Package Details

The experimentDB is a web-based application for the storage, organization and communication of experimental data with a focus on molecular biology and biochemical data. This application also stores data regarding reagents, including antibodies, constructs and other biomolecules as well as tracks the distribution of reagents. There is also some preliminary interfaces to other web resources.

Data Package

This package describes experimental data.

There are three main models in this package. These models cover experiments, results and protocols. There are model specifications described in experimentdb.models and views described in either experimentdb.views or experimentdb.urls for either custom or generic views respectively

Models

class experimentdb.data.models.Experiment(*args, **kwargs)

Experiment(experimentID, experiment, assay, experiment_date, comments, public, published, sample_storage)

exception DoesNotExist

exception Experiment.MultipleObjectsReturned

Experiment.antibodies

Experiment.cellline

Experiment.chemicals

Experiment.constructs

Experiment.get_absolute_url(*moreargs, **morekwargs)

Experiment.get_next_by_experiment_date(*moreargs, **morekwargs)

Experiment.get_previous_by_experiment_date(*moreargs, **morekwargs)

Experiment.project

Experiment.protein

Experiment.protocol

Experiment.researcher

Experiment.result_set

Experiment.siRNA

Experiment.strain

Experiment.subproject

class experimentdb.data.models.Protocol(*args, **kwargs)

Describes the protocol or protocols used to perform each experiment.

This model stores information about the protocol used for an experiment.

An experiment may have several protocols attached to it. For example, one could culture and transfect cells, then generate lysates then do some western blots.

Since migrating to a mediawiki based protocol storage system, the wiki_page attribute indicates the protocol wiki page. In this model, the protocol_revision attribute indicates the particular revision of the protocol used for that particular experiment. In this way a permalink can be generated to the specific protocol used for a particular experiment. To find the protocol revision number, mouse over the permanent link on the protocol and record the number at the end of the url.

exception DoesNotExist

exception Protocol.MultipleObjectsReturned

Protocol.experiment_set

Protocol.get_absolute_url(*moreargs, **morekwargs)

class experimentdb.data.models.Result(*args, **kwargs)

Result(id, experiment_id, conclusions, file1, file2, file3, rawscan1, rawscan2, rawscan3, rawscan4, rawscan5, result_figure1, result_figure2, public, published)

exception DoesNotExist

exception Result.MultipleObjectsReturned

Result.experiment

Result.get_absolute_url(*moreargs, **morekwargs)

class experimentdb.data.models.Sequencing(*args, **kwargs)

Sequencing(id, clone_name, construct_id, primer_id, file, sequence, correct, notes, date, sample_number, gel_number, lane_number)

exception DoesNotExist

exception Sequencing.MultipleObjectsReturned

Sequencing.construct

Sequencing.get_next_by_date(*moreargs, **morekwargs)

Sequencing.get_previous_by_date(*moreargs, **morekwargs)

Sequencing.primer

Views

This module provides the views for working with the data package. This module will generate index and detail views for experiments and protocols as well as for the form to enter new results through an experiment. Several other generic views are found in data.urls.

experimentdb.data.views.experiment(request, *args, **kwargs)

This renders a detailed page of an experiment.

The view will show the experiment, and all associated reagents, proteins, projects and results associated with this object.

experimentdb.data.views.experiment_edit(request, *args, **kwargs)

Renders a form to edit an experiment and associated formsets for experimental results.

Takes a request in the form of experiment/(experimentID)/edit and returns the experiment_result_form.html form.

experimentdb.data.views.index(request, *args, **kwargs)

This view shows a list of all experiments.

This list is ordered by the experiment date in descending order. This view could potentially be rendered by a generic view.

experimentdb.data.views.protocol_detail(request, *args, **kwargs)

This renders a view in which a protocol detail page is shown.

This view should be deprecated in favor of a redirection directly to the wiki page for this protocol

experimentdb.data.views.protocol_list(request, *args, **kwargs)

This renders a view in which all protocols are displayed.

In the case of deprecated protocols (i.e. protocols not marked as active), these are not shown. This view could also be rendered as a generic view.

experimentdb.data.views.result_new(request, *args, **kwargs)

This renders a form to add a new result.

This view will be sent from a particular experiment and will attach the result to that particular experiment.

Lookups

This is a configuration file for the ajax lookups for the data app.

See http://code.google.com/p/django-ajax-selects/ for information about configuring the ajax lookups.

class experimentdb.data.lookups.ProtocolLookup

This is the generic lookup for protocols.

It is to be used for all protocol requests and directs to the ‘protocol’ channel.

format_item(protocol)

the display of a currently selected object in the area below the search box. html is OK

format_result(protocol)

This controls the display of the dropdown menu.

This is set to show the unicode name of the protocol.

get_objects(ids)

given a list of ids, return the objects ordered as you would like them on the admin page. this is for displaying the currently selected items (in the case of a ManyToMany field)

get_query(q, request)

This sets up the query for the lookup.

The lookup searches the name of the protocol.

URLconfs

This package stores views for the data package.

Tests

Fixtures

Datasets Package

Models

class experimentdb.datasets.models.IL10_TNFa_Microarray(*args, **kwargs)

IL10_TNFa_Microarray(id, ill_ID, Control_1_2008, Control_2_2008, Control_1_2009, Control_2_2009, Control_3_2009, Control_4_2009, TNFa_1_2008, TNFa_2_2008, TNFa_1_2009, TNFa_2_2009, TNFa_3_2009, TNFa_4_2009, Both_1_2008, Both_2_2008, Both_1_2009, Both_2_2009, Both_3_2009, Both_4_2009, IL10_1_2008, IL10_2_2008, IL10_1_2009, IL10_2_2009, IL10_3_2009, IL10_4_2009, GeneSymbol, GeneID, GeneName)

exception DoesNotExist

exception IL10_TNFa_Microarray.MultipleObjectsReturned

class experimentdb.datasets.models.PI35P2_Binding_Screen_SP(*args, **kwargs)

PI35P2_Binding_Screen_SP(id, Gene_Name_id, Gain_of_Function, Loss_of_Function, Candidate, Comments)

exception DoesNotExist

PI35P2_Binding_Screen_SP.Gene_Name

exception PI35P2_Binding_Screen_SP.MultipleObjectsReturned

PI35P2_Binding_Screen_SP.get_Gain_of_Function_display(*moreargs, **morekwargs)

PI35P2_Binding_Screen_SP.get_Loss_of_Function_display(*moreargs, **morekwargs)

class experimentdb.datasets.models.SGD_GeneNames(*args, **kwargs)

SGD_GeneNames(Locus_name, Other_name, Description, Gene_product, Phenotype, ORF_name, SGDID)

Bait_GeneName

exception DoesNotExist

SGD_GeneNames.Hit_GeneName

exception SGD_GeneNames.MultipleObjectsReturned

SGD_GeneNames.PI3PBP_Gene_Name

SGD_GeneNames.get_absolute_url(*moreargs, **morekwargs)

SGD_GeneNames.sgd_phenotypes_set

class experimentdb.datasets.models.SGD_interactions(*args, **kwargs)

SGD_interactions(id, Feature_Name_Bait, Standard_Gene_Name_Bait_id, Feature_Name_Hit, Standard_Gene_Name_Hit_id, Experiment_Type, Genetic_or_Physical_Interaction, Source, Manually_Curated_or_High_Throughput, Notes, Phenotype, Reference, Citation)

exception DoesNotExist

exception SGD_interactions.MultipleObjectsReturned

SGD_interactions.Standard_Gene_Name_Bait

SGD_interactions.Standard_Gene_Name_Hit

class experimentdb.datasets.models.SGD_phenotypes(*args, **kwargs)

SGD_phenotypes(id, Feature_Name, Feature_Type, Gene_Name_id, SGDID, Reference, Experiment_Type, Mutant_Type, Allele, Strain_Background, Phenotype, Chemical, Condition, Details, Reporter)

exception DoesNotExist

SGD_phenotypes.Gene_Name

exception SGD_phenotypes.MultipleObjectsReturned

Views

experimentdb.datasets.views.sgd_gene_detail(request, gene)

URLconfs

Tests

Fixtures

Cloning Package

Models

class experimentdb.cloning.models.Cloning(*args, **kwargs)

This model stores details about the generation of new recombinant DNA molecules.

exception DoesNotExist

exception Cloning.MultipleObjectsReturned

Cloning.construct

Cloning.get_absolute_url(*moreargs, **morekwargs)

Cloning.get_cloning_type_display(*moreargs, **morekwargs)

Cloning.primer_3prime

Cloning.primer_5prime

Cloning.researcher

Cloning.sequencing

Cloning.vector

class experimentdb.cloning.models.Mutagenesis(*args, **kwargs)

This model contains data describing the generation of muationns in clones

exception DoesNotExist

exception Mutagenesis.MultipleObjectsReturned

Mutagenesis.antisense_primer

Mutagenesis.construct

Mutagenesis.get_absolute_url(*moreargs, **morekwargs)

Mutagenesis.get_next_by_date_completed(*moreargs, **morekwargs)

Mutagenesis.get_previous_by_date_completed(*moreargs, **morekwargs)

Mutagenesis.protocol

Mutagenesis.researcher

Mutagenesis.sense_primer

Mutagenesis.sequencing

Mutagenesis.template

Views

URLconfs

Tests

Fixtures

External Package

Models

This package contains the model information for the external app.

It defines the structure and behavior of the following models: - Contact - Vendor - Reference

class experimentdb.external.models.Contact(*args, **kwargs)

This model defines a contact.

This is intended to be a person who is involved in the research program, and may be but it not necessarily a database user. The required fields are first_name and last_name.

exception DoesNotExist

exception Contact.MultipleObjectsReturned

Contact.antibody_researcher

Contact.cell_researcher

Contact.chemical_researcher

Contact.cloning_set

Contact.construct_researcher

Contact.experiment_set

Contact.get_absolute_url(*moreargs, **morekwargs)

Contact.laboratory_set

Contact.mutagenesis_set

Contact.primer_researcher

Contact.project_set

Contact.reference_set

Contact.save()

The save is over-ridden to slugify the contact field into a slugfield named contactID.

Contact.strain_researcher

Contact.subproject_set

Contact.user

class experimentdb.external.models.Reference(*args, **kwargs)

This model contains objects of the class reference.

It is intended to keep track of specific papers that pertain to protocols, experiments or projects.

The only required field for this model is a title.

exception DoesNotExist

exception Reference.MultipleObjectsReturned

Reference.antibody_set

Reference.cell_set

Reference.chemical_set

Reference.construct_set

Reference.get_absolute_url(*moreargs, **morekwargs)

Reference.primer_set

Reference.project_set

Reference.researchers

Reference.strain_set

Reference.subproject_set

class experimentdb.external.models.Vendor(*args, **kwargs)

This model contains objects of the class vendor.

It is intended to be used to indicate companies from which reagents are obtained. The only required field is company.

exception DoesNotExist

exception Vendor.MultipleObjectsReturned

Vendor.antibody_vendor

Vendor.cell_vendor

Vendor.chemical_vendor

Vendor.construct_vendor

Vendor.get_absolute_url(*moreargs, **morekwargs)

Vendor.primer_vendor

Vendor.save()

The save is over-ridden to slugify the contact field into a slugfield named contactID.

Vendor.strain_vendor

Views

URLconfs

This folder contains the urlconf redirections for the external app.

There is separate files for vendor, contact and reference urls.

Tests

This package defines the tests for the external app.

It contains model tests for the models: - Vendor - Reference - Contact

There are currently no views associated with these models.

class experimentdb.external.tests.ContactModelTests(methodName='runTest')

Tests the model attributes of Contact objects contained in the reagents app.

setUp()

Instantiate the test client.

tearDown()

Depopulate created model instances from test database.

test_contact_absolute_url()

test_contact_slugify()

test_create_contact_minimal()

This is a test for creating a new primer object, with only the minimum fields being entered

class experimentdb.external.tests.ReferenceModelTests(methodName='runTest')

Tests the model attributes of Reference objects contained in the reagents app.

setUp()

Instantiate the test client.

tearDown()

Depopulate created model instances from test database.

test_create_reference_minimal()

This is a test for creating a new primer object, with only the minimum fields being entered

test_reference_absolute_url()

class experimentdb.external.tests.VendorModelTests(methodName='runTest')

Tests the model attributes of Vendor objects contained in the reagents app.

setUp()

Instantiate the test client.

tearDown()

Depopulate created model instances from test database.

test_create_vendor_minimal()

This is a test for creating a new primer object, with only the minimum fields being entered

test_vendor_absolute_url()

Fixtures

This folder contains test fixtures for the external app.

Currently there is one file with a sample object for each of: - Vendor - Contact - Reference

in the file test_external.json

Proteins Package

Models

class experimentdb.proteins.models.Protein(*args, **kwargs)

Protein(id, name)

exception DoesNotExist

exception Protein.MultipleObjectsReturned

Protein.antibody_set

Protein.cell_set

Protein.chemical_set

Protein.construct_set

Protein.experiment_set

Protein.get_absolute_url(*moreargs, **morekwargs)

Protein.primer_set

Protein.protein_family

Protein.proteindetail_set

Protein.strain_set

class experimentdb.proteins.models.ProteinDetail(*args, **kwargs)

ProteinDetail(id, name, protein_id, gene, species_id, geneID, RefSeqProtein, RefSeqProtein_gi, RefSeqNucleotide, RefSeqNucleotide_gi, WormBaseID, FlyBaseID, SGD_ID, public, published)

exception DoesNotExist

exception ProteinDetail.MultipleObjectsReturned

ProteinDetail.protein

ProteinDetail.species

class experimentdb.proteins.models.ProteinFamily(*args, **kwargs)

ProteinFamily(id, name, notes)

exception DoesNotExist

exception ProteinFamily.MultipleObjectsReturned

ProteinFamily.get_absolute_url(*moreargs, **morekwargs)

ProteinFamily.protein_set

class experimentdb.proteins.models.Species(*args, **kwargs)

Species(id, common_name, scientific_name, taxonomy_id)

exception DoesNotExist

exception Species.MultipleObjectsReturned

Species.proteindetail_set

Views

experimentdb.proteins.views.detail(request, *args, **kwargs)

experimentdb.proteins.views.index(request, *args, **kwargs)

experimentdb.proteins.views.protein_isoform_detail(request, *args, **kwargs)

fetch and parse a genbank protein record

Lookups

This is a configuration file for the ajax lookups for the proteins app.

See http://code.google.com/p/django-ajax-selects/ for information about configuring the ajax lookups.

class experimentdb.proteins.lookups.ProteinLookup

This is the generic lookup for antibodies.

It is to be used for all protein requests and directs to the ‘protein’ channel.

format_item(protein)

the display of a currently selected object in the area below the search box. html is OK

format_result(protein)

This controls the display of the dropdown menu.

This is set to show the unicode name of the protein.

get_objects(ids)

given a list of ids, return the objects ordered as you would like them on the admin page. this is for displaying the currently selected items (in the case of a ManyToMany field)

get_query(q, request)

This sets up the query for the lookup.

The lookup searches the name of the protein.

URLconfs

experimentdb.proteins.urls.restricted_change_protein(request, *args, **kwargs)

experimentdb.proteins.urls.restricted_create_protein(request, *args, **kwargs)

experimentdb.proteins.urls.restricted_delete_protein(request, *args, **kwargs)

experimentdb.proteins.urls.restricted_detail(request, *args, **kwargs)

experimentdb.proteins.urls.restricted_object_list(request, *args, **kwargs)

Tests

Fixtures

This folder contains data fixtures for the proteins app.

Currently there is one text fixture for Protein objects named test_protein.json.

Reagents Package

Models

This package describes the models in the reagents app.

The models are ReagentInfo, which is an abstract superclass of: - Primer - Cell - Antibody - Strain - Chemical - Construct

The ReagentInfo class provides generic fields to all the models, while each subclass provides extra specific fields. This package also contains a Selection model, to be used for antibiotic selections, and a specied model, to be used to indicate various species.

class experimentdb.reagents.models.Antibody(*args, **kwargs)

This model describes antibodies.

The required fields are name and source_species. This model is a subclass of ReagentInfo.

exception DoesNotExist

exception Antibody.MultipleObjectsReturned

Antibody.experiment_set

Antibody.get_absolute_url(*moreargs, **morekwargs)

Antibody.get_location_display(*moreargs, **morekwargs)

Antibody.get_source_species_display(*moreargs, **morekwargs)

Antibody.protein

Antibody.reference

Antibody.researcher

Antibody.save()

The save is over-ridden to slugify the name field into a slugfield.

Antibody.species

Antibody.vendor

class experimentdb.reagents.models.Cell(*args, **kwargs)

This model describes objects of the class Cell.

This model is intended to be used to store information about mammalian cell lines. The only required field is name. This model is a subclass of ReagentInfo.

exception DoesNotExist

exception Cell.MultipleObjectsReturned

Cell.cell_line_species

Cell.experiment_set

Cell.get_absolute_url(*moreargs, **morekwargs)

Cell.get_location_display(*moreargs, **morekwargs)

Cell.get_species_display(*moreargs, **morekwargs)

Cell.protein

Cell.reference

Cell.researcher

Cell.save()

The save is over-ridden to slugify the name field into a slugfield.

Cell.vendor

class experimentdb.reagents.models.Chemical(*args, **kwargs)

This model describes objects of the class Chemical.

It is intended to describe chemicals used in experiments. The only required field is name. This model is a subclass of ReagentInfo.

exception DoesNotExist

exception Chemical.MultipleObjectsReturned

Chemical.experiment_set

Chemical.get_absolute_url(*moreargs, **morekwargs)

Chemical.get_location_display(*moreargs, **morekwargs)

Chemical.protein

Chemical.reference

Chemical.researcher

Chemical.save()

The save is over-ridden to slugify the name field into a slugfield.

Chemical.vendor

class experimentdb.reagents.models.Construct(*args, **kwargs)

This model describes recombinant DNA objects.

The only required field is name. It is a subclass of ReagentInfo.

exception DoesNotExist

exception Construct.MultipleObjectsReturned

Construct.constructshipment_set

Construct.experiment_set

Construct.final_clone

Construct.get_absolute_url(*moreargs, **morekwargs)

Construct.get_location_display(*moreargs, **morekwargs)

Construct.mutant

Construct.protein

Construct.recipient_vector

Construct.reference

Construct.researcher

Construct.save()

The save is over-ridden to slugify the name field into a slugfield.

Construct.selection

Construct.sequencing_set

Construct.strain_set

Construct.template

Construct.vendor

class experimentdb.reagents.models.Primer(*args, **kwargs)

Model describing primer objects.

These objects can be of any short nucleotide type including primers, siRNA oligos or morpholinos. The required fields are the name and the type. The nonrequired fields include the sequence, the protein, the ordering date and all generic reagent info fields. This is a subclass of the ReagentInfo abstract base class.

3_Primer

5_Primer

exception DoesNotExist

exception Primer.MultipleObjectsReturned

Primer.antisense_primer

Primer.experiment_set

Primer.get_absolute_url(*moreargs, **morekwargs)

Primer.get_location_display(*moreargs, **morekwargs)

Primer.get_primer_type_display(*moreargs, **morekwargs)

Primer.protein

Primer.reference

Primer.researcher

Primer.save()

The save is over-ridden to slugify the name field into a slugfield.

Primer.sense_primer

Primer.sequencing_set

Primer.vendor

class experimentdb.reagents.models.ReagentInfo(*args, **kwargs)

Abstract base model for all reagents, will not be used in isolation, only as part of other models.

This superclass provides several generic fields, available to all reagents. The only required field of all reagents is name. It orders all reagents by name, although this may be over-ridden in the model. It also sets sets their __unicode__ representation to be “name”.

class Meta

ReagentInfo.get_location_display(*moreargs, **morekwargs)

ReagentInfo.protein

ReagentInfo.reference

ReagentInfo.researcher

ReagentInfo.vendor

class experimentdb.reagents.models.Selection(*args, **kwargs)

Model for selection conditions of transformants.

This object has one required field, being selection. An optional comments field is also available.

Initial data upon installation includes resistance to ampicillin or kanamycin. Other selective markers should be added at /experimentdb/selection/new

exception DoesNotExist

exception Selection.MultipleObjectsReturned

Selection.construct_set

Selection.get_absolute_url(*moreargs, **morekwargs)

Selection.save()

The save is over-ridden to slugify the selection field into a slugfield.

Selection.strain_set

class experimentdb.reagents.models.Species(*args, **kwargs)

Model for indicating specific species.

The only required field is common_name. This is used with Strain, Cell and Antibody objects. Currently the species field, with the old choices=SPECIES is present until data can be migrated. Upon installation, initial data is provided for rabbit, mouse, human, yeast and goat species. More species can be added at /experimentdb/species/new.

exception DoesNotExist

exception Species.MultipleObjectsReturned

Species.antibody_set

Species.cell_set

Species.get_absolute_url(*moreargs, **morekwargs)

Species.save()

The save is over-ridden to slugify the common_name field into a slugfield.

Species.strain_set

class experimentdb.reagents.models.Strain(*args, **kwargs)

Model describing biological strains.

This was devised to organize yeast strains, but can be used for bacteria or other organisms as well. The only required field is name. This is a subclass of ReagentInfo abstract class

exception DoesNotExist

exception Strain.MultipleObjectsReturned

Strain.background

Strain.experiment_set

Strain.get_absolute_url(*moreargs, **morekwargs)

Strain.get_location_display(*moreargs, **morekwargs)

Strain.get_species_display(*moreargs, **morekwargs)

Strain.plasmids

Strain.protein

Strain.reference

Strain.researcher

Strain.save()

The save is over-ridden to slugify the name field into a slugfield.

Strain.selection

Strain.strain_set

Strain.strain_species

Strain.vendor

Views

experimentdb.reagents.views.antibody_lookup(request)

A json lookup view for antibodies.

This view takes a get query item and returns a json dictionary of antibody objects matching that name

experimentdb.reagents.views.index(request, *args, **kwargs)

Lookups

This is a configuration file for the ajax lookups for the reagents app.

See http://code.google.com/p/django-ajax-selects/ for information about configuring the ajax lookups.

class experimentdb.reagents.lookups.AntibodyLookup

This is the generic lookup for antibodies.

It is to be used for all antibody requests and directs to the ‘antibody’ channel.

format_item(antibody)

the display of a currently selected object in the area below the search box. html is OK

format_result(antibody)

This controls the display of the dropdown menu.

This is set to show the unicode name of the antibody, as well as the vendor and the source species.

get_objects(ids)

given a list of ids, return the objects ordered as you would like them on the admin page. this is for displaying the currently selected items (in the case of a ManyToMany field)

get_query(q, request)

This sets up the query for the lookup.

The lookup searches the name of the antibody.

class experimentdb.reagents.lookups.CellLineLookup

This is the generic lookup for strains.

It is to be used for all cell line requests and directs to the ‘cell’ channel.

format_item(cell)

the display of a currently selected object in the area below the search box. html is OK

format_result(cell)

This controls the display of the dropdown menu.

This is set to show the unicode name of the cell line.

get_objects(ids)

given a list of ids, return the objects ordered as you would like them on the admin page. this is for displaying the currently selected items (in the case of a ManyToMany field)

get_query(q, request)

This sets up the query for the lookup.

The lookup searches the name of the cell.

class experimentdb.reagents.lookups.ChemicalLookup

This is the generic lookup for chemicals.

It is to be used for all chemical requests and directs to the ‘chemical’ channel.

format_item(chemical)

the display of a currently selected object in the area below the search box. html is OK

format_result(chemical)

This controls the display of the dropdown menu.

This is set to show the unicode name of the chemical.

get_objects(ids)

given a list of ids, return the objects ordered as you would like them on the admin page. this is for displaying the currently selected items (in the case of a ManyToMany field)

get_query(q, request)

This sets up the query for the lookup.

The lookup searches the name of the chemical.

class experimentdb.reagents.lookups.ConstructLookup

This is the generic lookup for constructs.

It is to be used for all construct requests and directs to the ‘construct’ channel.

format_item(construct)

the display of a currently selected object in the area below the search box. html is OK

format_result(construct)

This controls the display of the dropdown menu.

This is set to show the unicode name of the construct.

get_objects(ids)

given a list of ids, return the objects ordered as you would like them on the admin page. this is for displaying the currently selected items (in the case of a ManyToMany field)

get_query(q, request)

This sets up the query for the lookup.

The lookup searches the name of the construct.

class experimentdb.reagents.lookups.SiRNALookup

This is the generic lookup for siRNA.

It is to be used for all siRNA requests and directs to the ‘siRNA’ channel This channel will not search for all Primer objects, only the ones with primer_type=”siRNA”.

format_item(siRNA)

the display of a currently selected object in the area below the search box. html is OK

format_result(siRNA)

This controls the display of the dropdown menu.

This is set to show the unicode name of the siRNA line.

get_objects(ids)

given a list of ids, return the objects ordered as you would like them on the admin page. this is for displaying the currently selected items (in the case of a ManyToMany field)

get_query(q, request)

This sets up the query for the lookup.

The lookup searches the name of the siRNA.

class experimentdb.reagents.lookups.StrainLookup

This is the generic lookup for strains.

It is to be used for all strain requests and directs to the ‘strain’ channel.

format_item(strain)

the display of a currently selected object in the area below the search box. html is OK

format_result(strain)

This controls the display of the dropdown menu.

This is set to show the unicode name of the strain.

get_objects(ids)

given a list of ids, return the objects ordered as you would like them on the admin page. this is for displaying the currently selected items (in the case of a ManyToMany field)

get_query(q, request)

This sets up the query for the lookup.

The lookup searches the name of the strain.

URLconfs

URLconfs for reagent models.

In general these urls have the names model-list, model-detail, model-new, model-edit and model-delete.

Tests

This file contains tests for the reagents application.

These tests include model and view tests for Strain, Primer, Cell, Antibody, Construct, Chemical, Species and Selection objects.

class experimentdb.reagents.tests.AntibodyModelTests(methodName='runTest')

Tests the model attributes of Antibody objects contained in the reagents app.

setUp()

Instantiate the test client.

tearDown()

Depopulate created model instances from test database.

test_antibody_slugify()

This is a test for the antibody name being correctly slugified

test_create_antibody_all_fields()

This is a test for creating a new antibody object, with only the all fields being entered

test_create_antibody_minimal()

This is a test for creating a new antibody object, with only the minimum fields being entered

class experimentdb.reagents.tests.CellModelTests(methodName='runTest')

Tests the model attributes of Cell objects contained in the reagents app.

setUp()

Instantiate the test client.

tearDown()

Depopulate created model instances from test database.

test_cell_line_slugify()

This is a test for the cell line name being correctly slugified

test_create_cell_line_all_fields()

This is a test for creating a new cell_line object, with only the all fields being entered

test_create_cell_line_minimal()

This is a test for creating a new cell line object, with only the minimum fields being entered

class experimentdb.reagents.tests.ChemicalModelTests(methodName='runTest')

Tests the model attributes of Chemical objects contained in the reagents app.

setUp()

Instantiate the test client.

tearDown()

Depopulate created model instances from test database.

test_chemical_slugify()

This is a test for the cell line name being correctly slugified

test_create_chemical_all_fields()

This is a test for creating a new chemical object, with only the all fields being entered

test_create_chemical_minimal()

This is a test for creating a new chemical object, with only the minimum fields being entered

class experimentdb.reagents.tests.ConstructModelTests(methodName='runTest')

Tests the model attributes of Construct objects contained in the reagents app.

setUp()

Instantiate the test client.

tearDown()

Depopulate created model instances from test database.

test_construct_slugify()

This is a test for the construct name being correctly slugified

test_create_cell_line_minimal()

This is a test for creating a new construct object, with only the minimum fields being entered

test_create_construct_all_fields()

This is a test for creating a new construct object, with only the all fields being entered

class experimentdb.reagents.tests.PrimerModelTests(methodName='runTest')

Tests the model attributes of Primer objects contained in the reagents app.

setUp()

Instantiate the test client.

tearDown()

Depopulate created model instances from test database.

test_create_primer_all_fields()

This is a test for creating a new primer object, with only the all fields being entered

test_create_primer_minimal()

This is a test for creating a new primer object, with only the minimum fields being entered

test_primer_slugify()

This is a test for the primer name being correctly slugified

class experimentdb.reagents.tests.SelectionModelTests(methodName='runTest')

Tests the model attributes of Selection objects contained in the reagents app.

setUp()

Instantiate the test client.

tearDown()

Depopulate created model instances from test database.

test_create_selection_all_fields()

This is a test for creating a new selection object, with only the all fields being entered

test_create_selection_minimal()

This is a test for creating a new selection object, with only the minimum fields being entered

test_selection_slugify()

This is a test for the cell line name being correctly slugified

class experimentdb.reagents.tests.SpeciesModelTests(methodName='runTest')

Tests the model attributes of Species objects contained in the reagents app.

setUp()

Instantiate the test client.

tearDown()

Depopulate created model instances from test database.

test_create_species_all_fields()

This is a test for creating a new species object, with only the all fields being entered

test_create_species_minimal()

This is a test for creating a new species object, with only the minimum fields being entered

test_species_slugify()

This is a test for the cell line name being correctly slugified

class experimentdb.reagents.tests.StrainModelTests(methodName='runTest')

Tests the model attributes of Strain objects contained in the reagents app.

setUp()

Instantiate the test client.

tearDown()

Depopulate created model instances from test database.

test_create_strain_all_fields()

This is a test for creating a new strain object, with only the all fields being entered

test_create_strain_minimal()

This is a test for creating a new strain object, with only the minimum fields being entered

test_strain_slugify()

This is a test for the cell line name being correctly slugified

Fixtures

This folder contains fixtures for the reagents app.

Currently there are the following text fixtures - Species model named test_species.json - Selection model named test_selection.json - Strain model named test_strain.json - Construct model named test_construct.json

Sharing Package

Models

This package defines the database models for for the sharing application.

This application tracks shipments of constructs to other groups.

These tests include the following models: - Institution - Laboratory - Recipient - ConstructShipment

In the terms of this application, ConstructShipments are sent to Recipients, who are in Laboratories at Institutions.

class experimentdb.sharing.models.ConstructShipment(*args, **kwargs)

This class describes a shipment of constructs.

The required fields are constructs, ship_date, recipient (who is defined as part of a Laboratory and in turn an Institution).

exception DoesNotExist

exception ConstructShipment.MultipleObjectsReturned

ConstructShipment.constructs

ConstructShipment.get_absolute_url(*moreargs, **morekwargs)

ConstructShipment.get_next_by_ship_date(*moreargs, **morekwargs)

ConstructShipment.get_previous_by_ship_date(*moreargs, **morekwargs)

ConstructShipment.recipient

class experimentdb.sharing.models.Institution(*args, **kwargs)

This class defines Institution models.

The only required is institution. The institution describes part of the address (city/state/country) the rest is defined under Laboratory.

exception DoesNotExist

exception Institution.MultipleObjectsReturned

Institution.get_country_display(*moreargs, **morekwargs)

Institution.get_institution_type_display(*moreargs, **morekwargs)

Institution.laboratory_set

class experimentdb.sharing.models.Laboratory(*args, **kwargs)

This class describes groups or laboratories.

This class has two required fields, principal_investigator and institution. In this context, a laboratory could be a single person or a group of people at an institution. Typically the recipient of the shipment works at the laboratory. The laboratory may or may not also be a contact, as defined in the external app.

exception DoesNotExist

exception Laboratory.MultipleObjectsReturned

Laboratory.contact

Laboratory.institution

Laboratory.recipient_set

class experimentdb.sharing.models.Recipient(*args, **kwargs)

This class describes the recipient of a shipment.

The recipient could be the principal investigator, or a member of their group. The required fields for this model are first_name, last_name and lab.

exception DoesNotExist

exception Recipient.MultipleObjectsReturned

Recipient.constructshipment_set

Recipient.lab

Views

URLconfs

experimentdb.sharing.urls.change_shipment(request, *args, **kwargs)

experimentdb.sharing.urls.create_shipment(request, *args, **kwargs)

experimentdb.sharing.urls.delete_shipment(request, *args, **kwargs)

experimentdb.sharing.urls.shipment_detail(request, *args, **kwargs)

experimentdb.sharing.urls.shipment_list(request, *args, **kwargs)

Tests

This file contains tests for the sharing application.

These tests include model and view tests for the following models: - Institution - Laboratory - Recipient - ConstructShipment

class experimentdb.sharing.tests.ConstructShipmentModelTests(methodName='runTest')

Tests the model attributes of ConstructShipment objects contained in the reagents app.

setUp()

Instantiate the test client.

tearDown()

Depopulate created model instances from test database.

test_create_construct_shipment_all_fields()

This is a test for creating a new construct shipment object, with all fields being entered

test_create_construct_shipment_minimal()

This is a test for creating a new construct shipment, with only the minimum fields being entered

class experimentdb.sharing.tests.InstitutionModelTests(methodName='runTest')

Tests the model attributes of Laboratory objects contained in the reagents app.

setUp()

Instantiate the test client.

tearDown()

Depopulate created model instances from test database.

test_create_institution_all_fields()

This is a test for creating a new institution object, with all fields being entered

test_create_institution_minimal()

This is a test for creating a new institution, with only the minimum fields being entered

class experimentdb.sharing.tests.LaboratoryModelTests(methodName='runTest')

Tests the model attributes of Laboratory objects contained in the reagents app.

setUp()

Instantiate the test client.

tearDown()

Depopulate created model instances from test database.

test_create_laboratory_all_fields()

This is a test for creating a new recipient object, with all fields being entered

test_create_laboratory_minimal()

This is a test for creating a new laboratory, with only the minimum fields being entered

class experimentdb.sharing.tests.RecipientModelTests(methodName='runTest')

Tests the model attributes of Recipient objects contained in the reagents app.

setUp()

Instantiate the test client.

tearDown()

Depopulate created model instances from test database.

test_create_recipient_all_fields()

This is a test for creating a new recipient, with all fields being entered

test_create_recipient_minimal()

This is a test for creating a new recipient, with only the minimum fields being entered

Fixtures

This folder contains data fixtures for the sharing app.

Currently it contains the following test fixtures: - an Institution object as test_institution.json - a Laboratory object as test_laboratory.json - a Recipient object as test_recipient.json