diff generate_macros.py @ 0:cbc24be56f7b draft

planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/generate_macros.py	Tue Aug 29 04:13:09 2017 -0400
@@ -0,0 +1,227 @@
+#!/usr/bin/env python
+
+import enasearch
+
+spaces = '    '
+operator_names = {
+    "=": "equal",
+    "!=": "different",
+    "<": "lower",
+    "<=": "equal or lower",
+    ">": "higher",
+    ">=": "equal or higher",
+}
+
+
+def format_name(name, alternative_name):
+    """
+    Format name to remove None name and & in name
+    """
+    if name is None:
+        name = alternative_name
+    name = name.replace("&", "and")
+    return name
+
+
+def sort_by_name(dict):
+    """
+    Sort a dictionary on the values
+    """
+    return sorted(dict, key=dict.get)
+
+
+def write_analysis_fields():
+    """
+    Write the analysis fields
+    """
+    s = '%s<xml name="analysis_fields">\n' % (spaces)
+    fields = enasearch.get_returnable_fields(result="analysis", verbose=False)
+    for f in fields:
+        s += '%s<option value="%s">%s</option>\n' % (2 * spaces, f, f)
+    s += '%s</xml>\n' % (spaces)
+    return s
+
+
+def write_display_options():
+    """
+    Write the display options
+    """
+    s = '%s<xml name="display_options">\n' % (spaces)
+    when_s = '%s<xml name="when_display_options">\n' % (spaces)
+    options = enasearch.get_display_options(verbose=False)
+    for opt in options:
+        s += '%s<option value="%s">%s</option>\n' % (2 * spaces, opt, options[opt]['description'])
+        when_s += '%s<when value="%s">\n' % (2 * spaces, opt)
+        if opt == 'fasta' or opt == 'fastq':
+            when_s += '%s<param name="range_start" argument="--subseq_range" type="integer" optional="true" label="Start integer for subsequences"/>\n' % (3 * spaces)
+            when_s += '%s<param name="range_stop" argument="--subseq_range" type="integer" optional="true" label="Stop integer for subsequences"/>\n' % (3 * spaces)
+        else:
+            when_s += '%s<param argument="--offset" type="integer" optional="true" label="First record to get"/>\n' % (3 * spaces)
+            when_s += '%s<param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>\n' % (3 * spaces)
+        when_s += '%s</when>\n' % (2 * spaces)
+    s += '%s</xml>\n' % (spaces)
+    when_s += '%s</xml>\n' % (spaces)
+    s += when_s
+    return s
+
+
+def write_run_fields():
+    """
+    Write the run fields
+    """
+    s = '%s<xml name="run_fields">\n' % (spaces)
+    fields = enasearch.get_returnable_fields(result="read_run", verbose=False)
+    for f in fields:
+        s += '%s<option value="%s">%s</option>\n' % (2 * spaces, f, f)
+    s += '%s</xml>\n' % (spaces)
+    return s
+
+
+def write_taxonomy_results():
+    """
+    Write the possible taxonomy results
+    """
+    s = '%s<xml name="taxonomy_results">\n' % (spaces)
+    fields = enasearch.get_taxonomy_results(verbose=False)
+    for f in fields:
+        s += '%s<option value="%s">%s</option>\n' % (2 * spaces, f, fields[f]['description'])
+    s += '%s</xml>\n' % (spaces)
+    return s
+
+
+def write_result_parameters(fts=False):
+    """
+    Write the parameters that are dependant of results
+    """
+    res = enasearch.get_results(verbose=False)
+    options = enasearch.get_display_options(verbose=False)
+    ft = enasearch.get_filter_types(verbose=False)
+    # Format the filter type related parameters
+    ft_parameters = {}
+    for t in ft:
+        s = ''
+        if 'operators' in ft[t]:
+            s = '%s<param name="operation" type="select" label="Operator">\n' % (7 * spaces)
+            for o in ft[t]['operators']:
+                on = o
+                if o in operator_names:
+                    on = operator_names[o]
+                s += '%s<option value="%s">%s</option>\n' % (8 * spaces, on, on)
+            s += '%s</param>\n' % (7 * spaces)
+            if 'value' in ft[t]:
+                value_format = 'float' if t == 'Number' else 'text'
+                s += '%s<param name="value" type="%s" value="" label="%s"/>\n' % (7 * spaces, value_format, ft[t]['value'])
+            elif 'values' in ft[t]:
+                s += '%s<param name="value" type="select" label="Value">\n' % (7 * spaces)
+                for v in ft[t]['values']:
+                    s += '%s<option value="%s">%s</option>\n' % (8 * spaces, v, v)
+                s += '%s</param>\n' % (7 * spaces)
+        else:
+            s += '%s<conditional name="op">\n' % (7 * spaces)
+            s += '%s<param name="operation" type="select" label="Operation">\n' % (8 * spaces)
+            for op in ft[t]:
+                s += '%s<option value="%s">%s</option>\n' % (9 * spaces, op, ft[t][op]['description'])
+            s += '%s</param>\n' % (8 * spaces)
+            for op in ft[t]:
+                s += '%s<when value="%s">\n' % (8 * spaces, op)
+                s += '%s<param name="values" type="text" value="" label="%s" help="Values separated by simple comma"/>\n' % (9 * spaces, ",".join(ft[t][op]['parameters']))
+                s += '%s</when>\n' % (8 * spaces)
+            s += '%s</conditional>\n' % (7 * spaces)
+        ft_parameters[t] = s
+    # Start adding the conditional
+    s = '%s<conditional name="res">\n' % (2 * spaces)
+    # Add result parameter
+    s += '%s<param argument="--result" type="select" label="Result to return">\n' % (3 * spaces)
+    for r in res:
+        s += '%s<option value="%s">%s</option>\n' % (4 * spaces, r, res[r]['description'])
+    s += '%s</param>\n' % (3 * spaces)
+    for r in res:
+        sf = enasearch.get_sortable_fields(r)
+        ff = res[r]['filter_fields']
+        s += '%s<when value="%s">\n' % (3 * spaces, r)
+        if not fts:
+            s += '%s<repeat name="queries" title="Add a query">\n' % (4 * spaces)
+            # Add combination operator
+            s += '%s<param name="combination_operation" type="select" label="Combination operation">\n' % (5 * spaces)
+            s += '%s<option value="AND">AND</option>\n' % (6 * spaces)
+            s += '%s<option value="OR">OR</option>\n' % (6 * spaces)
+            s += '%s<option value="NOT">NOT</option>\n' % (6 * spaces)
+            s += '%s</param>\n' % (5 * spaces)
+            s += '%s<conditional name="filter_field">\n' % (5 * spaces)
+            s += '%s<param name="field" type="select" label="Field to query">\n' % (6 * spaces)
+            for f in ff:
+                s += '%s<option value="%s">%s</option>\n' % (7 * spaces, f, ff[f]['description'])
+            s += '%s</param>\n' % (6 * spaces)
+            for f in ff:
+                # Add the correct parameter given the type of field
+                typ = ff[f]['type'].capitalize()
+                if typ not in ft_parameters:
+                    if f == 'location':
+                        typ = 'Geospatial'
+                    else:
+                        continue
+                s += '%s<when value="%s">\n' % (6 * spaces, f)
+                s += ft_parameters[typ]
+                s += '%s</when>\n' % (6 * spaces)
+            s += '%s</conditional>\n' % (5 * spaces)
+            s += '%s</repeat>\n' % (4 * spaces)
+        # Add display opt
+        s += '%s<conditional name="display_opt">\n' % (4 * spaces)
+        s += '%s<param argument="--display" type="select" label="Display option to specify the display format">\n' % (5 * spaces)
+        s += '%s<expand macro="display_options"/>\n' % (6 * spaces)
+        s += '%s</param>\n' % (5 * spaces)
+        for opt in options:
+            s += '%s<when value="%s"' % (5 * spaces, opt)
+            if opt != 'fasta' and opt != 'fastq':
+                s += '>\n'
+                s += '%s<param argument="--offset" type="integer" optional="true" label="First record to get"/>\n' % (6 * spaces)
+                s += '%s<param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>\n' % (6 * spaces)
+                if opt == 'report':
+                    s += '%s<param argument="--fields" type="select" multiple="true" label="Fields to return">\n' % (6 * spaces)
+                    for f in res[r]['returnable_fields']:
+                        s += '%s<option value="%s">%s</option>\n' % (7 * spaces, f, f)
+                    s += '%s</param>\n' % (6 * spaces)
+                    s += '%s<param argument="--sortfields" type="select" optional="true" multiple="true" label="Fields to sort the results">\n' % (6 * spaces)
+                    for f in sf:
+                        s += '%s<option value="%s">%s</option>\n' % (7 * spaces, f, sf[f]['description'])
+                    s += '%s</param>\n' % (6 * spaces)
+                s += '%s</when>\n' % (5 * spaces)
+            else:
+                s += '/>\n'
+        s += '%s</conditional>\n' % (4 * spaces)
+        s += '%s</when>\n' % (3 * spaces)
+    s += '%s</conditional>\n' % (2 * spaces)
+    return s
+
+
+def write_search_data_parameters():
+    """
+    Write the parameters for search_data
+    """
+    fts = '%s<xml name="free_text_search">\n' % (spaces)
+    fts += write_result_parameters(True)
+    fts += '%s</xml>\n' % (spaces)
+    cts = '%s<xml name="conditional_text_search">\n' % (spaces)
+    cts += write_result_parameters(False)
+    cts += '%s</xml>\n' % (spaces)
+    return fts + cts
+
+
+def generate_search_macros(filepath):
+    """
+    Generate the content of the macro file
+    """
+    s = '<?xml version="1.0" ?>\n'
+    s += '<macros>\n'
+    s += write_analysis_fields()
+    s += write_display_options()
+    s += write_run_fields()
+    s += write_taxonomy_results()
+    s += write_search_data_parameters()
+    s += '</macros>\n'
+    with open(filepath, "w") as file:
+        file.write(s)
+
+
+if __name__ == '__main__':
+    generate_search_macros("search_macros.xml")