Attempt to split common initial data from wold lab specific database contents.

diff --git a/htsworkflow/frontend/bcmagic/fixtures/initial_data.json b/htsworkflow/frontend/bcmagic/fixtures/initial_data.json
index 7b48d0b8736f7b3742ddad72dee474e5da00e6bf..99decf24e868afcdd4dd40140363f4466163d4f0 100644 (file)
--- a/htsworkflow/frontend/bcmagic/fixtures/initial_data.json
+++ b/htsworkflow/frontend/bcmagic/fixtures/initial_data.json
@@ -32,22 +32,5 @@
   "model": "bcmagic.keywordmap",
   "fields": {"regex": "(?P<barcode_id>.+)",
              "url_template": "/inventory/{{barcode_id}}/",
-             "keyword": "invb"}},
- {"pk": 1,
-  "model": "bcmagic.printer",
-  "fields": {"name": "ZM400 1.25x1",
-             "label_height": 1.0,
-             "notes": "Everyday use labels",
-             "label_width": 1.25,
-             "label_shape": "Square",
-             "model": "Zebra ZM400",
-             "ip_address": "131.215.34.116"}},
- {"pk": 2,
-  "model": "bcmagic.printer",
-  "fields": {"name": "ZM400 3x3",
-             "label_height": 3.0,
-             "notes": "Larger everyday use labels",
-             "label_width": 3.0,
-             "label_shape": "Square",
-             "model": "Zebra ZM400",
-             "ip_address": "131.215.34.117"}}]
+             "keyword": "invb"}}
+]

diff --git a/htsworkflow/frontend/bcmagic/fixtures/woldlab.json b/htsworkflow/frontend/bcmagic/fixtures/woldlab.json
new file mode 100644 (file)
index 0000000..51fdaa2
--- /dev/null
+++ b/htsworkflow/frontend/bcmagic/fixtures/woldlab.json
@@ -0,0 +1,18 @@
+[{"pk": 1,
+  "model": "bcmagic.printer",
+  "fields": {"name": "ZM400 1.25x1",
+             "label_height": 1.0,
+             "notes": "Everyday use labels",
+             "label_width": 1.25,
+             "label_shape": "Square",
+             "model": "Zebra ZM400",
+             "ip_address": "131.215.34.116"}},
+ {"pk": 2,
+  "model": "bcmagic.printer",
+  "fields": {"name": "ZM400 3x3",
+             "label_height": 3.0,
+             "notes": "Larger everyday use labels",
+             "label_width": 3.0,
+             "label_shape": "Square",
+             "model": "Zebra ZM400",
+             "ip_address": "131.215.34.117"}}]

diff --git a/htsworkflow/frontend/experiments/fixtures/initial_data.json b/htsworkflow/frontend/experiments/fixtures/initial_data.json
index cf259760b28306c6fd5228bbe1c2e732b506a9ce..f3645021101f934c882b50418a9b5c5ff98b043c 100644 (file)
--- a/htsworkflow/frontend/experiments/fixtures/initial_data.json
+++ b/htsworkflow/frontend/experiments/fixtures/initial_data.json
@@ -118,93 +118,5 @@
       "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"
     }
-  },
-  { "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/htsworkflow/frontend/experiments/fixtures/woldlab.json b/htsworkflow/frontend/experiments/fixtures/woldlab.json
new file mode 100644 (file)
index 0000000..b058925
--- /dev/null
+++ b/htsworkflow/frontend/experiments/fixtures/woldlab.json
@@ -0,0 +1,89 @@
+[ { "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/htsworkflow/frontend/experiments/test_experiments.py b/htsworkflow/frontend/experiments/test_experiments.py
index 6678dd418293d7ece172fb990a4d8445b1aeed90..0a0c9419827c7b4e9cb1c6d12e99fcb9100626e0 100644 (file)
--- a/htsworkflow/frontend/experiments/test_experiments.py
+++ b/htsworkflow/frontend/experiments/test_experiments.py
@@ -81,6 +81,7 @@ class ClusterStationTestCases(TestCase):
 
 class SequencerTestCases(TestCase):
     fixtures = ['initial_data.json',
+                'woldlab.json',
                 'test_flowcells.json']
 
     def test_default(self):

diff --git a/htsworkflow/frontend/inventory/fixtures/initial_data.json b/htsworkflow/frontend/inventory/fixtures/initial_data.json
index 68944de17107df87f66ac9e0b1ec330aa77d6889..028c026e8d9515277b065f0b5b86d2989a8ea83c 100644 (file)
--- a/htsworkflow/frontend/inventory/fixtures/initial_data.json
+++ b/htsworkflow/frontend/inventory/fixtures/initial_data.json
@@ -3,36 +3,24 @@
      "model": "inventory.itemtype",
      "fields": {"name": "Hard Drive"}
     },
-    {"pk":   2, 
+    {"pk":   2,
      "model": "inventory.itemtype",
      "fields": {"name": "Illumina SR Cluster Generation Reagents"}
-    },       
-    {"pk":   3, 
+    },
+    {"pk":   3,
      "model": "inventory.itemtype",
      "fields": {"name": "Illumina Library Creation Reagents"}
     },
-    {"pk":   4, 
+    {"pk":   4,
      "model": "inventory.itemtype",
      "fields": {"name": "Illumina Sequencing Reagents"}
     },
-    {"pk":   5, 
+    {"pk":   5,
      "model": "inventory.itemtype",
      "fields": {"name": "Illumina PE Cluster Generation Reagents"}
     },
-    {"pk":   6, 
+    {"pk":   6,
      "model": "inventory.itemtype",
-     "fields": {"name": "Library"} 
-    },       
-
-    {"pk": 1, 
-     "model": "inventory.printertemplate", 
-     "fields": {"default": false, 
-                "item_type": 1, 
-                "printer": 2, 
-             "template": "^FX=========================\r\n^FX 3\"x3\" Label\r\n^FX=========================\r\n^XA\r\n\r\n\r\n^FX======== Left Side ===========\r\n\r\n^FX------------\r\n^FX ^LH changes the 0,0 point of all subsequent location references\r\n^FX------------\r\n\r\n^LH0,50\r\n\r\n^FX ---Header---\r\n\r\n^FO25,0\r\n^CF0,50\r\n^FB250,2,,C\r\n^FD{{ item.barcode_id }}^FS\r\n\r\n^FX ---Column 1: Flowcells---\r\n\r\n^FX-----------------\r\n^FX FB command for automatic text formatting:\r\n^FX ^FB[dot width of area], [max # of lines], [change line spacing], [justification: L, C, R, J], [hanging indent]\r\n^FX-----------------\r\n\r\n^CF0,30,30\r\n^FO75,125\r\n^FB275,19,,L\r\n^FD{% for flowcell in flowcell_id_list %}{{ flowcell }}{% if not forloop.last %}\\&{% endif %}{% endfor %}^FS\r\n^FX ---Date---\r\n\r\n^FO0,725\r\n^CF0,35\r\n^FB300,2,,C\r\n^FD{{ oldest_rundate|date:\"YMd\" }} - {{ latest_rundate|date:\"YMd\" }}^FS\r\n\r\n^FX ---Barcode---\r\n\r\n^FO135,795\r\n^BXN,3,200^FDinvb|{{ item.barcode_id }}^FS\r\n\r\n^FX======== Right Side ===========\r\n\r\n^LH300,60\r\n\r\n^FX ---Header---\r\n\r\n^FO0,0\r\n^CF0,50\r\n^FB600,2,,C\r\n^FD{{ barcode_id }}^FS\r\n\r\n^FX ---Dividing line---\r\n\r\n^FX---------------\r\n^FX GB command:\r\n^FX ^GB[box width], [box height], [border thickness], [color: B, W], [corner rounding: 0-8]^FS\r\n^FX---------------\r\n\r\n^FO0,100\r\n^GB0,600,10^FS\r\n\r\n^FX ---Column 2: Libraries 1-20---\r\n\r\n^CF0,30,30\r\n^FO75,100\r\n^FB100,20,,L\r\n^FD{% for lib_id in library_id_list_1_to_20 %}{{ lib_id }}{% if not forloop.last %}\\&{% endif %}{% endfor %}^FS\r\n\r\n^FX ---Column 3: Libraries 21-40---\r\n\r\n^CF0,30,30\r\n^FO200,100\r\n^FB100,20,,L\r\n^FD{% for lib_id in library_id_list_21_to_40 %}{{ lib_id }}{% if not forloop.last %}\\&{% endif %}{% endfor %}^FS\r\n\r\n^FX ---Column 4: Libraries 41-60---\r\n\r\n^CF0,30,30\r\n^FO325,100\r\n^FB100,20,,L\r\n^FD{% for lib_id in library_id_list_41_to_60 %}{{ lib_id }}{% if not forloop.last %}\\&{% endif %}{% endfor %}^FS\r\n\r\n^FX ---Column 5: Libraries 61-80---\r\n\r\n^CF0,30,30\r\n^FO450,100\r\n^FB100,20,,L\r\n^FD{% for lib_id in library_id_list_61_to_80 %}{{ lib_id }}{% if not forloop.last %}\\&{% endif %}{% endfor %}^FS\r\n\r\n^FX ---Date---\r\n\r\n^FO0,715\r\n^CF0,35\r\n^FB600,2,,C\r\n^FDRun Dates: {{ oldest_rundate|date:\"YMd\" }}-{{ latest_rundate|date:\"YMd\" }}^FS\r\n\r\n^FX ---Barcode---\r\n\r\n^FO255,785\r\n^BXN,3,200^FDinvb|{{ item.barcode_id }}^FS\r\n\r\n^LH0,0\r\n^FX ---End---\r\n^XZ\r\n"}},
- {"pk": 2, 
-  "model": "inventory.printertemplate", 
-  "fields": {"default": true, 
-             "item_type": 2, 
-             "printer": 1, 
-             "template": "^FX=========================\r\n^FX Harddrive Location Tracking Label\r\n^FX 300x375 dots\r\n^FX=========================\r\n\r\n^XA\r\n^LH 0,25\r\n\r\n^FO0,0\r\n^CF0,35\r\n^FB375,1,,C\r\n^FD{{ item.item_type.name }}:^FS\r\n\r\n^FX -------Text contains HD serial #-------------\r\n^FO15,75\r\n^CF0,42\r\n^FB325,3,,C\r\n^FD{% if use_uuid %}{{ item.uuid }}{% else %}{{ item.barcode_id }}{% endif %}^FS\r\n\r\n^FX -------Barcode contains HD serial #-----------\r\n^FO150,200\r\n^BXN,3,200\r\n^FD{% if use_uuid %}invu|{{ item.uuid }}{% else %}invb|{{ item.barcode_id }}{% endif %}^FS\r\n\r\n^XZ\r\n"}}]
+     "fields": {"name": "Library"}
+    }
+]

diff --git a/htsworkflow/frontend/inventory/fixtures/woldlab.json b/htsworkflow/frontend/inventory/fixtures/woldlab.json
new file mode 100644 (file)
index 0000000..35568b5
--- /dev/null
+++ b/htsworkflow/frontend/inventory/fixtures/woldlab.json
@@ -0,0 +1,13 @@
+[{"pk": 1,
+     "model": "inventory.printertemplate",
+     "fields": {"default": false,
+                "item_type": 1,
+                "printer": 2,
+             "template": "^FX=========================\r\n^FX 3\"x3\" Label\r\n^FX=========================\r\n^XA\r\n\r\n\r\n^FX======== Left Side ===========\r\n\r\n^FX------------\r\n^FX ^LH changes the 0,0 point of all subsequent location references\r\n^FX------------\r\n\r\n^LH0,50\r\n\r\n^FX ---Header---\r\n\r\n^FO25,0\r\n^CF0,50\r\n^FB250,2,,C\r\n^FD{{ item.barcode_id }}^FS\r\n\r\n^FX ---Column 1: Flowcells---\r\n\r\n^FX-----------------\r\n^FX FB command for automatic text formatting:\r\n^FX ^FB[dot width of area], [max # of lines], [change line spacing], [justification: L, C, R, J], [hanging indent]\r\n^FX-----------------\r\n\r\n^CF0,30,30\r\n^FO75,125\r\n^FB275,19,,L\r\n^FD{% for flowcell in flowcell_id_list %}{{ flowcell }}{% if not forloop.last %}\\&{% endif %}{% endfor %}^FS\r\n^FX ---Date---\r\n\r\n^FO0,725\r\n^CF0,35\r\n^FB300,2,,C\r\n^FD{{ oldest_rundate|date:\"YMd\" }} - {{ latest_rundate|date:\"YMd\" }}^FS\r\n\r\n^FX ---Barcode---\r\n\r\n^FO135,795\r\n^BXN,3,200^FDinvb|{{ item.barcode_id }}^FS\r\n\r\n^FX======== Right Side ===========\r\n\r\n^LH300,60\r\n\r\n^FX ---Header---\r\n\r\n^FO0,0\r\n^CF0,50\r\n^FB600,2,,C\r\n^FD{{ barcode_id }}^FS\r\n\r\n^FX ---Dividing line---\r\n\r\n^FX---------------\r\n^FX GB command:\r\n^FX ^GB[box width], [box height], [border thickness], [color: B, W], [corner rounding: 0-8]^FS\r\n^FX---------------\r\n\r\n^FO0,100\r\n^GB0,600,10^FS\r\n\r\n^FX ---Column 2: Libraries 1-20---\r\n\r\n^CF0,30,30\r\n^FO75,100\r\n^FB100,20,,L\r\n^FD{% for lib_id in library_id_list_1_to_20 %}{{ lib_id }}{% if not forloop.last %}\\&{% endif %}{% endfor %}^FS\r\n\r\n^FX ---Column 3: Libraries 21-40---\r\n\r\n^CF0,30,30\r\n^FO200,100\r\n^FB100,20,,L\r\n^FD{% for lib_id in library_id_list_21_to_40 %}{{ lib_id }}{% if not forloop.last %}\\&{% endif %}{% endfor %}^FS\r\n\r\n^FX ---Column 4: Libraries 41-60---\r\n\r\n^CF0,30,30\r\n^FO325,100\r\n^FB100,20,,L\r\n^FD{% for lib_id in library_id_list_41_to_60 %}{{ lib_id }}{% if not forloop.last %}\\&{% endif %}{% endfor %}^FS\r\n\r\n^FX ---Column 5: Libraries 61-80---\r\n\r\n^CF0,30,30\r\n^FO450,100\r\n^FB100,20,,L\r\n^FD{% for lib_id in library_id_list_61_to_80 %}{{ lib_id }}{% if not forloop.last %}\\&{% endif %}{% endfor %}^FS\r\n\r\n^FX ---Date---\r\n\r\n^FO0,715\r\n^CF0,35\r\n^FB600,2,,C\r\n^FDRun Dates: {{ oldest_rundate|date:\"YMd\" }}-{{ latest_rundate|date:\"YMd\" }}^FS\r\n\r\n^FX ---Barcode---\r\n\r\n^FO255,785\r\n^BXN,3,200^FDinvb|{{ item.barcode_id }}^FS\r\n\r\n^LH0,0\r\n^FX ---End---\r\n^XZ\r\n"}},
+ {"pk": 2,
+  "model": "inventory.printertemplate",
+  "fields": {"default": true,
+             "item_type": 2,
+             "printer": 1,
+             "template": "^FX=========================\r\n^FX Harddrive Location Tracking Label\r\n^FX 300x375 dots\r\n^FX=========================\r\n\r\n^XA\r\n^LH 0,25\r\n\r\n^FO0,0\r\n^CF0,35\r\n^FB375,1,,C\r\n^FD{{ item.item_type.name }}:^FS\r\n\r\n^FX -------Text contains HD serial #-------------\r\n^FO15,75\r\n^CF0,42\r\n^FB325,3,,C\r\n^FD{% if use_uuid %}{{ item.uuid }}{% else %}{{ item.barcode_id }}{% endif %}^FS\r\n\r\n^FX -------Barcode contains HD serial #-----------\r\n^FO150,200\r\n^BXN,3,200\r\n^FD{% if use_uuid %}invu|{{ item.uuid }}{% else %}invb|{{ item.barcode_id }}{% endif %}^FS\r\n\r\n^XZ\r\n"}}
+]

diff --git a/htsworkflow/frontend/samples/test_samples.py b/htsworkflow/frontend/samples/test_samples.py
index f4bfe5a429920075c66e2198775d67056fe0688d..38e0dc27bfaa74d3aa11b74b70429666f1c6c9e8 100644 (file)
--- a/htsworkflow/frontend/samples/test_samples.py
+++ b/htsworkflow/frontend/samples/test_samples.py
@@ -27,6 +27,7 @@ from htsworkflow.util.ethelp import validate_xhtml
 
 class LibraryTestCase(TestCase):
     fixtures = ['initial_data.json',
+                'woldlab.json',
                 'test_samples.json']
 
     def setUp(self):
@@ -54,6 +55,7 @@ class SampleWebTestCase(TestCase):
     (like returning json objects)
     """
     fixtures = ['initial_data.json',
+                'woldlab.json',
                 'test_samples.json']
 
     def test_library_info(self):
@@ -282,6 +284,7 @@ except ImportError,e:
 
 class TestRDFaLibrary(TestCase):
     fixtures = ['initial_data.json',
+                'woldlab.json',
                 'test_samples.json']
 
     def test_parse_rdfa(self):