': 'True'}) + }, + u'samples.experimenttype': { + 'Meta': {'object_name': 'ExperimentType'}, + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'name': ('django.db.models.fields.CharField', [], {'unique': 'True', 'max_length': '50'}) + }, + u'samples.htsuser': { + 'Meta': {'ordering': "['first_name', 'last_name', 'username']", 'object_name': 'HTSUser', '_ormbases': [u'auth.User']}, + u'user_ptr': ('django.db.models.fields.related.OneToOneField', [], {'to': u"orm['auth.User']", 'unique': 'True', 'primary_key': 'True'}) + }, + u'samples.library': { + 'Meta': {'ordering': "['-id']", 'object_name': 'Library'}, + 'account_number': ('django.db.models.fields.CharField', [], {'max_length': '100', 'null': 'True', 'blank': 'True'}), + 'affiliations': ('django.db.models.fields.related.ManyToManyField', [], {'symmetrical': 'False', 'related_name': "'library_affiliations'", 'null': 'True', 'to': u"orm['samples.Affiliation']"}), + 'amplified_from_sample': ('django.db.models.fields.related.ForeignKey', [], {'blank': 'True', 'related_name': "'amplified_into_sample'", 'null': 'True', 'to': u"orm['samples.Library']"}), + 'antibody': ('django.db.models.fields.related.ForeignKey', [], {'to': u"orm['samples.Antibody']", 'null': 'True', 'blank': 'True'}), + 'bioanalyzer_concentration': ('django.db.models.fields.DecimalField', [], {'null': 'True', 'max_digits': '5', 'decimal_places': '2', 'blank': 'True'}), + 'bioanalyzer_image_url': ('django.db.models.fields.URLField', [], {'default': "''", 'max_length': '200', 'blank': 'True'}), + 'bioanalyzer_summary': ('django.db.models.fields.TextField', [], {'default': "''", 'blank': 'True'}), + 'cell_line': ('django.db.models.fields.related.ForeignKey', [], {'to': u"orm['samples.Cellline']", 'null': 'True', 'blank': 'True'}), + 'condition': ('django.db.models.fields.related.ForeignKey', [], {'to': u"orm['samples.Condition']", 'null': 'True', 'blank': 'True'}), + 'creation_date': ('django.db.models.fields.DateField', [], {'null': 'True', 'blank': 'True'}), + 'experiment_type': ('django.db.models.fields.related.ForeignKey', [], {'to': u"orm['samples.ExperimentType']"}), + 'gel_cut_size': ('django.db.models.fields.IntegerField', [], {'default': '225', 'null': 'True', 'blank': 'True'}), + 'hidden': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'id': ('django.db.models.fields.CharField', [], {'max_length': '10', 'primary_key': 'True'}), + 'insert_size': ('django.db.models.fields.IntegerField', [], {'null': 'True', 'blank': 'True'}), + 'library_name': ('django.db.models.fields.CharField', [], {'unique': 'True', 'max_length': '100'}), + 'library_species': ('django.db.models.fields.related.ForeignKey', [], {'to': u"orm['samples.Species']"}), + 'library_type': ('django.db.models.fields.related.ForeignKey', [], {'to': u"orm['samples.LibraryType']", 'null': 'True', 'blank': 'True'}), + 'made_by': ('django.db.models.fields.CharField', [], {'default': "'Lorian'", 'max_length': '50', 'blank': 'True'}), + 'made_for': ('django.db.models.fields.CharField', [], {'max_length': '50', 'blank': 'True'}), + 'multiplex_id': ('django.db.models.fields.CharField', [], {'max_length': '128', 'null': 'True', 'blank': 'True'}), + 'notes': ('django.db.models.fields.TextField', [], {'blank': 'True'}), + 'replicate': ('django.db.models.fields.PositiveSmallIntegerField', [], {'null': 'True', 'blank': 'True'}), + 'stopping_point': ('django.db.models.fields.CharField', [], {'default': "'Done'", 'max_length': '25'}), + 'successful_pM': ('django.db.models.fields.DecimalField', [], {'null': 'True', 'max_digits': '9', 'decimal_places': '1', 'blank': 'True'}), + 'tags': ('django.db.models.fields.related.ManyToManyField', [], {'blank': 'True', 'related_name': "'library_tags'", 'null': 'True', 'symmetrical': 'False', 'to': u"orm['samples.Tag']"}), + 'ten_nM_dilution': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), + 'undiluted_concentration': ('django.db.models.fields.DecimalField', [], {'null': 'True', 'max_digits': '5', 'decimal_places': '2', 'blank': 'True'}) + }, + u'samples.librarytype': { + 'Meta': {'ordering': "['-id']", 'object_name': 'LibraryType'}, + 'can_multiplex': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'is_paired_end': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), + 'name': ('django.db.models.fields.CharField', [], {'unique': 'True', 'max_length': '255'}) + }, + u'samples.species': { + 'Meta': {'ordering': "['scientific_name']", 'object_name': 'Species'}, + 'common_name': ('django.db.models.fields.CharField', [], {'max_length': '256', 'blank': 'True'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'scientific_name': ('django.db.models.fields.CharField', [], {'max_length': '256', 'db_index': 'True'}) + }, + u'samples.tag': { + 'Meta': {'ordering': "['context', 'tag_name']", 'object_name': 'Tag'}, + 'context': ('django.db.models.fields.CharField', [], {'default': "'Library'", 'max_length': '50'}), + u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), + 'tag_name': ('django.db.models.fields.CharField', [], {'max_length': '100', 'db_index': 'True'}) + } + } + + complete_apps = ['experiments'] \ No newline at end of file diff --git a/htsworkflow/frontend/experiments/models.py b/htsworkflow/frontend/experiments/models.py index 508abc7..2da1fcf 100644 --- a/htsworkflow/frontend/experiments/models.py +++ b/htsworkflow/frontend/experiments/models.py @@ -3,6 +3,7 @@ import glob import logging import os import re +import sre_constants import types import uuid @@ -455,6 +456,12 @@ class FileType(models.Model): #return u"" % (self.name,) return self.name + def regex_is_valid(self): + try: + regex = re.compile(self.regex) + except sre_constants.error as e: + return False + return re.compile(self.regex) is not None def str_uuid(): """Helper function to set default UUID in DataFile""" -- 2.30.2