Merge pull request #1486 from antgonza/library_fields

Library fields
qiita-spots · Oct 5, 2015 · 3ff52c5 · 3ff52c5
2 parents 484a7a5 + 2cf65b4
commit 3ff52c5
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Showing 2 changed files with 19 additions and 60 deletions.
diff --git a/qiita_ware/ebi.py b/qiita_ware/ebi.py
@@ -107,9 +107,7 @@ class EBISubmission(object):
                                     'NEXTSEQ 500', 'UNSPECIFIED']}
     xmlns_xsi = "http://www.w3.org/2001/XMLSchema-instance"
     xsi_noNSL = "ftp://ftp.sra.ebi.ac.uk/meta/xsd/sra_1_3/SRA.%s.xsd"
-    experiment_library_fields = [
-        'library_strategy', 'library_source', 'library_selection',
-        'library_layout']
+    experiment_library_fields = ['library_strategy']
 
     def __init__(self, preprocessed_data_id, action):
         error_msgs = []
@@ -439,6 +437,18 @@ def generate_experiment_xml(self):
             library_name = ET.SubElement(library_descriptor, 'LIBRARY_NAME')
             library_name.text = self._get_library_name(sample_name)
 
+            # hardcoding some values,
+            # see https://github.com/biocore/qiita/issues/1485
+            library_source = ET.SubElement(library_descriptor,
+                                           "LIBRARY_SOURCE")
+            library_source.text = "METAGENOMIC"
+            library_selection = ET.SubElement(library_descriptor,
+                                              "LIBRARY_SELECTION")
+            library_selection.text = "PCR"
+            library_layout = ET.SubElement(library_descriptor,
+                                           "LIBRARY_LAYOUT")
+            ET.SubElement(library_layout, "SINGLE")
+
             lcp = ET.SubElement(library_descriptor,
                                 "LIBRARY_CONSTRUCTION_PROTOCOL")
             lcp.text = escape(clean_whitespace(

diff --git a/qiita_ware/test/test_ebi.py b/qiita_ware/test/test_ebi.py
@@ -740,6 +740,9 @@ def test_generate_send_sequences_cmd(self):
 640194" />
       <LIBRARY_DESCRIPTOR>
         <LIBRARY_NAME>1.SKB2.640194</LIBRARY_NAME>
+        <LIBRARY_SOURCE>METAGENOMIC</LIBRARY_SOURCE>
+        <LIBRARY_SELECTION>PCR</LIBRARY_SELECTION>
+        <LIBRARY_LAYOUT><SINGLE /></LIBRARY_LAYOUT>
         <LIBRARY_CONSTRUCTION_PROTOCOL>This analysis was done as in Caporaso \
 et al 2011 Genome research. The PCR primers (F515/R806) were developed \
 against the V4 region of the 16S rRNA (both bacteria and archaea), which we \
@@ -826,6 +829,9 @@ def test_generate_send_sequences_cmd(self):
 640195" />
       <LIBRARY_DESCRIPTOR>
         <LIBRARY_NAME>1.SKB3.640195</LIBRARY_NAME>
+        <LIBRARY_SOURCE>METAGENOMIC</LIBRARY_SOURCE>
+        <LIBRARY_SELECTION>PCR</LIBRARY_SELECTION>
+        <LIBRARY_LAYOUT><SINGLE /></LIBRARY_LAYOUT>
         <LIBRARY_CONSTRUCTION_PROTOCOL>This analysis was done as in Caporaso \
 et al 2011 Genome research. The PCR primers (F515/R806) were developed \
 against the V4 region of the 16S rRNA (both bacteria and archaea), which we \
@@ -982,18 +988,6 @@ def test_generate_send_sequences_cmd(self):
 </TESTING>
 """
 
-GENLIBDESC = """<design foo="bar">
-    <LIBRARY_DESCRIPTOR>
-        <LIBRARY_NAME>sample</LIBRARY_NAME>
-        <LIBRARY_STRATEGY>OTHER</LIBRARY_STRATEGY>
-        <LIBRARY_SOURCE>METAGENOMIC</LIBRARY_SOURCE>
-        <LIBRARY_SELECTION>unspecified</LIBRARY_SELECTION>
-        <LIBRARY_CONSTRUCTION_PROTOCOL>libconsprot
-        </LIBRARY_CONSTRUCTION_PROTOCOL>
-    </LIBRARY_DESCRIPTOR>
-</design>
-"""
-
 GENSPOTDESC = """<design foo="bar">
     <SPOT_DESCRIPTOR>
         <SPOT_DECODE_SPEC />
@@ -1007,51 +1001,6 @@ def test_generate_send_sequences_cmd(self):
 </design>
 """
 
-SAMPLE_TEMPLATE_ERROR = (
-    "sample_name\tcollection_timestamp\tdescription\thas_extracted_data\t"
-    "has_physical_specimen\thost_subject_id\tlatitude\tlongitude\t"
-    "physical_location\trequired_sample_info_status_id\tsample_type\t"
-    "str_column\n"
-    "sample1\t2014-05-29 12:24:51\tTest Sample 1\tTrue\tTrue\tNotIdentified\t"
-    "42.42\t41.41\tlocation1\t1\ttype1\tValue for sample 1\n"
-    "sample2\t2014-05-29 12:24:51\tTest Sample 2\tTrue\tTrue\tNotIdentified\t"
-    "4.2\t1.1\tlocation1\t1\ttype1\tValue for sample 2\n"
-    "sample3\t2014-05-29 12:24:51\tTest Sample 3\tTrue\tTrue\tNotIdentified\t"
-    "4.8\t4.41\tlocation1\t1\ttype1\tValue for sample 3\n")
-
-EXP_SAMPLE_TEMPLATE = (
-    "sample_name\tcollection_timestamp\tdescription\thas_extracted_data\t"
-    "has_physical_specimen\thost_subject_id\tlatitude\tlongitude\t"
-    "physical_location\trequired_sample_info_status_id\tsample_type\t"
-    "str_column\ttaxon_id\tscientific_name\n"
-    "sample1\t2014-05-29 12:24:51\tTest Sample 1\tTrue\tTrue\tNotIdentified\t"
-    "42.42\t41.41\tlocation1\t1\ttype1\tValue for sample 1\t9606\t"
-    "homo sapiens\n"
-    "sample2\t2014-05-29 12:24:51\tTest Sample 2\tTrue\tTrue\tNotIdentified\t"
-    "4.2\t1.1\tlocation1\t1\ttype1\tValue for sample 2\t9606\thomo sapiens\n"
-    "sample3\t2014-05-29 12:24:51\tTest Sample 3\tTrue\tTrue\tNotIdentified\t"
-    "4.8\t4.41\tlocation1\t1\ttype1\tValue for sample 3\t9606\thomo sapiens\n")
-
-EXP_PREP_TEMPLATE = (
-    "sample_name\tcenter_name\tcenter_project_name\tdata_type_id\t"
-    "temp_status_id\tstr_column\tplatform\texperiment_design_description"
-    "\tlibrary_construction_protocol"
-    "\nsample1\tANL\tTest Project\t2\t1\tValue for sample 3"
-    "\tILLUMINA\texp design\tlib protocol\n"
-    "sample2\tANL\tTest Project\t2\t1\tValue for sample 1"
-    "\tILLUMINA\texp design\tlib protocol\n"
-    "sample3\tANL\tTest Project\t2\t1\tValue for sample 2"
-    "\tILLUMINA\texp design\tlib protocol\n")
-
-EXP_PREP_TEMPLATE_FILTERED = (
-    "sample_name\tcenter_name\tcenter_project_name\tdata_type_id\t"
-    "temp_status_id\tstr_column\tplatform\texperiment_design_description"
-    "\tlibrary_construction_protocol"
-    "\nsample1\tANL\tTest Project\t2\t1\tValue for sample 3"
-    "\tILLUMINA\texp design\tlib protocol\n"
-    "sample2\tANL\tTest Project\t2\t1\tValue for sample 1"
-    "\tILLUMINA\texp design\tlib protocol\n")
-
 
 if __name__ == "__main__":
     main()