diff --git a/datatypes_conf.xml.sample b/datatypes_conf.xml.sample
index 59d7e438f46..8c6548f4728 100644
--- a/datatypes_conf.xml.sample
+++ b/datatypes_conf.xml.sample
@@ -162,9 +162,9 @@
-
+
-
+
diff --git a/test-data/rgenetics.bed b/test-data/rgenetics.bed
new file mode 100644
index 00000000000..db1c51170dc
--- /dev/null
+++ b/test-data/rgenetics.bed
@@ -0,0 +1 @@
+lÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿï¾î¸ÿÿüþ¿ÿ¿ûú¿¿ï/ÿÿþÿ﯎ê¸ëê°®¾î®ãê¸;ì/âïú¯ï¯Îê¼ïâ°¯þϪã¯ø+ì?âÿú¯ïëÿî¾ÿºþÿþ¯þï¿ÿ;ï?þÿÿÿïÿÿÿÿÿºÿÿþ¯þï¿ÿ»ÿÿþÿÿÿïëÿî¾ÿºþÿþ¯þï¿ÿ;ï?þÿÿÿÿÿÿÿþïÿÿÿþÿÿÿÿûÿûÿÿÿ»ÿïëÿî¾ÿºþÿþ¯þï¿ÿ;ï?þÿÿÿïëÿê¾ÿºúïþ¯îë¿þ;¯>âïþ»
\ No newline at end of file
diff --git a/test-data/rgenetics.bim b/test-data/rgenetics.bim
new file mode 100644
index 00000000000..bc4e0190bc9
--- /dev/null
+++ b/test-data/rgenetics.bim
@@ -0,0 +1,10 @@
+22 rs5992809 16.5965 16596539 0 C
+22 rs12168131 16.6573 16657262 G A
+22 rs390041 16.6629 16662916 T C
+22 rs437633 16.6697 16669684 A G
+22 rs450960 16.6909 16690858 T C
+22 rs450975 16.6909 16690887 T C
+22 rs451740 16.6912 16691174 T C
+22 rs8139723 16.6917 16691696 T C
+22 rs405490 16.6922 16692175 G A
+22 rs415170 16.6935 16693517 G C
diff --git a/test-data/rgenetics.fam b/test-data/rgenetics.fam
new file mode 100644
index 00000000000..5afdbe59307
--- /dev/null
+++ b/test-data/rgenetics.fam
@@ -0,0 +1,90 @@
+CH18526 NA18526 0 0 2 1
+CH18524 NA18524 0 0 1 1
+CH18529 NA18529 0 0 2 1
+CH18558 NA18558 0 0 1 1
+CH18532 NA18532 0 0 2 1
+CH18561 NA18561 0 0 1 1
+CH18562 NA18562 0 0 1 1
+CH18537 NA18537 0 0 2 2
+CH18603 NA18603 0 0 1 2
+CH18540 NA18540 0 0 2 1
+CH18605 NA18605 0 0 1 1
+CH18542 NA18542 0 0 2 1
+CH18545 NA18545 0 0 2 1
+CH18572 NA18572 0 0 1 2
+CH18547 NA18547 0 0 2 2
+CH18609 NA18609 0 0 1 1
+CH18550 NA18550 0 0 2 1
+CH18608 NA18608 0 0 1 1
+CH18552 NA18552 0 0 2 1
+CH18611 NA18611 0 0 1 1
+CH18555 NA18555 0 0 2 1
+CH18564 NA18564 0 0 2 2
+CH18566 NA18566 0 0 2 1
+CH18563 NA18563 0 0 1 1
+CH18570 NA18570 0 0 2 1
+CH18612 NA18612 0 0 1 2
+CH18571 NA18571 0 0 2 1
+CH18620 NA18620 0 0 1 1
+CH18621 NA18621 0 0 1 1
+CH18594 NA18594 0 0 2 1
+CH18622 NA18622 0 0 1 2
+CH18573 NA18573 0 0 2 2
+CH18623 NA18623 0 0 1 1
+CH18576 NA18576 0 0 2 1
+CH18577 NA18577 0 0 2 1
+CH18624 NA18624 0 0 1 1
+CH18579 NA18579 0 0 2 1
+CH18632 NA18632 0 0 1 2
+CH18582 NA18582 0 0 2 1
+CH18633 NA18633 0 0 1 1
+CH18635 NA18635 0 0 1 2
+CH18592 NA18592 0 0 2 1
+CH18636 NA18636 0 0 1 1
+CH18593 NA18593 0 0 2 2
+CH18637 NA18637 0 0 1 1
+JA18942 NA18942 0 0 2 2
+JA18940 NA18940 0 0 1 2
+JA18951 NA18951 0 0 2 2
+JA18943 NA18943 0 0 1 2
+JA18947 NA18947 0 0 2 2
+JA18944 NA18944 0 0 1 2
+JA18945 NA18945 0 0 1 2
+JA18949 NA18949 0 0 2 2
+JA18948 NA18948 0 0 1 2
+JA18952 NA18952 0 0 1 2
+JA18956 NA18956 0 0 2 2
+JA18964 NA18964 0 0 2 2
+JA18953 NA18953 0 0 1 1
+JA18968 NA18968 0 0 2 2
+JA18959 NA18959 0 0 1 2
+JA18969 NA18969 0 0 2 1
+JA18960 NA18960 0 0 1 2
+JA18961 NA18961 0 0 1 2
+JA18972 NA18972 0 0 2 2
+JA18965 NA18965 0 0 1 2
+JA18973 NA18973 0 0 2 2
+JA18966 NA18966 0 0 1 2
+JA18975 NA18975 0 0 2 2
+JA18967 NA18967 0 0 1 2
+JA18976 NA18976 0 0 2 1
+JA18978 NA18978 0 0 2 2
+JA18970 NA18970 0 0 1 1
+JA18980 NA18980 0 0 2 2
+JA18995 NA18995 0 0 1 1
+JA18981 NA18981 0 0 2 2
+JA18971 NA18971 0 0 1 2
+JA18974 NA18974 0 0 1 1
+JA18987 NA18987 0 0 2 2
+JA18990 NA18990 0 0 1 1
+JA18991 NA18991 0 0 2 2
+JA18994 NA18994 0 0 1 2
+JA18992 NA18992 0 0 2 2
+JA18997 NA18997 0 0 2 2
+JA18998 NA18998 0 0 2 2
+JA19000 NA19000 0 0 1 2
+JA19005 NA19005 0 0 1 2
+JA18999 NA18999 0 0 2 2
+JA19007 NA19007 0 0 1 2
+JA19003 NA19003 0 0 2 2
+JA19012 NA19012 0 0 1 2
diff --git a/test-data/tinywga.bed b/test-data/tinywga.bed
new file mode 100644
index 00000000000..db1c51170dc
--- /dev/null
+++ b/test-data/tinywga.bed
@@ -0,0 +1 @@
+lÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿï¾î¸ÿÿüþ¿ÿ¿ûú¿¿ï/ÿÿþÿ﯎ê¸ëê°®¾î®ãê¸;ì/âïú¯ï¯Îê¼ïâ°¯þϪã¯ø+ì?âÿú¯ïëÿî¾ÿºþÿþ¯þï¿ÿ;ï?þÿÿÿïÿÿÿÿÿºÿÿþ¯þï¿ÿ»ÿÿþÿÿÿïëÿî¾ÿºþÿþ¯þï¿ÿ;ï?þÿÿÿÿÿÿÿþïÿÿÿþÿÿÿÿûÿûÿÿÿ»ÿïëÿî¾ÿºþÿþ¯þï¿ÿ;ï?þÿÿÿïëÿê¾ÿºúïþ¯îë¿þ;¯>âïþ»
\ No newline at end of file
diff --git a/test-data/tinywga.bim b/test-data/tinywga.bim
new file mode 100644
index 00000000000..bc4e0190bc9
--- /dev/null
+++ b/test-data/tinywga.bim
@@ -0,0 +1,10 @@
+22 rs5992809 16.5965 16596539 0 C
+22 rs12168131 16.6573 16657262 G A
+22 rs390041 16.6629 16662916 T C
+22 rs437633 16.6697 16669684 A G
+22 rs450960 16.6909 16690858 T C
+22 rs450975 16.6909 16690887 T C
+22 rs451740 16.6912 16691174 T C
+22 rs8139723 16.6917 16691696 T C
+22 rs405490 16.6922 16692175 G A
+22 rs415170 16.6935 16693517 G C
diff --git a/test-data/tinywga.fam b/test-data/tinywga.fam
new file mode 100644
index 00000000000..5afdbe59307
--- /dev/null
+++ b/test-data/tinywga.fam
@@ -0,0 +1,90 @@
+CH18526 NA18526 0 0 2 1
+CH18524 NA18524 0 0 1 1
+CH18529 NA18529 0 0 2 1
+CH18558 NA18558 0 0 1 1
+CH18532 NA18532 0 0 2 1
+CH18561 NA18561 0 0 1 1
+CH18562 NA18562 0 0 1 1
+CH18537 NA18537 0 0 2 2
+CH18603 NA18603 0 0 1 2
+CH18540 NA18540 0 0 2 1
+CH18605 NA18605 0 0 1 1
+CH18542 NA18542 0 0 2 1
+CH18545 NA18545 0 0 2 1
+CH18572 NA18572 0 0 1 2
+CH18547 NA18547 0 0 2 2
+CH18609 NA18609 0 0 1 1
+CH18550 NA18550 0 0 2 1
+CH18608 NA18608 0 0 1 1
+CH18552 NA18552 0 0 2 1
+CH18611 NA18611 0 0 1 1
+CH18555 NA18555 0 0 2 1
+CH18564 NA18564 0 0 2 2
+CH18566 NA18566 0 0 2 1
+CH18563 NA18563 0 0 1 1
+CH18570 NA18570 0 0 2 1
+CH18612 NA18612 0 0 1 2
+CH18571 NA18571 0 0 2 1
+CH18620 NA18620 0 0 1 1
+CH18621 NA18621 0 0 1 1
+CH18594 NA18594 0 0 2 1
+CH18622 NA18622 0 0 1 2
+CH18573 NA18573 0 0 2 2
+CH18623 NA18623 0 0 1 1
+CH18576 NA18576 0 0 2 1
+CH18577 NA18577 0 0 2 1
+CH18624 NA18624 0 0 1 1
+CH18579 NA18579 0 0 2 1
+CH18632 NA18632 0 0 1 2
+CH18582 NA18582 0 0 2 1
+CH18633 NA18633 0 0 1 1
+CH18635 NA18635 0 0 1 2
+CH18592 NA18592 0 0 2 1
+CH18636 NA18636 0 0 1 1
+CH18593 NA18593 0 0 2 2
+CH18637 NA18637 0 0 1 1
+JA18942 NA18942 0 0 2 2
+JA18940 NA18940 0 0 1 2
+JA18951 NA18951 0 0 2 2
+JA18943 NA18943 0 0 1 2
+JA18947 NA18947 0 0 2 2
+JA18944 NA18944 0 0 1 2
+JA18945 NA18945 0 0 1 2
+JA18949 NA18949 0 0 2 2
+JA18948 NA18948 0 0 1 2
+JA18952 NA18952 0 0 1 2
+JA18956 NA18956 0 0 2 2
+JA18964 NA18964 0 0 2 2
+JA18953 NA18953 0 0 1 1
+JA18968 NA18968 0 0 2 2
+JA18959 NA18959 0 0 1 2
+JA18969 NA18969 0 0 2 1
+JA18960 NA18960 0 0 1 2
+JA18961 NA18961 0 0 1 2
+JA18972 NA18972 0 0 2 2
+JA18965 NA18965 0 0 1 2
+JA18973 NA18973 0 0 2 2
+JA18966 NA18966 0 0 1 2
+JA18975 NA18975 0 0 2 2
+JA18967 NA18967 0 0 1 2
+JA18976 NA18976 0 0 2 1
+JA18978 NA18978 0 0 2 2
+JA18970 NA18970 0 0 1 1
+JA18980 NA18980 0 0 2 2
+JA18995 NA18995 0 0 1 1
+JA18981 NA18981 0 0 2 2
+JA18971 NA18971 0 0 1 2
+JA18974 NA18974 0 0 1 1
+JA18987 NA18987 0 0 2 2
+JA18990 NA18990 0 0 1 1
+JA18991 NA18991 0 0 2 2
+JA18994 NA18994 0 0 1 2
+JA18992 NA18992 0 0 2 2
+JA18997 NA18997 0 0 2 2
+JA18998 NA18998 0 0 2 2
+JA19000 NA19000 0 0 1 2
+JA19005 NA19005 0 0 1 2
+JA18999 NA18999 0 0 2 2
+JA19007 NA19007 0 0 1 2
+JA19003 NA19003 0 0 2 2
+JA19012 NA19012 0 0 1 2
diff --git a/test-data/tinywga.map b/test-data/tinywga.map
new file mode 100644
index 00000000000..3357e68b3ec
--- /dev/null
+++ b/test-data/tinywga.map
@@ -0,0 +1,10 @@
+22 rs5992809 16.5965 16596539
+22 rs12168131 16.6573 16657262
+22 rs390041 16.6629 16662916
+22 rs437633 16.6697 16669684
+22 rs450960 16.6909 16690858
+22 rs450975 16.6909 16690887
+22 rs451740 16.6912 16691174
+22 rs8139723 16.6917 16691696
+22 rs405490 16.6922 16692175
+22 rs415170 16.6935 16693517
diff --git a/test-data/tinywga.ped b/test-data/tinywga.ped
new file mode 100644
index 00000000000..5972aade279
--- /dev/null
+++ b/test-data/tinywga.ped
@@ -0,0 +1,90 @@
+CH18526 NA18526 0 0 2 1 C C A A C C G G C C C C C C C C A A C C
+CH18524 NA18524 0 0 1 1 C C A A C C G G C C C C C C C C A A C C
+CH18529 NA18529 0 0 2 1 C C A A T C A G T C T C T C C C G A G C
+CH18558 NA18558 0 0 1 1 C C A A C C G G C C C C C C C C A A C C
+CH18532 NA18532 0 0 2 1 C C A A C C G G C C C C C C C C A A C C
+CH18561 NA18561 0 0 1 1 C C A A C C G G T C C C T C C C G A G C
+CH18562 NA18562 0 0 1 1 C C G A T C A G T C C C T C C C G A G C
+CH18537 NA18537 0 0 2 2 C C A A T C A G C C C C C C C C A A C C
+CH18603 NA18603 0 0 1 2 C C G A T C A G C C C C C C C C A A C C
+CH18540 NA18540 0 0 2 1 C C A A C C G G C C C C C C C C A A C C
+CH18605 NA18605 0 0 1 1 C C A A T T A A C C C C C C C C A A C C
+CH18542 NA18542 0 0 2 1 C C G A T C G G C C C C C C C C A A C C
+CH18545 NA18545 0 0 2 1 C C G A T C A G T C C C T C C C G A G C
+CH18572 NA18572 0 0 1 2 C C A A T C A G C C C C C C C C A A G C
+CH18547 NA18547 0 0 2 2 C C G A T C A G T C C C T C C C G A G C
+CH18609 NA18609 0 0 1 1 C C A A C C G G C C C C C C C C A A C C
+CH18550 NA18550 0 0 2 1 C C G G T T A A T C C C T C T C G A G C
+CH18608 NA18608 0 0 1 1 C C G A T C G G C C C C C C C C A A C C
+CH18552 NA18552 0 0 2 1 C C A A C C G G C C C C C C C C A A C C
+CH18611 NA18611 0 0 1 1 C C G A T C A G T C C C T C C C G A G C
+CH18555 NA18555 0 0 2 1 C C A A C C G G C C C C C C C C A A C C
+CH18564 NA18564 0 0 2 2 C C A A T C G G C C C C C C C C A A C C
+CH18566 NA18566 0 0 2 1 C C A A T C A G C C C C C C T C A A C C
+CH18563 NA18563 0 0 1 1 C C A A C C G G C C C C C C C C A A C C
+CH18570 NA18570 0 0 2 1 C C A A T C A G T C T C T C C C G A G C
+CH18612 NA18612 0 0 1 2 C C A A T C A A T C T C T C C C G A G C
+CH18571 NA18571 0 0 2 1 C C A A T C A G C C C C C C C C A A C C
+CH18620 NA18620 0 0 1 1 C C A A C C G G T C T C T C C C G A G C
+CH18621 NA18621 0 0 1 1 C C G G T T A A T C C C T C C C G A G C
+CH18594 NA18594 0 0 2 1 C C A A T T A A C C C C C C C C A A G C
+CH18622 NA18622 0 0 1 2 C C A A C C G G C C C C C C C C A A C C
+CH18573 NA18573 0 0 2 2 C C A A T C A G C C C C C C C C A A C C
+CH18623 NA18623 0 0 1 1 C C G A T C G G C C C C C C C C A A C C
+CH18576 NA18576 0 0 2 1 C C A A C C G G C C C C C C C C A A C C
+CH18577 NA18577 0 0 2 1 C C A A T C A G C C C C C C C C A A G C
+CH18624 NA18624 0 0 1 1 C C A A T C A G C C C C C C C C A A C C
+CH18579 NA18579 0 0 2 1 C C A A T C A G T C T C T C T C G A G C
+CH18632 NA18632 0 0 1 2 C C A A C C G G C C C C C C C C A A C C
+CH18582 NA18582 0 0 2 1 C C A A C C G G C C C C C C C C A A C C
+CH18633 NA18633 0 0 1 1 C C G A T C G G C C C C C C C C A A C C
+CH18635 NA18635 0 0 1 2 C C A A T C G G C C C C C C C C A A C C
+CH18592 NA18592 0 0 2 1 C C A A C C G G C C C C C C C C A A C C
+CH18636 NA18636 0 0 1 1 C C A A T C A A T C T C T C C C G A G C
+CH18593 NA18593 0 0 2 2 C C A A C C G G T C T C T C C C G A G C
+CH18637 NA18637 0 0 1 1 C C A A T C A G T C T C T C C C G A G C
+JA18942 NA18942 0 0 2 2 C C A A C C A G C C C C C C C C A A C C
+JA18940 NA18940 0 0 1 2 C C A A T C A G C C C C C C C C A A G C
+JA18951 NA18951 0 0 2 2 C C G A T C A G C C C C C C C C A A C C
+JA18943 NA18943 0 0 1 2 C C A A C C G G C C C C C C C C A A C C
+JA18947 NA18947 0 0 2 2 C C G A T T A A C C C C C C C C A A G C
+JA18944 NA18944 0 0 1 2 C C A A T C A G T C T C T C C C G A G C
+JA18945 NA18945 0 0 1 2 C C A A C C G G C C C C C C C C A A C C
+JA18949 NA18949 0 0 2 2 C C G A T C G G C C C C C C C C A A C C
+JA18948 NA18948 0 0 1 2 C C G A T C G G C C C C C C C C A A C C
+JA18952 NA18952 0 0 1 2 C C A A T C A G C C C C C C C C A A C C
+JA18956 NA18956 0 0 2 2 C C A A C C A G T C T C T C C C G A G C
+JA18964 NA18964 0 0 2 2 C C A A T T A A C C C C C C C C A A G C
+JA18953 NA18953 0 0 1 1 C C A A T C A G C C C C C C T C A A C C
+JA18968 NA18968 0 0 2 2 C C A A C C G G C C C C C C C C A A C C
+JA18959 NA18959 0 0 1 2 C C G A T C G G C C C C C C C C A A C C
+JA18969 NA18969 0 0 2 1 C C A A C C G G C C C C C C C C A A C C
+JA18960 NA18960 0 0 1 2 C C A A T C A G T C T C T C C C G A G C
+JA18961 NA18961 0 0 1 2 C C A A C C A G C C C C C C C C A A C C
+JA18972 NA18972 0 0 2 2 C C G A T T A A T T T C T T C C G G G G
+JA18965 NA18965 0 0 1 2 C C A A T T A A C C C C C C C C A A C C
+JA18973 NA18973 0 0 2 2 C C A A C C G G C C C C C C T C A A C C
+JA18966 NA18966 0 0 1 2 C C G A T C A G T C C C T C C C G A G C
+JA18975 NA18975 0 0 2 2 C C A A C C G G C C C C C C C C A A G C
+JA18967 NA18967 0 0 1 2 C C A A C C G G C C C C C C C C A A G C
+JA18976 NA18976 0 0 2 1 C C A A C C G G C C C C C C C C A A C C
+JA18978 NA18978 0 0 2 2 C C G A T C G G C C C C C C C C A A C C
+JA18970 NA18970 0 0 1 1 C C G G T T A A T T C C T T C C G G G G
+JA18980 NA18980 0 0 2 2 C C A A T C A G T C T C T C C C G A G C
+JA18995 NA18995 0 0 1 1 C C A A T T A A C C C C C C C C A A G G
+JA18981 NA18981 0 0 2 2 C C A A T C A G C C C C C C C C A A G C
+JA18971 NA18971 0 0 1 2 C C A A C C G G C C C C C C C C A A C C
+JA18974 NA18974 0 0 1 1 C C A A C C G G C C C C C C C C A A C C
+JA18987 NA18987 0 0 2 2 C C A A C C G G C C C C C C C C A A C C
+JA18990 NA18990 0 0 1 1 C C A A T C G G C C C C C C C C A A G C
+JA18991 NA18991 0 0 2 2 C C A A C C G G C C C C C C C C A A C C
+JA18994 NA18994 0 0 1 2 C C G A T C A G C C C C C C C C A A G C
+JA18992 NA18992 0 0 2 2 C C A A T C A G C C C C C C T C A A C C
+JA18997 NA18997 0 0 2 2 C C A A C C G G C C C C C C C C A A C C
+JA18998 NA18998 0 0 2 2 C C A A C C G G C C C C C C T C A A C C
+JA19000 NA19000 0 0 1 2 C C A A C C G G C C C C C C C C A A C C
+JA19005 NA19005 0 0 1 2 C C A A C C G G C C C C C C C C A A G C
+JA18999 NA18999 0 0 2 2 C C A A T C A G C C C C C C C C A A C C
+JA19007 NA19007 0 0 1 2 C C A A T C A G C C C C C C C C A A G C
+JA19003 NA19003 0 0 2 2 C C A A T C G G C C C C C C C C A A C C
+JA19012 NA19012 0 0 1 2 C C A A 0 0 G G C C C C C C 0 0 A A C C
diff --git a/test/base/twilltestcase.py b/test/base/twilltestcase.py
index 08532c1deb2..7afcf662453 100644
--- a/test/base/twilltestcase.py
+++ b/test/base/twilltestcase.py
@@ -83,7 +83,7 @@ class TwillTestCase( unittest.TestCase ):
tc.submit("runtool_btn")
self.home()
except AssertionError, err:
- errmsg = "The file (%s) doesn't exist." % filename
+ errmsg = "Uploading file resulted in the following exception. Make sure the file (%s) exists. " % filename
errmsg += str( err )
raise AssertionError( errmsg )
# Make sure every history item has a valid hid
@@ -116,7 +116,36 @@ class TwillTestCase( unittest.TestCase ):
raise AssertionError, "Invalid hid (%s) created when pasting %s" % ( hid, url_paste )
# Wait for upload processing to finish (TODO: this should be done in each test case instead)
self.wait()
-
+ def upload_composite_datatype_file( self, ftype, ped_file='', map_file='', bim_file='', bed_file='', fam_file='', dbkey='unspecified (?)', base_name='rgenetics' ):
+ """Tests uploading either of 2 different composite data types ( lped and pbed )"""
+ self.visit_url( "%s/tool_runner/index?tool_id=upload1" % self.url )
+ # Handle refresh_on_change
+ self.refresh_form( "file_type", ftype )
+ tc.fv( "1", "dbkey", dbkey )
+ tc.fv( "1", "files_metadata|base_name", base_name )
+ if ftype == 'lped':
+ # lped data types include a ped_file and a map_file
+ ped_file = self.get_filename( ped_file )
+ tc.formfile( "1", "files_0|file_data", ped_file )
+ map_file = self.get_filename( map_file )
+ tc.formfile( "1", "files_1|file_data", map_file )
+ elif ftype == 'pbed':
+ # pbed data types include a bim_file, a bed_file and a fam_file
+ bim_file = self.get_filename( bim_file )
+ tc.formfile( "1", "files_0|file_data", bim_file )
+ bed_file = self.get_filename( bed_file )
+ tc.formfile( "1", "files_1|file_data", bed_file )
+ fam_file = self.get_filename( fam_file )
+ tc.formfile( "1", "files_2|file_data", fam_file )
+ else:
+ raise AssertionError, "Unsupported composite data type (%s) received, currently only lped and pbed data types are supported." % ftype
+ tc.submit( "runtool_btn" )
+ self.check_page_for_string( 'The following job has been succesfully added to the queue:' )
+ check_str = 'Uploaded Composite Dataset (%s)' % ftype
+ self.check_page_for_string( check_str )
+ # Wait for upload processing to finish (TODO: this should be done in each test case instead)
+ self.wait()
+ self.check_history_for_string( check_str )
# Functions associated with histories
def check_history_for_errors( self ):
"""Raises an exception if there are errors in a history"""
@@ -522,7 +551,20 @@ class TwillTestCase( unittest.TestCase ):
errmsg += str( err )
raise AssertionError( errmsg )
os.remove(temp_name)
-
+ def verify_composite_datatype_file_content( self, file_name, hda_id ):
+ local_name = self.get_filename( file_name )
+ temp_name = self.get_filename( 'temp_%s' % file_name )
+ self.visit_url( "%s/datasets/%s/display/%s" % ( self.url, hda_id, file_name ) )
+ data = self.last_page()
+ file( temp_name, 'wb' ).write( data )
+ try:
+ self.files_diff( local_name, temp_name )
+ except AssertionError, err:
+ os.remove( temp_name )
+ errmsg = 'History item %s different than expected, difference:\n' % str( hda_id )
+ errmsg += str( err )
+ raise AssertionError( errmsg )
+ os.remove( temp_name )
def is_zipped( self, filename ):
if not zipfile.is_zipfile( filename ):
return False
@@ -722,7 +764,29 @@ class TwillTestCase( unittest.TestCase ):
# Add conditions for other control types here when necessary.
pass
tc.submit( button )
-
+ def refresh_form( self, control_name, value, form_no=0, **kwd ):
+ """Handles Galaxy's refresh_on_change for forms without ultimately submitting the form"""
+ # control_name is the name of the form field that requires refresh_on_change, and value is
+ # the value to which that field is being set.
+ for i, f in enumerate( self.showforms() ):
+ if i == form_no:
+ break
+ try:
+ control = f.find_control( name=control_name )
+ except:
+ # This assumes we always want the first control of the given name, which may not be ideal...
+ control = f.find_control( name=control_name, nr=0 )
+ # Check for refresh_on_change attribute, submit a change if required
+ if 'refresh_on_change' in control.attrs.keys():
+ # Clear Control and set to proper value
+ control.clear()
+ tc.fv( f.name, control.name, value )
+ # Create a new submit control, allows form to refresh, instead of going to next page
+ control = ClientForm.SubmitControl( 'SubmitControl', '___refresh_grouping___', {'name':'refresh_grouping'} )
+ control.add_to_form( f )
+ control.fixup()
+ # Submit for refresh
+ tc.submit( '___refresh_grouping___' )
def visit_page( self, page ):
# tc.go("./%s" % page)
if not page.startswith( "/" ):
diff --git a/test/functional/test_get_data.py b/test/functional/test_get_data.py
index a843b4d2167..835a255f112 100644
--- a/test/functional/test_get_data.py
+++ b/test/functional/test_get_data.py
@@ -45,6 +45,7 @@ class UploadData( TwillTestCase ):
self.delete_history( id=self.security.encode_id( history1.id ) )
def test_005_url_paste( self ):
"""Test url paste behavior"""
+ # Logged in as admin_user
# Deleting the current history should have created a new history
self.check_history_for_string( 'Your history is empty' )
history2 = galaxy.model.History.filter( and_( galaxy.model.History.table.c.deleted==False,
@@ -57,3 +58,38 @@ class UploadData( TwillTestCase ):
self.check_history_for_string( 'Pasted Entry' )
self.check_history_for_string( 'hello world' )
self.delete_history( id=self.security.encode_id( history2.id ) )
+ def test_010_upload_lped_composite_datatype_files( self ):
+ """Test uploading lped composite datatype files"""
+ # Logged in as admin_user
+ self.check_history_for_string( 'Your history is empty' )
+ history3 = galaxy.model.History.filter( and_( galaxy.model.History.table.c.deleted==False,
+ galaxy.model.History.table.c.user_id==admin_user.id ) ) \
+ .order_by( desc( galaxy.model.History.table.c.create_time ) ).first()
+ # lped data types include a ped_file and a map_file ( which is binary )
+ self.upload_composite_datatype_file( 'lped', ped_file='tinywga.ped', map_file='tinywga.map', base_name='rgenetics' )
+ # Get the latest hid for testing
+ hda1 = galaxy.model.HistoryDatasetAssociation.query() \
+ .order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ).first()
+ assert hda1 is not None, "Problem retrieving hda1 from database"
+ # We'll test against the resulting ped file and map file for correctness
+ self.verify_composite_datatype_file_content( 'rgenetics.ped', str( hda1.id ) )
+ self.verify_composite_datatype_file_content( 'rgenetics.map', str( hda1.id ) )
+ self.delete_history( id=self.security.encode_id( history3.id ) )
+ def test_015_upload_pbed_composite_datatype_files( self ):
+ """Test uploading pbed composite datatype files"""
+ # Logged in as admin_user
+ self.check_history_for_string( 'Your history is empty' )
+ history4 = galaxy.model.History.filter( and_( galaxy.model.History.table.c.deleted==False,
+ galaxy.model.History.table.c.user_id==admin_user.id ) ) \
+ .order_by( desc( galaxy.model.History.table.c.create_time ) ).first()
+ # pbed data types include a bim_file, a bed_file and a fam_file
+ self.upload_composite_datatype_file( 'pbed', bim_file='tinywga.bim', bed_file='tinywga.bed', fam_file='tinywga.fam', base_name='rgenetics' )
+ # Get the latest hid for testing
+ hda1 = galaxy.model.HistoryDatasetAssociation.query() \
+ .order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ).first()
+ assert hda1 is not None, "Problem retrieving hda1 from database"
+ # We'll test against the resulting ped file and map file for correctness
+ self.verify_composite_datatype_file_content( 'rgenetics.bim', str( hda1.id ) )
+ self.verify_composite_datatype_file_content( 'rgenetics.bed', str( hda1.id ) )
+ self.verify_composite_datatype_file_content( 'rgenetics.fam', str( hda1.id ) )
+ self.delete_history( id=self.security.encode_id( history4.id ) )