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Merged
merged 7 commits into from
Sep 12, 2018
+277 −191
Merged

Plugin outdate version #2664

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3d803d1
adding GUI changes for deprecated artifacts
antgonza Sep 10, 2018
500e340
fixing some tests
antgonza Sep 10, 2018
099e3f4
Merge branch 'dev' of https://github.com/biocore/qiita into plugin-ou…
antgonza Sep 11, 2018
3cb72ef
pull upstream dev
antgonza Sep 11, 2018
0d67fb2
addressing @ElDeveloper comments
antgonza Sep 12, 2018
bcd930e
fixing errors
antgonza Sep 12, 2018
61cc59d
fixing more errors
antgonza Sep 12, 2018
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31 changes: 31 additions & 0 deletions qiita_db/software.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1169,6 +1169,37 @@ def type(self):
qdb.sql_connection.TRN.add(sql, [self.id])
return qdb.sql_connection.TRN.execute_fetchlast()

@property
def deprecated(self):
"""Returns if the software is deprecated or not

Returns
-------
bool
Whether the software is deprecated or not
"""
with qdb.sql_connection.TRN:
sql = """SELECT deprecated
FROM qiita.software
WHERE software_id = %s"""
qdb.sql_connection.TRN.add(sql, [self.id])
return qdb.sql_connection.TRN.execute_fetchlast()

@deprecated.setter
def deprecated(self, deprecate):
"""Changes deprecated of the software

Parameters
----------
deprecate : bool
New software deprecate value
"""
with qdb.sql_connection.TRN:
sql = """UPDATE qiita.software SET deprecated = %s
WHERE software_id = %s"""
qdb.sql_connection.TRN.add(sql, [deprecate, self._id])
qdb.sql_connection.TRN.execute()

@property
def active(self):
"""Returns if the software is active or not
Expand Down
5 changes: 5 additions & 0 deletions qiita_db/support_files/patches/66.sql
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Expand Up @@ -8,3 +8,8 @@ SELECT 42;
ALTER TABLE qiita.study ADD specimen_id_column varchar(256);

COMMENT ON COLUMN qiita.study.specimen_id_column IS 'The name of the column that describes the specimen identifiers (such as what is written on the tubes).';

-- September 12, 2018
-- add deprecated to software table

ALTER TABLE qiita.software ADD deprecated bool default False;
2 changes: 2 additions & 0 deletions qiita_db/support_files/patches/python_patches/66.py
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Original file line number Diff line number Diff line change
Expand Up @@ -21,6 +21,8 @@ def create_command(software, name, description, parameters, outputs=None,
sql_param_values = []
sql_artifact_params = []
for pname, vals in parameters.items():
# vals should always have 2 elements as it should be:
# param_name: [parameter_type, default]
if len(vals) != 2:
raise QiitaDBError(
"Malformed parameters dictionary, the format should be "
Expand Down
5 changes: 4 additions & 1 deletion qiita_db/support_files/qiita-db.dbs
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Expand Up @@ -1259,6 +1259,9 @@
<column name="active" type="bool" jt="-7" mandatory="y" >
<defo>&#039;True&#039;</defo>
</column>
<column name="deprecated" type="bool" jt="-7" >
<defo>False</defo>
</column>
<index name="pk_software" unique="PRIMARY_KEY" >
<column name="software_id" />
</index>
Expand Down Expand Up @@ -1676,7 +1679,6 @@ Controlled Vocabulary]]></comment>
<entity schema="qiita" name="study_artifact" color="b2cdf7" x="1590" y="750" />
<entity schema="qiita" name="prep_template_processing_job" color="b2cdf7" x="1725" y="990" />
<entity schema="qiita" name="software_type" color="b2cdf7" x="2610" y="960" />
<entity schema="qiita" name="software" color="b2cdf7" x="2385" y="960" />
<entity schema="qiita" name="study_publication" color="b2cdf7" x="1845" y="720" />
<entity schema="qiita" name="investigation_study" color="c0d4f3" x="2025" y="360" />
<entity schema="qiita" name="investigation" color="c0d4f3" x="2250" y="315" />
Expand Down Expand Up @@ -1728,6 +1730,7 @@ Controlled Vocabulary]]></comment>
<entity schema="qiita" name="processing_job_validator" color="b2cdf7" x="2160" y="1410" />
<entity schema="qiita" name="processing_job" color="b2cdf7" x="1935" y="1140" />
<entity schema="qiita" name="study" color="d0def5" x="1785" y="240" />
<entity schema="qiita" name="software" color="b2cdf7" x="2385" y="960" />
<group name="Group_analyses" color="c4e0f9" >
<comment>analysis tables</comment>
<entity schema="qiita" name="analysis" />
Expand Down
209 changes: 108 additions & 101 deletions qiita_db/support_files/qiita-db.html
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Expand Up @@ -516,12 +516,7 @@
prep_template_processing_job references processing_job ( processing_job_id )</title>
</path>
<text x='1912' y='1045' transform='rotate(0 1912,1045)' title='Foreign Key fk_prep_template_processing_job_0
prep_template_processing_job references processing_job ( processing_job_id )' style='fill:#a1a0a0;'>processing_job_id</text><path transform='translate(7,0)' marker-start='url(#foot)' marker-end='url(#arrow)' d='M 2520 975 L 2595,975' >
<title>Foreign Key fk_software_software_type
software references software_type ( software_type_id )</title>
</path>
<text x='2527' y='970' transform='rotate(0 2527,970)' title='Foreign Key fk_software_software_type
software references software_type ( software_type_id )' style='fill:#a1a0a0;'>software_type_id</text><path transform='translate(7,0)' marker-start='url(#foot)' marker-end='url(#arrow)' d='M 1860 705 L 1860,615' >
prep_template_processing_job references processing_job ( processing_job_id )' style='fill:#a1a0a0;'>processing_job_id</text><path transform='translate(7,0)' marker-start='url(#foot)' marker-end='url(#arrow)' d='M 1860 705 L 1860,615' >
<title>Foreign Key fk_study_publication_study
study_publication references study ( study_id )</title>
</path>
Expand Down Expand Up @@ -811,7 +806,7 @@
term references ontology ( ontology_id )</title>
</path>
<text x='643' y='1450' transform='rotate(0 643,1450)' title='Foreign Key fk_term_ontology
term references ontology ( ontology_id )' style='fill:#a1a0a0;'>ontology_id</text><path transform='translate(7,0)' marker-start='url(#foot)' marker-end='url(#arrow)' d='M 2325 1275 L 2347,1275 Q 2355,1275 2355,1267 L 2355,1102 Q 2355,1095 2362,1095 L 2370,1095' >
term references ontology ( ontology_id )' style='fill:#a1a0a0;'>ontology_id</text><path transform='translate(7,0)' marker-start='url(#foot)' marker-end='url(#arrow)' d='M 2325 1275 L 2347,1275 Q 2355,1275 2355,1267 L 2355,1117 Q 2355,1110 2362,1110 L 2370,1110' >
<title>Foreign Key fk_soft_command_software
software_command references software ( software_id )</title>
</path>
Expand Down Expand Up @@ -861,7 +856,12 @@
study references timeseries_type ( timeseries_type_id )</title>
</path>
<text x='1972' y='535' transform='rotate(0 1972,535)' title='Foreign Key fk_study_timeseries_type
study references timeseries_type ( timeseries_type_id )' style='fill:#a1a0a0;'>timeseries_type_id</text><!-- ============= Table 'column_controlled_vocabularies' ============= -->
study references timeseries_type ( timeseries_type_id )' style='fill:#a1a0a0;'>timeseries_type_id</text><path transform='translate(7,0)' marker-start='url(#foot)' marker-end='url(#arrow)' d='M 2520 975 L 2595,975' >
<title>Foreign Key fk_software_software_type
software references software_type ( software_type_id )</title>
</path>
<text x='2527' y='970' transform='rotate(0 2527,970)' title='Foreign Key fk_software_software_type
software references software_type ( software_type_id )' style='fill:#a1a0a0;'>software_type_id</text><!-- ============= Table 'column_controlled_vocabularies' ============= -->
<rect class='table' x='270' y='1208' width='195' height='75' rx='7' ry='7' />
<path d='M 270.50 1234.50 L 270.50 1215.50 Q 270.50 1208.50 277.50 1208.50 L 457.50 1208.50 Q 464.50 1208.50 464.50 1215.50 L 464.50 1234.50 L270.50 1234.50 ' style='fill:url(#tableHeaderGradient0); stroke:none;' />
<a xlink:href='#column_controlled_vocabularies'><text x='280' y='1222' class='tableTitle'>column_controlled_vocabularies</text><title>Table qiita.column_controlled_vocabularies
Expand Down Expand Up @@ -1242,27 +1242,6 @@
<use id='nn' x='2612' y='1002' xlink:href='#nn'/><a xlink:href='#software_type.software_type'><text x='2628' y='1012'>software_type</text><title>software_type varchar not null</title></a>
<use id='nn' x='2612' y='1017' xlink:href='#nn'/><a xlink:href='#software_type.description'><text x='2628' y='1027'>description</text><title>description varchar not null</title></a>

<!-- ============= Table 'software' ============= -->
<rect class='table' x='2385' y='953' width='135' height='165' rx='7' ry='7' />
<path d='M 2385.50 979.50 L 2385.50 960.50 Q 2385.50 953.50 2392.50 953.50 L 2512.50 953.50 Q 2519.50 953.50 2519.50 960.50 L 2519.50 979.50 L2385.50 979.50 ' style='fill:url(#tableHeaderGradient3); stroke:none;' />
<a xlink:href='#software'><text x='2429' y='967' class='tableTitle'>software</text><title>Table qiita.software</title></a>
<use id='nn' x='2387' y='987' xlink:href='#nn'/><a xlink:href='#software.software_id'><use id='pk' x='2387' y='986' xlink:href='#pk'/><title>Primary Key ( software_id ) </title></a>
<a xlink:href='#software.software_id'><text x='2403' y='997'>software_id</text><title>software_id bigserial not null</title></a>
<a xlink:href='#software.software_id'><use id='ref' x='2508' y='986' xlink:href='#ref'/><title>Referred by default_workflow ( software_id )
Referred by oauth_software ( software_id )
Referred by software_artifact_type ( software_id )
Referred by software_command ( software_id )
Referred by software_publication ( software_id ) </title></a>
<use id='nn' x='2387' y='1002' xlink:href='#nn'/><a xlink:href='#software.name'><text x='2403' y='1012'>name</text><title>name varchar not null</title></a>
<use id='nn' x='2387' y='1017' xlink:href='#nn'/><a xlink:href='#software.version'><text x='2403' y='1027'>version</text><title>version varchar not null</title></a>
<use id='nn' x='2387' y='1032' xlink:href='#nn'/><a xlink:href='#software.description'><text x='2403' y='1042'>description</text><title>description varchar not null</title></a>
<use id='nn' x='2387' y='1047' xlink:href='#nn'/><a xlink:href='#software.environment_script'><text x='2403' y='1057'>environment_script</text><title>environment_script varchar not null</title></a>
<use id='nn' x='2387' y='1062' xlink:href='#nn'/><a xlink:href='#software.start_script'><text x='2403' y='1072'>start_script</text><title>start_script varchar not null</title></a>
<use id='nn' x='2387' y='1077' xlink:href='#nn'/><a xlink:href='#software.software_type_id'><use id='idx' x='2387' y='1076' xlink:href='#idx'/><title>Index ( software_type_id ) </title></a>
<a xlink:href='#software.software_type_id'><text x='2403' y='1087'>software_type_id</text><title>software_type_id bigint not null</title></a>
<a xlink:href='#software.software_type_id'><use id='fk' x='2508' y='1076' xlink:href='#fk'/><title>References software_type ( software_type_id ) </title></a>
<use id='nn' x='2387' y='1092' xlink:href='#nn'/><a xlink:href='#software.active'><text x='2403' y='1102'>active</text><title>active bool not null default &#039;True&#039;</title></a>

<!-- ============= Table 'study_publication' ============= -->
<rect class='table' x='1845' y='713' width='120' height='90' rx='7' ry='7' />
<path d='M 1845.50 739.50 L 1845.50 720.50 Q 1845.50 713.50 1852.50 713.50 L 1957.50 713.50 Q 1964.50 713.50 1964.50 720.50 L 1964.50 739.50 L1845.50 739.50 ' style='fill:url(#tableHeaderGradient3); stroke:none;' />
Expand Down Expand Up @@ -2038,6 +2017,28 @@
<a xlink:href='#study.specimen_id_column'><text x='1803' y='592'>specimen_id_column</text><title>specimen_id_column varchar&#040;256&#041;
The name of the column that describes the specimen identifiers &#040;such as what is written on the tubes&#041;&#046;</title></a>

<!-- ============= Table 'software' ============= -->
<rect class='table' x='2385' y='953' width='135' height='180' rx='7' ry='7' />
<path d='M 2385.50 979.50 L 2385.50 960.50 Q 2385.50 953.50 2392.50 953.50 L 2512.50 953.50 Q 2519.50 953.50 2519.50 960.50 L 2519.50 979.50 L2385.50 979.50 ' style='fill:url(#tableHeaderGradient3); stroke:none;' />
<a xlink:href='#software'><text x='2429' y='967' class='tableTitle'>software</text><title>Table qiita.software</title></a>
<use id='nn' x='2387' y='987' xlink:href='#nn'/><a xlink:href='#software.software_id'><use id='pk' x='2387' y='986' xlink:href='#pk'/><title>Primary Key ( software_id ) </title></a>
<a xlink:href='#software.software_id'><text x='2403' y='997'>software_id</text><title>software_id bigserial not null</title></a>
<a xlink:href='#software.software_id'><use id='ref' x='2508' y='986' xlink:href='#ref'/><title>Referred by default_workflow ( software_id )
Referred by oauth_software ( software_id )
Referred by software_artifact_type ( software_id )
Referred by software_command ( software_id )
Referred by software_publication ( software_id ) </title></a>
<use id='nn' x='2387' y='1002' xlink:href='#nn'/><a xlink:href='#software.name'><text x='2403' y='1012'>name</text><title>name varchar not null</title></a>
<use id='nn' x='2387' y='1017' xlink:href='#nn'/><a xlink:href='#software.version'><text x='2403' y='1027'>version</text><title>version varchar not null</title></a>
<use id='nn' x='2387' y='1032' xlink:href='#nn'/><a xlink:href='#software.description'><text x='2403' y='1042'>description</text><title>description varchar not null</title></a>
<use id='nn' x='2387' y='1047' xlink:href='#nn'/><a xlink:href='#software.environment_script'><text x='2403' y='1057'>environment_script</text><title>environment_script varchar not null</title></a>
<use id='nn' x='2387' y='1062' xlink:href='#nn'/><a xlink:href='#software.start_script'><text x='2403' y='1072'>start_script</text><title>start_script varchar not null</title></a>
<use id='nn' x='2387' y='1077' xlink:href='#nn'/><a xlink:href='#software.software_type_id'><use id='idx' x='2387' y='1076' xlink:href='#idx'/><title>Index ( software_type_id ) </title></a>
<a xlink:href='#software.software_type_id'><text x='2403' y='1087'>software_type_id</text><title>software_type_id bigint not null</title></a>
<a xlink:href='#software.software_type_id'><use id='fk' x='2508' y='1076' xlink:href='#fk'/><title>References software_type ( software_type_id ) </title></a>
<use id='nn' x='2387' y='1092' xlink:href='#nn'/><a xlink:href='#software.active'><text x='2403' y='1102'>active</text><title>active bool not null default &#039;True&#039;</title></a>
<a xlink:href='#software.deprecated'><text x='2403' y='1117'>deprecated</text><title>deprecated bool default False</title></a>

</g></svg>

<br/><br/>
Expand Down Expand Up @@ -3347,78 +3348,6 @@
</tbody>
</table>

<br/><br/>
<table class='bordered'>
<thead>
<tr><th colspan='4'><a name='software'>Table software</a></th></tr>
</thead>
<tbody>
<tr>
<td>*</td>
<td><a name='software.software_id'>software&#095;id</a></td>
<td> bigserial </td>
<td> </td>
</tr>
<tr>
<td>*</td>
<td><a name='software.name'>name</a></td>
<td> varchar </td>
<td> </td>
</tr>
<tr>
<td>*</td>
<td><a name='software.version'>version</a></td>
<td> varchar </td>
<td> </td>
</tr>
<tr>
<td>*</td>
<td><a name='software.description'>description</a></td>
<td> varchar </td>
<td> </td>
</tr>
<tr>
<td>*</td>
<td><a name='software.environment_script'>environment&#095;script</a></td>
<td> varchar </td>
<td> </td>
</tr>
<tr>
<td>*</td>
<td><a name='software.start_script'>start&#095;script</a></td>
<td> varchar </td>
<td> </td>
</tr>
<tr>
<td>*</td>
<td><a name='software.software_type_id'>software&#095;type&#095;id</a></td>
<td> bigint </td>
<td> </td>
</tr>
<tr>
<td>*</td>
<td><a name='software.active'>active</a></td>
<td> bool DEFO 'True' </td>
<td> </td>
</tr>
<tr><th colspan='4'><b>Indexes</b></th></tr>
<tr> <td>Pk</td><td>pk&#095;software</td>
<td> ON software&#095;id</td>
<td> </td>
</tr>
<tr> <td>&nbsp;</td><td>idx&#095;software</td>
<td> ON software&#095;type&#095;id</td>
<td> </td>
</tr>
<tr><th colspan='4'><b>Foreign Keys</b></th></tr>
<tr>
<td>&nbsp;</td><td>fk_software_software_type</td>
<td > ( software&#095;type&#095;id ) ref <a href='#software&#095;type'>software&#095;type</a> (software&#095;type&#095;id) </td>
<td> </td>
</tr>
</tbody>
</table>

<br/><br/>
<table class='bordered'>
<thead>
Expand Down Expand Up @@ -6170,4 +6099,82 @@
</tbody>
</table>

<br/><br/>
<table class='bordered'>
<thead>
<tr><th colspan='4'><a name='software'>Table software</a></th></tr>
</thead>
<tbody>
<tr>
<td>*</td>
<td><a name='software.software_id'>software&#095;id</a></td>
<td> bigserial </td>
<td> </td>
</tr>
<tr>
<td>*</td>
<td><a name='software.name'>name</a></td>
<td> varchar </td>
<td> </td>
</tr>
<tr>
<td>*</td>
<td><a name='software.version'>version</a></td>
<td> varchar </td>
<td> </td>
</tr>
<tr>
<td>*</td>
<td><a name='software.description'>description</a></td>
<td> varchar </td>
<td> </td>
</tr>
<tr>
<td>*</td>
<td><a name='software.environment_script'>environment&#095;script</a></td>
<td> varchar </td>
<td> </td>
</tr>
<tr>
<td>*</td>
<td><a name='software.start_script'>start&#095;script</a></td>
<td> varchar </td>
<td> </td>
</tr>
<tr>
<td>*</td>
<td><a name='software.software_type_id'>software&#095;type&#095;id</a></td>
<td> bigint </td>
<td> </td>
</tr>
<tr>
<td>*</td>
<td><a name='software.active'>active</a></td>
<td> bool DEFO 'True' </td>
<td> </td>
</tr>
<tr>
<td>&nbsp;</td>
<td><a name='software.deprecated'>deprecated</a></td>
<td> bool DEFO False </td>
<td> </td>
</tr>
<tr><th colspan='4'><b>Indexes</b></th></tr>
<tr> <td>Pk</td><td>pk&#095;software</td>
<td> ON software&#095;id</td>
<td> </td>
</tr>
<tr> <td>&nbsp;</td><td>idx&#095;software</td>
<td> ON software&#095;type&#095;id</td>
<td> </td>
</tr>
<tr><th colspan='4'><b>Foreign Keys</b></th></tr>
<tr>
<td>&nbsp;</td><td>fk_software_software_type</td>
<td > ( software&#095;type&#095;id ) ref <a href='#software&#095;type'>software&#095;type</a> (software&#095;type&#095;id) </td>
<td> </td>
</tr>
</tbody>
</table>

</body></html>
13 changes: 13 additions & 0 deletions qiita_db/test/test_software.py
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Expand Up @@ -750,6 +750,19 @@ def test_activate(self):
obs.activate()
self.assertTrue(obs.active)

def test_deprecated(self):
tester = qdb.software.Software(1)
self.assertFalse(tester.deprecated)

tester.deprecated = True
self.assertTrue(tester.deprecated)

tester.deprecated = False
self.assertFalse(tester.deprecated)

with self.assertRaises(ValueError):
tester.deprecated = 'error!'


@qiita_test_checker()
class DefaultParametersTests(TestCase):
Expand Down
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