aboutsummaryrefslogtreecommitdiff
diff options
context:
space:
mode:
Diffstat
-rw-r--r--doc/database.org165
-rw-r--r--doc/database.svg882
-rw-r--r--test/lib/NavigationTest.rb46
3 files changed, 1090 insertions, 3 deletions
diff --git a/doc/database.org b/doc/database.org
index e06ac1ff..2221c4fb 100644
--- a/doc/database.org
+++ b/doc/database.org
@@ -1,7 +1,11 @@
- github Document reduction issue
+* The small test database (2GB)
-* GeneNetwork Database
+The default install comes with a smaller database which includes a
+number of the BSD's and the Human liver dataset (GSE9588).
+
+* GeneNetwork database
** Estimated table sizes
@@ -487,7 +491,6 @@ select count(*) from ProbeSet limit 5;
-
** ProbeSetData
Probedata - main molecular data. Probesets, metabolome,
@@ -678,7 +681,21 @@ No longer used
** Species & Strain (should be sample)
-Menu
+select * from Species;
++----+-----------+----------------------+----------------+----------------------+-------------------------+------------+---------+
+| Id | SpeciesId | SpeciesName | Name | MenuName | FullName | TaxonomyId | OrderId |
++----+-----------+----------------------+----------------+----------------------+-------------------------+------------+---------+
+| 1 | 1 | Mouse | mouse | Mouse | Mus musculus | 10090 | 30 |
+| 2 | 2 | Rat | rat | Rat | Rattus norvegicus | 10116 | 40 |
+| 3 | 3 | Arabidopsis thaliana | arabidopsis | Arabidopsis thaliana | Arabidopsis thaliana | 3702 | 60 |
+| 4 | 4 | Human | human | Human | Homo sapiens | 9606 | 10 |
+| 5 | 5 | Barley | barley | Barley | Hordeum vulgare | 4513 | 70 |
+| 6 | 6 | Drosophila | drosophila | Drosophila | Drosophila melanogaster | 7227 | 50 |
+| 7 | 7 | Macaque monkey | macaque monkey | Macaque monkey | Macaca mulatta | 9544 | 20 |
+| 8 | 8 | Soybean | soybean | Soybean | Soybean | 3847 | 80 |
+| 9 | 9 | Tomato | tomato | Tomato | Tomato | 4081 | 90 |
++----+-----------+----------------------+----------------+----------------------+-------------------------+------------+---------+
+
** InbredSet
@@ -708,3 +725,145 @@ User selection - retained
** Vlookup
+* Fetching Data
+
+** Fetch phenotypes
+
+To get at phenotype data ProbeSetData is the main table (almost all
+important molecular assay data is in this table including probe set
+data, RNA-seq data, proteomic data, and metabolomic data. 2.5 billion
+rows March 2016)
+
+select count(*) from ProbeSetData limit 5;
++---------------+
+| count(*) |
++---------------+
+| 2,510,566,472 |
++---------------+
+
+select * from ProbeSetData limit 5;
++----+----------+-------+
+| Id | StrainId | value |
++----+----------+-------+
+| 1 | 1 | 5.742 |
+| 1 | 2 | 5.006 |
+| 1 | 3 | 6.079 |
+| 1 | 4 | 6.414 |
+| 1 | 5 | 4.885 |
++----+----------+-------+
+
+This table is used in
+
+: wqflask/base/do_search.py
+: wqflask/base/data_set.py
+: wqflask/utility/AJAX_table.py
+: wqflask/wqflask/correlation/show_corr_results.py
+
+In there we find 'ProbeSetData.Id = ProbeSetXRef.dataId'.
+
+select * from ProbeSetXRef limit 5;
++------------------+------------+--------+------------+--------------------+------------+-------------------+---------------------+-----------------+--------------------+--------+----------------------+------+
+| ProbeSetFreezeId | ProbeSetId | DataId | Locus_old | LRS_old | pValue_old | mean | se | Locus | LRS | pValue | additive | h2 |
++------------------+------------+--------+------------+--------------------+------------+-------------------+---------------------+-----------------+--------------------+--------+----------------------+------+
+| 1 | 1 | 1 | 10.095.400 | 13.3971627898894 | 0.163 | 5.48794285714286 | 0.08525787814808819 | rs13480619 | 12.590069931048001 | 0.269 | -0.28515625 | NULL |
+| 1 | 2 | 2 | D15Mit189 | 10.042057464356201 | 0.431 | 9.90165714285714 | 0.0374686634976217 | CEL-17_50896182 | 10.5970737900941 | 0.304 | -0.11678333333333299 | NULL |
+| 1 | 3 | 3 | D5Mit139 | 5.43678531742749 | 0.993 | 7.83948571428571 | 0.0457583416912569 | rs13478499 | 6.0970532702754 | 0.988 | 0.112957489878542 | NULL |
+| 1 | 4 | 4 | D1Mit511 | 9.87815279480766 | 0.483 | 8.315628571428569 | 0.0470396593931327 | rs6154379 | 11.774867551173099 | 0.286 | -0.157113725490196 | NULL |
+| 1 | 5 | 5 | D16H21S16 | 10.191723834264499 | 0.528 | 9.19345714285714 | 0.0354801718293322 | rs4199265 | 10.923263374016202 | 0.468 | 0.11476470588235299 | NULL |
++------------------+------------+--------+------------+--------------------+------------+-------------------+---------------------+-----------------+--------------------+--------+----------------------+------+
+
+i.e., for Strain Id 1 (DataId) 1, the locus '10.095.400' has a
+phenotype value of 5.742.
+
+GeneNetwork1 already has a limited REST interface, if you do
+
+: curl "http://robot.genenetwork.org/webqtl/main.py?cmd=get&probeset=1443823_s_at&db=HC_M2_0606_P"
+
+we get
+
+: ProbeSetID B6D2F1 C57BL/6J DBA/2J BXD1 BXD2 BXD5 BXD6 BXD8 BXD9 BXD11 BXD12 BXD13 BXD15 BXD16 BXD19 BXD20 BXD21 BXD22 BXD23 BXD24 BXD27 BXD28 BXD29 BXD31 BXD32 BXD33 BXD34 BXD38 BXD39 BXD40 BXD42 BXD67 BXD68 BXD43 BXD44 BXD45 BXD48 BXD50 BXD51 BXD55 BXD60 BXD61 BXD62 BXD63 BXD64 BXD65 BXD66 BXD69 BXD70 BXD73 BXD74 BXD75 BXD76 BXD77 BXD79 BXD73a BXD83 BXD84 BXD85 BXD86 BXD87 BXD89 BXD90 BXD65b BXD93 BXD94 A/J AKR/J C3H/HeJ C57BL/6ByJ CXB1 CXB2 CXB3 CXB4 CXB5 CXB6 CXB7 CXB8 CXB9 CXB10 CXB11 CXB12 CXB13 BXD48a 129S1/SvImJ BALB/cJ BALB/cByJ LG/J NOD/ShiLtJ PWD/PhJ BXD65a BXD98 BXD99 CAST/EiJ KK/HlJ WSB/EiJ NZO/HlLtJ PWK/PhJ D2B6F1
+: 1443823_s_at 15.251 15.626 14.716 15.198 14.918 15.057 15.232 14.968 14.87 15.084 15.192 14.924 15.343 15.226 15.364 15.36 14.792 14.908 15.344 14.948 15.08 15.021 15.176 15.14 14.796 15.443 14.636 14.921 15.22 15.62 14.816 15.39 15.428 14.982 15.05 15.13 14.722 14.636 15.242 15.527 14.825 14.416 15.125 15.362 15.226 15.176 15.328 14.895 15.141 15.634 14.922 14.764 15.122 15.448 15.398 15.089 14.765 15.234 15.302 14.774 14.979 15.212 15.29 15.012 15.041 15.448 14.34 14.338 14.809 15.046 14.816 15.232 14.933 15.255 15.21 14.766 14.8 15.506 15.749 15.274 15.599 15.673 14.651 14.692 14.552 14.563 14.164 14.546 15.044 14.695 15.162 14.772 14.645 15.493 14.75 14.786 15.003 15.148 15.221
+
+getTraitData is defined in the file [[https://github.com/genenetwork/genenetwork/blob/master/web/webqtl/textUI/cmdClass.py#L134][web/webqtl/textUI/cmdClass.py]].
+probe is None, so the code at line 199 is run
+
+query = "SELECT Strain.Name, %sData.value from %sData, Strain, %s,
+%sXRef WHERE %s.Name = '%s' and %sXRef.%sId = %s.Id and
+%sXRef.%sFreezeId = %d and %sXRef.DataId = %sData.Id and
+%sData.StrainId = Strain.Id order by Strain.Id" % (prefix, prefix,
+prefix, prefix, prefix, probeset,prefix, prefix, prefix, prefix,
+prefix, dbId, prefix, prefix, prefix)
+
+where prefix is ProbeSet (one presumes). So, let's see if we can do this by hand
+
+SELECT Strain.Name, ProbeSetData.value from ProbeSetData, Strain, ProbeSet,
+ProbeSetXRef WHERE ProbeSet.Name = '1443823_s_at' and ProbeSetXRef.ProbeSetId = ProbeSet.Id and
+ProbeSetXRef.ProbeSetFreezeId = $dbid and ProbeSetXRef.DataId = ProbeSetData.Id and
+ProbeSetData.StrainId = Strain.Id ORDER BY Strain.Id
+
+The $dbid is listed in the ProbeSetFreeze table,
+
+SELECT ProbeFreezeId,Name FROM ProbeSetFreeze WHERE Name='HC_M2_0606_P' limit 5;
+
++---------------+--------------+
+| ProbeFreezeId | Name |
++---------------+--------------+
+| 30 | HC_M2_0606_P |
++---------------+--------------+
+
+select id,name from ProbeSet WHERE Name = '1443823_s_at' limit 5;
++--------+--------------+
+| id | name |
++--------+--------------+
+| 106556 | 1443823_s_at |
++--------+--------------+
+
+So
+
+query = "SELECT Strain.Name, %sData.value from %sData, Strain, %s,
+%sXRef WHERE %s.Name = '%s' and %sXRef.%sId = %s.Id and
+%sXRef.%sFreezeId = %d and %sXRef.DataId = %sData.Id and
+%sData.StrainId = Strain.Id order by Strain.Id" % (prefix, prefix,
+prefix, prefix, prefix, probeset,prefix, prefix, prefix, prefix,
+prefix, dbId, prefix, prefix, prefix)
+
+CORRECT NAME:
+
+SELECT Strain.Name, ProbeSetData.value from ProbeSetData, Strain,
+ProbeSet, ProbeSetXRef WHERE ProbeSet.Name = 'at_probe' and
+ProbeSetXRef.ProbeSetId = ProbeSet.Id and
+ProbeSetXRef.ProbeSetFreezeId = dbid and ProbeSetXRef.DataId =
+ProbeSetData.Id and ProbeSetData.StrainId = Strain.Id order by
+Strain.Id
+
+
+select * from ProbeSetXRef WHERE probesetfreezeid=30 limit 5;
++------------------+------------+--------+------------+--------------------+------------+--------------------+--------------------+-----------------+--------------------+--------+-------------------+------+
+| ProbeSetFreezeId | ProbeSetId | DataId | Locus_old | LRS_old | pValue_old | mean | se | Locus | LRS | pValue | additive | h2 |
++------------------+------------+--------+------------+--------------------+------------+--------------------+--------------------+-----------------+--------------------+--------+-------------------+------+
+| 30 | 1 | 445962 | 01.059.350 | 7.1753152078069595 | 0.961 | 30.0646 | 1.79763935596594 | rs13475891 | 7.1753152078069204 | 0.973 | 4.71778125 | NULL |
+| 30 | 2 | 445963 | D4Mit156 | 7.58944292943285 | 0.724 | 232.38328571428602 | 9.00278909374791 | CEL-4_118751423 | 7.57513435426218 | 0.793 | 25.2660951417004 | NULL |
+| 30 | 3 | 445964 | D1Mit134 | 9.766065497826819 | 0.737 | 47.206 | 1.58413526287766 | mCV23431007 | 9.76606549782677 | 0.797 | -4.82405952380952 | NULL |
+| 30 | 4 | 445965 | D1Mit155 | 18.0045829157241 | 0.033 | 132.29248571428602 | 4.37799472291842 | rs3689947 | 17.9365068406286 | 0.049 | -16.945619047619 | NULL |
+| 30 | 5 | 445966 | D5Mit197 | 9.51068902627823 | 0.476 | 271.309971428571 | 7.4294268316065395 | rs6239372 | 10.4214974316601 | 0.41 | -25.6148045454546 | NULL |
++------------------+------------+--------+------------+--------------------+------------+--------------------+--------------------+-----------------+--------------------+--------+-------------------+------+
+
+So, apparently ProbeSetFreezeID points to the database identifier in
+ProbeSetFreeze which has the name of the 'DB'. OK, that kinda makes
+sense now. Meanwhile Probeset.name points to the phenotype name.
+
+ProbeSetXRef binds these tables together. Finally there is the data in
+
+select * from ProbeSetData limit 5;
++----+----------+-------+
+| Id | StrainId | value |
++----+----------+-------+
+| 1 | 1 | 5.742 |
+| 1 | 2 | 5.006 |
+| 1 | 3 | 6.079 |
+| 1 | 4 | 6.414 |
+| 1 | 5 | 4.885 |
++----+----------+-------+
+5 rows in set (0.00 sec)
+
+linked by ProbeSetXRef.dataid.
diff --git a/doc/database.svg b/doc/database.svg
new file mode 100644
index 00000000..9ddc2f47
--- /dev/null
+++ b/doc/database.svg
@@ -0,0 +1,882 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<!-- Created with Inkscape (http://www.inkscape.org/) -->
+
+<svg
+ xmlns:dc="http://purl.org/dc/elements/1.1/"
+ xmlns:cc="http://creativecommons.org/ns#"
+ xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+ xmlns:svg="http://www.w3.org/2000/svg"
+ xmlns="http://www.w3.org/2000/svg"
+ xmlns:sodipodi="http://sodipodi.sourceforge.net/DTD/sodipodi-0.dtd"
+ xmlns:inkscape="http://www.inkscape.org/namespaces/inkscape"
+ width="210mm"
+ height="297mm"
+ viewBox="0 0 744.09448819 1052.3622047"
+ id="svg2"
+ version="1.1"
+ inkscape:version="0.91 r13725"
+ sodipodi:docname="database.svg">
+ <defs
+ id="defs4">
+ <marker
+ inkscape:isstock="true"
+ style="overflow:visible;"
+ id="marker12489"
+ refX="0.0"
+ refY="0.0"
+ orient="auto"
+ inkscape:stockid="Arrow2Mend">
+ <path
+ transform="scale(0.6) rotate(180) translate(0,0)"
+ d="M 8.7185878,4.0337352 L -2.2072895,0.016013256 L 8.7185884,-4.0017078 C 6.9730900,-1.6296469 6.9831476,1.6157441 8.7185878,4.0337352 z "
+ style="fill-rule:evenodd;stroke-width:0.625;stroke-linejoin:round;stroke:#0000d7;stroke-opacity:1;fill:#0000d7;fill-opacity:1"
+ id="path12491" />
+ </marker>
+ <marker
+ inkscape:stockid="Arrow2Lend"
+ orient="auto"
+ refY="0.0"
+ refX="0.0"
+ id="Arrow2Lend"
+ style="overflow:visible;"
+ inkscape:isstock="true">
+ <path
+ id="path4445"
+ style="fill-rule:evenodd;stroke-width:0.62500000;stroke-linejoin:round;"
+ d="M 8.7185878,4.0337352 L -2.2072895,0.016013256 L 8.7185884,-4.0017078 C 6.9730900,-1.6296469 6.9831476,1.6157441 8.7185878,4.0337352 z "
+ transform="scale(1.1) rotate(180) translate(1,0)" />
+ </marker>
+ <marker
+ inkscape:isstock="true"
+ style="overflow:visible;"
+ id="marker11727"
+ refX="0.0"
+ refY="0.0"
+ orient="auto"
+ inkscape:stockid="Arrow2Mend">
+ <path
+ transform="scale(0.6) rotate(180) translate(0,0)"
+ d="M 8.7185878,4.0337352 L -2.2072895,0.016013256 L 8.7185884,-4.0017078 C 6.9730900,-1.6296469 6.9831476,1.6157441 8.7185878,4.0337352 z "
+ style="fill-rule:evenodd;stroke-width:0.625;stroke-linejoin:round;stroke:#0000da;stroke-opacity:1;fill:#0000da;fill-opacity:1"
+ id="path11729" />
+ </marker>
+ <marker
+ inkscape:isstock="true"
+ style="overflow:visible;"
+ id="marker11607"
+ refX="0.0"
+ refY="0.0"
+ orient="auto"
+ inkscape:stockid="Arrow2Lend">
+ <path
+ transform="scale(1.1) rotate(180) translate(1,0)"
+ d="M 8.7185878,4.0337352 L -2.2072895,0.016013256 L 8.7185884,-4.0017078 C 6.9730900,-1.6296469 6.9831476,1.6157441 8.7185878,4.0337352 z "
+ style="fill-rule:evenodd;stroke-width:0.625;stroke-linejoin:round;stroke:#0000da;stroke-opacity:1;fill:#0000da;fill-opacity:1"
+ id="path11609" />
+ </marker>
+ <marker
+ inkscape:stockid="Arrow1Lend"
+ orient="auto"
+ refY="0.0"
+ refX="0.0"
+ id="Arrow1Lend"
+ style="overflow:visible;"
+ inkscape:isstock="true">
+ <path
+ id="path4427"
+ d="M 0.0,0.0 L 5.0,-5.0 L -12.5,0.0 L 5.0,5.0 L 0.0,0.0 z "
+ style="fill-rule:evenodd;stroke:#0000a3;stroke-width:1pt;stroke-opacity:1;fill:#0000a3;fill-opacity:1"
+ transform="scale(0.8) rotate(180) translate(12.5,0)" />
+ </marker>
+ <marker
+ inkscape:stockid="Arrow2Mend"
+ orient="auto"
+ refY="0.0"
+ refX="0.0"
+ id="Arrow2Mend"
+ style="overflow:visible;"
+ inkscape:isstock="true"
+ inkscape:collect="always">
+ <path
+ id="path4451"
+ style="fill-rule:evenodd;stroke-width:0.625;stroke-linejoin:round;stroke:#0000d7;stroke-opacity:1;fill:#0000d7;fill-opacity:1"
+ d="M 8.7185878,4.0337352 L -2.2072895,0.016013256 L 8.7185884,-4.0017078 C 6.9730900,-1.6296469 6.9831476,1.6157441 8.7185878,4.0337352 z "
+ transform="scale(0.6) rotate(180) translate(0,0)" />
+ </marker>
+ <marker
+ inkscape:isstock="true"
+ style="overflow:visible;"
+ id="marker10561"
+ refX="0.0"
+ refY="0.0"
+ orient="auto"
+ inkscape:stockid="Arrow2Mend">
+ <path
+ transform="scale(0.6) rotate(180) translate(0,0)"
+ d="M 8.7185878,4.0337352 L -2.2072895,0.016013256 L 8.7185884,-4.0017078 C 6.9730900,-1.6296469 6.9831476,1.6157441 8.7185878,4.0337352 z "
+ style="fill-rule:evenodd;stroke-width:0.625;stroke-linejoin:round;stroke:#000000;stroke-opacity:1;fill:#000000;fill-opacity:1"
+ id="path10563" />
+ </marker>
+ <marker
+ inkscape:stockid="Arrow2Mstart"
+ orient="auto"
+ refY="0.0"
+ refX="0.0"
+ id="Arrow2Mstart"
+ style="overflow:visible"
+ inkscape:isstock="true">
+ <path
+ id="path4448"
+ style="fill-rule:evenodd;stroke-width:0.625;stroke-linejoin:round;stroke:#0000b1;stroke-opacity:1;fill:#0000b1;fill-opacity:1"
+ d="M 8.7185878,4.0337352 L -2.2072895,0.016013256 L 8.7185884,-4.0017078 C 6.9730900,-1.6296469 6.9831476,1.6157441 8.7185878,4.0337352 z "
+ transform="scale(0.6) translate(0,0)" />
+ </marker>
+ <marker
+ inkscape:stockid="TriangleOutM"
+ orient="auto"
+ refY="0.0"
+ refX="0.0"
+ id="TriangleOutM"
+ style="overflow:visible"
+ inkscape:isstock="true">
+ <path
+ id="path4569"
+ d="M 5.77,0.0 L -2.88,5.0 L -2.88,-5.0 L 5.77,0.0 z "
+ style="fill-rule:evenodd;stroke:#0000b1;stroke-width:1pt;stroke-opacity:1;fill:#0000b1;fill-opacity:1"
+ transform="scale(0.4)" />
+ </marker>
+ <marker
+ inkscape:stockid="Arrow1Lstart"
+ orient="auto"
+ refY="0.0"
+ refX="0.0"
+ id="Arrow1Lstart"
+ style="overflow:visible"
+ inkscape:isstock="true">
+ <path
+ id="path4424"
+ d="M 0.0,0.0 L 5.0,-5.0 L -12.5,0.0 L 5.0,5.0 L 0.0,0.0 z "
+ style="fill-rule:evenodd;stroke:#0000b1;stroke-width:1pt;stroke-opacity:1;fill:#0000b1;fill-opacity:1"
+ transform="scale(0.8) translate(12.5,0)" />
+ </marker>
+ <marker
+ inkscape:stockid="Arrow2Mstart"
+ orient="auto"
+ refY="0"
+ refX="0"
+ id="Arrow2Mstart-5"
+ style="overflow:visible"
+ inkscape:isstock="true">
+ <path
+ inkscape:connector-curvature="0"
+ id="path4448-2"
+ style="fill:#0000b1;fill-opacity:1;fill-rule:evenodd;stroke:#0000b1;stroke-width:0.625;stroke-linejoin:round;stroke-opacity:1"
+ d="M 8.7185878,4.0337352 -2.2072895,0.01601326 8.7185884,-4.0017078 c -1.7454984,2.3720609 -1.7354408,5.6174519 -6e-7,8.035443 z"
+ transform="scale(0.6,0.6)" />
+ </marker>
+ <marker
+ inkscape:stockid="Arrow2Mend"
+ orient="auto"
+ refY="0"
+ refX="0"
+ id="Arrow2Mend-8"
+ style="overflow:visible"
+ inkscape:isstock="true">
+ <path
+ inkscape:connector-curvature="0"
+ id="path4451-9"
+ style="fill:#0000b1;fill-opacity:1;fill-rule:evenodd;stroke:#0000b1;stroke-width:0.625;stroke-linejoin:round;stroke-opacity:1"
+ d="M 8.7185878,4.0337352 -2.2072895,0.01601326 8.7185884,-4.0017078 c -1.7454984,2.3720609 -1.7354408,5.6174519 -6e-7,8.035443 z"
+ transform="scale(-0.6,-0.6)" />
+ </marker>
+ <marker
+ inkscape:isstock="true"
+ style="overflow:visible"
+ id="marker12489-7"
+ refX="0"
+ refY="0"
+ orient="auto"
+ inkscape:stockid="Arrow2Mend">
+ <path
+ inkscape:connector-curvature="0"
+ transform="scale(-0.6,-0.6)"
+ d="M 8.7185878,4.0337352 -2.2072895,0.01601326 8.7185884,-4.0017078 c -1.7454984,2.3720609 -1.7354408,5.6174519 -6e-7,8.035443 z"
+ style="fill:#0000d7;fill-opacity:1;fill-rule:evenodd;stroke:#0000d7;stroke-width:0.625;stroke-linejoin:round;stroke-opacity:1"
+ id="path12491-4" />
+ </marker>
+ <marker
+ inkscape:isstock="true"
+ style="overflow:visible"
+ id="marker12489-7-2"
+ refX="0"
+ refY="0"
+ orient="auto"
+ inkscape:stockid="Arrow2Mend">
+ <path
+ inkscape:connector-curvature="0"
+ transform="scale(-0.6,-0.6)"
+ d="M 8.7185878,4.0337352 -2.2072895,0.01601326 8.7185884,-4.0017078 c -1.7454984,2.3720609 -1.7354408,5.6174519 -6e-7,8.035443 z"
+ style="fill:#0000d7;fill-opacity:1;fill-rule:evenodd;stroke:#0000d7;stroke-width:0.625;stroke-linejoin:round;stroke-opacity:1"
+ id="path12491-4-9" />
+ </marker>
+ </defs>
+ <sodipodi:namedview
+ id="base"
+ pagecolor="#ffffff"
+ bordercolor="#666666"
+ borderopacity="1.0"
+ inkscape:pageopacity="0.0"
+ inkscape:pageshadow="2"
+ inkscape:zoom="0.98994949"
+ inkscape:cx="361.50633"
+ inkscape:cy="527.18241"
+ inkscape:document-units="px"
+ inkscape:current-layer="layer1"
+ showgrid="false"
+ inkscape:window-width="1085"
+ inkscape:window-height="1276"
+ inkscape:window-x="28"
+ inkscape:window-y="142"
+ inkscape:window-maximized="0"
+ inkscape:snap-bbox="false"
+ inkscape:snap-nodes="true">
+ <inkscape:grid
+ type="xygrid"
+ id="grid3355" />
+ </sodipodi:namedview>
+ <metadata
+ id="metadata7">
+ <rdf:RDF>
+ <cc:Work
+ rdf:about="">
+ <dc:format>image/svg+xml</dc:format>
+ <dc:type
+ rdf:resource="http://purl.org/dc/dcmitype/StillImage" />
+ <dc:title />
+ </cc:Work>
+ </rdf:RDF>
+ </metadata>
+ <g
+ inkscape:label="Layer 1"
+ inkscape:groupmode="layer"
+ id="layer1">
+ <rect
+ style="fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:0.46889797px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1"
+ id="rect3357"
+ width="174.81682"
+ height="25.531101"
+ x="39.020161"
+ y="85.668076" />
+ <rect
+ style="fill:none"
+ id="rect4159"
+ width="280"
+ height="20"
+ x="40"
+ y="72.362206" />
+ <rect
+ style="fill:none"
+ id="rect4164"
+ width="290"
+ height="20"
+ x="40"
+ y="72.362206" />
+ <text
+ xml:space="preserve"
+ style="font-style:normal;font-weight:normal;font-size:12.5px;line-height:100%;font-family:sans-serif;letter-spacing:0px;word-spacing:0px;fill:#000000;fill-opacity:1;stroke:none;stroke-width:1px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1;-inkscape-font-specification:'sans-serif, Normal';font-stretch:normal;font-variant:normal;text-anchor:start;text-align:start;writing-mode:lr;"
+ x="40"
+ y="82.362206"
+ id="text4181"
+ sodipodi:linespacing="100%"><tspan
+ sodipodi:role="line"
+ id="tspan4183"
+ x="40"
+ y="82.362206">ProbesetData</tspan><tspan
+ sodipodi:role="line"
+ x="40"
+ y="107.36221"
+ id="tspan4185" /></text>
+ <text
+ xml:space="preserve"
+ style="font-style:normal;font-weight:normal;font-size:20px;line-height:125%;font-family:sans-serif;letter-spacing:0px;word-spacing:0px;fill:#000000;fill-opacity:1;stroke:none;stroke-width:1px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1"
+ x="100"
+ y="132.3622"
+ id="text4187"
+ sodipodi:linespacing="125%"><tspan
+ sodipodi:role="line"
+ id="tspan4189"
+ x="100"
+ y="132.3622" /></text>
+ <rect
+ style="fill:none"
+ id="rect4191"
+ width="80"
+ height="70.000008"
+ x="60"
+ y="92.362206" />
+ <text
+ xml:space="preserve"
+ style="font-style:normal;font-weight:normal;font-size:12.5px;line-height:125%;font-family:sans-serif;letter-spacing:0px;word-spacing:0px;fill:#000000;fill-opacity:1;stroke:none;stroke-width:1px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1;"
+ x="60"
+ y="102.3622"
+ id="text4208"
+ sodipodi:linespacing="125%"><tspan
+ sodipodi:role="line"
+ id="tspan4210"
+ x="60"
+ y="102.3622">id</tspan><tspan
+ sodipodi:role="line"
+ x="60"
+ y="127.3622"
+ id="tspan4212" /></text>
+ <text
+ xml:space="preserve"
+ style="font-style:normal;font-weight:normal;font-size:12.5px;line-height:100%;font-family:sans-serif;letter-spacing:0px;word-spacing:0px;fill:#000000;fill-opacity:1;stroke:none;stroke-width:1px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1;-inkscape-font-specification:'sans-serif, Normal';font-stretch:normal;font-variant:normal;text-anchor:start;text-align:start;writing-mode:lr;"
+ x="90"
+ y="102.3622"
+ id="text4214"
+ sodipodi:linespacing="100%"><tspan
+ sodipodi:role="line"
+ id="tspan4216"
+ x="90"
+ y="102.3622">strainid</tspan><tspan
+ sodipodi:role="line"
+ x="90"
+ y="127.3622"
+ id="tspan4218" /></text>
+ <text
+ xml:space="preserve"
+ style="font-style:normal;font-weight:normal;font-size:20px;line-height:125%;font-family:sans-serif;letter-spacing:0px;word-spacing:0px;fill:#000000;fill-opacity:1;stroke:none;stroke-width:1px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1"
+ x="210"
+ y="102.3622"
+ id="text4220"
+ sodipodi:linespacing="125%"><tspan
+ sodipodi:role="line"
+ x="210"
+ y="102.3622"
+ id="tspan4224" /><tspan
+ sodipodi:role="line"
+ x="210"
+ y="127.3622"
+ id="tspan4228" /></text>
+ <text
+ xml:space="preserve"
+ style="font-style:normal;font-weight:normal;font-size:12.5px;line-height:125%;font-family:sans-serif;letter-spacing:0px;word-spacing:0px;fill:#000000;fill-opacity:1;stroke:none;stroke-width:1px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1"
+ x="160.71428"
+ y="102.3622"
+ id="text4230"
+ sodipodi:linespacing="125%"><tspan
+ sodipodi:role="line"
+ id="tspan4232"
+ x="160.71428"
+ y="102.3622">value</tspan><tspan
+ sodipodi:role="line"
+ x="160.71428"
+ y="117.9872"
+ id="tspan4234" /></text>
+ <text
+ xml:space="preserve"
+ style="font-style:normal;font-weight:normal;font-size:12.5px;line-height:125%;font-family:sans-serif;letter-spacing:0px;word-spacing:0px;fill:#000000;fill-opacity:1;stroke:none;stroke-width:1px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1"
+ x="40"
+ y="162.3622"
+ id="text4236"
+ sodipodi:linespacing="125%"><tspan
+ sodipodi:role="line"
+ id="tspan4238"
+ x="40"
+ y="162.3622">ProbeSetXRef</tspan><tspan
+ sodipodi:role="line"
+ x="40"
+ y="177.9872"
+ id="tspan4240" /></text>
+ <rect
+ style="fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:0.69999564px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1"
+ id="rect3357-3"
+ width="393.15714"
+ height="25.300003"
+ x="39.849991"
+ y="171.49791" />
+ <text
+ xml:space="preserve"
+ style="font-style:normal;font-weight:normal;font-size:12.5px;line-height:125%;font-family:sans-serif;letter-spacing:0px;word-spacing:0px;fill:#000000;fill-opacity:1;stroke:none;stroke-width:1px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1"
+ x="60"
+ y="182.3622"
+ id="text4257"
+ sodipodi:linespacing="125%"><tspan
+ sodipodi:role="line"
+ id="tspan4259"
+ x="60"
+ y="182.3622">ProbeSetFreezeId</tspan><tspan
+ sodipodi:role="line"
+ x="60"
+ y="197.9872"
+ id="tspan4261" /></text>
+ <text
+ xml:space="preserve"
+ style="font-style:normal;font-weight:normal;font-size:12.5px;line-height:125%;font-family:sans-serif;letter-spacing:0px;word-spacing:0px;fill:#000000;fill-opacity:1;stroke:none;stroke-width:1px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1"
+ x="190"
+ y="182.3622"
+ id="text4263"
+ sodipodi:linespacing="125%"><tspan
+ sodipodi:role="line"
+ id="tspan4265"
+ x="190"
+ y="182.3622">ProbeSetID</tspan><tspan
+ sodipodi:role="line"
+ x="190"
+ y="197.9872"
+ id="tspan4267" /></text>
+ <text
+ xml:space="preserve"
+ style="font-style:normal;font-weight:normal;font-size:12.5px;line-height:125%;font-family:sans-serif;letter-spacing:0px;word-spacing:0px;fill:#000000;fill-opacity:1;stroke:none;stroke-width:1px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1"
+ x="290"
+ y="182.3622"
+ id="text4269"
+ sodipodi:linespacing="125%"><tspan
+ sodipodi:role="line"
+ id="tspan4271"
+ x="290"
+ y="182.3622">DataId</tspan><tspan
+ sodipodi:role="line"
+ x="290"
+ y="197.9872"
+ id="tspan4273" /></text>
+ <text
+ xml:space="preserve"
+ style="font-style:normal;font-weight:normal;font-size:12.5px;line-height:125%;font-family:sans-serif;letter-spacing:0px;word-spacing:0px;fill:#000000;fill-opacity:1;stroke:none;stroke-width:1px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1"
+ x="360"
+ y="182.3622"
+ id="text4275"
+ sodipodi:linespacing="125%"><tspan
+ sodipodi:role="line"
+ id="tspan4277"
+ x="360"
+ y="182.3622">pValue</tspan><tspan
+ sodipodi:role="line"
+ x="360"
+ y="197.9872"
+ id="tspan4279" /></text>
+ <rect
+ style="fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:0.50748467px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1"
+ id="rect3357-6"
+ width="205.08281"
+ height="25.492514"
+ x="249.75372"
+ y="87.830231" />
+ <text
+ xml:space="preserve"
+ style="font-style:normal;font-weight:normal;font-size:12.5px;line-height:125%;font-family:sans-serif;letter-spacing:0px;word-spacing:0px;fill:#000000;fill-opacity:1;stroke:none;stroke-width:1px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1"
+ x="250"
+ y="82.362206"
+ id="text4296"
+ sodipodi:linespacing="125%"><tspan
+ sodipodi:role="line"
+ x="250"
+ y="82.362206"
+ id="tspan12343">ProbesetFreeze</tspan><tspan
+ sodipodi:role="line"
+ x="250"
+ y="97.987206"
+ id="tspan4300" /></text>
+ <text
+ xml:space="preserve"
+ style="font-style:normal;font-weight:normal;font-size:12.5px;line-height:125%;font-family:sans-serif;letter-spacing:0px;word-spacing:0px;fill:#000000;fill-opacity:1;stroke:none;stroke-width:1px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1"
+ x="312.52795"
+ y="102.3622"
+ id="text4302"
+ sodipodi:linespacing="125%"><tspan
+ sodipodi:role="line"
+ x="312.52795"
+ y="102.3622"
+ id="tspan5260">ProbeFreezeId </tspan><tspan
+ sodipodi:role="line"
+ x="312.52795"
+ y="117.9872"
+ id="tspan4308" /><tspan
+ sodipodi:role="line"
+ x="312.52795"
+ y="133.6122"
+ id="tspan4306" /></text>
+ <text
+ xml:space="preserve"
+ style="font-style:normal;font-weight:normal;font-size:12.5px;line-height:125%;font-family:sans-serif;letter-spacing:0px;word-spacing:0px;fill:#000000;fill-opacity:1;stroke:none;stroke-width:1px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1"
+ x="404.24365"
+ y="102.3622"
+ id="text4310"
+ sodipodi:linespacing="125%"><tspan
+ sodipodi:role="line"
+ id="tspan4312"
+ x="404.24365"
+ y="102.3622">Name</tspan><tspan
+ sodipodi:role="line"
+ x="404.24365"
+ y="117.9872"
+ id="tspan4314" /></text>
+ <path
+ style="fill:none"
+ id="path4331"
+ sodipodi:type="arc"
+ sodipodi:cx="415"
+ sodipodi:cy="57.362206"
+ sodipodi:rx="15"
+ sodipodi:ry="15"
+ sodipodi:start="0"
+ sodipodi:end="0.30092023"
+ d="m 430,57.362206 a 15,15 0 0 1 -0.67404,4.445988 L 415,57.362206 Z" />
+ <path
+ style="fill:none"
+ id="path4333"
+ sodipodi:type="arc"
+ sodipodi:cx="415"
+ sodipodi:cy="57.362206"
+ sodipodi:rx="25"
+ sodipodi:ry="5"
+ sodipodi:start="0"
+ sodipodi:end="0.30092094"
+ d="m 440,57.362206 a 25,5 0 0 1 -1.1234,1.481999 L 415,57.362206 Z" />
+ <path
+ style="fill:none"
+ id="path4335"
+ sodipodi:type="arc"
+ sodipodi:cx="400"
+ sodipodi:cy="57.362206"
+ sodipodi:rx="10"
+ sodipodi:ry="15"
+ sodipodi:start="0"
+ sodipodi:end="0.30092094"
+ d="m 410,57.362206 a 10,15 0 0 1 -0.44936,4.445998 L 400,57.362206 Z" />
+ <path
+ style="fill:none"
+ id="path4337"
+ sodipodi:type="arc"
+ sodipodi:cx="336.88586"
+ sodipodi:cy="45.240116"
+ sodipodi:rx="30.304577"
+ sodipodi:ry="1.5152289"
+ sodipodi:start="0"
+ sodipodi:end="0.30092094"
+ d="m 367.19044,45.240116 a 30.304577,1.5152289 0 0 1 -1.36177,0.449114 l -28.94281,-0.449114 z" />
+ <path
+ style="fill:none"
+ id="path4341"
+ sodipodi:type="arc"
+ sodipodi:cx="279.81226"
+ sodipodi:cy="30.592905"
+ sodipodi:rx="10.101525"
+ sodipodi:ry="4.0406103"
+ sodipodi:start="0"
+ sodipodi:end="0.27257505"
+ d="m 289.91378,30.592905 a 10.101525,4.0406103 0 0 1 -0.37294,1.087782 l -9.72858,-1.087782 z" />
+ <path
+ style="fill:none"
+ id="path4343"
+ sodipodi:type="arc"
+ sodipodi:cx="294.96454"
+ sodipodi:cy="47.007885"
+ sodipodi:rx="5.0507627"
+ sodipodi:ry="12.374369"
+ sodipodi:start="0"
+ sodipodi:end="0.27257505"
+ d="m 300.0153,47.007885 a 5.0507627,12.374369 0 0 1 -0.18647,3.331332 l -4.86429,-3.331332 z" />
+ <path
+ style="fill:none"
+ id="path4345"
+ sodipodi:type="arc"
+ sodipodi:cx="314.15744"
+ sodipodi:cy="50.795956"
+ sodipodi:rx="17.172594"
+ sodipodi:ry="2.5253813"
+ sodipodi:start="0"
+ sodipodi:end="0.27257505"
+ d="m 331.33003,50.795956 a 17.172594,2.5253813 0 0 1 -0.63399,0.679863 l -16.5386,-0.679863 z" />
+ <path
+ style="fill:none"
+ id="path4347"
+ sodipodi:type="arc"
+ sodipodi:cx="372.49374"
+ sodipodi:cy="53.573875"
+ sodipodi:rx="36.112953"
+ sodipodi:ry="5.8083773"
+ sodipodi:start="0"
+ sodipodi:end="0.27257505"
+ d="m 408.6067,53.573875 a 36.112953,5.8083773 0 0 1 -1.33326,1.563687 l -34.7797,-1.563687 z" />
+ <path
+ style="opacity:0.92099998;fill:#1df5d5;fill-opacity:1;stroke:#000000;stroke-width:0.05549314;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:0.96610173"
+ id="path4362"
+ sodipodi:type="arc"
+ sodipodi:cx="432.99887"
+ sodipodi:cy="78.632385"
+ sodipodi:rx="26.093044"
+ sodipodi:ry="18.630219"
+ sodipodi:start="0.86050045"
+ sodipodi:end="0.81667097"
+ d="m 450.01305,92.757239 a 26.093044,18.630219 0 0 1 -36.6095,-1.82283 26.093044,18.630219 0 0 1 2.15172,-26.157287 26.093044,18.630219 0 0 1 36.65666,1.249611 26.093044,18.630219 0 0 1 -1.34842,26.184672"
+ sodipodi:open="true" />
+ <text
+ xml:space="preserve"
+ style="font-style:normal;font-weight:normal;font-size:12.5px;line-height:125%;font-family:sans-serif;letter-spacing:0px;word-spacing:0px;fill:#000000;fill-opacity:1;stroke:none;stroke-width:1px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1"
+ x="427.39667"
+ y="80.98439"
+ id="text4412"
+ sodipodi:linespacing="125%"><tspan
+ sodipodi:role="line"
+ id="tspan4414"
+ x="427.39667"
+ y="80.98439">DB</tspan><tspan
+ sodipodi:role="line"
+ x="427.39667"
+ y="96.60939"
+ id="tspan4416" /></text>
+ <rect
+ style="fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:0.63383168px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1"
+ id="rect3357-6-4"
+ width="263.54529"
+ height="30.944864"
+ x="473.30872"
+ y="-76.369919"
+ transform="scale(1,-1)" />
+ <text
+ xml:space="preserve"
+ style="font-style:normal;font-weight:normal;font-size:12.5px;line-height:125%;font-family:sans-serif;letter-spacing:0px;word-spacing:0px;fill:#000000;fill-opacity:1;stroke:none;stroke-width:1px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1"
+ x="475.78186"
+ y="35.138592"
+ id="text5279"
+ sodipodi:linespacing="125%"><tspan
+ sodipodi:role="line"
+ id="tspan5281"
+ x="475.78186"
+ y="35.138592">ProbeFreeze</tspan><tspan
+ sodipodi:role="line"
+ x="475.78186"
+ y="50.763592"
+ id="tspan5283" /></text>
+ <text
+ xml:space="preserve"
+ style="font-style:normal;font-weight:normal;font-size:12.5px;line-height:125%;font-family:sans-serif;letter-spacing:0px;word-spacing:0px;fill:#000000;fill-opacity:1;stroke:none;stroke-width:1px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1"
+ x="481.84277"
+ y="64.433014"
+ id="text5285"
+ sodipodi:linespacing="125%"><tspan
+ sodipodi:role="line"
+ id="tspan5287"
+ x="481.84277"
+ y="64.433014">id</tspan><tspan
+ sodipodi:role="line"
+ x="481.84277"
+ y="80.058014"
+ id="tspan5289" /></text>
+ <text
+ xml:space="preserve"
+ style="font-style:normal;font-weight:normal;font-size:12.5px;line-height:125%;font-family:sans-serif;letter-spacing:0px;word-spacing:0px;fill:#000000;fill-opacity:1;stroke:none;stroke-width:1px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1"
+ x="509.11688"
+ y="64.433014"
+ id="text5291"
+ sodipodi:linespacing="125%"><tspan
+ sodipodi:role="line"
+ id="tspan5293"
+ x="509.11688"
+ y="64.433014">ProbeFreezeId</tspan><tspan
+ sodipodi:role="line"
+ x="509.11688"
+ y="80.058006"
+ id="tspan5295" /></text>
+ <text
+ xml:space="preserve"
+ style="font-style:normal;font-weight:normal;font-size:12.5px;line-height:125%;font-family:sans-serif;letter-spacing:0px;word-spacing:0px;fill:#000000;fill-opacity:1;stroke:none;stroke-width:1px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1"
+ x="616.19305"
+ y="64.433014"
+ id="text5297"
+ sodipodi:linespacing="125%"><tspan
+ sodipodi:role="line"
+ id="tspan5299"
+ x="616.19305"
+ y="64.433014">TissueId</tspan></text>
+ <text
+ xml:space="preserve"
+ style="font-style:normal;font-weight:normal;font-size:12.5px;line-height:125%;font-family:sans-serif;letter-spacing:0px;word-spacing:0px;fill:#000000;fill-opacity:1;stroke:none;stroke-width:1px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1"
+ x="263.64981"
+ y="101.80865"
+ id="text5965"
+ sodipodi:linespacing="125%"><tspan
+ sodipodi:role="line"
+ id="tspan5967"
+ x="263.64981"
+ y="101.80865">id</tspan><tspan
+ sodipodi:role="line"
+ x="263.64981"
+ y="117.43365"
+ id="tspan5969" /></text>
+ <path
+ style="opacity:0.92099998;fill:#1df5d5;fill-opacity:1;stroke:#000000;stroke-width:0.04304412;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:0.96610173"
+ id="path4362-2"
+ sodipodi:type="arc"
+ sodipodi:cx="506.08649"
+ sodipodi:cy="83.625862"
+ sodipodi:rx="20.03821"
+ sodipodi:ry="14.595966"
+ sodipodi:start="0.86050045"
+ sodipodi:end="0.81667097"
+ d="m 519.15256,94.692071 a 20.03821,14.595966 0 0 1 -28.11434,-1.428108 20.03821,14.595966 0 0 1 1.65242,-20.493098 20.03821,14.595966 0 0 1 28.15056,0.979016 20.03821,14.595966 0 0 1 -1.03552,20.514553"
+ sodipodi:open="true" />
+ <text
+ xml:space="preserve"
+ style="font-style:normal;font-weight:normal;font-size:12.5px;line-height:125%;font-family:sans-serif;letter-spacing:0px;word-spacing:0px;fill:#000000;fill-opacity:1;stroke:none;stroke-width:1px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1"
+ x="501.03564"
+ y="86.656364"
+ id="text7497"
+ sodipodi:linespacing="125%"><tspan
+ sodipodi:role="line"
+ id="tspan7499"
+ x="501.03564"
+ y="86.656364">=</tspan></text>
+ <path
+ style="fill:none;fill-rule:evenodd;stroke:#0000a3;stroke-width:2.8;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1;stroke-miterlimit:4;stroke-dasharray:none;marker-end:url(#Arrow2Mend)"
+ d="m 385.87827,117.9711 c 0,0 59.599,62.62946 92.93404,22.22336 30.30457,-42.426411 30.30457,-42.426411 30.30457,-42.426411"
+ id="path11531"
+ inkscape:connector-curvature="0" />
+ <path
+ style="fill:none;fill-rule:evenodd;stroke:#0000da;stroke-width:4.50923538;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1;marker-end:url(#marker11727)"
+ d="M 303.7558,169.72606 71.513981,116.30022"
+ id="path11707"
+ inkscape:connector-curvature="0" />
+ <path
+ style="fill:none;fill-rule:evenodd;stroke:#0000d7;stroke-width:2;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1;stroke-miterlimit:4;stroke-dasharray:none;marker-end:url(#marker12489)"
+ d="m 138.3909,171.50919 130.30968,-59.599"
+ id="path12481"
+ inkscape:connector-curvature="0" />
+ <rect
+ style="fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:0.46889797px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1"
+ id="rect3357-8"
+ width="174.81682"
+ height="25.531101"
+ x="42.901268"
+ y="25.4035" />
+ <text
+ xml:space="preserve"
+ style="font-style:normal;font-weight:normal;font-size:12.5px;line-height:125%;font-family:sans-serif;letter-spacing:0px;word-spacing:0px;fill:#000000;fill-opacity:1;stroke:none;stroke-width:1px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1"
+ x="43.436558"
+ y="17.966"
+ id="text12592"
+ sodipodi:linespacing="125%"><tspan
+ sodipodi:role="line"
+ id="tspan12594"
+ x="43.436558"
+ y="17.966">Strain</tspan><tspan
+ sodipodi:role="line"
+ x="43.436558"
+ y="33.591"
+ id="tspan12596" /></text>
+ <text
+ xml:space="preserve"
+ style="font-style:normal;font-weight:normal;font-size:12.5px;line-height:125%;font-family:sans-serif;letter-spacing:0px;word-spacing:0px;fill:#000000;fill-opacity:1;stroke:none;stroke-width:1px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1"
+ x="55.558392"
+ y="41.199509"
+ id="text12598"
+ sodipodi:linespacing="125%"><tspan
+ sodipodi:role="line"
+ x="55.558392"
+ y="41.199509"
+ id="tspan12610">id</tspan><tspan
+ sodipodi:role="line"
+ x="55.558392"
+ y="56.824509"
+ id="tspan12602" /></text>
+ <text
+ xml:space="preserve"
+ style="font-style:normal;font-weight:normal;font-size:12.5px;line-height:125%;font-family:sans-serif;letter-spacing:0px;word-spacing:0px;fill:#000000;fill-opacity:1;stroke:none;stroke-width:1px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1"
+ x="101.01525"
+ y="40.189354"
+ id="text12604"
+ sodipodi:linespacing="125%"><tspan
+ sodipodi:role="line"
+ id="tspan12606"
+ x="101.01525"
+ y="40.189354">name</tspan><tspan
+ sodipodi:role="line"
+ x="101.01525"
+ y="55.814354"
+ id="tspan12608" /></text>
+ <path
+ style="fill:none;fill-rule:evenodd;stroke:#0000d7;stroke-width:0.96167564;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1;marker-end:url(#marker12489-7)"
+ d="M 108.99621,89.933268 65.230166,45.329821"
+ id="path12481-0"
+ inkscape:connector-curvature="0" />
+ <rect
+ style="fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:0.46889797px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1"
+ id="rect3357-8-7"
+ width="174.81682"
+ height="25.531101"
+ x="40.880962"
+ y="240.56599" />
+ <text
+ xml:space="preserve"
+ style="font-style:normal;font-weight:normal;font-size:12.5px;line-height:125%;font-family:sans-serif;letter-spacing:0px;word-spacing:0px;fill:#000000;fill-opacity:1;stroke:none;stroke-width:1px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1"
+ x="43.436558"
+ y="231.10818"
+ id="text14098"
+ sodipodi:linespacing="125%"><tspan
+ sodipodi:role="line"
+ id="tspan14100"
+ x="43.436558"
+ y="231.10818">ProbeSet</tspan><tspan
+ sodipodi:role="line"
+ x="43.436558"
+ y="246.73318"
+ id="tspan14102" /></text>
+ <text
+ xml:space="preserve"
+ style="font-style:normal;font-weight:normal;font-size:12.5px;line-height:125%;font-family:sans-serif;letter-spacing:0px;word-spacing:0px;fill:#000000;fill-opacity:1;stroke:none;stroke-width:1px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1"
+ x="53.538086"
+ y="257.37213"
+ id="text14104"
+ sodipodi:linespacing="125%"><tspan
+ sodipodi:role="line"
+ x="53.538086"
+ y="257.37213"
+ id="tspan14108">id</tspan></text>
+ <text
+ xml:space="preserve"
+ style="font-style:normal;font-weight:normal;font-size:12.5px;line-height:125%;font-family:sans-serif;letter-spacing:0px;word-spacing:0px;fill:#000000;fill-opacity:1;stroke:none;stroke-width:1px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1"
+ x="90.913734"
+ y="256.362"
+ id="text14112"
+ sodipodi:linespacing="125%"><tspan
+ sodipodi:role="line"
+ x="90.913734"
+ y="256.362"
+ id="tspan14116">name</tspan></text>
+ <text
+ xml:space="preserve"
+ style="font-style:normal;font-weight:normal;font-size:12.5px;line-height:125%;font-family:sans-serif;letter-spacing:0px;word-spacing:0px;fill:#000000;fill-opacity:1;stroke:none;stroke-width:1px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1"
+ x="144.45181"
+ y="255.35185"
+ id="text14120"
+ sodipodi:linespacing="125%"><tspan
+ sodipodi:role="line"
+ x="144.45181"
+ y="255.35185"
+ id="tspan14124">many infos</tspan></text>
+ <path
+ style="fill:none;fill-rule:evenodd;stroke:#0000d7;stroke-width:1.89054883;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1;marker-end:url(#marker12489-7-2)"
+ d="M 72.019909,251.65943 208.39464,196.3512"
+ id="path12481-0-6"
+ inkscape:connector-curvature="0"
+ inkscape:transform-center-x="-32.453094"
+ inkscape:transform-center-y="114.65633" />
+ <text
+ xml:space="preserve"
+ style="font-style:normal;font-weight:normal;font-size:12.5px;line-height:125%;font-family:sans-serif;letter-spacing:0px;word-spacing:0px;fill:#000000;fill-opacity:1;stroke:none;stroke-width:1px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1"
+ x="150.51273"
+ y="40.18935"
+ id="text3465"
+ sodipodi:linespacing="125%"><tspan
+ sodipodi:role="line"
+ id="tspan3467"
+ x="150.51273"
+ y="40.18935">speciesid</tspan><tspan
+ sodipodi:role="line"
+ x="150.51273"
+ y="55.81435"
+ id="tspan3469" /></text>
+ </g>
+</svg>
diff --git a/test/lib/NavigationTest.rb b/test/lib/NavigationTest.rb
new file mode 100644
index 00000000..26080d28
--- /dev/null
+++ b/test/lib/NavigationTest.rb
@@ -0,0 +1,46 @@
+# In these tests we navigate from the main page to a specific trait then hit the different mapping tool buttons (In this case pylMM and r/qtl) followed by computing the results (marker regressions).
+
+class NavigationTest
+end
+
+describe NavigationTest do
+ before do
+ @agent = Mechanize.new
+ @agent.agent.http.ca_file = '/etc/ssl/certs/ca-certificates.crt'
+ end
+
+ describe NavigationTest do
+ it "pyLMM mapping tool selection" do
+ page = @agent.get($host+'/show_trait?trait_id=1435395_s_at&dataset=HC_M2_0606_P')
+#Navigates to http://localhost:5003/show_trait?trait_id=1435395_s_at&dataset=HC_M2_0606_P and clicks respective buttons.
+ link = page.link_with(text: 'pyLMM')
+ page = link.click
+ puts page.uri
+ link = page.link_with(text: 'Compute')
+ page = link.click
+ puts page.uri
+ probe_link.uri.to_s.must_equal "/marker_regression"
+
+
+ end
+ end
+
+end
+
+describe NavigationTest do
+ it "R/qtl mapping tool selection" do
+ page = @agent.get($host+'/show_trait?trait_id=1435395_s_at&dataset=HC_M2_0606_P')
+ link = page.link_with(text: 'R/qtl')
+ page = link.click
+ puts page.uri
+ form.field_with(:name => 'Methods').options[2].select
+ link = page.link_with(text: 'Compute')
+ page = link.click
+ puts page.uri
+ probe_link.uri.to_s.must_equal "/marker_regression"
+
+
+ end
+ end
+
+
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-21 19:40:09 +0000