pytz>=2011
requests>=2.0
wsgiref==0.1.2
+factory_boy>=2.4
\ No newline at end of file
+++ /dev/null
-[
- {
- "model": "samples.Cellline",
- "pk": 1,
- "fields": {
- "cellline_name": "Unknown",
- "notes": "Unknown"
- }
- },
- {
- "model": "samples.Cellline",
- "pk": 2,
- "fields": {
- "cellline_name": "C2C12",
- "notes": ""
- }
- },
- {
- "model": "samples.Cellline",
- "pk": 3,
- "fields": {
- "cellline_name": "C2C12 60 hrs",
- "notes": "Unknown"
- }
- },
- { "pk": 1, "model": "samples.Condition",
- "fields": {
- "condition_name": "Unknown",
- "nickname": "",
- "notes": "Unknown"
- }
- },
- {
- "model": "samples.LibraryType",
- "pk": 1,
- "fields": {
- "name": "Single End (non-multiplexed)",
- "can_multiplex": false,
- "is_paired_end": false
- }
- },
- {
- "model": "samples.LibraryType",
- "pk": 2,
- "fields": {
- "name": "Paired End (non-multiplexed)",
- "can_multiplex": false,
- "is_paired_end": true
- }
- },
- {
- "model": "samples.LibraryType",
- "pk": 5,
- "fields": {
- "name": "Barcoded Illumina",
- "can_multiplex": true,
- "is_paired_end": true
- }
- },
- {
- "model": "samples.LibraryType",
- "pk": 7,
- "fields": {
- "name": "Barcoded Small RNA",
- "can_multiplex": true,
- "is_paired_end": true
- }
- },
- {
- "model": "samples.LibraryType",
- "pk": 8,
- "fields": {
- "name": "Nextera",
- "can_multiplex": true,
- "is_paired_end": true
- }
- },
- {
- "model": "samples.LibraryType",
- "pk": 9,
- "fields": {
- "name": "Dual Index Illumina",
- "can_multiplex": true,
- "is_paired_end": true
- }
- },
- {
- "model": "samples.ExperimentType",
- "pk": 1,
- "fields": {
- "name": "Unknown"
- }
- },
- {
- "model": "samples.ExperimentType",
- "pk": 2,
- "fields": {
- "name": "ChIP-seq"
- }
- },
- {
- "model": "samples.ExperimentType",
- "pk": 4,
- "fields": {
- "name": "RNA-seq"
- }
- },
- {
- "model": "samples.ExperimentType",
- "pk": 7,
- "fields": {
- "name": "De Novo"
- }
- },
- {
- "model": "samples.ExperimentType",
- "pk": 8,
- "fields": {
- "name": "Whole Genome"
- }
- },
- {
- "model": "samples.ExperimentType",
- "pk": 9,
- "fields": {
- "name": "Small RNA"
- }
- },
- {
- "model": "samples.ExperimentType",
- "pk": 10,
- "fields": {
- "name": "Multiplexed"
- }
- },
- {
- "model": "samples.Species",
- "pk": 2,
- "fields": {
- "scientific_name": "Drosophila melanogaster",
- "common_name": "fruit fly"
- }
- },
- {
- "model": "samples.Species",
- "pk": 3,
- "fields": {
- "scientific_name": "Caenorhabditis elegans",
- "common_name": ""
- }
- },
- {
- "model": "samples.Species",
- "pk": 6,
- "fields": {
- "scientific_name": "Arabidopsis thaliana"
- }
- },
- {
- "model": "samples.Species",
- "pk": 8,
- "fields": {
- "scientific_name": "Homo sapiens",
- "common_name": "human"
- }
- },
- {
- "model": "samples.Species",
- "pk": 9,
- "fields": {
- "scientific_name": "Mus musculus",
- "common_name": "mouse"
- }
- },
- {
- "model": "samples.Species",
- "pk": 10,
- "fields": {
- "scientific_name": "Strongylocentrotus purpuratus"
- }
- },
- {
- "pk": 1,
- "model": "samples.MultiplexIndex",
- "fields": {
- "multiplex_id": 1,
- "adapter_type": 8,
- "sequence": "ATCACG"
- }
- },
- {
- "pk": 2,
- "model": "samples.MultiplexIndex",
- "fields": {
- "multiplex_id": 2,
- "adapter_type": 8,
- "sequence": "CGATGT"
- }
- },
- {
- "pk": 3,
- "model": "samples.MultiplexIndex",
- "fields": {
- "multiplex_id": 3,
- "adapter_type": 8,
- "sequence": "TTAGGC"
- }
- },
- {
- "pk": 4,
- "model": "samples.MultiplexIndex",
- "fields": {
- "multiplex_id": 4,
- "adapter_type": 8,
- "sequence": "TGACCA"
- }
- },
- {
- "pk": 5,
- "model": "samples.MultiplexIndex",
- "fields": {
- "multiplex_id": 5,
- "adapter_type": 8,
- "sequence": "ACAGTG"
- }
- },
- {
- "pk": 6,
- "model": "samples.MultiplexIndex",
- "fields": {
- "multiplex_id": 6,
- "adapter_type": 8,
- "sequence": "GCCAAT"
- }
- },
- {
- "pk": 7,
- "model": "samples.MultiplexIndex",
- "fields": {
- "multiplex_id": 7,
- "adapter_type": 8,
- "sequence": "CAGATC"
- }
- },
- {
- "pk": 8,
- "model": "samples.MultiplexIndex",
- "fields": {
- "multiplex_id": 8,
- "adapter_type": 8,
- "sequence": "ACTTGA"
- }
- },
- {
- "pk": 9,
- "model": "samples.MultiplexIndex",
- "fields": {
- "multiplex_id": 9,
- "adapter_type": 8,
- "sequence": "GATCAG"
- }
- },
- {
- "pk": 10,
- "model": "samples.MultiplexIndex",
- "fields": {
- "multiplex_id": 10,
- "adapter_type": 8,
- "sequence": "TAGCTT"
- }
- },
- {
- "pk": 11,
- "model": "samples.MultiplexIndex",
- "fields": {
- "multiplex_id": 11,
- "adapter_type": 8,
- "sequence": "GGCTAC"
- }
- },
- {
- "pk": 12,
- "model": "samples.MultiplexIndex",
- "fields": {
- "multiplex_id": 12,
- "adapter_type": 8,
- "sequence": "CTTGTA"
- }
- },
- {
- "pk": 13,
- "model": "samples.MultiplexIndex",
- "fields": {
- "multiplex_id": 1,
- "adapter_type": 7,
- "sequence": "ATCACG"
- }
- },
- {
- "pk": 14,
- "model": "samples.MultiplexIndex",
- "fields": {
- "multiplex_id": 2,
- "adapter_type": 7,
- "sequence": "CGATGT"
- }
- },
- {
- "pk": 15,
- "model": "samples.MultiplexIndex",
- "fields": {
- "multiplex_id": 3,
- "adapter_type": 7,
- "sequence": "TTAGGC"
- }
- },
- {
- "pk": 16,
- "model": "samples.MultiplexIndex",
- "fields": {
- "multiplex_id": 4,
- "adapter_type": 7,
- "sequence": "TGACCA"
- }
- },
- {
- "pk": 17,
- "model": "samples.MultiplexIndex",
- "fields": {
- "multiplex_id": 5,
- "adapter_type": 7,
- "sequence": "ACAGTG"
- }
- },
- {
- "pk": 18,
- "model": "samples.MultiplexIndex",
- "fields": {
- "multiplex_id": 6,
- "adapter_type": 7,
- "sequence": "GCCAAT"
- }
- },
- {
- "pk": 19,
- "model": "samples.MultiplexIndex",
- "fields": {
- "multiplex_id": 7,
- "adapter_type": 7,
- "sequence": "CAGATC"
- }
- },
- {
- "pk": 20,
- "model": "samples.MultiplexIndex",
- "fields": {
- "multiplex_id": 8,
- "adapter_type": 7,
- "sequence": "ACTTGA"
- }
- },
- {
- "pk": 21,
- "model": "samples.MultiplexIndex",
- "fields": {
- "multiplex_id": 9,
- "adapter_type": 7,
- "sequence": "GATCAG"
- }
- },
- {
- "pk": 22,
- "model": "samples.MultiplexIndex",
- "fields": {
- "multiplex_id": 10,
- "adapter_type": 7,
- "sequence": "TAGCTT"
- }
- },
- {
- "pk": 23,
- "model": "samples.MultiplexIndex",
- "fields": {
- "multiplex_id": 11,
- "adapter_type": 7,
- "sequence": "GGCTAC"
- }
- },
- {
- "pk": 24,
- "model": "samples.MultiplexIndex",
- "fields": {
- "multiplex_id": 12,
- "adapter_type": 7,
- "sequence": "CTTGTA"
- }
- },
- {
- "pk": 25,
- "model": "samples.MultiplexIndex",
- "fields": {
- "multiplex_id": 13,
- "adapter_type": 7,
- "sequence": "AGTCAA"
- }
- },
- {
- "pk": 26,
- "model": "samples.MultiplexIndex",
- "fields": {
- "multiplex_id": 14,
- "adapter_type": 7,
- "sequence": "AGTTCC"
- }
- },
- {
- "pk": 27,
- "model": "samples.MultiplexIndex",
- "fields": {
- "multiplex_id": 15,
- "adapter_type": 7,
- "sequence": "ATGTCA"
- }
- },
- {
- "pk": 28,
- "model": "samples.MultiplexIndex",
- "fields": {
- "multiplex_id": 16,
- "adapter_type": 7,
- "sequence": "CCGTCC"
- }
- },
- {
- "pk": 29,
- "model": "samples.MultiplexIndex",
- "fields": {
- "multiplex_id": 17,
- "adapter_type": 7,
- "sequence": "GTAGAG"
- }
- },
- {
- "pk": 30,
- "model": "samples.MultiplexIndex",
- "fields": {
- "multiplex_id": 18,
- "adapter_type": 7,
- "sequence": "GTCCGC"
- }
- },
- {
- "pk": 31,
- "model": "samples.MultiplexIndex",
- "fields": {
- "multiplex_id": 19,
- "adapter_type": 7,
- "sequence": "GTGAAA"
- }
- },
- {
- "pk": 32,
- "model": "samples.MultiplexIndex",
- "fields": {
- "multiplex_id": 20,
- "adapter_type": 7,
- "sequence": "GTGGCC"
- }
- },
- {
- "pk": 33,
- "model": "samples.MultiplexIndex",
- "fields": {
- "multiplex_id": 21,
- "adapter_type": 7,
- "sequence": "GTTTCG"
- }
- },
- {
- "pk": 34,
- "model": "samples.MultiplexIndex",
- "fields": {
- "multiplex_id": 22,
- "adapter_type": 7,
- "sequence": "CGTACG"
- }
- },
- {
- "pk": 35,
- "model": "samples.MultiplexIndex",
- "fields": {
- "multiplex_id": 23,
- "adapter_type": 7,
- "sequence": "GAGTGG"
- }
- },
- {
- "pk": 36,
- "model": "samples.MultiplexIndex",
- "fields": {
- "multiplex_id": 24,
- "adapter_type": 7,
- "sequence": "GGTAGC"
- }
- },
- {
- "pk": 37,
- "model": "samples.MultiplexIndex",
- "fields": {
- "multiplex_id": 25,
- "adapter_type": 7,
- "sequence": "ACTGAT"
- }
- },
- {
- "pk": 38,
- "model": "samples.MultiplexIndex",
- "fields": {
- "multiplex_id": 26,
- "adapter_type": 7,
- "sequence": "ATGAGC"
- }
- },
- {
- "pk": 39,
- "model": "samples.MultiplexIndex",
- "fields": {
- "multiplex_id": 27,
- "adapter_type": 7,
- "sequence": "ATTCCT"
- }
- },
- {
- "pk": 40,
- "model": "samples.MultiplexIndex",
- "fields": {
- "multiplex_id": 28,
- "adapter_type": 7,
- "sequence": "CAAAAG"
- }
- },
- {
- "pk": 41,
- "model": "samples.MultiplexIndex",
- "fields": {
- "multiplex_id": 29,
- "adapter_type": 7,
- "sequence": "CAACTA"
- }
- },
- {
- "pk": 42,
- "model": "samples.MultiplexIndex",
- "fields": {
- "multiplex_id": 30,
- "adapter_type": 7,
- "sequence": "CACCGG"
- }
- },
- {
- "pk": 43,
- "model": "samples.MultiplexIndex",
- "fields": {
- "multiplex_id": 31,
- "adapter_type": 7,
- "sequence": "CACGAT"
- }
- },
- {
- "pk": 44,
- "model": "samples.MultiplexIndex",
- "fields": {
- "multiplex_id": 32,
- "adapter_type": 7,
- "sequence": "CACTCA"
- }
- },
- {
- "pk": 45,
- "model": "samples.MultiplexIndex",
- "fields": {
- "multiplex_id": 33,
- "adapter_type": 7,
- "sequence": "CAGGCG"
- }
- },
- {
- "pk": 46,
- "model": "samples.MultiplexIndex",
- "fields": {
- "multiplex_id": 34,
- "adapter_type": 7,
- "sequence": "CATGGC"
- }
- },
- {
- "pk": 47,
- "model": "samples.MultiplexIndex",
- "fields": {
- "multiplex_id": 35,
- "adapter_type": 7,
- "sequence": "CATTTT"
- }
- },
- {
- "pk": 48,
- "model": "samples.MultiplexIndex",
- "fields": {
- "multiplex_id": 36,
- "adapter_type": 7,
- "sequence": "CCAACA"
- }
- },
- {
- "pk": 49,
- "model": "samples.MultiplexIndex",
- "fields": {
- "multiplex_id": 37,
- "adapter_type": 7,
- "sequence": "CGGAAT"
- }
- },
- {
- "pk": 50,
- "model": "samples.MultiplexIndex",
- "fields": {
- "multiplex_id": 38,
- "adapter_type": 7,
- "sequence": "CTAGCT"
- }
- },
- {
- "pk": 51,
- "model": "samples.MultiplexIndex",
- "fields": {
- "multiplex_id": 39,
- "adapter_type": 7,
- "sequence": "CTATAC"
- }
- },
- {
- "pk": 52,
- "model": "samples.MultiplexIndex",
- "fields": {
- "multiplex_id": 40,
- "adapter_type": 7,
- "sequence": "CTCAGA"
- }
- },
- {
- "pk": 53,
- "model": "samples.MultiplexIndex",
- "fields": {
- "multiplex_id": 41,
- "adapter_type": 7,
- "sequence": "GACGAC"
- }
- },
- {
- "pk": 54,
- "model": "samples.MultiplexIndex",
- "fields": {
- "multiplex_id": 42,
- "adapter_type": 7,
- "sequence": "TAATCG"
- }
- },
- {
- "pk": 55,
- "model": "samples.MultiplexIndex",
- "fields": {
- "multiplex_id": 43,
- "adapter_type": 7,
- "sequence": "TACAGC"
- }
- },
- {
- "pk": 56,
- "model": "samples.MultiplexIndex",
- "fields": {
- "multiplex_id": 44,
- "adapter_type": 7,
- "sequence": "TATAAT"
- }
- },
- {
- "pk": 57,
- "model": "samples.MultiplexIndex",
- "fields": {
- "multiplex_id": 45,
- "adapter_type": 7,
- "sequence": "TCATTC"
- }
- },
- {
- "pk": 58,
- "model": "samples.MultiplexIndex",
- "fields": {
- "multiplex_id": 46,
- "adapter_type": 7,
- "sequence": "TCCCGA"
- }
- },
- {
- "pk": 59,
- "model": "samples.MultiplexIndex",
- "fields": {
- "multiplex_id": 47,
- "adapter_type": 7,
- "sequence": "TCGAAG"
- }
- },
- {
- "pk": 60,
- "model": "samples.MultiplexIndex",
- "fields": {
- "multiplex_id": 48,
- "adapter_type": 7,
- "sequence": "TCGGCA"
- }
- },
- {
- "pk": 61,
- "model": "samples.MultiplexIndex",
- "fields": {
- "multiplex_id": 1,
- "adapter_type": 5,
- "sequence": "ATCACG"
- }
- },
- {
- "pk": 62,
- "model": "samples.MultiplexIndex",
- "fields": {
- "multiplex_id": 2,
- "adapter_type": 5,
- "sequence": "CGATGT"
- }
- },
- {
- "pk": 63,
- "model": "samples.MultiplexIndex",
- "fields": {
- "multiplex_id": 3,
- "adapter_type": 5,
- "sequence": "TTAGGC"
- }
- },
- {
- "pk": 64,
- "model": "samples.MultiplexIndex",
- "fields": {
- "multiplex_id": 4,
- "adapter_type": 5,
- "sequence": "TGACCA"
- }
- },
- {
- "pk": 65,
- "model": "samples.MultiplexIndex",
- "fields": {
- "multiplex_id": 5,
- "adapter_type": 5,
- "sequence": "ACAGTG"
- }
- },
- {
- "pk": 66,
- "model": "samples.MultiplexIndex",
- "fields": {
- "multiplex_id": 6,
- "adapter_type": 5,
- "sequence": "GCCAAT"
- }
- },
- {
- "pk": 67,
- "model": "samples.MultiplexIndex",
- "fields": {
- "multiplex_id": 7,
- "adapter_type": 5,
- "sequence": "CAGATC"
- }
- },
- {
- "pk": 68,
- "model": "samples.MultiplexIndex",
- "fields": {
- "multiplex_id": 8,
- "adapter_type": 5,
- "sequence": "ACTTGA"
- }
- },
- {
- "pk": 69,
- "model": "samples.MultiplexIndex",
- "fields": {
- "multiplex_id": 9,
- "adapter_type": 5,
- "sequence": "GATCAG"
- }
- },
- {
- "pk": 70,
- "model": "samples.MultiplexIndex",
- "fields": {
- "multiplex_id": 10,
- "adapter_type": 5,
- "sequence": "TAGCTT"
- }
- },
- {
- "pk": 71,
- "model": "samples.MultiplexIndex",
- "fields": {
- "multiplex_id": 11,
- "adapter_type": 5,
- "sequence": "GGCTAC"
- }
- },
- {
- "pk": 72,
- "model": "samples.MultiplexIndex",
- "fields": {
- "multiplex_id": 12,
- "adapter_type": 5,
- "sequence": "CTTGTA"
- }
- },
- {"fields": {"adapter_type": 9,
- "multiplex_id": "N501",
- "sequence": "TAGATCGC"},
- "model": "samples.multiplexindex",
- "pk": 74
- },
- {"fields": {"adapter_type": 9,
- "multiplex_id": "N502",
- "sequence": "CTCTCTAT"},
- "model": "samples.multiplexindex",
- "pk": 75},
- {"fields": {"adapter_type": 9,
- "multiplex_id": "N503",
- "sequence": "TATCCTCT"},
- "model": "samples.multiplexindex",
- "pk": 76},
- {"fields": {"adapter_type": 9,
- "multiplex_id": "N504",
- "sequence": "AGAGTAGA"},
- "model": "samples.multiplexindex",
- "pk": 77},
- {"fields": {"adapter_type": 9,
- "multiplex_id": "N505",
- "sequence": "GTAAGGAG"},
- "model": "samples.multiplexindex",
- "pk": 78},
- {"fields": {"adapter_type": 9,
- "multiplex_id": "N506",
- "sequence": "ACTGCATA"},
- "model": "samples.multiplexindex",
- "pk": 79},
- {"fields": {"adapter_type": 9,
- "multiplex_id": "N507",
- "sequence": "AAGGAGTA"},
- "model": "samples.multiplexindex",
- "pk": 80},
- {"fields": {"adapter_type": 9,
- "multiplex_id": "N508",
- "sequence": "CTAAGCCT"},
- "model": "samples.multiplexindex",
- "pk": 81},
- {"fields": {"adapter_type": 9,
- "multiplex_id": "N701",
- "sequence": "TAAGGCGA"},
- "model": "samples.multiplexindex",
- "pk": 82},
- {"fields": {"adapter_type": 9,
- "multiplex_id": "N702",
- "sequence": "CGTACTAG"},
- "model": "samples.multiplexindex",
- "pk": 83},
- {"fields": {"adapter_type": 9,
- "multiplex_id": "N703",
- "sequence": "AGGCAGAA"},
- "model": "samples.multiplexindex",
- "pk": 84},
- {"fields": {"adapter_type": 9, "multiplex_id": "N704", "sequence": "TCCTGA"},
- "model": "samples.multiplexindex",
- "pk": 85},
- {"fields": {"adapter_type": 9,
- "multiplex_id": "N705",
- "sequence": "GGACTCCT"},
- "model": "samples.multiplexindex",
- "pk": 86},
- {"fields": {"adapter_type": 9,
- "multiplex_id": "N706",
- "sequence": "TAGGCATG"},
- "model": "samples.multiplexindex",
- "pk": 87},
- {"fields": {"adapter_type": 9,
- "multiplex_id": "N707",
- "sequence": "CTCTCTAC"},
- "model": "samples.multiplexindex",
- "pk": 88},
- {"fields": {"adapter_type": 9,
- "multiplex_id": "N708",
- "sequence": "CAGAGAGG"},
- "model": "samples.multiplexindex",
- "pk": 89},
- {"fields": {"adapter_type": 9,
- "multiplex_id": "N709",
- "sequence": "GCTACGCT"},
- "model": "samples.multiplexindex",
- "pk": 90},
- {"fields": {"adapter_type": 9,
- "multiplex_id": "N710",
- "sequence": "CGAGGCTG"},
- "model": "samples.multiplexindex",
- "pk": 91},
- {"fields": {"adapter_type": 9,
- "multiplex_id": "N711",
- "sequence": "AAGAGGCA"},
- "model": "samples.multiplexindex",
- "pk": 92},
- {"fields": {"adapter_type": 9,
- "multiplex_id": "N712",
- "sequence": "GTAGAGGA"},
- "model": "samples.multiplexindex",
- "pk": 93}
-]
+++ /dev/null
-[
- {"pk": 5, "model": "auth.user",
- "fields": {
- "username": "test",
- "first_name": "",
- "last_name": "",
- "is_active": true,
- "is_superuser": false,
- "is_staff": false,
- "last_login": "2009-01-01T00:00:01-0800",
- "groups": [],
- "user_permissions": [],
- "password": "sha1$foo$5e4eefec1144a04becfb7da79244f07c487fc345",
- "email": "",
- "date_joined": "2009-01-01T00:01:01-0800"
- }
- },
- {"pk": 1, "model": "samples.affiliation",
- "fields": {
- "users": [5],
- "name": "Alice",
- "contact": "Lab Boss",
- "email": "alice@some.where.else."
- }
- },
- {"pk": 2, "model": "samples.affiliation",
- "fields": { "name": "Bob",
- "contact": "Other Lab Boss",
- "email": "bob@some.where.else"
- }
- },
- {"pk": 3, "model": "samples.affiliation",
- "fields": {
- "users": [],
- "contact": "group 3",
- "name": "affiliation 3",
- "email": "pk3@example.com"
- }
- },
- {"pk": 4, "model": "samples.affiliation",
- "fields": {
- "users": [],
- "contact": "group 4",
- "name": "affiliation 4",
- "email": "pk1@example.com"
- }
- },
- {"pk": 5, "model": "samples.affiliation",
- "fields": {
- "users": [],
- "contact": "group 5",
- "name": "affiliation 5",
- "email": "pk5@example.com"
- }
- },
- {"pk": 153, "model": "experiments.flowcell",
- "fields": {
- "paired_end": true,
- "run_date": "2009-09-11T22:12:13-0800",
- "read_length": 75,
- "notes": "",
- "advanced_run": false,
- "control_lane": 2,
- "cluster_station": 3,
- "sequencer": 2,
- "flowcell_id": "303TUAAXX"
- }
- },
- {"pk": 1193, "model": "experiments.lane",
- "fields": {
- "comment": "No change in cluster numbers, despite slight increase in pM",
- "library": "10981",
- "cluster_estimate": 129000,
- "flowcell": 153,
- "lane_number": 1,
- "pM": "8"
- }
- },
- {"pk": 1197, "model": "experiments.lane",
- "fields": {
- "comment": "stuff",
- "library": "11016",
- "cluster_estimate": 140000,
- "flowcell": 153,
- "lane_number": 5,
- "pM": "7",
- "status": 2
- }
- },
- {"pk": "10981", "model": "samples.library",
- "fields": {
- "ten_nM_dilution": false,
- "gel_cut_size": 400,
- "library_name": "Paired End Multiplexed Sp-BAC",
- "creation_date": "2009-07-21",
- "cell_line": 1,
- "library_species": 2,
- "library_type": null,
- "made_by": "Igor",
- "affiliations": [
- 2
- ],
- "replicate": 1,
- "condition": 1,
- "hidden": false,
- "stopping_point": "Done",
- "tags": [],
- "made_for": "Andy Cameron",
- "amplified_from_sample": null,
- "notes": "Combined 10957-10968",
- "undiluted_concentration": "5.1",
- "successful_pM": null,
- "experiment_type": 10,
- "antibody": null
- }
- },
- {
- "pk": "11016",
- "model": "samples.library",
- "fields": {
- "ten_nM_dilution": false,
- "gel_cut_size": 325,
- "library_name": "Paired End Pfl #3 MP 7/24/9 a",
- "creation_date": "2009-08-06",
- "cell_line": 1,
- "library_species": 9,
- "library_type": 2,
- "made_by": "Lorian",
- "affiliations": [
- 3
- ],
- "replicate": 1,
- "condition": 1,
- "hidden": false,
- "stopping_point": "1Aa",
- "tags": [],
- "made_for": "",
- "amplified_from_sample": "11003",
- "notes": "7/31/2009 16:08:22\tColor: Blue",
- "undiluted_concentration": "35.5",
- "successful_pM": null,
- "experiment_type": 8,
- "antibody": null
- }
- },
- {
- "pk": "11039",
- "model": "samples.library",
- "fields": {
- "ten_nM_dilution": false,
- "gel_cut_size": 300,
- "library_name": "Paired ends 99 GM12892",
- "creation_date": "2009-08-25",
- "cell_line": 1,
- "library_species": 8,
- "library_type": 2,
- "made_by": "Brian Williams",
- "affiliations": [
- 1,
- 2,
- 4
- ],
- "replicate": 1,
- "condition": 1,
- "hidden": false,
- "stopping_point": "1Aa",
- "tags": [],
- "made_for": "Brian Williams",
- "amplified_from_sample": null,
- "notes": "fragment size = 300 bp, Amicon filtered\r\nnanodrop: 56.3",
- "undiluted_concentration": "28.7",
- "successful_pM": null,
- "experiment_type": 4,
- "antibody": null
- }
- },
- {
- "pk": "11003",
- "model": "samples.library",
- "fields": {
- "ten_nM_dilution": false,
- "gel_cut_size": 325,
- "library_name": "Paired End Pfl #3 MP 7/24/9",
- "creation_date": "2009-08-05",
- "cell_line": 1,
- "library_species": 8,
- "library_type": 2,
- "made_by": "Lorian",
- "affiliations": [
- 4
- ],
- "replicate": 1,
- "condition": 1,
- "hidden": true,
- "stopping_point": "1A",
- "tags": [],
- "made_for": "",
- "amplified_from_sample": null,
- "notes": "7/31/2009 16:08:22\tColor: Blue",
- "undiluted_concentration": null,
- "successful_pM": null,
- "experiment_type": 8,
- "antibody": null
- }
- },
- {
- "pk": "11005",
- "model": "samples.library",
- "fields": {
- "ten_nM_dilution": false,
- "gel_cut_size": 325,
- "library_name": "null cell line",
- "creation_date": "2009-08-05",
- "cell_line": null,
- "library_species": 8,
- "library_type": 2,
- "made_by": "Lorian",
- "affiliations": [
- 4
- ],
- "replicate": 1,
- "condition": 1,
- "hidden": true,
- "stopping_point": "1A",
- "tags": [],
- "made_for": "",
- "amplified_from_sample": null,
- "notes": "7/31/2009 16:08:22\tColor: Blue",
- "undiluted_concentration": null,
- "successful_pM": null,
- "experiment_type": 8,
- "antibody": null
- }
- }
-]
--- /dev/null
+# -*- coding: utf-8 -*-
+from __future__ import unicode_literals
+
+from django.db import models, migrations
+from django.conf import settings
+
+
+class Migration(migrations.Migration):
+
+ dependencies = [
+ ('auth', '0001_initial'),
+ ]
+
+ operations = [
+ migrations.CreateModel(
+ name='Affiliation',
+ fields=[
+ ('id', models.AutoField(verbose_name='ID', serialize=False, auto_created=True, primary_key=True)),
+ ('name', models.CharField(max_length=256, verbose_name=b'Name', db_index=True)),
+ ('contact', models.CharField(max_length=256, null=True, verbose_name=b'Lab Name', blank=True)),
+ ('email', models.EmailField(max_length=75, null=True, blank=True)),
+ ],
+ options={
+ 'ordering': ['name', 'contact'],
+ },
+ bases=(models.Model,),
+ ),
+ migrations.CreateModel(
+ name='Antibody',
+ fields=[
+ ('id', models.AutoField(verbose_name='ID', serialize=False, auto_created=True, primary_key=True)),
+ ('antigene', models.CharField(max_length=500, db_index=True)),
+ ('nickname', models.CharField(db_index=True, max_length=20, null=True, blank=True)),
+ ('catalog', models.CharField(max_length=50, null=True, blank=True)),
+ ('antibodies', models.CharField(max_length=500, db_index=True)),
+ ('source', models.CharField(db_index=True, max_length=500, null=True, blank=True)),
+ ('biology', models.TextField(null=True, blank=True)),
+ ('notes', models.TextField(null=True, blank=True)),
+ ],
+ options={
+ 'ordering': ['antigene'],
+ 'verbose_name_plural': 'antibodies',
+ },
+ bases=(models.Model,),
+ ),
+ migrations.CreateModel(
+ name='Cellline',
+ fields=[
+ ('id', models.AutoField(verbose_name='ID', serialize=False, auto_created=True, primary_key=True)),
+ ('cellline_name', models.CharField(unique=True, max_length=100, db_index=True)),
+ ('nickname', models.CharField(db_index=True, max_length=20, null=True, blank=True)),
+ ('notes', models.TextField(blank=True)),
+ ],
+ options={
+ 'ordering': ['cellline_name'],
+ },
+ bases=(models.Model,),
+ ),
+ migrations.CreateModel(
+ name='Condition',
+ fields=[
+ ('id', models.AutoField(verbose_name='ID', serialize=False, auto_created=True, primary_key=True)),
+ ('condition_name', models.CharField(unique=True, max_length=2000, db_index=True)),
+ ('nickname', models.CharField(db_index=True, max_length=20, null=True, verbose_name=b'Short Name', blank=True)),
+ ('notes', models.TextField(blank=True)),
+ ],
+ options={
+ 'ordering': ['condition_name'],
+ },
+ bases=(models.Model,),
+ ),
+ migrations.CreateModel(
+ name='ExperimentType',
+ fields=[
+ ('id', models.AutoField(verbose_name='ID', serialize=False, auto_created=True, primary_key=True)),
+ ('name', models.CharField(unique=True, max_length=50)),
+ ],
+ options={
+ },
+ bases=(models.Model,),
+ ),
+ migrations.CreateModel(
+ name='HTSUser',
+ fields=[
+ ('user_ptr', models.OneToOneField(parent_link=True, auto_created=True, primary_key=True, serialize=False, to=settings.AUTH_USER_MODEL)),
+ ],
+ options={
+ 'ordering': ['first_name', 'last_name', 'username'],
+ },
+ bases=('auth.user',),
+ ),
+ migrations.CreateModel(
+ name='Library',
+ fields=[
+ ('id', models.CharField(max_length=10, serialize=False, primary_key=True)),
+ ('library_name', models.CharField(unique=True, max_length=100)),
+ ('hidden', models.BooleanField(default=False)),
+ ('account_number', models.CharField(max_length=100, null=True, blank=True)),
+ ('replicate', models.PositiveSmallIntegerField(blank=True, null=True, choices=[(1, 1), (2, 2), (3, 3), (4, 4), (5, 5), (6, 6)])),
+ ('multiplex_id', models.CharField(max_length=128, null=True, verbose_name=b'Index ID', blank=True)),
+ ('creation_date', models.DateField(null=True, blank=True)),
+ ('made_for', models.CharField(max_length=50, verbose_name=b'ChIP/DNA/RNA Made By', blank=True)),
+ ('made_by', models.CharField(default=b'Lorian', max_length=50, blank=True)),
+ ('stopping_point', models.CharField(default=b'Done', max_length=25, choices=[(b'?', b'Unknown'), (b'Sample', b'Raw sample'), (b'Progress', b'In progress'), (b'1A', b'Ligation, then gel'), (b'PCR', b'Ligation, then PCR'), (b'1Ab', b'Ligation, PCR, then gel'), (b'1Ac', b'Ligation, gel, then 12x PCR'), (b'1Aa', b'Ligation, gel, then 18x PCR'), (b'2A', b'Ligation, PCR, gel, PCR'), (b'Done', b'Completed')])),
+ ('undiluted_concentration', models.DecimalField(decimal_places=2, max_digits=5, blank=True, help_text='Undiluted concentration (ng/\xb5l)', null=True, verbose_name=b'Concentration')),
+ ('successful_pM', models.DecimalField(null=True, max_digits=9, decimal_places=1, blank=True)),
+ ('ten_nM_dilution', models.BooleanField(default=False)),
+ ('gel_cut_size', models.IntegerField(default=225, null=True, blank=True)),
+ ('insert_size', models.IntegerField(null=True, blank=True)),
+ ('notes', models.TextField(blank=True)),
+ ('bioanalyzer_summary', models.TextField(default=b'', blank=True)),
+ ('bioanalyzer_concentration', models.DecimalField(help_text='(ng/\xb5l)', null=True, max_digits=5, decimal_places=2, blank=True)),
+ ('bioanalyzer_image_url', models.URLField(default=b'', blank=True)),
+ ('affiliations', models.ManyToManyField(related_name=b'library_affiliations', null=True, to='samples.Affiliation')),
+ ('amplified_from_sample', models.ForeignKey(related_name=b'amplified_into_sample', blank=True, to='samples.Library', null=True)),
+ ('antibody', models.ForeignKey(blank=True, to='samples.Antibody', null=True)),
+ ('cell_line', models.ForeignKey(verbose_name=b'Background', blank=True, to='samples.Cellline', null=True)),
+ ('condition', models.ForeignKey(blank=True, to='samples.Condition', null=True)),
+ ('experiment_type', models.ForeignKey(to='samples.ExperimentType')),
+ ],
+ options={
+ 'ordering': ['-id'],
+ 'verbose_name_plural': 'libraries',
+ },
+ bases=(models.Model,),
+ ),
+ migrations.CreateModel(
+ name='LibraryType',
+ fields=[
+ ('id', models.AutoField(verbose_name='ID', serialize=False, auto_created=True, primary_key=True)),
+ ('name', models.CharField(unique=True, max_length=255, verbose_name=b'Adapter Type')),
+ ('is_paired_end', models.BooleanField(default=True, help_text=b'can you do a paired end run with this adapter')),
+ ('can_multiplex', models.BooleanField(default=True, help_text=b'Does this adapter provide multiplexing?')),
+ ],
+ options={
+ 'ordering': ['-id'],
+ },
+ bases=(models.Model,),
+ ),
+ migrations.CreateModel(
+ name='MultiplexIndex',
+ fields=[
+ ('id', models.AutoField(verbose_name='ID', serialize=False, auto_created=True, primary_key=True)),
+ ('multiplex_id', models.CharField(max_length=6)),
+ ('sequence', models.CharField(max_length=12, null=True, blank=True)),
+ ('adapter_type', models.ForeignKey(to='samples.LibraryType')),
+ ],
+ options={
+ 'verbose_name_plural': 'multiplex indicies',
+ },
+ bases=(models.Model,),
+ ),
+ migrations.CreateModel(
+ name='Species',
+ fields=[
+ ('id', models.AutoField(verbose_name='ID', serialize=False, auto_created=True, primary_key=True)),
+ ('scientific_name', models.CharField(max_length=256, db_index=True)),
+ ('common_name', models.CharField(max_length=256, blank=True)),
+ ],
+ options={
+ 'ordering': ['scientific_name'],
+ 'verbose_name_plural': 'species',
+ },
+ bases=(models.Model,),
+ ),
+ migrations.CreateModel(
+ name='Tag',
+ fields=[
+ ('id', models.AutoField(verbose_name='ID', serialize=False, auto_created=True, primary_key=True)),
+ ('tag_name', models.CharField(max_length=100, db_index=True)),
+ ('context', models.CharField(default=b'Library', max_length=50, choices=[(b'Library', b'Library'), (b'ANY', b'ANY')])),
+ ],
+ options={
+ 'ordering': ['context', 'tag_name'],
+ },
+ bases=(models.Model,),
+ ),
+ migrations.AlterUniqueTogether(
+ name='multiplexindex',
+ unique_together=set([('adapter_type', 'multiplex_id')]),
+ ),
+ migrations.AddField(
+ model_name='library',
+ name='library_species',
+ field=models.ForeignKey(to='samples.Species'),
+ preserve_default=True,
+ ),
+ migrations.AddField(
+ model_name='library',
+ name='library_type',
+ field=models.ForeignKey(verbose_name=b'Adapter Type', blank=True, to='samples.LibraryType', null=True),
+ preserve_default=True,
+ ),
+ migrations.AddField(
+ model_name='library',
+ name='tags',
+ field=models.ManyToManyField(related_name=b'library_tags', null=True, to='samples.Tag', blank=True),
+ preserve_default=True,
+ ),
+ migrations.AddField(
+ model_name='affiliation',
+ name='users',
+ field=models.ManyToManyField(to='samples.HTSUser', null=True, blank=True),
+ preserve_default=True,
+ ),
+ migrations.AlterUniqueTogether(
+ name='affiliation',
+ unique_together=set([('name', 'contact')]),
+ ),
+ ]
--- /dev/null
+import datetime
+
+import factory
+from factory.django import DjangoModelFactory
+from . import models
+
+class AffiliationFactory(DjangoModelFactory):
+ class Meta:
+ model = models.Affiliation
+
+ name = 'affiliation'
+ contact = 'contact name'
+ email = factory.LazyAttribute(lambda obj: '%s@example.com' % obj.name)
+
+ @factory.post_generation
+ def users(self, create, extracted, **kwargs):
+ if not create:
+ return
+
+ if extracted:
+ for user in extracted:
+ self.users.add(user)
+
+class AntibodyFactory(DjangoModelFactory):
+ class Meta:
+ model = models.Antibody
+
+ antigen = 'antigen'
+ nickname = 'short name'
+ catalog = 'catalog #'
+ antibodies = 'antibody'
+ source = 'source'
+ biology = 'some biological description'
+ notes = 'some notes'
+
+
+class CelllineFactory(DjangoModelFactory):
+ class Meta:
+ model = models.Cellline
+
+ cellline_name = 'Test'
+ nickname = 'Test'
+ notes = 'Notes'
+
+
+class ConditionFactory(DjangoModelFactory):
+ class Meta:
+ model = models.Condition
+
+ condition_name = 'condition name'
+ nicname = 'nickname'
+ notes = 'notes'
+
+class ExperimentTypeFactory(DjangoModelFactory):
+ class Meta:
+ model = models.ExperimentType
+
+ name = 'experiment type name'
+
+class HTSUserFactory(DjangoModelFactory):
+ class Meta:
+ model = models.HTSUser
+
+ username = 'username'
+ email = factory.LazyAttribute(lambda obj: '%s@example.org' % obj.username)
+
+#class Tag
+
+class SpeciesFactory(DjangoModelFactory):
+ class Meta:
+ model = models.Species
+
+ scientific_name = 'test sapiens'
+ common_name = 'test human'
+
+
+class LibraryFactory(DjangoModelFactory):
+ class Meta:
+ model = models.Library
+
+ id = '10001'
+ library_name = 'C1C1 test'
+ library_species = factory.SubFactory(SpeciesFactory)
+ experiment_type = factory.SubFactory(ExperimentTypeFactory)
+ creation_date = datetime.datetime.now()
+ gel_cut_size = 400
+ made_for = 'scientist unit 2007'
+ made_by = 'microfluidics bot 7321'
+ stopping_point = '2A'
+ undiluted_concentration = '5.01'
+ hidden = False
from __future__ import absolute_import, print_function
import datetime
+import unittest
+import json
-try:
- import json
-except ImportError, e:
- import simplejson as json
-
-from django.test import TestCase
-from django.test.utils import setup_test_environment, \
- teardown_test_environment
-from django.db import connection
+from django.test import TestCase, RequestFactory
from django.conf import settings
from .models import Affiliation, ExperimentType, Species, Library
-
-from .views import library_dict, library_json
+from .views import library_dict, library_json, library
+from .samples_factory import *
from htsworkflow.auth import apidata
from htsworkflow.util.conversion import unicode_or_none
from htsworkflow.util.ethelp import validate_xhtml
class LibraryTestCase(TestCase):
- fixtures = ['initial_data.json',
- 'woldlab.json',
- 'test_samples.json']
+ def testOrganism(self):
+ human = SpeciesFactory(common_name='human')
+ self.assertEquals(human.common_name, 'human')
+ library = LibraryFactory(library_species=human)
+ self.assertEquals(library.organism(), 'human')
- def setUp(self):
- create_db(self)
+ def testAddingOneAffiliation(self):
+ affiliation = AffiliationFactory.create(name='Alice')
+ library = LibraryFactory()
+ library.affiliations.add(affiliation)
- def testOrganism(self):
- self.assertEquals(self.library_10001.organism(), 'human')
+ self.assertEqual(len(library.affiliations.all()), 1)
+ self.assertEqual(library.affiliation(), 'Alice (contact name)')
+
+ def testMultipleAffiliations(self):
+ alice = AffiliationFactory.create(name='Alice')
+ bob = AffiliationFactory.create(name='Bob')
- def testAffiliations(self):
- self.library_10001.affiliations.add(self.affiliation_alice)
- self.library_10002.affiliations.add(
- self.affiliation_alice,
- self.affiliation_bob
- )
- self.failUnless(len(self.library_10001.affiliations.all()), 1)
- self.failUnless(self.library_10001.affiliation(), 'Alice')
+ library = Library.make_test_object()
+ library.affiliations.add(alice, bob)
- self.failUnless(len(self.library_10002.affiliations.all()), 2)
- self.failUnless(self.library_10001.affiliation(), 'Alice, Bob')
+ self.assertEqual(len(library.affiliations.all()), 2)
+ self.assertEqual(library.affiliation(),
+ 'Alice (contact name), Bob (contact name)')
class SampleWebTestCase(TestCase):
Test returning data from our database in rest like ways.
(like returning json objects)
"""
- fixtures = ['initial_data.json',
- 'woldlab.json',
- 'test_samples.json']
-
- def test_library_info(self):
- for lib in Library.objects.all():
- lib_dict = library_dict(lib.id)
- url = '/samples/library/%s/json' % (lib.id,)
- lib_response = self.client.get(url, apidata)
- self.failUnlessEqual(lib_response.status_code, 200)
- lib_json = json.loads(lib_response.content)
-
- for d in [lib_dict, lib_json]:
- # amplified_from_sample is a link to the library table,
- # I want to use the "id" for the data lookups not
- # the embedded primary key.
- # It gets slightly confusing on how to implement sending the right id
- # since amplified_from_sample can be null
- #self.failUnlessEqual(d['amplified_from_sample'], lib.amplified_from_sample)
- self.failUnlessEqual(d['antibody_id'], lib.antibody_id)
- self.failUnlessEqual(d['cell_line_id'], lib.cell_line_id)
- self.failUnlessEqual(d['cell_line'], unicode_or_none(lib.cell_line))
- self.failUnlessEqual(d['experiment_type'], lib.experiment_type.name)
- self.failUnlessEqual(d['experiment_type_id'], lib.experiment_type_id)
- self.failUnlessEqual(d['gel_cut_size'], lib.gel_cut_size)
- self.failUnlessEqual(d['hidden'], lib.hidden)
- self.failUnlessEqual(d['id'], lib.id)
- self.failUnlessEqual(d['insert_size'], lib.insert_size)
- self.failUnlessEqual(d['library_name'], lib.library_name)
- self.failUnlessEqual(d['library_species'], lib.library_species.scientific_name)
- self.failUnlessEqual(d['library_species_id'], lib.library_species_id)
- self.failUnlessEqual(d['library_type_id'], lib.library_type_id)
- if lib.library_type_id is not None:
- self.failUnlessEqual(d['library_type'], lib.library_type.name)
- else:
- self.failUnlessEqual(d['library_type'], None)
- self.failUnlessEqual(d['made_for'], lib.made_for)
- self.failUnlessEqual(d['made_by'], lib.made_by)
- self.failUnlessEqual(d['notes'], lib.notes)
- self.failUnlessEqual(d['replicate'], lib.replicate)
- self.failUnlessEqual(d['stopping_point'], lib.stopping_point)
- self.failUnlessEqual(d['successful_pM'], lib.successful_pM)
- self.failUnlessEqual(d['undiluted_concentration'],
- unicode(lib.undiluted_concentration))
+ def test_library_dict(self):
+ library = LibraryFactory.create()
+ lib_dict = library_dict(library.id)
+ url = '/samples/library/%s/json' % (library.id,)
+ lib_response = self.client.get(url, apidata)
+ lib_json = json.loads(lib_response.content)
+
+
+ for d in [lib_dict, lib_json]:
+ # amplified_from_sample is a link to the library table,
+ # I want to use the "id" for the data lookups not
+ # the embedded primary key.
+ # It gets slightly confusing on how to implement sending the right id
+ # since amplified_from_sample can be null
+ #self.failUnlessEqual(d['amplified_from_sample'], lib.amplified_from_sample)
+ self.failUnlessEqual(d['antibody_id'], library.antibody_id)
+ self.failUnlessEqual(d['cell_line_id'], library.cell_line_id)
+ self.failUnlessEqual(d['cell_line'], unicode_or_none(library.cell_line))
+ self.failUnlessEqual(d['experiment_type'], library.experiment_type.name)
+ self.failUnlessEqual(d['experiment_type_id'], library.experiment_type_id)
+ self.failUnlessEqual(d['gel_cut_size'], library.gel_cut_size)
+ self.failUnlessEqual(d['hidden'], library.hidden)
+ self.failUnlessEqual(d['id'], library.id)
+ self.failUnlessEqual(d['insert_size'], library.insert_size)
+ self.failUnlessEqual(d['library_name'], library.library_name)
+ self.failUnlessEqual(d['library_species'], library.library_species.scientific_name)
+ self.failUnlessEqual(d['library_species_id'], library.library_species_id)
+ self.failUnlessEqual(d['library_type_id'], library.library_type_id)
+ self.failUnlessEqual(d['library_type'], None)
+ self.failUnlessEqual(d['made_for'], library.made_for)
+ self.failUnlessEqual(d['made_by'], library.made_by)
+ self.failUnlessEqual(d['notes'], library.notes)
+ self.failUnlessEqual(d['replicate'], library.replicate)
+ self.failUnlessEqual(d['stopping_point'], library.stopping_point)
+ self.failUnlessEqual(d['successful_pM'], library.successful_pM)
+ self.failUnlessEqual(d['undiluted_concentration'],
+ unicode(library.undiluted_concentration))
+
+
+ def junk(self):
# some specific tests
- if lib.id == '10981':
+ if library.id == '10981':
# test a case where there is no known status
lane_set = {u'status': u'Unknown',
u'paired_end': True,
u'status_code': None}
self.failUnlessEqual(len(d['lane_set']), 1)
self.failUnlessEqual(d['lane_set'][0], lane_set)
- elif lib.id == '11016':
+ elif library.id == '11016':
# test a case where there is a status
lane_set = {u'status': 'Good',
u'paired_end': True,
def test_library_no_key(self):
"""
- Make sure we get a 302 if we're not logged in
+ Make sure we get a 403 if we're not logged in
"""
- response = self.client.get('/samples/library/10981/json')
- self.failUnlessEqual(response.status_code, 403)
- response = self.client.get('/samples/library/10981/json', apidata)
+ library = LibraryFactory.create()
+
+ url = '/samples/library/{}/json'.format(library.id)
+ response = self.client.get(url, apidata)
self.failUnlessEqual(response.status_code, 200)
+ response = self.client.get(url)
+ self.failUnlessEqual(response.status_code, 403)
def test_library_rdf(self):
+ library = LibraryFactory.create()
+
import RDF
from htsworkflow.util.rdfhelp import get_model, \
dump_model, \
libraryOntology
model = get_model()
- response = self.client.get('/library/10981/')
+ response = self.client.get(library.get_absolute_url())
self.assertEqual(response.status_code, 200)
content = response.content
load_string_into_model(model, 'rdfa', content)
}"""
query = RDF.SPARQLQuery(body)
for r in query.execute(model):
- self.assertEqual(fromTypedNode(r['library_id']), u'10981')
+ self.assertEqual(fromTypedNode(r['library_id']),
+ library.id)
self.assertEqual(fromTypedNode(r['name']),
- u'Paired End Multiplexed Sp-BAC')
- self.assertEqual(fromTypedNode(r['gel_cut']), 400)
- self.assertEqual(fromTypedNode(r['made_by']), u'Igor')
+ library.name)
+ self.assertEqual(fromTypedNode(r['gel_cut']),
+ library.gel_cut)
+ self.assertEqual(fromTypedNode(r['made_by']),
+ library.made_by)
state = validate_xhtml(content)
if state is not None:
rdfNS = RDF.NS("http://www.w3.org/1999/02/22-rdf-syntax-ns#")
xsdNS = RDF.NS("http://www.w3.org/2001/XMLSchema#")
libNS = RDF.NS("http://jumpgate.caltech.edu/wiki/LibraryOntology#")
+
+ from htsworkflow.util.rdfhelp import dump_model
except ImportError,e:
HAVE_RDF = False
class TestRDFaLibrary(TestCase):
- fixtures = ['initial_data.json',
- 'woldlab.json',
- 'test_samples.json']
+ def setUp(self):
+ self.request = RequestFactory()
+
def test_parse_rdfa(self):
+
model = get_rdf_memory_model()
parser = RDF.Parser(name='rdfa')
- url = '/library/10981/'
+
+ bob = AffiliationFactory.create(name='Bob')
+
+ lib_object = LibraryFactory()
+ lib_object.affiliations.add(bob)
+ url = '/library/{}/'.format(lib_object.id)
+ ## request = self.request.get(url)
+ ## lib_response = library(request)
lib_response = self.client.get(url)
+ with open('/tmp/body.html', 'w') as outstream:
+ outstream.write(lib_response.content)
self.failIfEqual(len(lib_response.content), 0)
parser.parse_string_into_model(model,
lib_response.content,
'http://localhost'+url)
+ with open('/tmp/test.ttl', 'w') as outstream:
+ dump_model(model, outstream)
# http://jumpgate.caltech.edu/wiki/LibraryOntology#affiliation>
self.check_literal_object(model, ['Bob'], p=libNS['affiliation'])
- self.check_literal_object(model, ['Multiplexed'], p=libNS['experiment_type'])
+ self.check_literal_object(model,
+ ['experiment type name'],
+ p=libNS['experiment_type'])
self.check_literal_object(model, ['400'], p=libNS['gel_cut'])
- self.check_literal_object(model, ['Igor'], p=libNS['made_by'])
- self.check_literal_object(model, ['Paired End Multiplexed Sp-BAC'], p=libNS['name'])
- self.check_literal_object(model, ['Drosophila melanogaster'], p=libNS['species_name'])
-
- self.check_uri_object(model,
- [u'http://localhost/lane/1193'],
- p=libNS['has_lane'])
-
- fc_uri = RDF.Uri('http://localhost/flowcell/303TUAAXX/')
- self.check_literal_object(model,
- [u"303TUAAXX"],
- s=fc_uri, p=libNS['flowcell_id'])
+ self.check_literal_object(model,
+ ['microfluidics bot 7321'],
+ p=libNS['made_by'])
+ self.check_literal_object(model,
+ ['C1C1 test'],
+ p=libNS['name'])
+ self.check_literal_object(model,
+ ['test sapiens'],
+ p=libNS['species_name'])
+
def check_literal_object(self, model, values, s=None, p=None, o=None):
statements = list(model.find_statements(
projects / htsworkflow.git / commitdiff