DataTables load using AJAX, Search by metadata on studies page #1006
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@@ -98,12 +98,14 @@ | |
| from __future__ import division | ||
| from future.utils import viewitems | ||
| from copy import deepcopy | ||
| from itertools import chain | ||
| import warnings | ||
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| from qiita_core.exceptions import IncompetentQiitaDeveloperError | ||
| from .base import QiitaObject | ||
| from .exceptions import (QiitaDBStatusError, QiitaDBColumnError, QiitaDBError) | ||
| from .util import (check_required_columns, check_table_cols, convert_to_id, | ||
| get_environmental_packages, get_table_cols, infer_status) | ||
| from .sql_connection import SQLConnectionHandler | ||
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@@ -142,7 +144,12 @@ class Study(QiitaObject): | |
| """ | ||
| _table = "study" | ||
| # The following columns are considered not part of the study info | ||
| _non_info = frozenset(["email", "study_title"]) | ||
| # The following tables are considered part of info | ||
| _info_cols = frozenset(chain( | ||
| get_table_cols('study'), get_table_cols('study_status'), | ||
| get_table_cols('timeseries_type'), get_table_cols('portal_type'), | ||
| get_table_cols('study_pmid'))) | ||
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| def _lock_non_sandbox(self, conn_handler): | ||
| """Raises QiitaDBStatusError if study is non-sandboxed""" | ||
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@@ -198,6 +205,45 @@ def get_by_status(cls, status): | |
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| return studies | ||
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| @classmethod | ||
| def get_info(cls, study_ids=None, info_cols=None): | ||
| """Returns study data for a set of study_ids | ||
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| Parameters | ||
| ---------- | ||
| study_ids : list of ints, optional | ||
| Studies to get information for. Defauls to all studies | ||
| info_cols: list of str, optional | ||
| Information columns to retrieve. Defaults to all study data | ||
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| Returns | ||
| ------- | ||
| list of DictCursor | ||
| Table-like structure of metadata, one study per row. Can be | ||
| accessed as a list of dictionaries, keyed on column name. | ||
| """ | ||
| if info_cols is None: | ||
| info_cols = cls._info_cols | ||
| elif not cls._info_cols.issuperset(info_cols): | ||
| warnings.warn("Non-info columns passed: %s" % ", ".join( | ||
|
There was a problem hiding this comment. Is this a warning or an error? There was a problem hiding this comment. A warning, as suggested by @adamrp. |
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| set(info_cols) - cls._info_cols)) | ||
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| search_cols = ",".join(sorted(cls._info_cols.intersection(info_cols))) | ||
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There was a problem hiding this comment. Might raise a warning if the user requests information columns that are not in |
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| sql = """SELECT {0} FROM ( | ||
| qiita.study | ||
| JOIN qiita.timeseries_type USING (timeseries_type_id) | ||
| JOIN qiita.portal_type USING (portal_type_id) | ||
| LEFT JOIN (SELECT study_id, array_agg(pmid ORDER BY pmid) as | ||
| pmid FROM qiita.study_pmid GROUP BY study_id) sp USING (study_id) | ||
| )""".format(search_cols) | ||
| if study_ids is not None: | ||
| sql = "{0} WHERE study_id in ({1})".format( | ||
| sql, ','.join(str(s) for s in study_ids)) | ||
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| conn_handler = SQLConnectionHandler() | ||
| return conn_handler.execute_fetchall(sql) | ||
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| @classmethod | ||
| def exists(cls, study_title): | ||
| """Check if a study exists based on study_title, which is unique | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,6 @@ | ||
| -- March 19, 2015 | ||
| -- Rename columns to be more descriptive and allow easier joins | ||
| ALTER TABLE qiita.processed_data_status RENAME COLUMN description TO processed_data_status_description; | ||
| ALTER TABLE qiita.portal_type RENAME COLUMN description TO portal_description; | ||
| ALTER TABLE qiita.investigation RENAME COLUMN description TO investigation_description; | ||
| ALTER TABLE qiita.investigation RENAME COLUMN name TO investigation_name; |
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None of this information will change at runtime, right? If so, I think this could be cached in
qiita_pet.__init__and done onceThere was a problem hiding this comment.
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ah! nevermind, it is at the static scope of the object. it is done once