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.

diff --git a/htsworkflow/frontend/experiments/admin.py b/htsworkflow/frontend/experiments/admin.py
index e9419dc4a480771c09ea0987a3b2034f5ffeb55a..1a27a17c6ffc2a1e19898947960a50347a89643f 100644 (file)
--- 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 (file)
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 508abc71d770d3dfd53d9d0350cd09262e8b3e13..2da1fcf120228a2e46312a355066ddf1488aaba7 100644 (file)
--- 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"<FileType: %s>" % (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"""