1. RGMQL
  2. NAMESPACE
Browse code

added logic to handle remote dataset, change name

Simone authored on 13/05/2021 14:35:27
Showing 1 changed files
NAMESPACE
History View file @ b15d477
... ... 
@@ -52,6 +52,7 @@ export(sample_region)
52 52 
 export(save_query)
53 53 
 export(save_query_fromfile)
54 54 
 export(semijoin)
55 
+export(show_all_metadata)
55 56 
 export(show_datasets_list)
56 57 
 export(show_job_log)
57 58 
 export(show_jobs_list)
Browse code

update with some news

Simone authored on 21/03/2021 14:34:30
Showing 1 changed files
NAMESPACE
History View file @ 73652f4
1 1 
old mode 100644
2 2 
new mode 100755
... ... 
@@ -14,6 +14,7 @@ export(DGE)
14 14 
 export(DL)
15 15 
 export(DLE)
16 16 
 export(DOWN)
17 
+export(FULL)
17 18 
 export(MAX)
18 19 
 export(MD)
19 20 
 export(MEDIAN)
Browse code

The GMQLDataset class does not need to extend DataTable

Virtual class DataTable will be removed from the S4Vectors package
in the near future.

Hervé Pagès authored on 02/05/2020 09:03:41
Showing 1 changed files
NAMESPACE
History View file @ 278508b
... ... 
@@ -79,7 +79,6 @@ import(RGMQLlib)
79 79 
 import(httr)
80 80 
 import(xml2)
81 81 
 importClassesFrom(GenomicRanges,GRangesList)
82 
-importClassesFrom(S4Vectors,DataTable)
83 82 
 importFrom(BiocGenerics,setdiff)
84 83 
 importFrom(BiocGenerics,union)
85 84 
 importFrom(GenomicRanges,GRangesList)
Browse code

fix and register

Simone authored on 25/01/2018 10:37:53
Showing 1 changed files
NAMESPACE
History View file @ 13c0781
... ... 
@@ -42,6 +42,7 @@ export(login_gmql)
42 42 
 export(logout_gmql)
43 43 
 export(read_GRangesList)
44 44 
 export(read_gmql)
45 
+export(register_gmql)
45 46 
 export(remote_processing)
46 47 
 export(run_query)
47 48 
 export(run_query_fromfile)
Browse code

minor fix

Simone authored on 11/01/2018 13:10:15
Showing 1 changed files
NAMESPACE
History View file @ 1869707
... ... 
@@ -40,8 +40,8 @@ export(import_gmql)
40 40 
 export(init_gmql)
41 41 
 export(login_gmql)
42 42 
 export(logout_gmql)
43 
-export(read_GMQL)
44 43 
 export(read_GRangesList)
44 
+export(read_gmql)
45 45 
 export(remote_processing)
46 46 
 export(run_query)
47 47 
 export(run_query_fromfile)
Browse code

check fix

Simone authored on 03/01/2018 11:26:05
Showing 1 changed files
NAMESPACE
History View file @ 2f53c9a
... ... 
@@ -74,7 +74,7 @@ exportMethods(setdiff)
74 74 
 exportMethods(take)
75 75 
 exportMethods(union)
76 76 
 import(GenomicRanges)
77 
-import(RGMQLScalaLib)
77 
+import(RGMQLlib)
78 78 
 import(httr)
79 79 
 import(xml2)
80 80 
 importClassesFrom(GenomicRanges,GRangesList)
Browse code

fix

Simone authored on 02/01/2018 22:01:09
Showing 1 changed files
NAMESPACE
History View file @ 4bc0d16
... ... 
@@ -7,6 +7,7 @@ export(AVG)
7 7 
 export(BAG)
8 8 
 export(BAGD)
9 9 
 export(COUNT)
10 
+export(COUNTSAMP)
10 11 
 export(DESC)
11 12 
 export(DG)
12 13 
 export(DGE)
... ... 
@@ -39,8 +40,8 @@ export(import_gmql)
39 40 
 export(init_gmql)
40 41 
 export(login_gmql)
41 42 
 export(logout_gmql)
42 
-export(read)
43 
-export(read_dataset)
43 
+export(read_GMQL)
44 
+export(read_GRangesList)
44 45 
 export(remote_processing)
45 46 
 export(run_query)
46 47 
 export(run_query_fromfile)
... ... 
@@ -73,6 +74,7 @@ exportMethods(setdiff)
73 74 
 exportMethods(take)
74 75 
 exportMethods(union)
75 76 
 import(GenomicRanges)
77 
+import(RGMQLScalaLib)
76 78 
 import(httr)
77 79 
 import(xml2)
78 80 
 importClassesFrom(GenomicRanges,GRangesList)
... ... 
@@ -96,6 +98,7 @@ importFrom(methods,is)
96 98 
 importFrom(methods,isClass)
97 99 
 importFrom(methods,new)
98 100 
 importFrom(plyr,revalue)
101 
+importFrom(rJava,.jaddClassPath)
99 102 
 importFrom(rJava,.jarray)
100 103 
 importFrom(rJava,.jevalArray)
101 104 
 importFrom(rJava,.jinit)
Browse code

fix

Simone authored on 28/12/2017 14:43:57
Showing 1 changed files
NAMESPACE
History View file @ d5fc647
... ... 
@@ -28,7 +28,7 @@ export(SUM)
28 28 
 export(UP)
29 29 
 export(compile_query)
30 30 
 export(compile_query_fromfile)
31 
-export(condition_evaluation)
31 
+export(conds)
32 32 
 export(delete_dataset)
33 33 
 export(download_as_GRangesList)
34 34 
 export(download_dataset)
Browse code

fix error

Simone authored on 15/12/2017 12:37:00
Showing 1 changed files
NAMESPACE
History View file @ c93d851
... ... 
@@ -8,14 +8,11 @@ export(BAG)
8 8 
 export(BAGD)
9 9 
 export(COUNT)
10 10 
 export(DESC)
11 
-export(DF)
12 11 
 export(DG)
13 12 
 export(DGE)
14 13 
 export(DL)
15 14 
 export(DLE)
16 15 
 export(DOWN)
17 
-export(EX)
18 
-export(FN)
19 16 
 export(MAX)
20 17 
 export(MD)
21 18 
 export(MEDIAN)
... ... 
@@ -31,6 +28,7 @@ export(SUM)
31 28 
 export(UP)
32 29 
 export(compile_query)
33 30 
 export(compile_query_fromfile)
31 
+export(condition_evaluation)
34 32 
 export(delete_dataset)
35 33 
 export(download_as_GRangesList)
36 34 
 export(download_dataset)
Browse code

fix

Simone authored on 10/12/2017 16:29:05
Showing 1 changed files
NAMESPACE
History View file @ 83eb062
... ... 
@@ -57,6 +57,7 @@ export(show_jobs_list)
57 57 
 export(show_queries_list)
58 58 
 export(show_samples_list)
59 59 
 export(show_schema)
60 
+export(stop_gmql)
60 61 
 export(stop_job)
61 62 
 export(trace_job)
62 63 
 export(upload_dataset)
... ... 
@@ -80,6 +81,7 @@ importClassesFrom(GenomicRanges,GRangesList)
80 81 
 importClassesFrom(S4Vectors,DataTable)
81 82 
 importFrom(BiocGenerics,setdiff)
82 83 
 importFrom(BiocGenerics,union)
84 
+importFrom(GenomicRanges,GRangesList)
83 85 
 importFrom(GenomicRanges,makeGRangesFromDataFrame)
84 86 
 importFrom(S4Vectors,aggregate)
85 87 
 importFrom(S4Vectors,merge)
Browse code

fix and clean

Simone authored on 06/12/2017 17:47:26
Showing 1 changed files
NAMESPACE
History View file @ e5131ba
... ... 
@@ -29,7 +29,6 @@ export(SQRT)
29 29 
 export(STD)
30 30 
 export(SUM)
31 31 
 export(UP)
32 
-export(collect)
33 32 
 export(compile_query)
34 33 
 export(compile_query_fromfile)
35 34 
 export(delete_dataset)
... ... 
@@ -86,8 +85,12 @@ importFrom(S4Vectors,aggregate)
86 85 
 importFrom(S4Vectors,merge)
87 86 
 importFrom(S4Vectors,metadata)
88 87 
 importFrom(data.table,fread)
88 
+importFrom(dplyr,arrange)
89 89 
 importFrom(dplyr,bind_cols)
90 
+importFrom(dplyr,collect)
90 91 
 importFrom(dplyr,filter)
92 
+importFrom(dplyr,group_by)
93 
+importFrom(dplyr,select)
91 94 
 importFrom(glue,glue)
92 95 
 importFrom(methods,is)
93 96 
 importFrom(methods,isClass)
Browse code

add group, fixed some function

Simone authored on 05/12/2017 10:34:47
Showing 1 changed files
NAMESPACE
History View file @ c760228
... ... 
@@ -67,6 +67,7 @@ exportMethods(collect)
67 67 
 exportMethods(cover)
68 68 
 exportMethods(extend)
69 69 
 exportMethods(filter)
70 
+exportMethods(group_by)
70 71 
 exportMethods(map)
71 72 
 exportMethods(merge)
72 73 
 exportMethods(select)
... ... 
@@ -78,10 +79,16 @@ import(httr)
78 79 
 import(xml2)
79 80 
 importClassesFrom(GenomicRanges,GRangesList)
80 81 
 importClassesFrom(S4Vectors,DataTable)
82 
+importFrom(BiocGenerics,setdiff)
83 
+importFrom(BiocGenerics,union)
81 84 
 importFrom(GenomicRanges,makeGRangesFromDataFrame)
85 
+importFrom(S4Vectors,aggregate)
86 
+importFrom(S4Vectors,merge)
82 87 
 importFrom(S4Vectors,metadata)
83 88 
 importFrom(data.table,fread)
84 89 
 importFrom(dplyr,bind_cols)
90 
+importFrom(dplyr,filter)
91 
+importFrom(glue,glue)
85 92 
 importFrom(methods,is)
86 93 
 importFrom(methods,isClass)
87 94 
 importFrom(methods,new)
Browse code

clean files and folder

Simone authored on 21/11/2017 13:43:55
Showing 1 changed files
NAMESPACE
History View file @ 48ab60c
... ... 
@@ -29,7 +29,6 @@ export(SQRT)
29 29 
 export(STD)
30 30 
 export(SUM)
31 31 
 export(UP)
32 
-export(arrange)
33 32 
 export(collect)
34 33 
 export(compile_query)
35 34 
 export(compile_query_fromfile)
... ... 
@@ -52,7 +51,6 @@ export(sample_metadata)
52 51 
 export(sample_region)
53 52 
 export(save_query)
54 53 
 export(save_query_fromfile)
55 
-export(select)
56 54 
 export(semijoin)
57 55 
 export(show_datasets_list)
58 56 
 export(show_job_log)
... ... 
@@ -61,7 +59,6 @@ export(show_queries_list)
61 59 
 export(show_samples_list)
62 60 
 export(show_schema)
63 61 
 export(stop_job)
64 
-export(take)
65 62 
 export(trace_job)
66 63 
 export(upload_dataset)
67 64 
 exportMethods(aggregate)
Browse code

new build

Simone authored on 19/11/2017 00:55:04
Showing 1 changed files
NAMESPACE
History View file @ fce655e
... ... 
@@ -29,6 +29,8 @@ export(SQRT)
29 29 
 export(STD)
30 30 
 export(SUM)
31 31 
 export(UP)
32 
+export(arrange)
33 
+export(collect)
32 34 
 export(compile_query)
33 35 
 export(compile_query_fromfile)
34 36 
 export(delete_dataset)
... ... 
@@ -41,7 +43,6 @@ export(import_gmql)
41 43 
 export(init_gmql)
42 44 
 export(login_gmql)
43 45 
 export(logout_gmql)
44 
-export(materialize)
45 46 
 export(read)
46 47 
 export(read_dataset)
47 48 
 export(remote_processing)
... ... 
@@ -51,6 +52,7 @@ export(sample_metadata)
51 52 
 export(sample_region)
52 53 
 export(save_query)
53 54 
 export(save_query_fromfile)
55 
+export(select)
54 56 
 export(semijoin)
55 57 
 export(show_datasets_list)
56 58 
 export(show_job_log)
... ... 
@@ -63,15 +65,15 @@ export(take)
63 65 
 export(trace_job)
64 66 
 export(upload_dataset)
65 67 
 exportMethods(aggregate)
68 
+exportMethods(arrange)
69 
+exportMethods(collect)
66 70 
 exportMethods(cover)
67 71 
 exportMethods(extend)
68 72 
 exportMethods(filter)
69 
-exportMethods(join)
70 73 
 exportMethods(map)
71 
-exportMethods(materialize)
74 
+exportMethods(merge)
75 
+exportMethods(select)
72 76 
 exportMethods(setdiff)
73 
-exportMethods(sort)
74 
-exportMethods(subset)
75 77 
 exportMethods(take)
76 78 
 exportMethods(union)
77 79 
 import(GenomicRanges)
Browse code

S4 methods and change help

Simone authored on 17/11/2017 14:45:18
Showing 1 changed files
NAMESPACE
History View file @ 65260a4
... ... 
@@ -8,13 +8,14 @@ export(BAG)
8 8 
 export(BAGD)
9 9 
 export(COUNT)
10 10 
 export(DESC)
11 
+export(DF)
11 12 
 export(DG)
12 13 
 export(DGE)
13 14 
 export(DL)
14 15 
 export(DLE)
15 16 
 export(DOWN)
16 
-export(EXACT)
17 
-export(FULL)
17 
+export(EX)
18 
+export(FN)
18 19 
 export(MAX)
19 20 
 export(MD)
20 21 
 export(MEDIAN)
... ... 
@@ -50,6 +51,7 @@ export(sample_metadata)
50 51 
 export(sample_region)
51 52 
 export(save_query)
52 53 
 export(save_query_fromfile)
54 
+export(semijoin)
53 55 
 export(show_datasets_list)
54 56 
 export(show_job_log)
55 57 
 export(show_jobs_list)
... ... 
@@ -70,6 +72,7 @@ exportMethods(materialize)
70 72 
 exportMethods(setdiff)
71 73 
 exportMethods(sort)
72 74 
 exportMethods(subset)
75 
+exportMethods(take)
73 76 
 exportMethods(union)
74 77 
 import(GenomicRanges)
75 78 
 import(httr)
Browse code

start new build

Simone authored on 16/11/2017 12:08:21
Showing 1 changed files
NAMESPACE
History View file @ 702b843
... ... 
@@ -76,7 +76,6 @@ import(httr)
76 76 
 import(xml2)
77 77 
 importClassesFrom(GenomicRanges,GRangesList)
78 78 
 importClassesFrom(S4Vectors,DataTable)
79 
-importFrom(BiocGenerics,subset)
80 79 
 importFrom(GenomicRanges,makeGRangesFromDataFrame)
81 80 
 importFrom(S4Vectors,metadata)
82 81 
 importFrom(data.table,fread)
Browse code

map to s4 - start new build

Simone authored on 16/11/2017 10:37:54
Showing 1 changed files
NAMESPACE
History View file @ b3e9c8a
... ... 
@@ -30,7 +30,6 @@ export(SUM)
30 30 
 export(UP)
31 31 
 export(compile_query)
32 32 
 export(compile_query_fromfile)
33 
-export(cover)
34 33 
 export(delete_dataset)
35 34 
 export(download_as_GRangesList)
36 35 
 export(download_dataset)
... ... 
@@ -41,7 +40,6 @@ export(import_gmql)
41 40 
 export(init_gmql)
42 41 
 export(login_gmql)
43 42 
 export(logout_gmql)
44 
-export(map)
45 43 
 export(materialize)
46 44 
 export(read)
47 45 
 export(read_dataset)
... ... 
@@ -64,10 +62,11 @@ export(trace_job)
64 62 
 export(upload_dataset)
65 63 
 exportMethods(aggregate)
66 64 
 exportMethods(cover)
65 
+exportMethods(extend)
67 66 
 exportMethods(filter)
68 67 
 exportMethods(join)
68 
+exportMethods(map)
69 69 
 exportMethods(materialize)
70 
-exportMethods(mutate)
71 70 
 exportMethods(setdiff)
72 71 
 exportMethods(sort)
73 72 
 exportMethods(subset)
... ... 
@@ -77,6 +76,7 @@ import(httr)
77 76 
 import(xml2)
78 77 
 importClassesFrom(GenomicRanges,GRangesList)
79 78 
 importClassesFrom(S4Vectors,DataTable)
79 
+importFrom(BiocGenerics,subset)
80 80 
 importFrom(GenomicRanges,makeGRangesFromDataFrame)
81 81 
 importFrom(S4Vectors,metadata)
82 82 
 importFrom(data.table,fread)
Browse code

start new build

Simone authored on 15/11/2017 07:36:20
Showing 1 changed files
NAMESPACE
History View file @ db89f91
... ... 
@@ -30,6 +30,7 @@ export(SUM)
30 30 
 export(UP)
31 31 
 export(compile_query)
32 32 
 export(compile_query_fromfile)
33 
+export(cover)
33 34 
 export(delete_dataset)
34 35 
 export(download_as_GRangesList)
35 36 
 export(download_dataset)
Browse code

start new build

Simone authored on 14/11/2017 17:42:59
Showing 1 changed files
NAMESPACE
History View file @ 68a0f34
... ... 
@@ -30,7 +30,6 @@ export(SUM)
30 30 
 export(UP)
31 31 
 export(compile_query)
32 32 
 export(compile_query_fromfile)
33 
-export(cover)
34 33 
 export(delete_dataset)
35 34 
 export(download_as_GRangesList)
36 35 
 export(download_dataset)
... ... 
@@ -39,7 +38,6 @@ export(export_gmql)
39 38 
 export(filter_and_extract)
40 39 
 export(import_gmql)
41 40 
 export(init_gmql)
42 
-export(join)
43 41 
 export(login_gmql)
44 42 
 export(logout_gmql)
45 43 
 export(map)
... ... 
@@ -83,6 +81,8 @@ importFrom(S4Vectors,metadata)
83 81 
 importFrom(data.table,fread)
84 82 
 importFrom(dplyr,bind_cols)
85 83 
 importFrom(methods,is)
84 
+importFrom(methods,isClass)
85 
+importFrom(methods,new)
86 86 
 importFrom(plyr,revalue)
87 87 
 importFrom(rJava,.jarray)
88 88 
 importFrom(rJava,.jevalArray)
Browse code

S4 methods

Simone authored on 14/11/2017 15:58:33
Showing 1 changed files
NAMESPACE
History View file @ 07f76a5
... ... 
@@ -32,15 +32,11 @@ export(compile_query)
32 32 
 export(compile_query_fromfile)
33 33 
 export(cover)
34 34 
 export(delete_dataset)
35 
-export(difference)
36 35 
 export(download_as_GRangesList)
37 36 
 export(download_dataset)
38 37 
 export(execute)
39 38 
 export(export_gmql)
40 
-export(extend)
41 39 
 export(filter_and_extract)
42 
-export(flat)
43 
-export(histogram)
44 40 
 export(import_gmql)
45 41 
 export(init_gmql)
46 42 
 export(join)
... ... 
@@ -48,9 +44,6 @@ export(login_gmql)
48 44 
 export(logout_gmql)
49 45 
 export(map)
50 46 
 export(materialize)
51 
-export(merge)
52 
-export(order)
53 
-export(project)
54 47 
 export(read)
55 48 
 export(read_dataset)
56 49 
 export(remote_processing)
... ... 
@@ -60,7 +53,6 @@ export(sample_metadata)
60 53 
 export(sample_region)
61 54 
 export(save_query)
62 55 
 export(save_query_fromfile)
63 
-export(select)
64 56 
 export(show_datasets_list)
65 57 
 export(show_job_log)
66 58 
 export(show_jobs_list)
... ... 
@@ -68,15 +60,24 @@ export(show_queries_list)
68 60 
 export(show_samples_list)
69 61 
 export(show_schema)
70 62 
 export(stop_job)
71 
-export(summit)
72 63 
 export(take)
73 64 
 export(trace_job)
74 
-export(union)
75 65 
 export(upload_dataset)
66 
+exportMethods(aggregate)
67 
+exportMethods(cover)
68 
+exportMethods(filter)
69 
+exportMethods(join)
70 
+exportMethods(materialize)
71 
+exportMethods(mutate)
72 
+exportMethods(setdiff)
73 
+exportMethods(sort)
74 
+exportMethods(subset)
75 
+exportMethods(union)
76 76 
 import(GenomicRanges)
77 77 
 import(httr)
78 78 
 import(xml2)
79 79 
 importClassesFrom(GenomicRanges,GRangesList)
80 
+importClassesFrom(S4Vectors,DataTable)
80 81 
 importFrom(GenomicRanges,makeGRangesFromDataFrame)
81 82 
 importFrom(S4Vectors,metadata)
82 83 
 importFrom(data.table,fread)
Browse code

new build

Simone authored on 09/11/2017 15:46:50
Showing 1 changed files
NAMESPACE
History View file @ c6364b5
... ... 
@@ -53,7 +53,6 @@ export(order)
53 53 
 export(project)
54 54 
 export(read)
55 55 
 export(read_dataset)
56 
-export(register_gmql)
57 56 
 export(remote_processing)
58 57 
 export(run_query)
59 58 
 export(run_query_fromfile)
Browse code

change function name, completed vignette and descrption

Simone authored on 08/11/2017 13:30:29
Showing 1 changed files
NAMESPACE
History View file @ 94a33e5
... ... 
@@ -1,10 +1,12 @@
1 1 
 # Generated by roxygen2: do not edit by hand
2 2
3 
+export(ALL)
4 
+export(ANY)
3 5 
 export(ASC)
4 6 
 export(AVG)
5 7 
 export(BAG)
8 
+export(BAGD)
6 9 
 export(COUNT)
7 
-export(DEF)
8 10 
 export(DESC)
9 11 
 export(DG)
10 12 
 export(DGE)
... ... 
@@ -16,62 +18,62 @@ export(FULL)
16 18 
 export(MAX)
17 19 
 export(MD)
18 20 
 export(MEDIAN)
21 
+export(META)
19 22 
 export(MIN)
23 
+export(NIL)
20 24 
 export(Q1)
21 25 
 export(Q2)
22 26 
 export(Q3)
27 
+export(SQRT)
23 28 
 export(STD)
24 29 
 export(SUM)
25 
-export(TFARMatrix)
26 
-export(TFARMemAtrix)
27 30 
 export(UP)
28 
-export(compileQuery)
29 
-export(compileQuery.fromfile)
31 
+export(compile_query)
32 
+export(compile_query_fromfile)
30 33 
 export(cover)
31 
-export(deleteDataset)
34 
+export(delete_dataset)
32 35 
 export(difference)
33 
-export(downloadDataset)
34 
-export(downloadDatasetToGrangesList)
36 
+export(download_as_GRangesList)
37 
+export(download_dataset)
35 38 
 export(execute)
36 
-export(exportGMQL.gdm)
37 
-export(exportGMQL.gtf)
39 
+export(export_gmql)
38 40 
 export(extend)
41 
+export(filter_and_extract)
39 42 
 export(flat)
40 43 
 export(histogram)
41 
-export(importGMQL.gdm)
42 
-export(importGMQL.gtf)
43 
-export(initGMQL)
44 
+export(import_gmql)
45 
+export(init_gmql)
44 46 
 export(join)
45 
-export(login.GMQL)
46 
-export(logout.GMQL)
47 
+export(login_gmql)
48 
+export(logout_gmql)
47 49 
 export(map)
48 50 
 export(materialize)
49 51 
 export(merge)
50 
-export(metadataFromSample)
51 52 
 export(order)
52 53 
 export(project)
53 54 
 export(read)
54 
-export(readDataset)
55 
-export(regionFromSample)
56 
-export(register.GMQL)
55 
+export(read_dataset)
56 
+export(register_gmql)
57 57 
 export(remote_processing)
58 
-export(runQuery)
59 
-export(runQuery.fromfile)
60 
-export(saveQuery)
61 
-export(saveQuery.fromfile)
58 
+export(run_query)
59 
+export(run_query_fromfile)
60 
+export(sample_metadata)
61 
+export(sample_region)
62 
+export(save_query)
63 
+export(save_query_fromfile)
62 64 
 export(select)
63 
-export(showDatasets)
64 
-export(showJobLog)
65 
-export(showJobs)
66 
-export(showQueries)
67 
-export(showSamplesFromDataset)
68 
-export(showSchemaFromDataset)
69 
-export(stopJob)
65 
+export(show_datasets_list)
66 
+export(show_job_log)
67 
+export(show_jobs_list)
68 
+export(show_queries_list)
69 
+export(show_samples_list)
70 
+export(show_schema)
71 
+export(stop_job)
70 72 
 export(summit)
71 73 
 export(take)
72 
-export(traceJob)
74 
+export(trace_job)
73 75 
 export(union)
74 
-export(uploadSamples)
76 
+export(upload_dataset)
75 77 
 import(GenomicRanges)
76 78 
 import(httr)
77 79 
 import(xml2)
Browse code

passing to rJava

Simone authored on 16/10/2017 16:18:37
Showing 1 changed files
NAMESPACE
History View file @ 43d9e4a
... ... 
@@ -1,30 +1,76 @@
1 1 
 # Generated by roxygen2: do not edit by hand
2 2
3 
+export(ASC)
4 
+export(AVG)
5 
+export(BAG)
6 
+export(COUNT)
7 
+export(DEF)
8 
+export(DESC)
9 
+export(DG)
10 
+export(DGE)
11 
+export(DL)
12 
+export(DLE)
13 
+export(DOWN)
14 
+export(EXACT)
15 
+export(FULL)
16 
+export(MAX)
17 
+export(MD)
18 
+export(MEDIAN)
19 
+export(MIN)
20 
+export(Q1)
21 
+export(Q2)
22 
+export(Q3)
23 
+export(STD)
24 
+export(SUM)
3 25 
 export(TFARMatrix)
4 26 
 export(TFARMemAtrix)
27 
+export(UP)
28 
+export(compileQuery)
29 
+export(compileQuery.fromfile)
30 
+export(cover)
5 31 
 export(deleteDataset)
32 
+export(difference)
6 33 
 export(downloadDataset)
7 34 
 export(downloadDatasetToGrangesList)
35 
+export(execute)
8 36 
 export(exportGMQL.gdm)
9 37 
 export(exportGMQL.gtf)
10 38 
 export(extend)
39 
+export(flat)
40 
+export(histogram)
11 41 
 export(importGMQL.gdm)
12 42 
 export(importGMQL.gtf)
13 43 
 export(initGMQL)
44 
+export(join)
14 45 
 export(login.GMQL)
15 46 
 export(logout.GMQL)
47 
+export(map)
48 
+export(materialize)
49 
+export(merge)
16 50 
 export(metadataFromSample)
51 
+export(order)
52 
+export(project)
17 53 
 export(read)
18 54 
 export(readDataset)
19 55 
 export(regionFromSample)
20 56 
 export(register.GMQL)
21 57 
 export(remote_processing)
58 
+export(runQuery)
59 
+export(runQuery.fromfile)
22 60 
 export(saveQuery)
23 61 
 export(saveQuery.fromfile)
62 
+export(select)
24 63 
 export(showDatasets)
64 
+export(showJobLog)
65 
+export(showJobs)
25 66 
 export(showQueries)
26 67 
 export(showSamplesFromDataset)
27 68 
 export(showSchemaFromDataset)
69 
+export(stopJob)
70 
+export(summit)
71 
+export(take)
72 
+export(traceJob)
73 
+export(union)
28 74 
 export(uploadSamples)
29 75 
 import(GenomicRanges)
30 76 
 import(httr)
... ... 
@@ -36,12 +82,15 @@ importFrom(data.table,fread)
36 82 
 importFrom(dplyr,bind_cols)
37 83 
 importFrom(methods,is)
38 84 
 importFrom(plyr,revalue)
85 
+importFrom(rJava,.jarray)
86 
+importFrom(rJava,.jevalArray)
39 87 
 importFrom(rJava,.jinit)
40 88 
 importFrom(rJava,.jnull)
41 89 
 importFrom(rJava,.jpackage)
42 90 
 importFrom(rJava,J)
43 91 
 importFrom(rtracklayer,export)
44 92 
 importFrom(rtracklayer,import)
93 
+importFrom(stats,setNames)
45 94 
 importFrom(utils,read.delim)
46 95 
 importFrom(utils,unzip)
47 96 
 importFrom(utils,write.table)
Browse code

fix import dependence

Simone authored on 15/10/2017 19:26:05
Showing 1 changed files
NAMESPACE
History View file @ 6d7d26d
... ... 
@@ -28,7 +28,6 @@ export(showSchemaFromDataset)
28 28 
 export(uploadSamples)
29 29 
 import(GenomicRanges)
30 30 
 import(httr)
31 
-import(rJava)
32 31 
 import(xml2)
33 32 
 importClassesFrom(GenomicRanges,GRangesList)
34 33 
 importFrom(GenomicRanges,makeGRangesFromDataFrame)
... ... 
@@ -38,8 +37,9 @@ importFrom(dplyr,bind_cols)
38 37 
 importFrom(methods,is)
39 38 
 importFrom(plyr,revalue)
40 39 
 importFrom(rJava,.jinit)
41 
-importFrom(rJava,.jnew)
40 
+importFrom(rJava,.jnull)
42 41 
 importFrom(rJava,.jpackage)
42 
+importFrom(rJava,J)
43 43 
 importFrom(rtracklayer,export)
44 44 
 importFrom(rtracklayer,import)
45 45 
 importFrom(utils,read.delim)
Browse code

delete rscala

Simone authored on 15/10/2017 18:21:39
Showing 1 changed files
NAMESPACE
History View file @ 019c45d
... ... 
@@ -1,78 +1,34 @@
1 1 
 # Generated by roxygen2: do not edit by hand
2 2
3 
-export(ASC)
4 
-export(AVG)
5 
-export(BAG)
6 
-export(COUNT)
7 
-export(DEF)
8 
-export(DESC)
9 
-export(DGE)
10 
-export(DLE)
11 
-export(DOWN)
12 
-export(EXACT)
13 
-export(FULL)
14 
-export(MAX)
15 
-export(MD)
16 
-export(MEDIAN)
17 
-export(MIN)
18 
-export(Q1)
19 
-export(Q2)
20 
-export(Q3)
21 
-export(STD)
22 
-export(SUM)
23 3 
 export(TFARMatrix)
24 4 
 export(TFARMemAtrix)
25 
-export(UP)
26 
-export(compileQuery)
27 
-export(compileQuery.fromfile)
28 
-export(cover)
29 5 
 export(deleteDataset)
30 
-export(difference)
31 6 
 export(downloadDataset)
32 7 
 export(downloadDatasetToGrangesList)
33 
-export(execute)
34 8 
 export(exportGMQL.gdm)
35 9 
 export(exportGMQL.gtf)
36 10 
 export(extend)
37 
-export(flat)
38 
-export(histogram)
39 11 
 export(importGMQL.gdm)
40 12 
 export(importGMQL.gtf)
41 13 
 export(initGMQL)
42 
-export(join)
43 14 
 export(login.GMQL)
44 15 
 export(logout.GMQL)
45 
-export(map)
46 
-export(materialize)
47 
-export(merge)
48 16 
 export(metadataFromSample)
49 
-export(order)
50 
-export(project)
51 17 
 export(read)
52 18 
 export(readDataset)
53 19 
 export(regionFromSample)
54 20 
 export(register.GMQL)
55 21 
 export(remote_processing)
56 
-export(runQuery)
57 
-export(runQuery.fromfile)
58 22 
 export(saveQuery)
59 23 
 export(saveQuery.fromfile)
60 
-export(select)
61 24 
 export(showDatasets)
62 
-export(showJobLog)
63 
-export(showJobs)
64 25 
 export(showQueries)
65 26 
 export(showSamplesFromDataset)
66 27 
 export(showSchemaFromDataset)
67 
-export(stopJob)
68 
-export(summit)
69 
-export(take)
70 
-export(traceJob)
71 
-export(union)
72 28 
 export(uploadSamples)
73 29 
 import(GenomicRanges)
74 30 
 import(httr)
75 
-import(rscala)
31 
+import(rJava)
76 32 
 import(xml2)
77 33 
 importClassesFrom(GenomicRanges,GRangesList)
78 34 
 importFrom(GenomicRanges,makeGRangesFromDataFrame)
... ... 
@@ -81,9 +37,11 @@ importFrom(data.table,fread)
81 37 
 importFrom(dplyr,bind_cols)
82 38 
 importFrom(methods,is)
83 39 
 importFrom(plyr,revalue)
40 
+importFrom(rJava,.jinit)
41 
+importFrom(rJava,.jnew)
42 
+importFrom(rJava,.jpackage)
84 43 
 importFrom(rtracklayer,export)
85 44 
 importFrom(rtracklayer,import)
86 
-importFrom(stats,setNames)
87 45 
 importFrom(utils,read.delim)
88 46 
 importFrom(utils,unzip)
89 47 
 importFrom(utils,write.table)
Browse code

readme, namespace

Simone authored on 10/10/2017 11:00:24
Showing 1 changed files
NAMESPACE
History View file @ 71a94bb
... ... 
@@ -85,4 +85,5 @@ importFrom(rtracklayer,export)
85 85 
 importFrom(rtracklayer,import)
86 86 
 importFrom(stats,setNames)
87 87 
 importFrom(utils,read.delim)
88 
+importFrom(utils,unzip)
88 89 
 importFrom(utils,write.table)
Browse code

check and biocheck OK

Simone authored on 03/10/2017 17:36:09
Showing 1 changed files
NAMESPACE
History View file @ b48daf4
... ... 
@@ -83,5 +83,6 @@ importFrom(methods,is)
83 83 
 importFrom(plyr,revalue)
84 84 
 importFrom(rtracklayer,export)
85 85 
 importFrom(rtracklayer,import)
86 
+importFrom(stats,setNames)
86 87 
 importFrom(utils,read.delim)
87 88 
 importFrom(utils,write.table)
Browse code

fix join add description and example on distal object and join function

Simone authored on 28/09/2017 10:13:09
Showing 1 changed files
NAMESPACE
History View file @ 2deed4e
... ... 
@@ -81,7 +81,6 @@ importFrom(data.table,fread)
81 81 
 importFrom(dplyr,bind_cols)
82 82 
 importFrom(methods,is)
83 83 
 importFrom(plyr,revalue)
84 
-importFrom(rscala,scalaNull)
85 84 
 importFrom(rtracklayer,export)
86 85 
 importFrom(rtracklayer,import)
87 86 
 importFrom(utils,read.delim)
Browse code

add daggraph class and improveved manual

Simone authored on 14/08/2017 10:57:32
Showing 1 changed files
NAMESPACE
History View file @ 9ffd28f
... ... 
@@ -13,6 +13,7 @@ export(EXACT)
13 13 
 export(FULL)
14 14 
 export(MAX)
15 15 
 export(MD)
16 
+export(MEDIAN)
16 17 
 export(MIN)
17 18 
 export(Q1)
18 19 
 export(Q2)
... ... 
@@ -30,7 +31,6 @@ export(difference)
30 31 
 export(downloadDataset)
31 32 
 export(downloadDatasetToGrangesList)
32 33 
 export(execute)
33 
-export(export)
34 34 
 export(exportGMQL.gdm)
35 35 
 export(exportGMQL.gtf)
36 36 
 export(extend)
Browse code

add TODO list and fix on null value

Simone authored on 27/07/2017 07:13:14
Showing 1 changed files
NAMESPACE
History View file @ bdfe862
... ... 
@@ -48,7 +48,6 @@ export(merge)
48 48 
 export(metadataFromSample)
49 49 
 export(order)
50 50 
 export(project)
51 
-export(prova)
52 51 
 export(read)
53 52 
 export(readDataset)
54 53 
 export(regionFromSample)
Browse code

minor fix

Simone authored on 25/07/2017 06:56:22
Showing 1 changed files
NAMESPACE
History View file @ 22ffdce
... ... 
@@ -48,6 +48,7 @@ export(merge)
48 48 
 export(metadataFromSample)
49 49 
 export(order)
50 50 
 export(project)
51 
+export(prova)
51 52 
 export(read)
52 53 
 export(readDataset)
53 54 
 export(regionFromSample)
... ... 
@@ -81,6 +82,7 @@ importFrom(data.table,fread)
81 82 
 importFrom(dplyr,bind_cols)
82 83 
 importFrom(methods,is)
83 84 
 importFrom(plyr,revalue)
85 
+importFrom(rscala,scalaNull)
84 86 
 importFrom(rtracklayer,export)
85 87 
 importFrom(rtracklayer,import)
86 88 
 importFrom(utils,read.delim)
Browse code

delete rootfolder

Simone authored on 18/06/2017 17:18:08
Showing 1 changed files
NAMESPACE
History View file @ 50c5964
1 1 
new file mode 100644
... ... 
@@ -0,0 +1,87 @@
1 
+# Generated by roxygen2: do not edit by hand
2 
+
3 
+export(ASC)
4 
+export(AVG)
5 
+export(BAG)
6 
+export(COUNT)
7 
+export(DEF)
8 
+export(DESC)
9 
+export(DGE)
10 
+export(DLE)
11 
+export(DOWN)
12 
+export(EXACT)
13 
+export(FULL)
14 
+export(MAX)
15 
+export(MD)
16 
+export(MIN)
17 
+export(Q1)
18 
+export(Q2)
19 
+export(Q3)
20 
+export(STD)
21 
+export(SUM)
22 
+export(TFARMatrix)
23 
+export(TFARMemAtrix)
24 
+export(UP)
25 
+export(compileQuery)
26 
+export(compileQuery.fromfile)
27 
+export(cover)
28 
+export(deleteDataset)
29 
+export(difference)
30 
+export(downloadDataset)
31 
+export(downloadDatasetToGrangesList)
32 
+export(execute)
33 
+export(export)
34 
+export(exportGMQL.gdm)
35 
+export(exportGMQL.gtf)
36 
+export(extend)
37 
+export(flat)
38 
+export(histogram)
39 
+export(importGMQL.gdm)
40 
+export(importGMQL.gtf)
41 
+export(initGMQL)
42 
+export(join)
43 
+export(login.GMQL)
44 
+export(logout.GMQL)
45 
+export(map)
46 
+export(materialize)
47 
+export(merge)
48 
+export(metadataFromSample)
49 
+export(order)
50 
+export(project)
51 
+export(read)
52 
+export(readDataset)
53 
+export(regionFromSample)
54 
+export(register.GMQL)
55 
+export(remote_processing)
56 
+export(runQuery)
57 
+export(runQuery.fromfile)
58 
+export(saveQuery)
59 
+export(saveQuery.fromfile)
60 
+export(select)
61 
+export(showDatasets)
62 
+export(showJobLog)
63 
+export(showJobs)
64 
+export(showQueries)
65 
+export(showSamplesFromDataset)
66 
+export(showSchemaFromDataset)
67 
+export(stopJob)
68 
+export(summit)
69 
+export(take)
70 
+export(traceJob)
71 
+export(union)
72 
+export(uploadSamples)
73 
+import(GenomicRanges)
74 
+import(httr)
75 
+import(rscala)
76 
+import(xml2)
77 
+importClassesFrom(GenomicRanges,GRangesList)
78 
+importFrom(GenomicRanges,makeGRangesFromDataFrame)
79 
+importFrom(S4Vectors,metadata)
80 
+importFrom(data.table,fread)
81 
+importFrom(dplyr,bind_cols)
82 
+importFrom(methods,is)
83 
+importFrom(plyr,revalue)
84 
+importFrom(rtracklayer,export)
85 
+importFrom(rtracklayer,import)
86 
+importFrom(utils,read.delim)
87 
+importFrom(utils,write.table)