Convert experiments modules to use factories instead of fixtures.

And then propogate those changes throughout the test cases

diff --git a/experiments/experiments_factory.py b/experiments/experiments_factory.py
new file mode 100644 (file)
index 0000000..49421ee
--- /dev/null
+++ b/experiments/experiments_factory.py
@@ -0,0 +1,85 @@
+import datetime
+
+import factory
+from factory.django import DjangoModelFactory
+from . import models
+from samples.samples_factory import LibraryFactory
+
+
+class ClusterStationFactory(DjangoModelFactory):
+    class Meta:
+        model = models.ClusterStation
+
+    name = factory.Sequence(lambda x: 'cluster station %d' % (x,))
+    isdefault = True
+
+
+class SequencerFactory(DjangoModelFactory):
+    class Meta:
+        model = models.Sequencer
+
+    name = factory.Sequence(lambda x: 'sequencer %d' % (x,))
+    instrument_name = factory.Sequence(lambda x: 'instrument name %d' % (x,))
+    serial_number = factory.Sequence(lambda x: 'squencer serial number %d' % (x,))
+    model = 'HiSeq 1'
+    active = True
+    isdefault = True
+    comment = 'example sequencer'
+
+
+class FlowCellFactory(DjangoModelFactory):
+    class Meta:
+        model = models.FlowCell
+
+    flowcell_id = '1234AAAAXX'
+    run_date = datetime.datetime.now()
+    advanced_run = False
+    paired_end = True
+    read_length = 100
+    control_lane = 0
+    cluster_station = factory.SubFactory(ClusterStationFactory)
+    sequencer = factory.SubFactory(SequencerFactory)
+    notes = 'flowcell notes'
+
+
+class LaneFactory(DjangoModelFactory):
+    class Meta:
+        model = models.Lane
+
+    flowcell = factory.SubFactory(FlowCellFactory)
+    lane_number = 1
+    library = factory.SubFactory(LibraryFactory)
+    pM = 1.2
+    cluster_estimate = 12345
+    status = 2
+    comment = 'lane comment'
+
+
+class DataRunFactory(DjangoModelFactory):
+    class Meta:
+        model = models.DataRun
+
+    flowcell = factory.SubFactory(FlowCellFactory)
+    runfolder_name = '102030_UAW-EAS22_1234AAAAXX'
+    result_dir = runfolder_name + '/Unaligned'
+    run_start_time = datetime.datetime.now()
+    cycle_start = 1
+    cycle_stop = 101
+    run_status = 2
+    image_software = 'RTA'
+    image_version = '1.1'
+    basecall_software = 'RTA'
+    basecall_version = '2.2'
+    alignment_software = 'eland'
+    alignment_version = '2.2'
+    comment = 'comment'
+
+
+class FileTypeFactory(DjangoModelFactory):
+    class Meta:
+        model = models.FileType
+
+    name = 'file type'
+    mimetype = 'application/file'
+    regex = '.file$'
+

diff --git a/experiments/fixtures/initial_data.json b/experiments/fixtures/initial_data.json
deleted file mode 100644 (file)
index f364502..0000000
--- a/experiments/fixtures/initial_data.json
+++ /dev/null
@@ -1,122 +0,0 @@
-[
-  { "model": "experiments.FileType",
-    "pk": 1,
-    "fields": {
-      "name": "run_xml",
-      "mimetype": "application/vnd.htsworkflow-run-xml",
-      "regex": "run.*\\.xml\\Z(?ms)"
-    }
-  },
-  { "model": "experiments.FileType",
-    "pk": 2,
-    "fields": {
-      "name": "Summary.htm",
-      "mimetype": "text/html",
-      "regex": "Summary\\.htm\\Z(?ms)"
-    }
-  },
-
-  { "model": "experiments.FileType",
-    "pk": 3,
-    "fields": {
-      "name": "IVC All",
-      "mimetype": "image/png",
-      "regex": "s_(?P<lane>[0-9])_all\\.png\\Z(?ms)"
-    }
-  },
-  { "model": "experiments.FileType",
-    "pk": 4,
-    "fields": {
-      "name": "IVC Call",
-      "mimetype": "image/png",
-      "regex": "s_(?P<lane>[0-9])_call\\.png\\Z(?ms)"
-    }
-  },
-  { "model": "experiments.FileType",
-    "pk": 5,
-    "fields": {
-      "name": "IVC Percent All",
-      "mimetype": "image/png",
-      "regex": "s_(?P<lane>[0-9])_percent_all\\.png\\Z(?ms)"
-    }
-  },
-  { "model": "experiments.FileType",
-    "pk": 6,
-    "fields": {
-      "name": "IVC Percent Base",
-      "mimetype": "image/png",
-      "regex": "s_(?P<lane>[0-9])_percent_base\\.png\\Z(?ms)"
-    }
-  },
-  { "model": "experiments.FileType",
-    "pk": 7,
-    "fields": {
-      "name": "IVC Percent Call",
-      "mimetype": "image/png",
-      "regex": "s_(?P<lane>[0-9])_percent_call\\.png\\Z(?ms)"
-    }
-  },
-  { "model": "experiments.FileType",
-    "pk": 8,
-    "fields": {
-      "name": "GERALD Scores",
-      "regex": "scores\\.tar\\.bz2\\Z(?ms)"
-    }
-  },
-  { "model": "experiments.FileType",
-    "pk": 9,
-    "fields": {
-      "name": "ELAND Result",
-      "mimetype": "chemical/seq-na-eland",
-      "regex": "s_(?P<lane>[0-9])((?P<end>[1-4])_)?_eland_result\\.txt\\.bz2\\Z(?ms)"
-    }
-  },
-  { "model": "experiments.FileType",
-    "pk": 10,
-    "fields": {
-      "name": "ELAND Multi",
-      "mimetype": "chemical/seq-na-eland",
-      "regex": "s_(?P<lane>[0-9])((?P<end>[1-4])_)?_eland_multi\\.txt\\.bz2\\Z(?ms)"
-    }
-  },
-  { "model": "experiments.FileType",
-    "pk": 11,
-    "fields": {
-      "name": "ELAND Extended",
-      "mimetype": "chemical/seq-na-eland",
-      "regex": "s_(?P<lane>[0-9])((?P<end>[1-4])_)?_eland_extended\\.txt\\.bz2\\Z(?ms)"
-    }
-  },
-  { "model": "experiments.FileType",
-    "pk": 12,
-    "fields": {
-      "name": "ELAND Export",
-      "mimetype": "chemical/seq-na-eland",
-      "regex": "s_(?P<lane>[0-9])((?P<end>[1-4])_)?_export\\.txt\\.bz2\\Z(?ms)"
-    }
-  },
-  { "model": "experiments.FileType",
-    "pk": 13,
-    "fields": {
-      "name": "SRF",
-      "mimetype": "chemical/seq-na-srf",
-      "regex": ".*_(?P<lane>[1-8])\\.srf\\Z(?ms)"
-    }
-  },
-  { "model": "experiments.FileType",
-    "pk": 14,
-    "fields": {
-      "name": "QSEQ tarfile",
-      "mimetype": "chemical/seq-na-qseq",
-      "regex": ".*_l(?P<lane>[1-8])_r(?P<end>[1-4])\\.tar\\.bz2\\Z(?ms)"
-    }
-  },
-  { "model": "experiments.FileType",
-    "pk": 15,
-    "fields": {
-      "name": "HiSeq Fastq",
-      "mimetype": "chemical/seq-na-fastq",
-      "regex": "(?P<library>[0-9]+)_(NoIndex|[AGCT]+)_L(?P<lane>[0-9]+)_R(?P<end>[12])_(?P<split>[0-9]+)\\.fastq\\.gz"
-    }
-  }
-]

diff --git a/experiments/fixtures/test_flowcells.json b/experiments/fixtures/test_flowcells.json
deleted file mode 100644 (file)
index 15d00c6..0000000
--- a/experiments/fixtures/test_flowcells.json
+++ /dev/null
@@ -1,1273 +0,0 @@
-[
-    {"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$5e4eefec1144a04becfb7da79244f07c487fc345",
-       "email": "",
-       "date_joined": "2009-01-01T00:01:01-0800"
-       }
-   },
-   {"pk": 5, "model": "samples.htsuser",
-    "fields" : {}
-   },
-   {"pk": 6, "model": "auth.user",
-   "fields": {
-       "username": "admintest",
-       "first_name": "",
-       "last_name": "",
-       "is_active": true,
-       "is_superuser": false,
-       "is_staff": true,
-       "last_login": "2009-01-01T00:00:01-0800",
-       "groups": [],
-       "user_permissions": [],
-       "password": "sha1$foo$5e4eefec1144a04becfb7da79244f07c487fc345",
-       "email": "",
-       "date_joined": "2009-01-01T00:01:01-0800"
-       }
-   },
-   {"pk": 6, "model": "samples.htsuser",
-    "fields" : {}
-   },
-   {"pk": 7, "model": "auth.user",
-   "fields": {
-       "username": "supertest",
-       "first_name": "",
-       "last_name": "",
-       "is_active": true,
-       "is_superuser": true,
-       "is_staff": true,
-       "last_login": "2009-01-01T00:00:01-0800",
-       "groups": [],
-       "user_permissions": [],
-       "password": "sha1$foo$5e4eefec1144a04becfb7da79244f07c487fc345",
-       "email": "",
-       "date_joined": "2009-01-01T00:01:01-0800"
-       }
-   },
-   {"pk": 7, "model": "samples.htsuser",
-    "fields" : {}
-   },
-   {"pk": 1, "model": "samples.affiliation",
-     "fields": {
-         "users": [5],
-         "contact": "group 1",
-         "name": "affiliation 1",
-         "email": "pk1@example.com"
-         }
-     },
-    {"pk": 2, "model": "samples.affiliation",
-     "fields": {
-         "users": [6],
-         "contact": "group 2",
-         "name": "affiliation 2",
-         "email": "pk2@example.com"
-         }
-     },
-    {"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": 1, "model": "experiments.clusterstation",
-  "fields": {"name": "old", "isdefault": false}},
- {"pk": 2, "model": "experiments.clusterstation",
-  "fields": {"name": "loaner", "isdefault": true}},
- {"pk": 3, "model": "experiments.clusterstation",
-  "fields": {"name": "new", "isdefault": false}},
- {"pk": 1, "model": "experiments.sequencer",
-  "fields": { "name": "Rotifer (HWI-EAS229)",
-              "model": "Illumina Genome Analyzer I",
-              "active": false,
-              "isdefault": false }},
- {"pk": 2, "model": "experiments.sequencer",
-  "fields": {"name": "Tardigrade",
-             "instrument_name": "ILLUMINA-EC5D15",
-             "model": "Illumina Genome Analyzer IIx",
-             "active": true,
-             "isdefault": true}
- },
- {"pk": 3, "model": "experiments.sequencer",
-  "fields": {"name": "Sequenced somewhere else.",
-             "model": "Unknown",
-             "active": true,
-             "isdefault": false}},
- {"pk": 153, "model": "experiments.flowcell",
-  "fields": {
-      "paired_end": true,
-      "run_date": "2007-09-27T22:12:13-0800",
-      "read_length": 36,
-      "notes": "",
-      "advanced_run": false,
-      "control_lane": 2,
-      "cluster_station": 3,
-      "sequencer": 2,
-      "flowcell_id": "FC12150"
-      }
-  },
-  {"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": 1192, "model": "experiments.lane",
-    "fields": {
-        "comment": "Other library",
-        "library": "11070",
-        "cluster_estimate": 132000,
-        "flowcell": 153,
-        "lane_number": 1,
-        "pM": "7"
-        }
-    },
-
-  {"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": 10,
-            "library_type": null,
-            "made_by": "Igor",
-            "affiliations": [
-                1,2
-            ],
-            "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": 1194, "model": "experiments.lane",
-   "fields": {
-       "comment": "",
-       "library": "11016",
-       "cluster_estimate": 152000,
-       "flowcell": 153,
-       "lane_number": 2,
-       "pM": "7"
-       }
-   },
-    {
-        "pk": "11006",
-        "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": [
-                3
-            ],
-            "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": "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": 2,
-            "library_type": 2,
-            "made_by": "Lorian",
-            "affiliations": [
-                2
-            ],
-            "replicate": 1,
-            "condition": 1,
-            "hidden": false,
-            "stopping_point": "1Aa",
-            "tags": [],
-            "made_for": "",
-            "amplified_from_sample": 11006,
-            "notes": "7/31/2009 16:08:22\tColor: Blue",
-            "undiluted_concentration": "35.5",
-            "successful_pM": null,
-            "experiment_type": 8,
-            "antibody": null
-        }
-    },
-  {"pk": 1195, "model": "experiments.lane",
-   "fields": {
-       "comment": "",
-       "library": "SL039",
-       "cluster_estimate": 162000,
-       "flowcell": 153,
-       "lane_number": 3,
-       "pM": "7"
-       }
-   },
-    {
-        "pk": "SL039",
-        "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": [
-                3,4
-            ],
-            "replicate": 1,
-            "condition": 1,
-            "hidden": false,
-            "stopping_point": "1Aa",
-            "tags": [],
-            "made_for": "Brian Williams",
-            "amplified_from_sample": 11006,
-            "notes": "fragment size = 300 bp, Amicon filtered\r\nnanodrop: 56.3",
-            "undiluted_concentration": "28.7",
-            "successful_pM": null,
-            "experiment_type": 4,
-            "antibody": null
-        }
-    },
-  {"pk": 1196, "model": "experiments.lane",
-   "fields": {
-       "comment": "This lane's library had the second lowest concentration of all the libraries built at the same time (2.05ng/ul)",
-       "library": "11060",
-       "cluster_estimate": 24000,
-       "flowcell": 153,
-       "lane_number": 4,
-       "pM": "7"
-       }
-   },
-    {
-        "pk": "11060",
-        "model": "samples.library",
-        "fields": {
-            "ten_nM_dilution": false,
-            "gel_cut_size": 300,
-            "library_name": "Paired ends 100 VC_CN_4_M_MBB1185_s1",
-            "creation_date": "2009-09-01",
-            "cell_line": 1,
-            "library_species": 8,
-            "library_type": 2,
-            "made_by": "Brian Williams",
-            "affiliations": [
-                5
-            ],
-            "replicate": 1,
-            "condition": 1,
-            "hidden": false,
-            "stopping_point": "1Aa",
-            "tags": [],
-            "made_for": "Brian Williams",
-            "amplified_from_sample": 11006,
-            "notes": "300 bp gel fragment, Amicon filtered\r\nnanodrop: 24.2",
-            "undiluted_concentration": "2.05",
-            "successful_pM": null,
-            "experiment_type": 4,
-            "antibody": null
-        }
-    },
-  {"pk": 1197, "model": "experiments.lane",
-   "fields": {
-       "comment": "stuff",
-       "library": "11061",
-       "cluster_estimate": 140000,
-       "flowcell": 153,
-       "lane_number": 5,
-       "pM": "7",
-       "status": 2
-       }
-   },
-    {
-        "pk": "11061",
-        "model": "samples.library",
-        "fields": {
-            "ten_nM_dilution": false,
-            "gel_cut_size": 300,
-            "library_name": "Paired ends 101 VC_CN_4_M_MBB1185_s2",
-            "creation_date": "2009-09-01",
-            "cell_line": 1,
-            "library_species": 8,
-            "library_type": 2,
-            "made_by": "Brian Williams",
-            "affiliations": [
-                2,4
-            ],
-            "replicate": 1,
-            "condition": 1,
-            "hidden": false,
-            "stopping_point": "1Aa",
-            "tags": [],
-            "made_for": "Brian Williams",
-            "amplified_from_sample": null,
-            "notes": "300 bp gel fragment, Amicon filtered\r\nnanodrop: 33.1",
-            "undiluted_concentration": "12.9",
-            "successful_pM": null,
-            "experiment_type": 4,
-            "antibody": null
-        }
-    },
-  {"pk": 1198, "model": "experiments.lane",
-   "fields": {
-       "comment": "This lane's library had the lowest concentration of all the libraries built at the same time (1.2ng/ul)",
-       "library": "11062",
-       "cluster_estimate": 2000,
-       "flowcell": 153,
-       "lane_number": 6,
-       "pM": "7",
-       "status": 0
-       }
-   },
-    {
-        "pk": "11062",
-        "model": "samples.library",
-        "fields": {
-            "ten_nM_dilution": false,
-            "gel_cut_size": 300,
-            "library_name": "Paired ends 102 VC_AU_8_M_MBB4721_s1",
-            "creation_date": "2009-09-01",
-            "cell_line": 1,
-            "library_species": 8,
-            "library_type": 2,
-            "made_by": "Brian Williams",
-            "affiliations": [
-                4,5
-            ],
-            "replicate": 1,
-            "condition": 1,
-            "hidden": false,
-            "stopping_point": "1Aa",
-            "tags": [],
-            "made_for": "Brian Williams",
-            "amplified_from_sample": null,
-            "notes": "300 bp gel fragment, Amicon filtered\r\nnanodrop: 13.9",
-            "undiluted_concentration": "1.2",
-            "successful_pM": null,
-            "experiment_type": 4,
-            "antibody": null
-        }
-    },
-  {"pk": 1199, "model": "experiments.lane",
-   "fields": {
-       "comment": "",
-       "library": "11063",
-       "cluster_estimate": 120000,
-       "flowcell": 153,
-       "lane_number": 7,
-       "pM": "7"
-       }
-   },
-    {
-        "pk": "11063",
-        "model": "samples.library",
-        "fields": {
-            "ten_nM_dilution": false,
-            "gel_cut_size": 300,
-            "library_name": "Paired ends 103 VC_AU_8_M_MBB4721_s2",
-            "creation_date": "2009-09-01",
-            "cell_line": 1,
-            "library_species": 8,
-            "library_type": 2,
-            "made_by": "Brian Williams",
-            "affiliations": [
-                1,3
-            ],
-            "replicate": 1,
-            "condition": 1,
-            "hidden": false,
-            "stopping_point": "1Aa",
-            "tags": [],
-            "made_for": "Brian Williams",
-            "amplified_from_sample": null,
-            "notes": "300 bp gel fragment, Amicon filtered\r\nnanodrop: 46.9",
-            "undiluted_concentration": "24.5",
-            "successful_pM": null,
-            "experiment_type": 4,
-            "antibody": null
-        }
-    },
-  {"pk": 1200, "model": "experiments.lane",
-   "fields": {
-       "comment": "This lane's library had the third lowest concentration of all the libraries built at the same time (5.21ng/ul), but gave perfectly normal cluster numbers",
-       "library": "11064",
-       "cluster_estimate": 157000,
-       "flowcell": 153,
-       "lane_number": 8,
-       "pM": "7"
-       }
-   },
-    {
-        "pk": "11064",
-        "model": "samples.library",
-        "fields": {
-            "ten_nM_dilution": false,
-            "gel_cut_size": 300,
-            "library_name": "Paired ends 104 VC_CN_7_M_MBB4898_s1",
-            "creation_date": "2009-09-01",
-            "cell_line": 1,
-            "library_species": 8,
-            "library_type": 2,
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-            "stopping_point": "1Aa",
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-        "model": "samples.library",
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-            "gel_cut_size": 300,
-            "library_name": "Paired ends 95 Gilberto_d3_control_LTA",
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-            "notes": "fragment size = 300 bp, Amicon filtered\r\nnanodrop: 67.1",
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-            "gel_cut_size": 225,
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-            "gel_cut_size": 225,
-            "library_name": "HNDM3 HLH hnd-1 strain mex-3 fed anti-hlh-1 2% fix plate a",
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-        "pk": "11057",
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-            "gel_cut_size": 225,
-            "library_name": "HNDM3 4H8 hnd-1 strain mex-3 fed 4H8 2% fix plate a",
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-            "notes": "8/26/2009 14:46:56\tColor: Orange.",
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-            "library_type": 2,
-            "made_by": "Yuling Jiao",
-            "affiliations": [
-                2
-            ],
-            "replicate": 1,
-            "condition": null,
-            "hidden": false,
-            "stopping_point": "Done",
-            "tags": [],
-            "made_for": "",
-            "amplified_from_sample": null,
-            "notes": "nanodrop: Xng/ul.",
-            "undiluted_concentration": "18.3",
-            "successful_pM": null,
-            "experiment_type": 4,
-            "antibody": null
-        }
-    },
-  {"pk": 1184, "model": "experiments.lane",
-   "fields": {
-       "comment": "",
-       "library": "11070",
-       "cluster_estimate": 182000,
-       "flowcell": 151,
-       "lane_number": 8,
-       "pM": "7"
-       }
-   },
-    {
-        "pk": "11070",
-        "model": "samples.library",
-        "fields": {
-            "ten_nM_dilution": false,
-            "gel_cut_size": 300,
-            "library_name": "Paired End AG-5d-1 AG domain of floral meristem day 5, rep 1",
-            "creation_date": "2009-09-02",
-            "cell_line": null,
-            "library_species": 6,
-            "library_type": 2,
-            "made_by": "Yuling Jiao",
-            "affiliations": [
-                3
-            ],
-            "replicate": 1,
-            "condition": null,
-            "hidden": false,
-            "stopping_point": "Done",
-            "tags": [],
-            "made_for": "",
-            "amplified_from_sample": null,
-            "notes": "nanodrop: 40ng/ul\r\nCalibrated qbit with standards.\r\nMeasured 2ul library with qbit using HS kit.\r\n",
-            "undiluted_concentration": "20.3",
-            "successful_pM": null,
-            "experiment_type": 4,
-            "antibody": null
-        }
-     },
- {"pk": 200, "model": "experiments.flowcell",
-  "fields": {
-      "paired_end": true,
-      "run_date": "2007-09-27T22:12:13-0800",
-      "read_length": 36,
-      "notes": "",
-      "advanced_run": false,
-      "control_lane": 2,
-      "cluster_station": 3,
-      "sequencer": 2,
-      "flowcell_id": "30012AAXX (failed)"
-      }
-  },
-  {"pk": 201, "model": "experiments.lane",
-   "fields": {
-       "comment": "",
-       "library": "11070",
-       "cluster_estimate": 182000,
-       "flowcell": 200,
-       "lane_number": 8,
-       "pM": "7"
-       }
-   }
-]

diff --git a/experiments/fixtures/woldlab.json b/experiments/fixtures/woldlab.json
deleted file mode 100644 (file)
index b058925..0000000
--- a/experiments/fixtures/woldlab.json
+++ /dev/null
@@ -1,89 +0,0 @@
-[ { "model": "experiments.Sequencer",
-    "pk": 1,
-    "fields": {
-      "name": "Rotifer",
-      "instrument_name": "ILLUMINA-33A494",
-      "serial_number": "",
-      "model": "Illumina Genome Analyzer II",
-      "active": false,
-      "isdefault": false,
-      "comment": "after 2010 pipeline name, was exchanged for hiseq"
-    }
-  },
-  { "model": "experiments.Sequencer",
-    "pk": 2,
-    "fields": {
-      "name": "Tardigrade",
-      "instrument_name": "ILLUMINA-EC5D15",
-      "serial_number": "",
-      "model": "Illumina Genome Analyzer IIx",
-      "active": true,
-      "isdefault": false,
-      "comment": "after 2010 pipeline name"
-    }
-  },
-  { "model": "experiments.Sequencer",
-    "pk": 3,
-    "fields": {
-      "name": "Elsewhere",
-      "instrument_name": "",
-      "serial_number": "",
-      "model": "Unknown",
-      "active": false,
-      "isdefault": false,
-      "comment": "Sequenced somewhere else"
-    }
-  },
-  { "model": "experiments.Sequencer",
-    "pk": 4,
-    "fields": {
-      "name": "Volvox",
-      "instrument_name": "HWI-ST0787",
-      "serial_number": "",
-      "model": "Illumina HiSeq 2000",
-      "active": true,
-      "isdefault": true,
-      "comment": ""
-    }
-  },
-  { "model": "experiments.Sequencer",
-    "pk": 5,
-    "fields": {
-      "name": "Tardigrade (older)",
-      "instrument_name": "HWUSI-EAS627",
-      "serial_number": "",
-      "model": "Illumina Genome Analyzer II",
-      "active": false,
-      "isdefault": false,
-      "comment": "earlier version of tardigrade"
-    }
-  },
-  { "model": "experiments.Sequencer",
-    "pk": 6,
-    "fields": {
-      "name": "Rotifer (older)",
-      "instrument_name": "HWUSI-EAS229",
-      "serial_number": "",
-      "model": "Illumina Genome Analyzer II",
-      "active": false,
-      "isdefault": false,
-      "comment": "earlier rotifer name"
-    }
-  },
-  { "model": "experiments.Sequencer",
-    "pk": 7,
-    "fields": {
-      "name": "First sequencer",
-      "instrument_name": "USI-EAS44",
-      "serial_number": "",
-      "model": "Illumina Genome Analyzer I",
-      "active": false,
-      "isdefault": false,
-      "comment": "our first sequencer"
-    }
-  },
-  { "model": "experiments.ClusterStation",
-    "pk": 3,
-    "fields": { "name": "new", "isdefault": false }
-  }
-]

diff --git a/experiments/test_experiments.py b/experiments/test_experiments.py
index ba27db4706bb18da6a58639321fd517d897fdbd1..f0c36104de1ec00376e2eaba4da1022c8229bddb 100644 (file)
--- a/experiments/test_experiments.py
+++ b/experiments/test_experiments.py
@@ -20,9 +20,14 @@ from django.test.utils import setup_test_environment, teardown_test_environment
 from django.db import connection
 from django.conf import settings
 
-from .models import ClusterStation, DataRun, Sequencer, FlowCell, FileType, \
+from .models import ClusterStation, cluster_station_default, \
+    DataRun, Sequencer, FlowCell, FileType, \
     find_file_type_metadata_from_filename
+from samples.models import HTSUser
 from .experiments import flowcell_information, lanes_for
+from .experiments_factory import ClusterStationFactory, FlowCellFactory, LaneFactory
+from samples.samples_factory import AffiliationFactory, HTSUserFactory, \
+    LibraryFactory, LibraryTypeFactory, MultiplexIndexFactory
 from htsworkflow.auth import apidata
 from htsworkflow.util.ethelp import validate_xhtml
 
@@ -36,14 +41,23 @@ from django.db import connection
 
 
 class ExperimentsTestCases(TestCase):
-    fixtures = ['initial_data.json',
-                'test_flowcells.json',
-                ]
-
     def setUp(self):
+        # Generate at least one fleshed out example flowcell
         self.tempdir = tempfile.mkdtemp(prefix='htsw-test-experiments-')
         settings.RESULT_HOME_DIR = self.tempdir
 
+        self.password = 'password'
+        self.user_odd = HTSUserFactory(username='user-odd')
+        self.user_odd.set_password(self.password)
+        self.affiliation_odd = AffiliationFactory(name='affiliation-odd', users=[self.user_odd])
+        self.user_even = HTSUserFactory(username='user-even')
+        self.user_even.set_password(self.password)
+        self.affiliation_even = AffiliationFactory(name='affiliation-even', users=[self.user_even])
+        self.admin = HTSUserFactory.create(username='admin', is_staff=True, is_superuser=True)
+        self.admin.set_password(self.password)
+        self.admin.save()
+
+        self.fc12150 = FlowCellFactory(flowcell_id='FC12150')
         self.fc1_id = 'FC12150'
         self.fc1_root = os.path.join(self.tempdir, self.fc1_id)
         os.mkdir(self.fc1_root)
@@ -53,12 +67,30 @@ class ExperimentsTestCases(TestCase):
         shutil.copy(os.path.join(TESTDATA_DIR, runxml),
                     os.path.join(self.fc1_dir, runxml))
         for i in range(1,9):
+            affiliation = self.affiliation_odd if i % 2 == 1 else self.affiliation_even
+            library = LibraryFactory(id="1215" + str(i))
+            library.affiliations.add(affiliation)
+            lane = LaneFactory(flowcell=self.fc12150, lane_number=i, library=library)
             shutil.copy(
                 os.path.join(TESTDATA_DIR,
                              'woldlab_070829_USI-EAS44_0017_FC11055_1.srf'),
                 os.path.join(self.fc1_dir,
                              'woldlab_070829_SERIAL_FC12150_%d.srf' %(i,))
                 )
+        self.fc12150.save()
+
+        self.fc42jtn = FlowCellFactory(flowcell_id='42JTNAAXX')
+        self.fc42jtn_lanes = []
+        for i in range(1,9):
+            affiliation = self.affiliation_odd if i % 2 == 1 else self.affiliation_even
+            library_type = LibraryTypeFactory(can_multiplex=True)
+            multiplex_index = MultiplexIndexFactory(adapter_type=library_type)
+            library = LibraryFactory(id="1300" + str(i),
+                                     library_type=library_type,
+                                     multiplex_id=multiplex_index.multiplex_id)
+            library.affiliations.add(affiliation)
+            lane = LaneFactory(flowcell=self.fc42jtn, lane_number=(i % 2) + 1, library=library)
+            self.fc42jtn_lanes.append(lane)
 
         self.fc2_dir = os.path.join(self.tempdir, '42JTNAAXX')
         os.mkdir(self.fc2_dir)
@@ -73,6 +105,10 @@ class ExperimentsTestCases(TestCase):
         """
         Check the code that packs the django objects into simple types.
         """
+        fc12150 = self.fc12150
+        fc42jtn = self.fc42jtn
+        fc42ju1 = FlowCellFactory(flowcell_id='42JU1AAXX')
+
         for fc_id in [u'FC12150', u"42JTNAAXX", "42JU1AAXX"]:
             fc_dict = flowcell_information(fc_id)
             fc_django = FlowCell.objects.get(flowcell_id=fc_id)
@@ -142,15 +178,16 @@ class ExperimentsTestCases(TestCase):
         self.assertEqual(response.status_code, 200)
         flowcell = json.loads(response.content)['result']
 
+        # library id is 12150 + lane number (1-8), so 12153
         lane_contents = flowcell['lane_set']['3']
         lane_library = lane_contents[0]
-        self.assertEqual(lane_library['library_id'], 'SL039')
+        self.assertEqual(lane_library['library_id'], '12153')
 
-        response = self.client.get('/samples/library/SL039/json', apidata)
+        response = self.client.get('/samples/library/12153/json', apidata)
         self.assertEqual(response.status_code, 200)
-        library_sl039 = json.loads(response.content)['result']
+        library_12153 = json.loads(response.content)['result']
 
-        self.assertEqual(library_sl039['library_id'], 'SL039')
+        self.assertEqual(library_12153['library_id'], '12153')
 
     def test_raw_id_field(self):
         """
@@ -164,10 +201,9 @@ class ExperimentsTestCases(TestCase):
         This tests to make sure that the value entered in the raw library id field matches
         the library id looked up.
         """
-        expected_ids = [u'10981',u'11016',u'SL039',u'11060',
-                        u'11061',u'11062',u'11063',u'11064']
-        self.client.login(username='supertest', password='BJOKL5kAj6aFZ6A5')
-        response = self.client.get('/admin/experiments/flowcell/153/')
+        expected_ids = [ u'1215{}'.format(i) for i in range(1,9) ]
+        self.assertTrue(self.client.login(username=self.admin.username, password=self.password))
+        response = self.client.get('/admin/experiments/flowcell/{}/'.format(self.fc12150.id))
 
         tree = fromstring(response.content)
         for i in range(0,8):
@@ -185,8 +221,8 @@ class ExperimentsTestCases(TestCase):
         Make sure the library page includes links to the flowcell pages.
         That work with flowcell IDs that have parenthetical comments.
         """
-        self.client.login(username='supertest', password='BJOKL5kAj6aFZ6A5')
-        response = self.client.get('/library/11070/')
+        self.assertTrue(self.client.login(username=self.admin.username, password=self.password))
+        response = self.client.get('/library/12151/')
         self.assertEqual(response.status_code, 200)
         status = validate_xhtml(response.content)
         if status is not None: self.assertTrue(status)
@@ -194,45 +230,41 @@ class ExperimentsTestCases(TestCase):
         tree = fromstring(response.content)
         flowcell_spans = tree.xpath('//span[@property="libns:flowcell_id"]',
                                     namespaces=NSMAP)
-        self.assertEqual(flowcell_spans[1].text, '30012AAXX (failed)')
+        self.assertEqual(flowcell_spans[1].text, 'FC12150')
         failed_fc_span = flowcell_spans[1]
         failed_fc_a = failed_fc_span.getparent()
         # make sure some of our RDF made it.
         self.assertEqual(failed_fc_a.get('typeof'), 'libns:IlluminaFlowcell')
-        self.assertEqual(failed_fc_a.get('href'), '/flowcell/30012AAXX/')
+        self.assertEqual(failed_fc_a.get('href'), '/flowcell/FC12150/')
         fc_response = self.client.get(failed_fc_a.get('href'))
         self.assertEqual(fc_response.status_code, 200)
         status = validate_xhtml(response.content)
         if status is not None: self.assertTrue(status)
 
-        fc_lane_response = self.client.get('/flowcell/30012AAXX/8/')
+        fc_lane_response = self.client.get('/flowcell/FC12150/8/')
         self.assertEqual(fc_lane_response.status_code, 200)
         status = validate_xhtml(response.content)
         if status is not None: self.assertTrue(status)
 
-
     def test_pooled_multiplex_id(self):
-        fc_dict = flowcell_information('42JU1AAXX')
-        lane_contents = fc_dict['lane_set'][3]
-        self.assertEqual(len(lane_contents), 2)
-        lane_dict = multi_lane_to_dict(lane_contents)
-
-        self.assertEqual(lane_dict['12044']['index_sequence'],
-                         {u'1': u'ATCACG',
-                          u'2': u'CGATGT',
-                          u'3': u'TTAGGC'})
-        self.assertEqual(lane_dict['11045']['index_sequence'],
-                         {u'1': u'ATCACG'})
+        fc_dict = flowcell_information(self.fc42jtn.flowcell_id)
 
+        lane_contents = fc_dict['lane_set'][2]
+        self.assertEqual(len(lane_contents), len(self.fc42jtn_lanes) / 2)
+        lane_dict = multi_lane_to_dict(lane_contents)
 
+        self.assertTrue(self.fc42jtn_lanes[0].library.multiplex_id in \
+                        lane_dict['13001']['index_sequence'])
+        self.assertTrue(self.fc42jtn_lanes[2].library.multiplex_id in \
+                        lane_dict['13003']['index_sequence'])
 
     def test_lanes_for(self):
         """
         Check the code that packs the django objects into simple types.
         """
-        user = 'test'
+        user = self.user_odd.username
         lanes = lanes_for(user)
-        self.assertEqual(len(lanes), 5)
+        self.assertEqual(len(lanes), 8)
 
         response = self.client.get('/experiments/lanes_for/%s/json' % (user,), apidata)
         lanes_json = json.loads(response.content)['result']
@@ -247,12 +279,12 @@ class ExperimentsTestCases(TestCase):
         """
         Do we get something meaningful back when the user isn't attached to anything?
         """
-        user = 'supertest'
-        lanes = lanes_for(user)
+        user = HTSUserFactory.create(username='supertest')
+        lanes = lanes_for(user.username)
         self.assertEqual(len(lanes), 0)
 
         response = self.client.get('/experiments/lanes_for/%s/json' % (user,), apidata)
-        lanes_json = json.loads(response.content)
+        self.assertEqual(response.status_code, 404)
 
     def test_lanes_for_no_user(self):
         """
@@ -291,11 +323,11 @@ class ExperimentsTestCases(TestCase):
 
         srf4 = result_dict['FC12150/C1-37/woldlab_070829_SERIAL_FC12150_4.srf']
         self.assertEqual(srf4.file_type, srf_file_type)
-        self.assertEqual(srf4.library_id, '11060')
+        self.assertEqual(srf4.library_id, '12154')
         self.assertEqual(srf4.data_run.flowcell.flowcell_id, 'FC12150')
         self.assertEqual(
             srf4.data_run.flowcell.lane_set.get(lane_number=4).library_id,
-            '11060')
+            '12154')
         self.assertEqual(
             srf4.pathname,
             os.path.join(settings.RESULT_HOME_DIR, srf4.relative_pathname))
@@ -346,15 +378,15 @@ class ExperimentsTestCases(TestCase):
 
         model = get_model()
 
-        expected = {'1': ['11034'],
-                    '2': ['11036'],
-                    '3': ['12044','11045'],
-                    '4': ['11047','13044'],
-                    '5': ['11055'],
-                    '6': ['11067'],
-                    '7': ['11069'],
-                    '8': ['11070']}
-        url = '/flowcell/42JU1AAXX/'
+        expected = {'1': ['12151'],
+                    '2': ['12152'],
+                    '3': ['12153'],
+                    '4': ['12154'],
+                    '5': ['12155'],
+                    '6': ['12156'],
+                    '7': ['12157'],
+                    '8': ['12158']}
+        url = '/flowcell/{}/'.format(self.fc12150.flowcell_id)
         response = self.client.get(url)
         self.assertEqual(response.status_code, 200)
         status = validate_xhtml(response.content)
@@ -378,18 +410,14 @@ class ExperimentsTestCases(TestCase):
         count = 0
         for r in query.execute(model):
             count += 1
-            self.assertEqual(fromTypedNode(r['flowcell_id']), u'42JU1AAXX')
+            self.assertEqual(fromTypedNode(r['flowcell_id']), u'FC12150')
             lane_id = fromTypedNode(r['lane_id'])
             library_id = fromTypedNode(r['library_id'])
             self.assertTrue(library_id in expected[lane_id])
-        self.assertEqual(count, 10)
+        self.assertEqual(count, 8)
 
 
 class TestFileType(TestCase):
-    fixtures = ['initial_data.json',
-                'test_flowcells.json',
-                ]
-
     def test_file_type_unicode(self):
         file_type_objects = FileType.objects
         name = 'QSEQ tarfile'
@@ -448,34 +476,56 @@ class TestFileType(TestCase):
             self.assertEqual(result.get('end', None), end)
 
 class TestEmailNotify(TestCase):
-    fixtures = ['initial_data.json',
-                'test_flowcells.json']
+    def setUp(self):
+        self.password = 'foo27'
+        self.user = HTSUserFactory.create(username='test')
+        self.user.set_password(self.password)
+        self.user.save()
+        self.admin = HTSUserFactory.create(username='admintest', is_staff=True)
+        self.admin.set_password(self.password)
+        self.admin.save()
+        self.super = HTSUserFactory.create(username='supertest', is_staff=True, is_superuser=True)
+        self.super.set_password(self.password)
+        self.super.save()
+
+        self.library = LibraryFactory.create()
+        self.affiliation = AffiliationFactory()
+        self.affiliation.users.add(self.user)
+        self.library.affiliations.add(self.affiliation)
+        self.fc = FlowCellFactory.create()
+        self.lane = LaneFactory(flowcell=self.fc, lane_number=1, library=self.library)
+
+        self.url = '/experiments/started/{}/'.format(self.fc.id)
 
     def test_started_email_not_logged_in(self):
-        response = self.client.get('/experiments/started/153/')
+        response = self.client.get(self.url)
         self.assertEqual(response.status_code, 302)
 
     def test_started_email_logged_in_user(self):
-        self.client.login(username='test', password='BJOKL5kAj6aFZ6A5')
-        response = self.client.get('/experiments/started/153/')
+        self.assertTrue(self.client.login(username=self.user.username, password=self.password))
+        response = self.client.get(self.url)
         self.assertEqual(response.status_code, 302)
 
     def test_started_email_logged_in_staff(self):
-        self.client.login(username='admintest', password='BJOKL5kAj6aFZ6A5')
-        response = self.client.get('/experiments/started/153/')
+        self.assertTrue(self.admin.is_staff)
+        admin = HTSUser.objects.get(username=self.admin.username)
+        self.assertTrue(admin.is_staff)
+        self.assertTrue(admin.check_password(self.password))
+        self.assertTrue(self.client.login(username=self.admin.username, password=self.password))
+        response = self.client.get(self.url)
         self.assertEqual(response.status_code, 200)
 
     def test_started_email_send(self):
-        self.client.login(username='admintest', password='BJOKL5kAj6aFZ6A5')
-        response = self.client.get('/experiments/started/153/')
+        self.assertTrue(self.client.login(username=self.admin.username, password=self.password))
+        response = self.client.get(self.url)
         self.assertEqual(response.status_code, 200)
 
-        self.assertTrue('pk1@example.com' in response.content)
-        self.assertTrue('Lane #8 : (11064) Paired ends 104' in response.content)
+        self.assertTrue(self.affiliation.email in response.content)
+        self.assertTrue(self.library.library_name in response.content)
 
-        response = self.client.get('/experiments/started/153/', {'send':'1','bcc':'on'})
+        response = self.client.get(self.url, {'send':'1','bcc':'on'})
         self.assertEqual(response.status_code, 200)
-        self.assertEqual(len(mail.outbox), 4)
+        self.assertEqual(len(mail.outbox), 2)
         bcc = set(settings.NOTIFICATION_BCC).copy()
         bcc.update(set(settings.MANAGERS))
         for m in mail.outbox:
@@ -486,12 +536,14 @@ class TestEmailNotify(TestCase):
         """
         Can we navigate between the flowcell and email forms properly?
         """
-        self.client.login(username='supertest', password='BJOKL5kAj6aFZ6A5')
-        response = self.client.get('/experiments/started/153/')
+        admin_url = '/admin/experiments/flowcell/{}/'.format(self.fc.id)
+        self.client.login(username=self.admin.username, password=self.password)
+        response = self.client.get(self.url)
         self.assertEqual(response.status_code, 200)
-        self.assertTrue(re.search('Flowcell FC12150', response.content))
+        #print("email navigation content:", response.content)
+        self.assertTrue(re.search(self.fc.flowcell_id, response.content))
         # require that navigation back to the admin page exists
-        self.assertTrue(re.search('<a href="/admin/experiments/flowcell/153/">[^<]+</a>', response.content))
+        self.assertTrue(re.search('<a href="{}">[^<]+</a>'.format(admin_url), response.content))
 
 def multi_lane_to_dict(lane):
     """Convert a list of lane entries into a dictionary indexed by library ID
@@ -499,9 +551,10 @@ def multi_lane_to_dict(lane):
     return dict( ((x['library_id'],x) for x in lane) )
 
 class TestSequencer(TestCase):
-    fixtures = ['initial_data.json',
-                'test_flowcells.json',
-                ]
+    def setUp(self):
+        self.fc12150 = FlowCellFactory(flowcell_id='FC12150')
+        self.library = LibraryFactory(id="12150")
+        self.lane = LaneFactory(flowcell=self.fc12150, lane_number=1, library=self.library)
 
     def test_name_generation(self):
         seq = Sequencer()
@@ -512,11 +565,9 @@ class TestSequencer(TestCase):
         self.assertEqual(unicode(seq), "Seq1 (HWI-SEQ1)")
 
     def test_lookup(self):
-        fc = FlowCell.objects.get(pk=153)
-        self.assertEqual(fc.sequencer.model,
-                             "Illumina Genome Analyzer IIx")
-        self.assertEqual(fc.sequencer.instrument_name,
-                             "ILLUMINA-EC5D15")
+        fc = self.fc12150
+        self.assertEqual(fc.sequencer.model, 'HiSeq 1')
+        self.assertTrue(fc.sequencer.instrument_name.startswith('instrument name')),
         # well actually we let the browser tack on the host name
         url = fc.get_absolute_url()
         self.assertEqual(url, '/flowcell/FC12150/')
@@ -530,20 +581,21 @@ class TestSequencer(TestCase):
         self.assertEqual(seq_by[0].attrib['rel'], 'libns:sequenced_by')
         seq = seq_by[0].getchildren()
         self.assertEqual(len(seq), 1)
-        self.assertEqual(seq[0].attrib['about'], '/sequencer/2')
+        sequencer = '/sequencer/' + str(self.fc12150.sequencer.id)
+        self.assertEqual(seq[0].attrib['about'], sequencer)
         self.assertEqual(seq[0].attrib['typeof'], 'libns:Sequencer')
 
         name = seq[0].xpath('./span[@property="libns:sequencer_name"]')
         self.assertEqual(len(name), 1)
-        self.assertEqual(name[0].text, 'Tardigrade')
+        self.assertTrue(name[0].text.startswith('sequencer '))
         instrument = seq[0].xpath(
             './span[@property="libns:sequencer_instrument"]')
         self.assertEqual(len(instrument), 1)
-        self.assertEqual(instrument[0].text, 'ILLUMINA-EC5D15')
+        self.assertTrue(instrument[0].text.startswith('instrument name'))
         model = seq[0].xpath(
             './span[@property="libns:sequencer_model"]')
         self.assertEqual(len(model), 1)
-        self.assertEqual(model[0].text, 'Illumina Genome Analyzer IIx')
+        self.assertEqual(model[0].text, 'HiSeq 1')
 
     def test_flowcell_with_rdf_validation(self):
         from htsworkflow.util.rdfhelp import add_default_schemas, \
@@ -578,7 +630,7 @@ class TestSequencer(TestCase):
         add_default_schemas(model)
         inference = Infer(model)
 
-        url = '/lane/1193'
+        url = '/lane/{}'.format(self.lane.id)
         response = self.client.get(url)
         self.assertEqual(response.status_code, 200)
         status = validate_xhtml(response.content)